http://www.mdpi.com/journal/genes Latest open access articles published in Genes at http://www.mdpi.com/journal/genes/ http://www.mdpi.com/2073-4425/3/1/115/ In the plant pathogenic bacterium, Pseudomonas syringae, the exopolysaccharide levan is synthesized by extracellular levansucrase (Lsc), which is encoded by two conserved 1,296-bp genes termed lscB and lscC in P. syringae strain PG4180. A third gene, lscA, is homologous to the 1,248-bp lsc gene of the bacterium Erwinia amylovora, causing fire blight. However, lscA is not expressed in P. syringae strain PG4180. Herein, PG4180 lscA was shown to be expressed from its native promoter in the Lsc-deficient E. amylovora mutant, Ea7/74-LS6, suggesting that lscA might be closely related to the E. amylovora lsc gene. Nucleotide sequence analysis revealed that lscB and lscC homologs in several P. syringae strains are part of a highly conserved 1.8-kb region containing the ORF, flanked by 450-452-bp and 49-51-bp up- and downstream sequences, respectively. Interestingly, the 450-452-bp upstream sequence, along with the initial 48-bp ORF sequence encoding for the N-terminal 16 amino acid residues of Lsc, were found to be highly similar to the respective sequence of a putatively prophage-borne glycosyl hydrolase-encoding gene in several P. syringae genomes. Minimal promoter regions of lscB and lscC were mapped in PG4180 by deletion analysis and were found to be located in similar positions upstream of lsc genes in three P. syringae genomes. Thus, a putative 498-500-bp promoter element was identified, which possesses the prophage-associated com gene and DNA encoding common N-terminal sequences of all 1,296-bp Lsc and two glycosyl hydrolases. Since the gene product of the non-expressed 1,248-bp lscA is lacking this conserved N-terminal region but is otherwise highly homologous to those of lscB and lscC, it was concluded that lscA might have been the ancestral lsc gene in E. amylovora and P. syringae. Our data indicated that its highly expressed paralogs in P. syringae are probably derived from subsequent recombination events initiated by insertion of the 498-500-bp promoter element, described herein, containing a translational start site. http://www.mdpi.com/2073-4425/3/1/115/ Fri, 10 Feb 2012 00:00:00 CET Genes 2012-02-10 3 1 Article 115 137 2073-4425 Genomic Distribution and Divergence of Levansucrase-Coding Genes in Pseudomonas syringae 2012-02-10 doi: 10.3390/genes3010115 Abhishek Srivastava Nehaya Al-Karablieh Shaunak Khandekar Arifa Sharmin Helge Weingart Matthias S. Ullrich http://www.mdpi.com/2073-4425/3/1/90/ Although radiation carcinogenesis has been shown both experimentally and epidemiologically, the use of ionizing radiation is also one of the major modalities in cancer treatment. Various known cellular and molecular events are involved in carcinogenesis. Apart from the known phenomena, there could be implications for carcinogenesis and cancer prevention due to other biological processes such as the bystander effect, the abscopal effect, intrinsic radiosensitivity and radioadaptation. Bystander effects have consequences for mutation initiated cancer paradigms of radiation carcinogenesis, which provide the mechanistic justification for low-dose risk estimates. The abscopal effect is potentially important for tumor control and is mediated through cytokines and/or the immune system (mainly cell-mediated immunity). It results from loss of growth and stimulatory and/or immunosuppressive factors from the tumor. Intrinsic radiosensitivity is a feature of some cancer prone chromosomal breakage syndromes such as ataxia telangectiasia. Radiosensitivity is manifested as higher chromosomal aberrations and DNA repair impairment is now known as a good biomarker for breast cancer screening and prediction of prognosis. However, it is not yet known whether this effect is good or bad for those receiving radiation or radiomimetic agents for treatment. Radiation hormesis is another major concern for carcinogenesis. This process which protects cells from higher doses of radiation or radio mimic chemicals, may lead to the escape of cells from mitotic death or apoptosis and put cells with a lower amount of damage into the process of cancer induction. Therefore, any of these biological phenomena could have impact on another process giving rise to genome instability of cells which are not in the field of radiation but still receiving a lower amount of radiation. For prevention of radiation induced carcinogenesis or risk assessment as well as for successful radiation therapy, all these phenomena should be taken into account. http://www.mdpi.com/2073-4425/3/1/90/ Fri, 20 Jan 2012 00:00:00 CET Genes 2012-01-20 3 1 Review 90 114 2073-4425 Biological Complexities in Radiation Carcinogenesis and Cancer Radiotherapy: Impact of New Biological Paradigms 2012-01-20 doi: 10.3390/genes3010090 Hossein Mozdarani http://www.mdpi.com/2073-4425/3/1/88/ Following publication of our article [1], we found errors in analyses performed by the corresponding author (DJS) related to the phylogenetic relationship between Xylella species and the other xanthomonads. These errors do not make any difference to the main findings and conclusions reported in our paper. For example, the phylogenetic positions of NCPPB1131, NCPPB1132 and NCPPB4393 within the Group 1 Xanthomonas species are unaffected. However, we wish to apologize to the authors of a previous work [2] for creating any negative impression on the quality of their phylogenetic analyses and to take this opportunity to rectify the errors. [...] http://www.mdpi.com/2073-4425/3/1/88/ Wed, 11 Jan 2012 00:00:00 CET Genes 2012-01-11 3 1 Correction 88 89 2073-4425 Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050–1065. 2012-01-11 doi: 10.3390/genes3010088 David J Studholme Arthur Wasukira Konrad Paszkiewicz Valente Aritua Richard Thwaites Julian Smith Murray Grant http://www.mdpi.com/2073-4425/3/1/81/ Genomic sequences across diverse species seem to align towards a common ancestry, eventually implying that eons ago some universal antecedent organism would have lived on the face of Earth. However, when evolution is understood not only as a biological process but as a general thermodynamic process, it becomes apparent that the quest for the last universal common ancestor is unattainable. Ambiguities in alignments are unavoidable because the driving forces and paths of evolution cannot be separated from each other. Thus tracking down life’s origin is by its nature a non-computable task. The thermodynamic tenet clarifies that evolution is a path-dependent process of least-time consumption of free energy. The natural process is without a demarcation line between animate and inanimate. http://www.mdpi.com/2073-4425/3/1/81/ Mon, 09 Jan 2012 00:00:00 CET Genes 2012-01-09 3 1 Article 81 87 2073-4425 Looking for the Last Universal Common Ancestor (LUCA) 2012-01-09 doi: 10.3390/genes3010081 Minna Koskela Arto Annila http://www.mdpi.com/2073-4425/3/1/62/ Pseudomonas cichorii harbors the hrp genes. hrp-mutants lose their virulence on eggplant but not on lettuce. A phosphinothricin N-acetyltransferase gene (pat) is located between hrpL and an aldehyde dehydrogenase gene (aldH) in the genome of P. cichorii. Comparison of nucleotide sequences and composition of the genes among pseudomonads suggests a common ancestor of hrp and pat between P. cichorii strains and P. viridiflava strains harboring the single hrp pathogenicity island. In contrast, phylogenetic diversification of aldH corresponded to species diversification amongst pseudomonads. In this study, the involvement of aldH and pat in P. cichorii virulence was analyzed. An aldH-deleted mutant (ΔaldH) and a pat-deleted mutant (Δpat) lost their virulence on eggplant but not on lettuce. P. cichorii expressed both genes in eggplant leaves, independent of HrpL, the transcriptional activator for the hrp. Inoculation into Asteraceae species susceptible to P. cichorii showed that the involvement of hrp, pat and aldH in P. cichorii virulence is independent of each other and has no relationship with the phylogeny of Asteraceae species based on the nucleotide sequences of ndhF and rbcL. It is thus thought that not only the hrp genes but also pat and aldH are implicated in the diversity of P. cichorii virulence on susceptible host plant species. http://www.mdpi.com/2073-4425/3/1/62/ Tue, 27 Dec 2011 00:00:00 CET Genes 2011-12-27 3 1 Article 62 80 2073-4425 Implication of an Aldehyde Dehydrogenase Gene and a Phosphinothricin N-Acetyltransferase Gene in the Diversity of Pseudomonas cichorii Virulence 2011-12-27 doi: 10.3390/genes3010062 Masayuki Tanaka Ullah Md Wali Hitoshi Nakayashiki Tatsuya Fukuda Hiroyuki Mizumoto Kouhei Ohnishi Akinori Kiba Yasufumi Hikichi http://www.mdpi.com/2073-4425/3/1/35/ Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses. http://www.mdpi.com/2073-4425/3/1/35/ Wed, 21 Dec 2011 00:00:00 CET Genes 2011-12-21 3 1 Article 35 61 2073-4425 Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia 2011-12-21 doi: 10.3390/genes3010035 Damien Mornico Lucie Miché Gilles Béna Nico Nouwen André Verméglio David Vallenet Alexander A.T. Smith Eric Giraud Claudine Médigue Lionel Moulin http://www.mdpi.com/2073-4425/3/1/19/ Both external radiation exposure and internal radionuclide contamination are well known risk factors in the development of thyroid epithelial tumors. The identification of specific molecular markers deregulated in radiation-induced thyroid tumors is important for the etiological diagnosis since neither histological features nor genetic alterations can discriminate between sporadic and radiation-induced tumors. Identification of highly discriminating markers in radiation-induced tumors is challenging as it relies on the ability to identify marker deregulation which is associated with a cellular stress that occurred many years before in the thyroid cells. The existence of such a signature is still controversial, as it was not found in several studies while a highly discriminating signature was found in both post-radiotherapy and post-Chernobyl series in other studies. Overall, published studies searching for radiation-induced thyroid tumor specificities, using transcriptomic, proteomic and comparative genomic hybridization approaches, and bearing in mind the analytical constraints required to analyze such small series of tumors, suggest that such a molecular signature could be found. In comparison with sporadic tumors, we highlight molecular similarities and specificities in tumors occurring after high-dose external radiation exposure, such as radiotherapy, and in post-Chernobyl tumors that occurred after internal 131I contamination. We discuss the relevance of signature extrapolation from series of tumors developing after high and low doses in the identification of tumors induced at very low doses of radiation. http://www.mdpi.com/2073-4425/3/1/19/ Wed, 21 Dec 2011 00:00:00 CET Genes 2011-12-21 3 1 Review 19 34 2073-4425 Discriminating Gene Expression Signature of Radiation-Induced Thyroid Tumors after Either External Exposure or Internal Contamination 2011-12-21 doi: 10.3390/genes3010019 Catherine Ory Nicolas Ugolin Martin Schlumberger Paul Hofman Sylvie Chevillard http://www.mdpi.com/2073-4425/3/1/1/ Animals have co-evolved with mutualistic microbial communities, known as the microbiota, which are essential for organ development and function. We hypothesize that modern animal husbandry practices exert an impact on the intestinal microbiota. In this study, we compared the structure of the fecal microbiota between feral and domestic goats using the G2 PhyloChip and assessed the presence of five tetracycline resistance genes [tet(M), tet(S), tet(O), tet(Q) and tet(W)] by PCR. Feces were collected from 10 goats: 5 domestic from a farm in the main island of Puerto Rico and 5 feral from the remote dry island of Mona. There were 42 bacterial phyla from 153 families detected in the goats’ feces. A total of 84 PhyloChip-OTUs were different in the fecal microbiota of feral and domestic goat. Both feral and domestic goats carried antibiotic resistance genes tet(O) and tet(W), but domestic goats additionally carried tet(Q). Diet, host genetics and antibiotic exposure are likely determinant factors in shaping the intestinal microbiota and may explain the differences observed between feral and domestic goats fecal microbiota. http://www.mdpi.com/2073-4425/3/1/1/ Wed, 21 Dec 2011 00:00:00 CET Genes 2011-12-21 3 1 Article 1 18 2073-4425 Comparison of the Fecal Microbiota in Feral and Domestic Goats 2011-12-21 doi: 10.3390/genes3010001 Kassandra M. De Jesús-Laboy Filipa Godoy-Vitorino Yvette M. Piceno Lauren M. Tom Ida G. Pantoja-Feliciano Michelle J. Rivera-Rivera Gary L. Andersen María G. Domínguez-Bello http://www.mdpi.com/2073-4425/2/4/1050/ We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors. http://www.mdpi.com/2073-4425/2/4/1050/ Fri, 02 Dec 2011 00:00:00 CET Genes 2011-12-02 2 4 Communication 1050 1065 2073-4425 Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade 2011-12-02 doi: 10.3390/genes2041050 David J. Studholme Arthur Wasukira Konrad Paszkiewicz Valente Aritua Richard Thwaites Julian Smith Murray Grant http://www.mdpi.com/2073-4425/2/4/1033/ In developed countries, more than half of all cancer patients receive radiotherapy at some stage in the management of their disease. However, a radiation-induced secondary malignancy can be the price of success if the primary cancer is cured or at least controlled. Therefore, there is increasing concern regarding radiation-related second cancer risks in long-term radiotherapy survivors and a corresponding need to be able to predict cancer risks at high radiation doses. Of particular interest are second cancer risk estimates for new radiation treatment modalities such as intensity modulated radiotherapy, intensity modulated arc-therapy, proton and heavy ion radiotherapy. The long term risks from such modern radiotherapy treatment techniques have not yet been determined and are unlikely to become apparent for many years, due to the long latency time for solid tumor induction. Most information on the dose-response of radiation-induced cancer is derived from data on the A-bomb survivors who were exposed to γ-rays and neutrons. Since, for radiation protection purposes, the dose span of main interest is between zero and one Gy, the analysis of the A-bomb survivors is usually focused on this range. With increasing cure rates, estimates of cancer risk for doses larger than one Gy are becoming more important for radiotherapy patients. Therefore in this review, emphasis was placed on doses relevant for radiotherapy with respect to radiation induced solid cancer. Simple radiation protection models should be used only with extreme care for risk estimates in radiotherapy, since they are developed exclusively for low dose. When applied to scatter radiation, such models can predict only a fraction of observed second malignancies. Better semi-empirical models include the effect of dose fractionation and represent the dose-response relationships more accurately. The involved uncertainties are still huge for most of the organs and tissues. A major reason for this is that the underlying processes of the induction of carcinoma and sarcoma are not well known. Most uncertainties are related to the time patterns of cancer induction, the population specific dependencies and to the organ specific cancer induction rates. For radiotherapy treatment plan optimization these factors are irrelevant, as a treatment plan comparison is performed for a patient of specific age, sex, etc. If a treatment plan is compared relative to another one only the shape of the dose-response curve (the so called risk-equivalent dose) is of importance and errors can be minimized. http://www.mdpi.com/2073-4425/2/4/1033/ Tue, 29 Nov 2011 00:00:00 CET Genes 2011-11-29 2 4 Review 1033 1049 2073-4425 Modeling the Risk of Secondary Malignancies after Radiotherapy 2011-11-29 doi: 10.3390/genes2041033 Uwe Schneider http://www.mdpi.com/2073-4425/2/4/1017/ Alphaproteobacteria show a great versatility in adapting to a broad range of environments and lifestyles, with the association between bacteria and plants as one of the most intriguing, spanning from relatively unspecific nonsymbiotic association (as rhizospheric or endophytic strains) to the highly species-specific interaction of rhizobia. To shed some light on possible common genetic features in such a heterogeneous set of plant associations, the genomes of 92 Alphaproteobacteria strains were analyzed with a fuzzy orthologs-species detection approach. This showed that the different habitats and lifestyles of plant-associated bacteria (soil, plant colonizers, symbiont) are partially reflected by the trend to have larger genomes with respect to nonplant-associated species. A relatively large set of genes specific to symbiotic bacteria (73 orthologous groups) was found, with a remarkable presence of regulators, sugar transporters, metabolic enzymes, nodulation genes and several genes with unknown function that could be good candidates for further characterization. Interestingly, 15 orthologous groupspresent in all plant-associated bacteria (symbiotic and nonsymbiotic), but absent in nonplant-associated bacteria, were also found, whose functions were mainly related to regulation of gene expression and electron transport. Two of these orthologous groups were also detected in fully sequenced plant-associated Betaproteobacteria and Gammaproteobacteria. Overall these results lead us to hypothesize that plant-bacteria associations, though quite variable, are partially supported by a conserved set of unsuspected gene functions. http://www.mdpi.com/2073-4425/2/4/1017/ Tue, 29 Nov 2011 00:00:00 CET Genes 2011-11-29 2 4 Article 1017 1032 2073-4425 Plant-Bacteria Association and Symbiosis: Are There Common Genomic Traits in Alphaproteobacteria? 2011-11-29 doi: 10.3390/genes2041017 Francesco Pini Marco Galardini Marco Bazzicalupo Alessio Mengoni http://www.mdpi.com/2073-4425/2/4/998/ The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles. http://www.mdpi.com/2073-4425/2/4/998/ Tue, 29 Nov 2011 00:00:00 CET Genes 2011-11-29 2 4 Review 998 1016 2073-4425 Antifragility and Tinkering in Biology (and in Business) Flexibility Provides an Efficient Epigenetic Way to Manage Risk 2011-11-29 doi: 10.3390/genes2040998 Antoine Danchin Philippe M. Binder Stanislas Noria http://www.mdpi.com/2073-4425/2/4/980/ Plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. Phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology and overcoming highly developed adaptive immune responses. Emerging research, however, has highlighted the ability of seemingly dedicated human pathogens to cause plant disease, and specialized plant pathogens to cause human disease. Such microbes represent interesting systems for studying the evolution of cross-kingdom pathogenicity, and the benefits and tradeoffs of exploiting multiple hosts with drastically different morphologies and physiologies. This review will explore cross-kingdom pathogenicity, where plants and humans are common hosts. We illustrate that while cross-kingdom pathogenicity appears to be maintained, the directionality of host association (plant to human, or human to plant) is difficult to determine. Cross-kingdom human pathogens, and their potential plant reservoirs, have important implications for the emergence of infectious diseases. http://www.mdpi.com/2073-4425/2/4/980/ Mon, 28 Nov 2011 00:00:00 CET Genes 2011-11-28 2 4 Review 980 997 2073-4425 Insights into Cross-Kingdom Plant Pathogenic Bacteria 2011-11-28 doi: 10.3390/genes2040980 Morgan W.B. Kirzinger Geetanchaly Nadarasah John Stavrinides http://www.mdpi.com/2073-4425/2/4/957/ Pseudomonas savastanoi pv. savastanoi is the causal agent of Olive knot disease, relying on the Type Three Secretion System (TTSS) for its pathogenicity. In this regard, nothing was known about the two other pathovars belonging to this species, pv. nerii and pv. fraxini, characterized by a different host range. Here we report on the organization of the entire TTSS cluster on the three pathovars, and a phylogenetic analysis including the TTSS of those bacteria belonging to the P. syringae complex sequenced so far, highlighting the evolution of each operon (hrpC, hrpJ, hrpRS, hrpU and hrpZ). Moreover, by Real-Time PCR we analyzed the in vitro expression of four main TTSS genes, revealing different activation patterns in the three pathovars, hypothetically related to their diverse virulence behaviors. http://www.mdpi.com/2073-4425/2/4/957/ Fri, 25 Nov 2011 00:00:00 CET Genes 2011-11-25 2 4 Article 957 979 2073-4425 Type Three Secretion System in Pseudomonas savastanoi Pathovars: Does Timing Matter? 2011-11-25 doi: 10.3390/genes2040957 Stefania Tegli Andrea Gori Matteo Cerboneschi Maria Grazia Cipriani Angelo Sisto http://www.mdpi.com/2073-4425/2/4/925/ Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2]. http://www.mdpi.com/2073-4425/2/4/925/ Fri, 18 Nov 2011 00:00:00 CET Genes 2011-11-18 2 4 Article 925 956 2073-4425 Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales 2011-11-18 doi: 10.3390/genes2040925 Jan Reinkensmeier Jan-Philip Schlüter Robert Giegerich Anke Becker http://www.mdpi.com/2073-4425/2/4/912/ The metabolic and regulatory capabilities of an organism are implicit in its protein content. This is often hard to estimate, however, due to ascertainment biases inherent in the available genome annotations. Its complement of recognizable functional protein domains and their combinations convey essentially the same information and at the same time are much more readily accessible, although protein domain models trained for one phylogenetic group frequently fail on distantly related sequences. Pooling related domain models based on their GO-annotation in combination with de novo gene prediction methods provides estimates that seem to be less affected by phylogenetic biases. We show here for 18 diverse representatives from all eukaryotic kingdoms that a pooled analysis of the tendencies for co-occurrence or avoidance of protein domains is indeed feasible. This type of analysis can reveal general large-scale patterns in the domain co-occurrence and helps to identify lineage-specific variations in the evolution of protein domains. Somewhat surprisingly, we do not find strong ubiquitous patterns governing the evolutionary behavior of specific functional classes. Instead, there are strong variations between the major groups of Eukaryotes, pointing at systematic differences in their evolutionary constraints. http://www.mdpi.com/2073-4425/2/4/912/ Wed, 09 Nov 2011 00:00:00 CET Genes 2011-11-09 2 4 Article 912 924 2073-4425 Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions 2011-11-09 doi: 10.3390/genes2040912 Arli A. Parikesit Peter F. Stadler Sonja J. Prohaska http://www.mdpi.com/2073-4425/2/4/869/ The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups. http://www.mdpi.com/2073-4425/2/4/869/ Tue, 08 Nov 2011 00:00:00 CET Genes 2011-11-08 2 4 Article 869 911 2073-4425 Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms 2011-11-08 doi: 10.3390/genes2040869 Arshan Nasir Aisha Naeem Muhammad Jawad Khan Horacio D. Lopez Nicora Gustavo Caetano-Anollés http://www.mdpi.com/2073-4425/2/4/853/ Plasmids are mobile genetic elements that provide their hosts with many beneficial traits including in some cases the ability to degrade different aromatic compounds. To fulfill the knowledge gap regarding catabolic plasmids of the Baltic Sea water, a total of 209 biodegrading bacterial strains were isolated and screened for the presence of these mobile genetic elements. We found that both large and small plasmids are common in the cultivable Baltic Sea bacterioplankton and are particularly prevalent among bacterial genera Pseudomonas and Acinetobacter. Out of 61 plasmid-containing strains (29% of all isolates), 34 strains were found to carry large plasmids, which could be associated with the biodegradative capabilities of the host bacterial strains. Focusing on the diversity of IncP-9 plasmids, self-transmissible m-toluate (TOL) and salicylate (SAL) plasmids were detected. Sequencing the repA gene of IncP-9 carrying isolates revealed a high diversity within IncP-9 plasmid family, as well as extended the assumed bacterial host species range of the IncP-9 representatives. This study is the first insight into the genetic pool of the IncP-9 catabolic plasmids in the Baltic Sea bacterioplankton. http://www.mdpi.com/2073-4425/2/4/853/ Fri, 04 Nov 2011 00:00:00 CET Genes 2011-11-04 2 4 Article 853 868 2073-4425 Occurrence of Plasmids in the Aromatic Degrading Bacterioplankton of the Baltic Sea 2011-11-04 doi: 10.3390/genes2040853 Jekaterina Jutkina Eeva Heinaru Eve Vedler Jaanis Juhanson Ain Heinaru http://www.mdpi.com/2073-4425/2/4/841/ Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization. To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively. The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community. http://www.mdpi.com/2073-4425/2/4/841/ Wed, 02 Nov 2011 00:00:00 CET Genes 2011-11-02 2 4 Review 841 852 2073-4425 Information Management of Genome Enabled Data Streams for Pseudomonas syringae on the Pseudomonas-Plant Interaction (PPI) Website 2011-11-02 doi: 10.3390/genes2040841 Magdalen Lindeberg http://www.mdpi.com/2073-4425/2/4/829/ Both centromeric alpha-satellite sequences as well as centromeric protein A (CENP-A) are highly variable in eukaryotes. CENP-A, a histone H3 variant, is thought to act as the epigenetic “mark” for assembly of centromeric proteins. While most of the histone fold domain (HFD) of the CENP-A is fairly well conserved, a portion of this HFD as well as the N-terminal tail show adaptive variation in both plants and animals. Such variation may establish reproductive barriers that may lead to speciation. The family Percidae contains over 200 species most of which are within the subfamily Etheostomatinae. This subfamily represents a species rich radiation of freshwater fishes in North America and these species exhibit both allopatric and sympatric distributions. In order to study the evolution of CENP-A in percid fish species, we have isolated and characterized the CENP-A gene from Etheostoma tallapoosae by PCR based gene walking. As a result of this study we have demonstrated that the Tallapoosa darter CENP-A gene HFD sequences can be isolated from genomic DNA by nested PCR in a manner that does not lead to the amplification of the highly sequence related histone H3 gene. We also demonstrated that PCR based walking can be subsequently used to isolate the rest of the CENP-A gene and adjacent gene sequences. These adjacent gene sequences provide us with a primer binding sites for PCR isolation of the CENP-A gene from other percid species of fishes. An initial comparison of three percid species shows that the N-terminal tail of the percid CENP-A gene shows adaptive evolution. http://www.mdpi.com/2073-4425/2/4/829/ Mon, 31 Oct 2011 00:00:00 CET Genes 2011-10-31 2 4 Article 829 840 2073-4425 Isolation and Characterization of the Etheostoma tallapoosae (Teleostei: Percidae) CENP-A Gene 2011-10-31 doi: 10.3390/genes2040829 Dyanna M. Fountain Leos G. Kral http://www.mdpi.com/2073-4425/2/4/804/ Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods. http://www.mdpi.com/2073-4425/2/4/804/ Mon, 31 Oct 2011 00:00:00 CET Genes 2011-10-31 2 4 Review 804 828 2073-4425 Ecological and Temporal Constraints in the Evolution of Bacterial Genomes 2011-10-31 doi: 10.3390/genes2040804 Luis Boto Jose Luis Martínez http://www.mdpi.com/2073-4425/2/4/788/ Previously we revealed that flagellin proteins in Pseudomonas syringae pv. tabaci 6605 (Pta 6605) were glycosylated with a trisaccharide, modified viosamine (mVio)-rhamnose-rhamnose and that glycosylation was required for virulence. We further identified some glycosylation-related genes, including vioA, vioB, vioT, fgt1, and fgt2. In this study, we newly identified vioR and vioM in a so-called viosamine island as biosynthetic genes for glycosylation of mVio in Pta 6605 by the mass spectrometry (MS) of flagellin glycan in the respective mutants. Furthermore, characterization of the mVio-related genes and MS analyses of flagellin glycans in other pathovars of P. syringae revealed that mVio-related genes were essential for mVio biosynthesis in flagellin glycans, and that P. syringae pv. syringae B728a, which does not possess a viosamine island, has a different structure of glycan in its flagellin protein. http://www.mdpi.com/2073-4425/2/4/788/ Fri, 28 Oct 2011 00:00:00 CEST Genes 2011-10-28 2 4 Article 788 803 2073-4425 Identification of Genes Involved in the Glycosylation of Modified Viosamine of Flagellins in Pseudomonas syringae by Mass Spectrometry 2011-10-28 doi: 10.3390/genes2040788 Masanobu Yamamoto Mayumi Ohnishi-Kameyama Chi L. Nguyen Fumiko Taguchi Kazuhiro Chiku Tadashi Ishii Hiroshi Ono Mitsuru Yoshida Yuki Ichinose http://www.mdpi.com/2073-4425/2/4/763/ The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes. http://www.mdpi.com/2073-4425/2/4/763/ Fri, 28 Oct 2011 00:00:00 CEST Genes 2011-10-28 2 4 Article 763 787 2073-4425 Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T 2011-10-28 doi: 10.3390/genes2040763 Takakazu Kaneko Hiroko Maita Hideki Hirakawa Nobukazu Uchiike Kiwamu Minamisawa Akiko Watanabe Shusei Sato http://www.mdpi.com/2073-4425/2/4/748/ Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and our knowledge of function through a limited set of in-vitro biochemical studies. How these intersect through evolution is described in the first part of the review. In the second part, our understanding of a series of questions is addressed. This includes how sequences evolve within structures, how evolutionary processes enable structural transitions, how the folding process can change through evolution and what the fitness impacts of this might be. Moving beyond static structures, the evolution of protein kinetics (including normal modes) is discussed, as is the evolution of conformational ensembles and structurally disordered proteins. This ties back to a question of the role of neostructuralization and how it relates to selection on sequences for functions. The relationship between metastability, the fitness landscape, sequence divergence, and organismal effective population size is explored. Lastly, a brief discussion of modeling the evolution of sequences of ordered and disordered proteins is entertained. http://www.mdpi.com/2073-4425/2/4/748/ Fri, 28 Oct 2011 00:00:00 CEST Genes 2011-10-28 2 4 Review 748 762 2073-4425 The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint 2011-10-28 doi: 10.3390/genes2040748 Jessica Siltberg-Liberles Johan A. Grahnen David A. Liberles http://www.mdpi.com/2073-4425/2/4/736/ Chromobacterium violaceum is a gram-negative betaproteobacterium that has been isolated from various Brazilian ecosystems. Its genome contains the cyn operon, which gives it the ability to metabolize highly toxic cyanate into ammonium and carbon dioxide. We used a proteomics approach to investigate the effects of cyanate on the metabolism of this bacterium. The proteome of cells grown with and without cyanate was compared on 2-D gels. Differential spots were digested and identified by mass spectrometry. The bacterium was able to grow at concentrations of up to 1 mM cyanate. Eighteen spots were differentially expressed in the presence of cyanate, of which 16 were downregulated and only two were upregulated. An additional 12 spots were detected only in extracts of cells unexposed to cyanate, and one was expressed only by the exposed cells. Fourteen spots were identified, corresponding to 13 different proteins. We conclude that cyanate promotes expression of enzymes that combat oxidative stress and represses enzymes of the citric acid cycle, strongly affecting the energetic metabolism of the cell. Other proteins that were under-expressed in bacteria exposed to cyanate are involved in amino-acid metabolism or are hypothetical proteins, demonstrating that cyanate also affects expression of genes that are not part of the cyn operon. http://www.mdpi.com/2073-4425/2/4/736/ Wed, 19 Oct 2011 00:00:00 CEST Genes 2011-10-19 2 4 Article 736 747 2073-4425 Proteomics Analysis of the Effects of Cyanate on Chromobacterium violaceum Metabolism 2011-10-19 doi: 10.3390/genes2040736 Rafael A. Baraúna Alessandra Ciprandi Agenor V. Santos Marta S.P. Carepo Evonnildo C. Gonçalves Maria P.C. Schneider Artur Silva http://www.mdpi.com/2073-4425/2/4/706/ Type IV pili (T4P) are hair-like appendages found on the surface of a wide range of bacteria belonging to the β-, γ-, and δ-Proteobacteria, Cyanobacteria and Firmicutes. They constitute an efficient device for a particular type of bacterial surface motility, named twitching, and are involved in several other bacterial activities and functions, including surface adherence, colonization, biofilm formation, genetic material uptake and virulence. Tens of genes are involved in T4P synthesis and regulation, with the majority of them being generally named pil/fim genes. Despite the multiple functionality of T4P and their well-established role in pathogenicity of animal pathogenic bacteria, relatively little attention has been given to the role of T4P in plant pathogenic bacteria. Only in recent years studies have begun to examine with more attention the relevance of these surface appendages for virulence of plant bacterial pathogens. The aim of this review is to summarize the current knowledge about T4P genetic machinery and its role in the interactions between phytopathogenic bacteria and their plant hosts. http://www.mdpi.com/2073-4425/2/4/706/ Tue, 18 Oct 2011 00:00:00 CEST Genes 2011-10-18 2 4 Review 706 735 2073-4425 Involvement of Type IV Pili in Pathogenicity of Plant Pathogenic Bacteria 2011-10-18 doi: 10.3390/genes2040706 Saul Burdman Ofir Bahar Jennifer K. Parker Leonardo De La Fuente http://www.mdpi.com/2073-4425/2/4/689/ The throughput and single-base resolution of RNA-Sequencing (RNA-Seq) have contributed to a dramatic change in transcriptomic-based inquiries and resulted in many new insights into the complexities of bacterial transcriptomes. RNA-Seq could contribute to similar advances in our understanding of plant pathogenic bacteria but it is still a technology under development with limitations and unknowns that need to be considered. Here, we review some new developments for RNA-Seq and highlight recent findings for host-associated bacteria. We also discuss the technical and statistical challenges in the practical application of RNA-Seq for studying bacterial transcriptomes and describe some of the currently available solutions. http://www.mdpi.com/2073-4425/2/4/689/ Thu, 13 Oct 2011 00:00:00 CEST Genes 2011-10-13 2 4 Review 689 705 2073-4425 RNA-Seq for Plant Pathogenic Bacteria 2011-10-13 doi: 10.3390/genes2040689 Jeffrey A. Kimbrel Yanming Di Jason S. Cumbie Jeff H. Chang http://www.mdpi.com/2073-4425/2/4/671/ Considering how biological macromolecules first evolved, probably within a marine environment, it seems likely the very earliest peptides were not encoded by nucleic acids, or at least not via the genetic code as we know it. An objective of the present work is to demonstrate that sequence-independent peptides, or peptides with variable and unreliable lengths and sequences, have the potential to perform a variety of chemically useful functions such as anion and cation binding and membrane and channel formation as well as simple types of catalysis. These functions tend to be performed with the assistance of the main chain CONH atoms rather than the more variable or limited side chain atoms of the peptides presumed to exist then. http://www.mdpi.com/2073-4425/2/4/671/ Mon, 26 Sep 2011 00:00:00 CEST Genes 2011-09-26 2 4 Article 671 688 2073-4425 Functional Capabilities of the Earliest Peptides and the Emergence of Life 2011-09-26 doi: 10.3390/genes2040671 E. James Milner-White Michael J. Russell http://www.mdpi.com/2073-4425/2/4/661/ Despite intensive investigation for decades, the principle of higher-order organization of mitotic chromosomes is unclear. Here, I describe a novel model that emphasizes a critical role of interactions of homologous DNA repeats (repetitive elements; repetitive sequences) in mitotic chromosome architecture. According to the model, DNA repeats are assembled, via repeat interactions (pairing), into compact core structures that govern the arrangement of chromatins in mitotic chromosomes. Tandem repeat assemblies form a chromosomal axis to coordinate chromatins in the longitudinal dimension, while dispersed repeat assemblies form chromosomal nodes around the axis to organize chromatins in the halo. The chromosomal axis and nodes constitute a firm skeleton on which non-skeletal chromatins can be anchored, folded, and supercoiled. http://www.mdpi.com/2073-4425/2/4/661/ Mon, 26 Sep 2011 00:00:00 CEST Genes 2011-09-26 2 4 Article 661 670 2073-4425 A Model of DNA Repeat-Assembled Mitotic Chromosomal Skeleton 2011-09-26 doi: 10.3390/genes2040661 Shao-Jun Tang http://www.mdpi.com/2073-4425/2/3/640/ Pseudomonas syringae is pathogenic in a wide variety of plants, causing diseases with economic impacts. Pseudomonas syringae pathovars produce several toxins that can function as virulence factors and contribute to disease symptoms. These virulence factors include antimetabolite toxins, such as tabtoxin, phaseolotoxin and mangotoxin, which target enzymes in the pathways of amino acid metabolism. The antimetabolite toxins are generally located in gene clusters present in the flexible genomes of specific strains. These gene clusters are typically present in blocks of genes that appear to be integrated into specific sites in the P. syringae core genome. A general overview of the genetic organization and biosynthetic and regulatory functions of these genetic traits of the antimetabolite toxins will be given in the present work. http://www.mdpi.com/2073-4425/2/3/640/ Thu, 15 Sep 2011 00:00:00 CEST Genes 2011-09-15 2 3 Review 640 660 2073-4425 Genes Involved in the Production of Antimetabolite Toxins by Pseudomonas syringae Pathovars 2011-09-15 doi: 10.3390/genes2030640 Eva Arrebola Francisco M Cazorla Alejandro Pérez-García Antonio de Vicente http://www.mdpi.com/2073-4425/2/3/627/ Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia, including E. amylovora, E. pyrifoliae, E. tasmaniensis, and E. billingiae, have provided us near complete genetic information about this pathogen and its closely-related species. This review describes in silico subtractive hybridization-based comparative genomic analyses of eight genomes currently available, and highlights what we have learned from these comparative analyses, as well as genetic and functional genomic studies. Sequence analyses reinforce the assumption that E. amylovora is a relatively homogeneous species and support the current classification scheme of E. amylovora and its related species. The potential evolutionary origin of these Erwinia species is also proposed. The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized. Future research directions are also suggested. http://www.mdpi.com/2073-4425/2/3/627/ Thu, 15 Sep 2011 00:00:00 CEST Genes 2011-09-15 2 3 Review 627 639 2073-4425 Comparative Genomics of Erwinia amylovora and Related Erwinia Species—What do We Learn? 2011-09-15 doi: 10.3390/genes2030627 Youfu Zhao Mingsheng Qi http://www.mdpi.com/2073-4425/2/3/608/ Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse “sampling” of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature. http://www.mdpi.com/2073-4425/2/3/608/ Tue, 16 Aug 2011 00:00:00 CEST Genes 2011-08-16 2 3 Article 608 626 2073-4425 Protein Folding Absent Selection 2011-08-16 doi: 10.3390/genes2030608 Thomas H. LaBean Tauseef R. Butt Stuart A. Kauffman Erik A. Schultes http://www.mdpi.com/2073-4425/2/3/599/ We found some errors in the published versions of Figure S2, Figure S3 and Figure S8 of our paper [1]. The correct Figures are presented below. http://www.mdpi.com/2073-4425/2/3/599/ Tue, 16 Aug 2011 00:00:00 CEST Genes 2011-08-16 2 3 Correction 599 607 2073-4425 Correction: Nagy, A., et al. Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors. Genes 2011, 2, 449-501. 2011-08-16 doi: 10.3390/genes2030599 Alinda Nagy György Szláma Eszter Szarka Mária Trexler László Bányai László Patthy http://www.mdpi.com/2073-4425/2/3/578/ In the accompanying papers we have shown that sequence errors of public databases and confusion of paralogs and epaktologs (proteins that are related only through the independent acquisition of the same domain types) significantly distort the picture that emerges from comparison of the domain architecture (DA) of multidomain Metazoan proteins since they introduce a strong bias in favor of terminal over internal DA change. The issue of whether terminal or internal DA changes occur with greater probability has very important implications for the DA evolution of multidomain proteins since gene fusion can add domains only at terminal positions, whereas domain-shuffling is capable of inserting domains both at internal and terminal positions. As a corollary, overestimation of terminal DA changes may be misinterpreted as evidence for a dominant role of gene fusion in DA evolution. In this manuscript we show that in several recent studies of DA evolution of Metazoa the authors used databases that are significantly contaminated with incomplete, abnormal and mispredicted sequences (e.g., UniProtKB/TrEMBL, EnsEMBL) and/or the authors failed to separate paralogs and epaktologs, explaining why these studies concluded that the major mechanism for gains of new domains in metazoan proteins is gene fusion. In contrast with the latter conclusion, our studies on high quality orthologous and paralogous Swiss-Prot sequences confirm that shuffling of mobile domains had a major role in the evolution of multidomain proteins of Metazoa and especially those formed in early vertebrates. http://www.mdpi.com/2073-4425/2/3/578/ Fri, 05 Aug 2011 00:00:00 CEST Genes 2011-08-05 2 3 Article 578 598 2073-4425 Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms 2011-08-05 doi: 10.3390/genes2030578 Alinda Nagy Laszlo Patthy http://www.mdpi.com/2073-4425/2/3/562/ In human pre-mRNA splicing, infrequent errors occur resulting in erroneous splice products as shown in a genome-wide approach. One characteristic subgroup consists of products lacking one cassette exon. The noise in the splicing process, represented by those misspliced products, can be increased by cold shock treatment or by inhibiting the nonsense mediated decay. Here, we investigated whether the splicing noise frequency increases with age in vivo in peripheral bloods cells or in vitro in cultured and aged fibroblasts from healthy donors. Splicing noise frequency was measured for four erroneously skipped NF1 exons and one exon of RABAC1, AATF and PCGF2 by RT-qPCR. Measurements were validated in cultured fibroblasts treated with cold shock or puromycin. Intragenic but not interpersonal differences were detected in splicing noise frequencies in vivo in peripheral blood cells of 11 healthy donors (15 y–85 y) and in in vitro senescent fibroblasts from three further donors. No correlation to the age of the donors was found in the splicing noise frequencies. Our data demonstrates that splicing error frequencies are not altered by age in peripheral blood cells or in vitro aged fibroblasts in the tested exons of the four investigated genes, indicating a high importance of correct splicing in these proliferating aged cells. http://www.mdpi.com/2073-4425/2/3/562/ Tue, 02 Aug 2011 00:00:00 CEST Genes 2011-08-02 2 3 Article 562 577 2073-4425 Aberrant Single Exon Skipping is not Altered by Age in Exons of NF1, RABAC1, AATF or PCGF2 in Human Blood Cells and Fibroblasts 2011-08-02 doi: 10.3390/genes2030562 Kevin Mellert Michael Uhl Josef Högel Markus Lamla Ralf Kemkemer Dieter Kaufmann http://www.mdpi.com/2073-4425/2/3/516/ In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of multidomain proteins in Metazoa. To estimate the contribution of this type of error we have used as reference UniProtKB/Swiss-Prot sequences from protein families with well-characterized evolutionary histories. We have used two types of paralogy-group construction procedures and monitored the impact of various parameters on the separation of true paralogs from epaktologs on correctly annotated Swiss-Prot entries of multidomain proteins. Our studies have shown that, although public protein family databases are contaminated with epaktologs, analysis of the structure of sequence similarity networks of multidomain proteins provides an efficient means for the separation of epaktologs and paralogs. We have also demonstrated that contamination of protein families with epaktologs increases the apparent rate of DA change and introduces a bias in DA differences in as much as it increases the proportion of terminal over internal DA differences.We have shown that confusing paralogous and epaktologous multidomain proteins significantly increases the apparent rate of DA change in Metazoa and introduces a positional bias in favor of terminal over internal DA changes. Our findings caution that earlier studies based on analysis of datasets of protein families that were contaminated with epaktologs may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. A reassessment of the DA evolution of multidomain proteins is presented in an accompanying paper [1]. http://www.mdpi.com/2073-4425/2/3/516/ Tue, 02 Aug 2011 00:00:00 CEST Genes 2011-08-02 2 3 Article 516 561 2073-4425 Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs 2011-08-02 doi: 10.3390/genes2030516 Alinda Nagy László Bányai László Patthy http://www.mdpi.com/2073-4425/2/3/502/ Eukaryotic genomes contain a large amount of DNA repeats (also known as repetitive DNA, repetitive elements, and repetitive sequences). Here, I propose a role of repetitive DNA in the formation of higher-order structures of chromosomes. The central idea of this theory is that chromatin regions with repetitive sequences pair with regions harboring homologous repeats and that such somatic repeat pairing (RP) assembles repetitive DNA chromatin into compact chromosomal domains that specify chromatin folding in a site-directed manner. According to this theory, DNA repeats are not randomly distributed in the genome. Instead, they form a core framework that coordinates the architecture of chromosomes. In contrast to the viewpoint that DNA repeats are genomic ‘junk’, this theory advocates that repetitive sequences are chromatin organizer modules that determine chromatin-chromatin contact points within chromosomes. This novel concept, if correct, would suggest that DNA repeats in the linear genome encode a blueprint for higher-order chromosomal organization. http://www.mdpi.com/2073-4425/2/3/502/ Tue, 02 Aug 2011 00:00:00 CEST Genes 2011-08-02 2 3 Article 502 515 2073-4425 Chromatin Organization by Repetitive Elements (CORE): A Genomic Principle for the Higher-Order Structure of Chromosomes 2011-08-02 doi: 10.3390/genes2030502 Shao-Jun Tang http://www.mdpi.com/2073-4425/2/3/449/ In view of the fact that appearance of novel protein domain architectures (DA) is closely associated with biological innovations, there is a growing interest in the genome-scale reconstruction of the evolutionary history of the domain architectures of multidomain proteins. In such analyses, however, it is usually ignored that a significant proportion of Metazoan sequences analyzed is mispredicted and that this may seriously affect the validity of the conclusions. To estimate the contribution of errors in gene prediction to differences in DA of predicted proteins, we have used the high quality manually curated UniProtKB/Swiss-Prot database as a reference. For genome-scale analysis of domain architectures of predicted proteins we focused on RefSeq, EnsEMBL and NCBI’s GNOMON predicted sequences of Metazoan species with completely sequenced genomes. Comparison of the DA of UniProtKB/Swiss-Prot sequences of worm, fly, zebrafish, frog, chick, mouse, rat and orangutan with those of human Swiss-Prot entries have identified relatively few cases where orthologs had different DA, although the percentage with different DA increased with evolutionary distance. In contrast with this, comparison of the DA of human, orangutan, rat, mouse, chicken, frog, zebrafish, worm and fly RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences with those of the corresponding/orthologous human Swiss-Prot entries identified a significantly higher proportion of domain architecture differences than in the case of the comparison of Swiss-Prot entries. Analysis of RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences with DAs different from those of their Swiss-Prot orthologs confirmed that the higher rate of domain architecture differences is due to errors in gene prediction, the majority of which could be corrected with our FixPred protocol. We have also demonstrated that contamination of databases with incomplete, abnormal or mispredicted sequences introduces a bias in DA differences in as much as it increases the proportion of terminal over internal DA differences. Here we have shown that in the case of RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences of Metazoan species, the contribution of gene prediction errors to domain architecture differences of orthologs is comparable to or greater than those due to true gene rearrangements. We have also demonstrated that domain architecture comparison may serve as a useful tool for the quality control of gene predictions and may thus guide the correction of sequence errors. Our findings caution that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. A reassessment of the DA evolution of orthologous and paralogous proteins is presented in an accompanying paper [1]. http://www.mdpi.com/2073-4425/2/3/449/ Wed, 13 Jul 2011 00:00:00 CEST Genes 2011-07-13 2 3 Article 449 501 2073-4425 Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors 2011-07-13 doi: 10.3390/genes2030449 Alinda Nagy György Szláma Eszter Szarka Mária Trexler László Bányai László Patthy http://www.mdpi.com/2073-4425/2/3/420/ Pluripotent stem cells hold great promise for cell-based therapies in regenerative medicine. However, critical to understanding and exploiting mechanisms of cell lineage specification, epigenetic reprogramming, and the optimal environment for maintaining and differentiating pluripotent stem cells is a fundamental knowledge of how these events occur in normal embryogenesis. The early mouse embryo has provided an excellent model to interrogate events crucial in cell lineage commitment and plasticity, as well as for embryo-derived lineage-specific stem cells and induced pluripotent stem (iPS) cells. Here we provide an overview of cell lineage specification in the early (preimplantation) mouse embryo focusing on the transcriptional circuitry and epigenetic marks necessary for successive differentiation events leading to the formation of the blastocyst. http://www.mdpi.com/2073-4425/2/3/420/ Wed, 13 Jul 2011 00:00:00 CEST Genes 2011-07-13 2 3 Review 420 448 2073-4425 Understanding the Molecular Circuitry of Cell Lineage Specification in the Early Mouse Embryo 2011-07-13 doi: 10.3390/genes2030420 Anna Bergsmedh Mary E. Donohoe Rebecca-Ayme Hughes Anna-Katerina Hadjantonakis http://www.mdpi.com/2073-4425/2/3/397/ Recurrent translocations are well known hallmarks of many human solid tumors and hematological disorders, where patient- and breakpoint-specific information may facilitate prognostication and individualized therapy. In thyroid carcinomas, the proto-oncogenes RET and NTRK1 are often found to be activated through chromosomal rearrangements. However, many sporadic tumors and papillary thyroid carcinomas (PTCs) arising in patients with a history of exposure to elevated levels of ionizing irradiation do not carry these known abnormalities. We developed a rapid scheme to screen tumor cell metaphase spreads and identify candidate genes of tumorigenesis and neoplastic progression for subsequent functional studies. Using a series of overnight fluorescence in situ hybridization (FISH) experiments with pools comprised of bacterial artificial chromosome (BAC) clones, it now becomes possible to rapidly refine breakpoint maps and, within one week, progress from the low resolution Spectral Karyotyping (SKY) maps or Giemsa-banding (G-banding) karyotypes to fully integrated, high resolution physical maps including a list of candiate genes in the critical regions. http://www.mdpi.com/2073-4425/2/3/397/ Tue, 28 Jun 2011 00:00:00 CEST Genes 2011-06-28 2 3 Article 397 419 2073-4425 Delineating Chromosomal Breakpoints in Radiation-Induced Papillary Thyroid Cancer 2011-06-28 doi: 10.3390/genes2030397 Heinz-Ulrich G. Weier Yuko Ito Johnson Kwan Jan Smida Jingly F. Weier Ludwig Hieber Chun-Mei Lu Lars Lehmann Mei Wang Haig J. Kassabian Hui Zeng Benjamin O’Brien http://www.mdpi.com/2073-4425/2/2/394/ Gene conversion is an outcome of recombination, causing non-reciprocal transfer of a DNA fragment. Several decades later than the discovery of crossing over, gene conversion was first recognized in fungi when non-Mendelian allelic distortion was observed. Gene conversion occurs when a double-strand break is repaired by using homologous sequences in the genome. In meiosis, there is a strong preference to use the orthologous region (allelic gene conversion), which causes non-Mendelian allelic distortion, but paralogous or duplicated regions can also be used for the repair (inter-locus gene conversion, also referred to as non-allelic and ectopic gene conversion). The focus of this special issue is the latter, interlocus gene conversion; the rate is lower than allelic gene conversion but it has more impact on phenotype because more drastic changes in DNA sequence are involved. http://www.mdpi.com/2073-4425/2/2/394/ Fri, 17 Jun 2011 00:00:00 CEST Genes 2011-06-17 2 2 Editorial 394 396 2073-4425 Special Issue: Gene Conversion in Duplicated Genes 2011-06-17 doi: 10.3390/genes2020394 Hideki Innan http://www.mdpi.com/2073-4425/2/2/384/ Acute myeloid leukemia (AML) can develop as a secondary malignancy following radiotherapy, but also following low-dose environmental or occupational radiation exposure. Therapy-related AML frequently carries deletions of chromosome 5q and/or 7, but for low-dose exposure associated AML this has not been described. For the present study we performed genome-wide screens for loss-of-heterozygosity (LOH) in a set of 19 AML cases that developed after radiation-exposure following the Chernobyl accident. Using Affymetrix SNP arrays we found large regions of LOH in 16 of the cases. Eight cases (42%) demonstrated LOH at 5q and/or 7, which is a known marker of complex karyotypic changes and poor prognosis. We could show here for the first time that exposure to low-dose ionizing radiation induces AML with molecular alterations similar to those seen in therapy-related cases. http://www.mdpi.com/2073-4425/2/2/384/ Tue, 31 May 2011 00:00:00 CEST Genes 2011-05-31 2 2 Article 384 393 2073-4425 Allelic Imbalances in Radiation—Associated Acute Myeloid Leukemia 2011-05-31 doi: 10.3390/genes2020384 Sergiy V. Klymenko Jan Smida Michael J. Atkinson Volodymir G. Bebeshko Michaela Nathrath Michael Rosemann http://www.mdpi.com/2073-4425/2/2/374/ The risk of developing thyroid cancer increases considerably after exposure to external or internal radiation, especially in children below the age of 10. After the Chernobyl reactor accident, the yearly incidence of childhood thyroid cancer in Belarus increased to approximately 40 per 1.000.000 in girls and to roughly 20 per 1.000.000 in boys compared to approximately 0.5 cases per 1.000.000 prior to the accident. Typically, young children with thyroid cancer after radiation exposure present in ≈95% of the cases as papillary cancers, in ≈50% as invasive tumors growing outside the thyroid capsule, in ≈65% with lymph node metastases and in ≈15% with distant metastases. A joint Belarusian-German project starting in April 1993 that combined treatment with surgery and radioiodine was organized in 237 selected children from Belarus who were exposed to the Chernobyl fallout and had advanced stages of thyroid cancer. The study group included 141 girls and 96 boys. Their median age at the time of the accident was 1.7 years; whereas the median age at the time of diagnosis was 12.4 years. With the exception of two cases with follicular histology, the majority of the patients had been diagnosed with papillary thyroid cancers. In 63%, the tumor had grown outside the thyroid capsule and invaded the tissue of the neck (pT4). Nearly all of the selected cases (96%) showed-up with lymph node metastases (pN1) and 43% of the patients with distant metastases mainly to the lungs (pM1). In 58% of the children, complete remissions of thyroid cancer could be achieved until December 31st 2010 and in 34% of the children, stable partial remissions; in the remaining 8% of the patients, partial remissions were observed. The risk of radiation-induced thyroid cancer increased considerably in children and adolescents who were affected by the Chernobyl reactor accident. In spite of the fact, that thyroid cancers in young children seem to behave more aggressively than in older patients, the results of combined treatment with thyroidectomy, radioiodine therapy and thyroid hormone replacement are excellent. http://www.mdpi.com/2073-4425/2/2/374/ Tue, 31 May 2011 00:00:00 CEST Genes 2011-05-31 2 2 Review 374 383 2073-4425 Clinical Experiences with Radiation Induced Thyroid Cancer after Chernobyl 2011-05-31 doi: 10.3390/genes2020374 Christoph Reiners http://www.mdpi.com/2073-4425/2/2/360/ LINE-1 (Long Interspersed Nuclear elements) and HERVs (Human Endogenous Retroviruses) are two families of retrotransposons which together account for about 28% of the human genome. Genes harbored within LINE-1 and HERV retrotransposons, particularly that encoding the reverse transcriptase (RT) enzyme, are generally expressed at low levels in differentiated cells, but their expression is up-regulated in embryonic tissues and transformed cells. Here we review evidence indicating that the LINE-1-encoded RT plays regulatory roles in early embryonic development. Indeed, antisense-mediated inhibition of expression of a highly expressed LINE-1 family in mouse zygotes caused developmental arrest at the two- or four-cell embryo stages. Development is also arrested when the embryo endogenous RT activity is pharmacologically inhibited by nevirapine, an RT inhibitor currently employed in AIDS treatment. The arrest of embryonic development is irreversible even after RT inhibition is removed and it is associated with subverted gene expression profiles. These data indicate an early requirement for LINE-1-encoded RT to support early developmental progression. Consistent with this, recent findings indicate that a reverse transcription wave is triggered in the zygote a few hours after fertilization and is propagated at least through the first two rounds of cell division. On the whole these findings suggest that reverse transcription is strictly required in early embryos as a key component of a novel RT-dependent mechanism that regulated the proper unfolding of the developmental program. http://www.mdpi.com/2073-4425/2/2/360/ Wed, 18 May 2011 00:00:00 CEST Genes 2011-05-18 2 2 Review 360 373 2073-4425 A Reverse Transcriptase-Dependent Mechanism Is Essential for Murine Preimplantation Development 2011-05-18 doi: 10.3390/genes2020360 Ilaria Sciamanna Patrizia Vitullo Angela Curatolo Corrado Spadafora http://www.mdpi.com/2073-4425/2/2/345/ Fertilization is a very complex biological process that requires the perfect cooperation between two highly specialized cells: the male and female gametes. The oocyte provides the physical space where this process takes place, most of the energetic need, and half of the genetic contribution. The spermatozoon mostly contributes the other half of the chromosomes and it is specialized to reach and to penetrate the oocyte. Notably, the mouse oocyte and early embryo are transcriptionally inactive. Hence, they fully depend on the maternal mRNAs and proteins stored during oocyte maturation to drive the onset of development. The new embryo develops autonomously around the four-cell stage, when maternal supplies are exhausted and the zygotic genome is activated in mice. This oocyte-to-embryo transition needs an efficient and tightly regulated translation of the maternally-inherited mRNAs, which likely contributes to embryonic genome activation. Full understanding of post-transcriptional regulation of gene expression in early embryos is crucial to understand the reprogramming of the embryonic genome, it might help driving reprogramming of stem cells in vitro and will likely improve in vitro culturing of mammalian embryos for assisted reproduction. Nevertheless, the knowledge of the mechanism(s) underlying this fundamental step in embryogenesis is still scarce, especially if compared to other model organisms. We will review here the current knowledge on the post-transcriptional control of gene expression in mouse early embryos and discuss some of the unanswered questions concerning this fascinating field of biology. http://www.mdpi.com/2073-4425/2/2/345/ Wed, 06 Apr 2011 00:00:00 CEST Genes 2011-04-06 2 2 Review 345 359 2073-4425 Post-Transcriptional Control of Gene Expression in Mouse Early Embryo Development: A View from the Tip of the Iceberg 2011-04-06 doi: 10.3390/genes2020345 Enrica Bianchi Claudio Sette http://www.mdpi.com/2073-4425/2/2/332/ Currently in vitro culture of mouse preimplantation embryos has become a very important technique to investigate different mechanisms of early embryogenesis. However, there is a big difference in the preimplantation development between mammalian species. Despite close relatedness to mice, in vitro cultivation of rat preimplantation embryos is still delicate and needs further investigation and optimizations. In this study we have compared the in vitro developmental potential of mouse and rat embryos cultured at different culture conditions in parallel experiments. Interestingly, mouse zygotes developed in vitro until blastocyst stage even in inadequate medium without any phosphates and with low osmolarity which was formulated especially for cultivation of rat embryos. Rat parthenotes and zygotes developed in M16 medium formulated for mouse embryos only till 2-cell stage and further development is blocked completely at this stage. Moreover, developmental ability of rat embryos in vitro was significantly lower in comparison with mouse even in special rat mR1ECM medium. Mouse and rat embryos at 2-cell stage obtained in vivo developed until blastocyst stages significantly more efficiently compared to zygotes. Culture of mouse zygotes in glass capillaries resulted in a significantly higher rate of morula and blastocyst development compared with dishes. The Well-of-the-Well system resulted in a significant improvement when compared with dishes for the culture of rat zygotes only until morula stage. Reduced oxygen tension increased the developmental rate of rat but not mouse zygotes until blastocyst stage. This study demonstrates that development of early preimplantation embryos is altered by different culture conditions and show strong differences even between two related species such as mice and rats. Therefore, for understanding the fundamental mechanisms of early mammalian development it is very important to use embryos of various species. http://www.mdpi.com/2073-4425/2/2/332/ Fri, 01 Apr 2011 00:00:00 CEST Genes 2011-04-01 2 2 Article 332 344 2073-4425 Effect of Culture Conditions on Viability of Mouse and Rat Embryos Developed in Vitro 2011-04-01 doi: 10.3390/genes2020332 Elena Popova Michael Bader Alexander Krivokharchenko http://www.mdpi.com/2073-4425/2/2/313/ Interlocus gene conversion occurs such that a certain length of DNA fragment is non-reciprocally transferred (copied and pasted) between paralogous regions. To understand the rate and tract length of gene conversion, there are two major approaches. One is based on mutation-accumulation experiments, and the other uses natural DNA sequence variation. In this review, we overview the two major approaches and discuss their advantages and disadvantages. In addition, to demonstrate the importance of statistical analysis of empirical and evolutionary data for estimating tract length, we apply a maximum likelihood method to several data sets. http://www.mdpi.com/2073-4425/2/2/313/ Fri, 25 Mar 2011 00:00:00 CET Genes 2011-03-25 2 2 Article 313 331 2073-4425 The Rate and Tract Length of Gene Conversion between Duplicated Genes 2011-03-25 doi: 10.3390/genes2020313 Sayaka P. Mansai Tomoyuki Kado Hideki Innan http://www.mdpi.com/2073-4425/2/2/298/ Early embryonic development is a multi-step process that is intensively regulated by various signaling pathways. Because of the complexity of the embryo and the interactions between the germ layers, it is very difficult to fully understand how these signals regulate embryo patterning. Recently, pluripotent stem cell lines derived from different developmental stages have provided an in vitro system for investigating molecular mechanisms regulating cell fate decisions. In this review, we summarize the major functions of the BMP, FGF, Nodal and Wnt signaling pathways, which have well-established roles in vertebrate embryogenesis. Then, we highlight recent studies in pluripotent stem cells that have revealed the stage-specific roles of BMP，FGF and Nodal pathways during neural differentiation. These findings enhance our understanding of the stepwise regulation of embryo patterning by particular signaling pathways and provide new insight into the mechanisms underlying early embryonic development. http://www.mdpi.com/2073-4425/2/2/298/ Thu, 24 Mar 2011 00:00:00 CET Genes 2011-03-24 2 2 Review 298 312 2073-4425 Pluripotent Stem Cell Studies Elucidate the Underlying Mechanisms of Early Embryonic Development 2011-03-24 doi: 10.3390/genes2020298 Lingyu Li Naihe Jing http://www.mdpi.com/2073-4425/2/1/280/ Developmental biology, regenerative medicine and cancer biology are more and more interested in understanding the molecular mechanisms controlling pluripotency and self-renewal in stem cells. Pluripotency is maintained by a synergistic interplay between extrinsic stimuli and intrinsic circuitries, which allow sustainment of the undifferentiated and self-renewing state. Nevertheless, even though a lot of efforts have been made in the past years, the precise mechanisms regulating these processes remain unclear. One of the key extrinsic factors is leukemia inhibitory factor (LIF) that is largely used for the cultivation and derivation of mouse embryonic and induced pluripotent stem cells. LIF acts through the LIFR/gp130 receptor and activates STAT3, an important regulator of mouse embryonic stem cell self-renewal. STAT3 is known to inhibit differentiation into both mesoderm and endoderm lineages by preventing the activation of lineage-specific differentiation programs. However, LIF activates also parallel circuitries like the PI3K-pathway and the MEK/ERK-pathway, but its mechanisms of action remain to be better elucidated. This review article aims at summarizing the actual knowledge on the importance of LIF in the maintenance of pluripotency and self-renewal in embryonic and induced pluripotent stem cells. http://www.mdpi.com/2073-4425/2/1/280/ Wed, 09 Mar 2011 00:00:00 CET Genes 2011-03-09 2 1 Review 280 297 2073-4425 The Role of the Leukemia Inhibitory Factor (LIF) — Pathway in Derivation and Maintenance of Murine Pluripotent Stem Cells 2011-03-09 doi: 10.3390/genes2010280 Urs Graf Elisa A. Casanova Paolo Cinelli http://www.mdpi.com/2073-4425/2/1/260/ Meiosis is a highly conserved process, which is stringently regulated in all organisms, from fungi through to humans. Two major events define meiosis in eukaryotes. The first is the pairing, or synapsis, of homologous chromosomes and the second is the exchange of genetic information in a process called meiotic recombination. Synapsis is mediated by the meiosis-specific synaptonemal complex structure in combination with the cohesins that tether sister chromatids together along chromosome arms through prophase I. Previously, we identified FKBP6 as a novel component of the mammalian synaptonemal complex. Further studies demonstrated an interaction between FKBP6 and the NIMA-related kinase-1, NEK1. To further investigate the role of NEK1 in mammalian meiosis, we have examined gametogenesis in the spontaneous mutant, Nek1kat2J. Homozygous mutant animals show decreased testis size, defects in testis morphology, and in cohesin removal at late prophase I of meiosis, causing complete male infertility. Cohesin protein SMC3 remains localized to the meiotic chromosome cores at diplonema in the Nek1 mutant, and also in the related Fkbp6 mutant, while in wild type cells SMC3 is removed from the cores at the end of prophase I and becomes more diffuse throughout the DAPI stained region of the nucleus. These data implicate NEK1 as a possible kinase involved in cohesin redistribution in murine spermatocytes. http://www.mdpi.com/2073-4425/2/1/260/ Mon, 07 Mar 2011 00:00:00 CET Genes 2011-03-07 2 1 Article 260 279 2073-4425 NEK1 Facilitates Cohesin Removal during Mammalian Spermatogenesis 2011-03-07 doi: 10.3390/genes2010260 Kim Holloway Elle C. Roberson Kelly L. Corbett Nadine K. Kolas Edward Nieves Paula E. Cohen http://www.mdpi.com/2073-4425/2/1/229/ E-cadherin; pluripotency; embryonic stem cell; induced pluripotent stem cell; iPS; ES; signaling pathways; Activin; Nodal http://www.mdpi.com/2073-4425/2/1/229/ Fri, 25 Feb 2011 00:00:00 CET Genes 2011-02-25 2 1 Review 229 259 2073-4425 The Function of E-Cadherin in Stem Cell Pluripotency and Self-Renewal 2011-02-25 doi: 10.3390/genes2010229 Francesca Soncin Christopher M. Ward http://www.mdpi.com/2073-4425/2/1/219/ Embryonic stem (ES) cells can differentiate into multiple types of cells belonging to all three germ layers. Although ES cells are clonally established, they display heterogeneous responses upon the induction of differentiation, resulting in a mixture of various types of differentiated cells. Our recent reports have shown that Hes1 regulates the fate choice of ES cells by repressing Notch signaling, and that the oscillatory expression of Hes1 contributes to various differentiation responses in ES cells. Here we discuss the mechanism regulating the intracellular dynamics in ES cells and how to trigger the lineage choice from pluripotent ES cells. http://www.mdpi.com/2073-4425/2/1/219/ Tue, 22 Feb 2011 00:00:00 CET Genes 2011-02-22 2 1 Article 219 228 2073-4425 Hes1 Oscillations Contribute to Heterogeneous Differentiation Responses in Embryonic Stem Cells 2011-02-22 doi: 10.3390/genes2010219 Taeko Kobayashi Ryoichiro Kageyama http://www.mdpi.com/2073-4425/2/1/210/ The SET and MYND (SMYD) family of lysine methyltransferases is defined by a SET domain that is split into two segments by a MYND domain, followed by a cysteine-rich post-SET domain. While members of the SMYD family are important in the SET-mediated regulation of gene transcription, pathological consequences have also been associated with aberrant expression of SMYD proteins. The last decade has witnessed a rapid increase in the studies and corresponding understanding of these highly impactful enzymes. Herein, we review the current body of knowledge related to the SMYD family of lysine methyltransferases and their role in transcriptional regulation, epigenetics, and tumorigenesis. http://www.mdpi.com/2073-4425/2/1/210/ Mon, 21 Feb 2011 00:00:00 CET Genes 2011-02-21 2 1 Review 210 218 2073-4425 SET/MYND Lysine Methyltransferases Regulate Gene Transcription and Protein Activity 2011-02-21 doi: 10.3390/genes2010210 Kristin Leinhart Mark Brown http://www.mdpi.com/2073-4425/2/1/191/ Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples. http://www.mdpi.com/2073-4425/2/1/191/ Fri, 18 Feb 2011 00:00:00 CET Genes 2011-02-18 2 1 Article 191 209 2073-4425 Neutral and Non-Neutral Evolution of Duplicated Genes with Gene Conversion 2011-02-18 doi: 10.3390/genes2010191 Jeffrey A. Fawcett Hideki Innan http://www.mdpi.com/2073-4425/2/1/169/ Mitochondria have their own genomic DNA. Unlike the nuclear genome, each cell contains hundreds to thousands of copies of mitochondrial DNA (mtDNA). The copies of mtDNA tend to have heterogeneous sequences, due to the high frequency of mutagenesis, but are quickly homogenized within a cell (“homoplasmy”) during vegetative cell growth or through a few sexual generations. Heteroplasmy is strongly associated with mitochondrial diseases, diabetes and aging. Recent studies revealed that the yeast cell has the machinery to homogenize mtDNA, using a common DNA processing pathway with gene conversion; i.e., both genetic events are initiated by a double-stranded break, which is processed into 3' single-stranded tails. One of the tails is base-paired with the complementary sequence of the recipient double-stranded DNA to form a D-loop (homologous pairing), in which repair DNA synthesis is initiated to restore the sequence lost by the breakage. Gene conversion generates sequence diversity, depending on the divergence between the donor and recipient sequences, especially when it occurs among a number of copies of a DNA sequence family with some sequence variations, such as in immunoglobulin diversification in chicken. MtDNA can be regarded as a sequence family, in which the members tend to be diversified by a high frequency of spontaneous mutagenesis. Thus, it would be interesting to determine why and how double-stranded breakage and D-loop formation induce sequence homogenization in mitochondria and sequence diversification in nuclear DNA. We will review the mechanisms and roles of mtDNA homoplasmy, in contrast to nuclear gene conversion, which diversifies gene and genome sequences, to provide clues toward understanding how the common DNA processing pathway results in such divergent outcomes. http://www.mdpi.com/2073-4425/2/1/169/ Mon, 14 Feb 2011 00:00:00 CET Genes 2011-02-14 2 1 Review 169 190 2073-4425 Enlightenment of Yeast Mitochondrial Homoplasmy: Diversified Roles of Gene Conversion 2011-02-14 doi: 10.3390/genes2010169 Feng Ling Tsutomu Mikawa Takehiko Shibata http://www.mdpi.com/2073-4425/2/1/152/ The study of meiosis is limited because of the intrinsic nature of gametogenesis in mammals. One way to overcome these limitations would be the use of culture systems that would allow meiotic progression in vitro. There have been some attempts to culture mammalian meiocytes in recent years. In this review we will summarize all the efforts to-date in order to culture mammalian sperm and oocyte precursor cells. http://www.mdpi.com/2073-4425/2/1/152/ Mon, 14 Feb 2011 00:00:00 CET Genes 2011-02-14 2 1 Review 152 168 2073-4425 Meiosis in a Bottle: New Approaches to Overcome Mammalian Meiocyte Study Limitations 2011-02-14 doi: 10.3390/genes2010152 Ignasi Roig Miguel Angel Brieno-Enriquez Montserrat Garcia Caldes http://www.mdpi.com/2073-4425/2/1/131/ The evolutionary impact of gene duplication events has been a theme of Drosophila genetics dating back to the Morgan School. While considerable attention has been placed on the genetic novelties that duplicates are capable of introducing, and the role that positive selection plays in their early stages of duplicate evolution, much less attention has been given to the potential consequences of ectopic (non-allelic) gene conversion on these evolutionary processes. In this paper we consider the historical origins of ectopic gene conversion models and present a synthesis of the current Drosophila data in light of several primary questions in the field. http://www.mdpi.com/2073-4425/2/1/131/ Fri, 11 Feb 2011 00:00:00 CET Genes 2011-02-11 2 1 Review 131 151 2073-4425 Gene Duplication and Ectopic Gene Conversion in Drosophila 2011-02-11 doi: 10.3390/genes2010131 J. Roman Arguello Tim Connallon http://www.mdpi.com/2073-4425/2/1/107/ Neural stem cells (NSCs) are capable of producing a variety of neural cell types, and are indispensable for the development of the mammalian brain. NSCs can be induced in vitro from pluripotent stem cells, including embryonic stem cells and induced-pluripotent stem cells. Although the transplantation of these exogenous NSCs is a potential strategy for improving presently untreatable neurological conditions, there are several obstacles to its implementation, including tumorigenic, immunological, and ethical problems. Recent studies have revealed that NSCs also reside in the adult brain. The endogenous NSCs are activated in response to disease or trauma, and produce new neurons and glia, suggesting they have the potential to regenerate damaged brain tissue while avoiding the above-mentioned problems. Here we present an overview of the possibility and limitations of using endogenous NSCs in regenerative medicine. http://www.mdpi.com/2073-4425/2/1/107/ Fri, 14 Jan 2011 00:00:00 CET Genes 2011-01-14 2 1 Review 107 130 2073-4425 Prospects and Limitations of Using Endogenous Neural Stem Cells for Brain Regeneration 2011-01-14 doi: 10.3390/genes2010107 Naoko Kaneko Eisuke Kako Kazunobu Sawamoto http://www.mdpi.com/2073-4425/2/1/81/ The dramatic discovery that somatic cells could be reprogrammed to induced pluripotent stem cells (iPSCs), by the expression of just four factors, has opened new opportunities for regenerative medicine and novel ways of modeling human diseases. Extensive research over the short time since the first iPSCs were generated has yielded the ability to reprogram various cell types using a diverse range of methods. However the duration, efficiency, and safety of induced reprogramming have remained a persistent limitation to achieving a robust experimental and therapeutic system. The field has worked to resolve these issues through technological advances using non-integrative approaches, factor replacement or complementation with microRNA, shRNA and drugs. Despite these advances, the molecular mechanisms underlying the reprogramming process remain poorly understood. Recently, through the use of inducible secondary reprogramming systems, researchers have now accessed more rigorous mechanistic experiments to decipher this complex process. In this review we will discuss some of the major recent findings in reprogramming, pertaining to proliferation and cellular senescence, epigenetic and chromatin remodeling, and other complex cellular processes such as morphological changes and mesenchymal-to-epithelial transition. We will focus on the implications of this work in the construction of a mechanistic understanding of reprogramming and discuss unexplored areas in this rapidly expanding field. http://www.mdpi.com/2073-4425/2/1/81/ Thu, 13 Jan 2011 00:00:00 CET Genes 2011-01-13 2 1 Review 81 106 2073-4425 Looking into the Black Box: Insights into the Mechanisms of Somatic Cell Reprogramming 2011-01-13 doi: 10.3390/genes2010081 Laurent David Payman Samavarchi-Tehrani Azadeh Golipour Jeffrey L. Wrana http://www.mdpi.com/2073-4425/2/1/59/ Polycomb group proteins (PcG) are major epigenetic regulators, essential for establishing heritable expression patterns of developmental control genes. The mouse PcG family member M33/Cbx2 (Chromobox homolog protein 2) is a component of the Polycomb-Repressive Complex 1 (PRC1). Targeted deletion of Cbx2/M33 in mice results in homeotic transformations of the axial skeleton, growth retardation and male-to-female sex reversal. In this study, we tested whether Cbx2 is involved in the control of chromatin remodeling processes during meiosis. Our analysis revealed sex reversal in 28.6% of  XY−/− embryos, in which a hypoplastic testis and a contralateral ovary were observed in close proximity to the kidney, while the remaining male mutant fetuses exhibited bilateral testicular hypoplasia. Notably, germ cells recovered from Cbx2(XY−/−) testes on day 18.5 of fetal development exhibited premature meiosis onset with synaptonemal complex formation suggesting a role for Cbx2 in the control of meiotic entry in male germ cells. Mutant females exhibited small ovaries with significant germ cell loss and a high proportion of oocytes with abnormal synapsis and non-homologous interactions at the pachytene stage as well as formation of univalents at diplotene. These defects were associated with failure to resolve DNA double strand breaks marked by persistent gH2AX and Rad51 foci at the late pachytene stage. Importantly, two factors required for meiotic silencing of asynapsed chromatin, ubiquitinated histone H2A (ubH2A) and the chromatin remodeling protein BRCA1, co-localized with fully synapsed chromosome axes in the majority of Cbx2(−/−) oocytes. These results provide novel evidence that Cbx2 plays a critical and previously unrecognized role in germ cell viability, meiosis onset and homologous chromosome synapsis in the mammalian germline. http://www.mdpi.com/2073-4425/2/1/59/ Tue, 11 Jan 2011 00:00:00 CET Genes 2011-01-11 2 1 Article 59 80 2073-4425 Role of Polycomb Group Protein Cbx2/M33 in Meiosis Onset and Maintenance of Chromosome Stability in the Mammalian Germline 2011-01-11 doi: 10.3390/genes2010059 Claudia Baumann Rabindranath De La Fuente http://www.mdpi.com/2073-4425/2/1/48/ Gene conversion is a type of homologous recombination that leads to transfer of genetic information among homologous DNA sequences. It can be categorized into two classes: homogenizing and diversifying gene conversions. The former class results in neutralization and homogenization of any sequence variation among repetitive DNA sequences, and thus is important for concerted evolution. On the other hand, the latter functions to increase genetic diversity at the recombination-recipient loci. Thus, these two types of gene conversion play opposite roles in genome dynamics. Diversifying gene conversion is observed in the immunoglobulin (Ig) loci of chicken, rabbit, and other animals, and directs the diversification of Ig variable segments and acquisition of functional Ig repertoires. This type of gene conversion is initiated by the biased occurrence of recombination initiation events (e.g., DNA single- or double-strand breaks) on the recipient DNA site followed by unidirectional homologous recombination from multiple template sequences. Transcription and DNA accessibility is also important in the regulation of biased recombination initiation. In this review, we will discuss the biological significance and possible mechanisms of diversifying gene conversion in somatic cells of eukaryotes. http://www.mdpi.com/2073-4425/2/1/48/ Mon, 10 Jan 2011 00:00:00 CET Genes 2011-01-10 2 1 Review 48 58 2073-4425 Genetic Diversification by Somatic Gene Conversion 2011-01-10 doi: 10.3390/genes2010048 Kohei Kurosawa Kunihiro Ohta http://www.mdpi.com/2073-4425/2/1/36/ The TSPY gene stands out from all other human protein-coding genes because of its high copy number and tandemly-repeated organization. Here, we review its evolutionary history in great apes in order to assess whether these unusual properties are more likely to result from a relaxation of constraint or an unusual functional role. Detailed comparisons with chimpanzee are possible because a finished sequence of the chimpanzee Y chromosome is available, together with more limited data from other apes. These comparisons suggest that the human-chimpanzee ancestral Y chromosome carried a tandem array of TSPY genes which expanded on the human lineage while undergoing multiple duplication events followed by pseudogene formation on the chimpanzee lineage. The protein coding region is the most highly conserved of the multi-copy Y genes in human-chimpanzee comparisons, and the analysis of the dN/dS ratio indicates that TSPY is evolutionarily highly constrained, but may have experienced positive selection after the human-chimpanzee split. We therefore conclude that the exceptionally high copy number in humans is most likely due to a human-specific but unknown functional role, possibly involving rapid production of a large amount of TSPY protein at some stage during spermatogenesis. http://www.mdpi.com/2073-4425/2/1/36/ Mon, 10 Jan 2011 00:00:00 CET Genes 2011-01-10 2 1 Review 36 47 2073-4425 An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes 2011-01-10 doi: 10.3390/genes2010036 Yali Xue Chris Tyler-Smith http://www.mdpi.com/2073-4425/2/1/21/ In spite of evolutionary conservation of meiosis, many of the genes that control mammalian meiosis are still unknown. We report here that the ENU-induced repro4 mutation, identified in a screen to uncover genes that control mouse meiosis, causes failure of spermatocytes to exit meiotic prophase I via the G2/MI transition. Major events of meiotic prophase I occurred normally in affected spermatocytes and known regulators of the meiotic G2/MI transition were present and functional. Deep sequencing of mutant DNA revealed a mutation located in an intron of the Mtap2 gene, encoding microtubule-associated protein 2, and levels of Mtap2 transcript were reduced in mutant testes. This evidence implicates MTAP2 as required directly or indirectly for completion of meiosis and normal spermatogenesis in mammals. http://www.mdpi.com/2073-4425/2/1/21/ Mon, 10 Jan 2011 00:00:00 CET Genes 2011-01-10 2 1 Article 21 35 2073-4425 A Mutation in Mtap2 Is Associated with Arrest of Mammalian Spermatocytes before the First Meiotic Division 2011-01-10 doi: 10.3390/genes2010021 Fengyun Sun Mary Ann Handel http://www.mdpi.com/2073-4425/2/1/1/ Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60–70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families. http://www.mdpi.com/2073-4425/2/1/1/ Mon, 10 Jan 2011 00:00:00 CET Genes 2011-01-10 2 1 Review 1 20 2073-4425 Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization 2011-01-10 doi: 10.3390/genes2010001 Xi-Yin Wang Andrew H. Paterson http://www.mdpi.com/2073-4425/1/3/550/ Gene conversion is a specific type of homologous recombination that involves the unidirectional transfer of genetic material from a ‘donor’ sequence to a highly homologous ‘acceptor’. We have recently reviewed the molecular mechanisms underlying gene conversion, explored the key part that this process has played in fashioning extant human genes, and performed a meta-analysis of gene-conversion events known to have caused human genetic disease. Here we shall briefly summarize some of the latest developments in the study of pathogenic gene conversion events, including (i) the emerging idea of minimal efficient sequence homology (MESH) for homologous recombination, (ii) the local DNA sequence features that appear to predispose to gene conversion, (iii) a mechanistic comparison of gene conversion and transient hypermutability, and (iv) recently reported examples of pathogenic gene conversion events. http://www.mdpi.com/2073-4425/1/3/550/ Wed, 22 Dec 2010 00:00:00 CET Genes 2010-12-22 1 3 Review 550 563 2073-4425 Gene Conversion in Human Genetic Disease 2010-12-22 doi: 10.3390/genes1030550 Jian-Min Chen Claude Férec David N. Cooper http://www.mdpi.com/2073-4425/1/3/521/ Meiotic recombination is initiated by the induction of programmed DNA double strand breaks (DSBs). DSB repair promotes homologous interactions and pairing and leads to the formation of crossovers (COs), which are required for the proper reductional segregation at the first meiotic division. In mammals, several hundred DSBs are generated at the beginning of meiotic prophase by the catalytic activity of SPO11. Currently it is not well understood how the frequency and timing of DSB formation and their localization are regulated. Several approaches in humans and mice have provided an extensive description of the localization of initiation events based on CO mapping, leading to the identification and characterization of preferred sites (hotspots) of initiation. This review presents the current knowledge about the proteins known to be involved in this process, the sites where initiation takes place, and the factors that control hotspot localization. http://www.mdpi.com/2073-4425/1/3/521/ Wed, 22 Dec 2010 00:00:00 CET Genes 2010-12-22 1 3 Review 521 549 2073-4425 Initiation of Meiotic Recombination in Mammals 2010-12-22 doi: 10.3390/genes1030521 Rajeev Kumar Bernard De Massy http://www.mdpi.com/2073-4425/1/3/505/ Meiosis yields haploid gametes following two successive divisions of a germ cell in the absence of intervening DNA replication. Balanced segregation of homologous chromosomes in Meiosis I is aided by a proteinaceous structure, the synaptonemal complex (SC). The objective of this study was to determine total average autosomal SC lengths in spermatocytes in three commonly used mouse strains (129S4/SvJae, C57BL/6J, and BALB/c). Our experiments revealed that the total autosomal SC length in BALB/c spermatocytes is 9% shorter than in the two other strains. Shorter SCs are also observed in spermatocytes of (BALB/c × 129S4/SvJae) and (C57BL/6J × BALB/c) F1 hybrids suggesting a genetic basis of SC length regulation. Along these lines, we studied expression of a selected group of genes implicated in meiotic chromosome architecture. We found that BALB/c testes express up to 6-fold less of Rec8 mRNA and 4-fold less of REC8 protein. These results suggest that the mechanism that defines the SC length operates via a REC8‑dependent process. Finally, our results demonstrate that genetic background can have an effect on meiotic studies in mice. http://www.mdpi.com/2073-4425/1/3/505/ Wed, 15 Dec 2010 00:00:00 CET Genes 2010-12-15 1 3 Article 505 520 2073-4425 Synaptonemal Complex Length Variation in Wild-Type Male Mice 2010-12-15 doi: 10.3390/genes1030505 Neil M. Vranis Godfried W. Van der Heijden Safia Malki Alex Bortvin http://www.mdpi.com/2073-4425/1/3/495/ Sister chromatid cohesion is essential for cell division. During meiosis, it is also required for proper synapsis of pairs of sister chromatids and for chiasma formation and maintenance. Since mammalian oocytes remain arrested in late prophase for a very long period—up to five decades in humans—the preservation of cohesion throughout this period is a formidable challenge. Mouse models with cohesin deficiencies and aging wild-type mice showed that this challenge is not fully met: cohesion weakens and deteriorates with increasing age. These recent findings have highly significant implications for our comprehension of the genesis of aneuploidies. http://www.mdpi.com/2073-4425/1/3/495/ Mon, 13 Dec 2010 00:00:00 CET Genes 2010-12-13 1 3 Review 495 504 2073-4425 Cohesin in Oocytes—Tough Enough for Mammalian Meiosis? 2010-12-13 doi: 10.3390/genes1030495 Ekaterina Revenkova Caroline Adelfalk Rolf Jessberger http://www.mdpi.com/2073-4425/1/3/484/ During the first meiotic prophase, the cohesin complex is localized to the chromosome axis and contributes to chromosome organization, pairing, synapsis, and recombination. The PDS5 protein, an accessory factor of the cohesin complex, is known to be a component of meiotic chromosome cores in fungi and to be implicated in meiotic chromosome structure and function. We found by immunoblotting experiments that a mammalian PDS5 protein, PDS5B, is abundantly expressed in mouse testis compared to other tissues. Immunofluorescence labeling experiments revealed that PDS5B is highly expressed in spermatogonia and that most PDS5B is depleted from chromatin as cells enter meiosis. During the first meiotic prophase, PDS5B associates with the axial cores of chromosomes. The axial association of PDS5B was observed also in the absence of synaptonemal complex proteins, such as SYCP1 and SYCP3, suggesting that PDS5B is an integral part of the chromosome axis as defined by the cohesin complex. These results suggest that PDS5B modulates cohesin functions in spermatocytes as well as in spermatogonia, contributing to meiotic chromosome structure and function. http://www.mdpi.com/2073-4425/1/3/484/ Mon, 13 Dec 2010 00:00:00 CET Genes 2010-12-13 1 3 Article 484 494 2073-4425 The Mouse Cohesin-Associated Protein PDS5B Is Expressed in Testicular Cells and Is Associated with the Meiotic Chromosome Axes 2010-12-13 doi: 10.3390/genes1030484 Tomoyuki Fukuda Christer Hoog http://www.mdpi.com/2073-4425/1/3/469/ Male spermatogenesis is an essential and complex process necessary to gain totipotency and allow a whole new organism to develop upon fertilization. While single-gene based studies have provided insights into the mechanisms underlying spermatogenesis, detailed global profiling of all the key meiotic stages is required to fully define these processes. Here, by isolating highly enriched mouse meiotic cell populations, we have generated a comprehensive gene expression atlas of mammalian meiosis. Our data define unique signatures for the specific stages of meiosis, including global chromosome X inactivation and reactivation. The data also reveal profound switches in global gene expression at the initiation of pachynema that are reminiscent of the commitment to meiosis observed in budding yeast. Overall, this meiotic atlas provides an exhaustive blueprint and resource for mammalian gametogenesis and meiosis. http://www.mdpi.com/2073-4425/1/3/469/ Mon, 13 Dec 2010 00:00:00 CET Genes 2010-12-13 1 3 Article 469 483 2073-4425 A Global Expression Switch Marks Pachytene Initiation during Mouse Male Meiosis 2010-12-13 doi: 10.3390/genes1030469 Mohammad Fallahi Irina V. Getun Zhen K. Wu Philippe R.J. Bois http://www.mdpi.com/2073-4425/1/3/452/ Interlocus gene conversion, the nonreciprocal exchange of genetic material between genes, is facilitated by high levels of sequence identity between DNA sequences and has the dual effect of homogenizing intergenic sequences while increasing intragenic variation. Gene conversion can have important consequences for the evolution of paralogs subsequent to gene duplication, as well as result in misinterpretations regarding their evolution. We review the current state of research on gene conversion in paralogs within Caenorhabditis elegans and its congeneric species, including the relative rates of gene conversion, the range of observable conversion tracts, the genomic variables that strongly influence the frequency of gene conversion and its contribution to concerted evolution of multigene families. Additionally, we discuss recent studies that examine the phenotypic and population-genetic effects of interlocus gene conversion between the sex-determination locus fog-2 and its paralog ftr-1 in natural and experimental populations of C. elegans. In light of the limitations of gene conversion detection methods that rely solely on the statistical distribution of identical nucleotides between paralogs, we suggest that analyses of gene conversion in C. elegans take advantage of mutation accumulation experiments and sequencing projects of related Caenorhabditis species. http://www.mdpi.com/2073-4425/1/3/452/ Thu, 09 Dec 2010 00:00:00 CET Genes 2010-12-09 1 3 Review 452 468 2073-4425 Genomic and Population-Level Effects of Gene Conversion in Caenorhabditis Paralogs 2010-12-09 doi: 10.3390/genes1030452 Vaishali Katju Ulfar Bergthorsson http://www.mdpi.com/2073-4425/1/3/440/ The RING domain-containing protein CCNB1IP1 (Cyclin B1 Interacting Protein 1) is a putative ubiquitin E3 ligase that is essential for chiasmata formation, and hence fertility, in mice. Previous studies in cultured cells indicated that CCNB1IP1 targets Cyclin B for degradation, thus playing a role in cell cycle regulation. Mice homozygous for a mutant allele (mei4) of Ccnb1ip1 display no detectable phenotype other than meiotic failure from an absence of chiasmata. CCNB1IP1 is not conserved in key model organisms such as yeast and Drosophila, and there are no features of the protein that implicate clear mechanisms for a role in recombination. To gain insight into CCNB1IP1’s function in meiotic cells, we raised a specific antibody and determined that the protein appears in pachynema. This indicates that CCNB1IP1 is involved with crossover intermediate maturation, rather than early (leptotene) specification of a subset of SPO11-induced double strand breaks towards the crossover pathway. Additionally, a yeast 2-hybrid (Y2H) screen revealed that CCNB1IP1 interacts with SUMO2 and a set of proteins enriched for consensus sumoylation sites. The Y2H studies, combined with scrutiny of CCNB1IP1 domains, implicate this protein as an E3 ligase of the sumoylation cascade. We hypothesize CCNB1IP1 represents a novel meiosis-specific SUMO E3 ligase critical to resolution of recombination intermediates into mature chiasmata. http://www.mdpi.com/2073-4425/1/3/440/ Thu, 02 Dec 2010 00:00:00 CET Genes 2010-12-02 1 3 Article 440 451 2073-4425 Evidence Implicating CCNB1IP1, a RING Domain-Containing Protein Required for Meiotic Crossing Over in Mice, as an E3 SUMO Ligase 2010-12-02 doi: 10.3390/genes1030440 Edward R. Strong John C. Schimenti http://www.mdpi.com/2073-4425/1/3/427/ Gene conversion (conversion), the unidirectional transfer of DNA sequence information, occurs as a byproduct of recombinational repair of broken or damaged DNA molecules. Whereas excision repair processes replace damaged DNA by copying the complementary sequence from the undamaged strand of duplex DNA, recombinational mechanisms copy similar sequence, usually in another molecule, to replace the damaged sequence. In mitotic cells the other molecule is usually a sister chromatid, and the repair does not lead to genetic change. Less often a homologous chromosome or homologous sequence in an ectopic position is used. Conversion results from repair in two ways. First, if there was a double-strand gap at the site of a break, homologous sequence will be used as the template for synthesis to fill the gap, thus transferring sequence information in both strands. Second, recombinational repair uses complementary base pairing, and the heteroduplex molecule so formed is a source of conversion, both as heteroduplex and when donor (undamaged template) information is retained after correction of mismatched bases in heteroduplex. There are mechanisms that favour the use of sister molecules that must fail before ectopic homology can be used. Meiotic recombination events lead to the formation of crossovers required in meiosis for orderly segregation of pairs of homologous chromosomes. These events result from recombinational repair of programmed double-strand breaks, but in contrast with mitotic recombination, meiotic recombinational events occur predominantly between homologous chromosomes, so that transfer of sequence differences by conversion is very frequent. Transient recombination events that do not form crossovers form both between homologous chromosomes and between regions of ectopic homology, and leave their mark in the occurrence of frequent non-crossover conversion, including ectopic conversion. http://www.mdpi.com/2073-4425/1/3/427/ Mon, 29 Nov 2010 00:00:00 CET Genes 2010-11-29 1 3 Review 427 439 2073-4425 Mechanisms of Ectopic Gene Conversion 2010-11-29 doi: 10.3390/genes1030427 P.J. Hastings http://www.mdpi.com/2073-4425/1/3/413/ Xenopus embryos provide a rich source of pluripotent cells that can be differentiated into functional organs. Since the molecular principles of vertebrate organogenesis appear to be conserved between Xenopus and mammals, this system can provide useful guidelines for the directional manipulation of human embryonic stem cells. Pluripotent Xenopus cells can be easily isolated from the animal pole of blastula stage Xenopus embryos. These so called “animal cap” cells represent prospective ectodermal cells, but give rise to endodermal, mesodermal and neuro-ectodermal derivatives if treated with the appropriate factors. These factors include evolutionary conserved modulators of the key developmental signal transduction pathways that can be supplied either by mRNA microinjection or direct application of recombinant proteins. This relatively simple system has added to our understanding of pancreas, liver, kidney, eye and heart development. In particular, recent studies have used animal cap cells to generate ectopic eyes and hearts, setting the stage for future work aimed at programming pluripotent cells for regenerative medicine. http://www.mdpi.com/2073-4425/1/3/413/ Thu, 18 Nov 2010 00:00:00 CET Genes 2010-11-18 1 3 Review 413 426 2073-4425 Programming Pluripotent Precursor Cells Derived from Xenopus Embryos to Generate Specific Tissues and Organs 2010-11-18 doi: 10.3390/genes1030413 Annette Borchers Tomas Pieler http://www.mdpi.com/2073-4425/1/3/388/ Cytogenetic analysis of head and neck squamous cell carcinoma (HNSCC) established several biomarkers that have been correlated to clinical parameters during the past years. Adequate cell culture model systems are required for functional studies investigating those potential prognostic markers in HNSCC. We have used a cell line, CAL 33, for the establishment of a cell culture model in order to perform functional analyses of interesting candidate genes and proteins. The cell line was cytogenetically characterized using array CGH, spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH). As a starting point for the investigation of genetic markers predicting radiosensitivity in tumor cells, irradiation experiments were carried out and radiation responses of CAL 33 have been determined. Radiosensitivity of CAL 33 cells was intermediate when compared to published data on tumor cell lines. http://www.mdpi.com/2073-4425/1/3/388/ Thu, 11 Nov 2010 00:00:00 CET Genes 2010-11-11 1 3 Article 388 412 2073-4425 Establishment and Molecular Cytogenetic Characterization of a Cell Culture Model of Head and Neck Squamous Cell Carcinoma (HNSCC) 2010-11-11 doi: 10.3390/genes1030388 Verena L. Bauer Ludwig Hieber Quirin Schaeffner Johannes Weber Herbert Braselmann Reinhard Huber Axel Walch Horst Zitzelsberger http://www.mdpi.com/2073-4425/1/3/385/ Next Generation Sequencing (NGS) refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger) sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance). The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche), Illumina (formerly Solexa) Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies) and the Heliscope (Helicos Corporation). The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...] http://www.mdpi.com/2073-4425/1/3/385/ Wed, 27 Oct 2010 00:00:00 CEST Genes 2010-10-27 1 3 Editorial 385 387 2073-4425 Special Issue: Next Generation DNA Sequencing 2010-10-27 doi: 10.3390/genes1030385 Paul Richardson http://www.mdpi.com/2073-4425/1/3/371/ Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques. http://www.mdpi.com/2073-4425/1/3/371/ Tue, 26 Oct 2010 00:00:00 CEST Genes 2010-10-26 1 3 Article 371 384 2073-4425 Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes 2010-10-26 doi: 10.3390/genes1030371 Jennifer L. Edwards Darren L. Smith John Connolly James E. McDonald Michael J. Cox Ian Joint Clive Edwards Alan J. McCarthy http://www.mdpi.com/2073-4425/1/3/357/ Introns are common among all eukaryotes, while only a limited number of introns are found in prokaryotes. Globin and globin-like proteins are widely distributed in nature, being found even in prokaryotes and a wide range of patterns of intron-exon have been reported in several eukaryotic globin genes. Globin genes in invertebrates show considerable variation in the positions of introns; globins can be found without introns, with only one intron or with three introns in different positions. In this work we analyzed the introns in the myoglobin gene from Biomphalaria glabrata, B. straminea and B. tenagophila. In the Biomphalaria genus, the myoglobin gene has three introns; these were amplified by PCR and analyzed by PCR-RFLP. Results showed that the size (number or nucleotides) and the nucleotide sequence of the coding gene of the myoglobin are variable in the three species. We observed the presence of size polymorphisms in intron 2 and 3; this characterizes a homozygous/heterozygous profile and it indicates the existence of two alleles which are different in size in each species of Biomphalaria. This polymorphism could be explored for specific identification of Biomphalaria individuals. http://www.mdpi.com/2073-4425/1/3/357/ Wed, 20 Oct 2010 00:00:00 CEST Genes 2010-10-20 1 3 Article 357 370 2073-4425 Size Polymorphism in Alleles of the Myoglobin Gene from Biomphalaria Mollusks 2010-10-20 doi: 10.3390/genes1030357 Kádima N. Teixeira Karyne N. Souza Teofânia H.D.A. Vidigal Cristiane A. Brito Alexandre M.C. Santos Marcelo M. Santoro http://www.mdpi.com/2073-4425/1/3/349/ The importance of gene conversion for the evolution of gene families is reviewed. Four problems concerning gene conversion, i.e., concerted evolution, generation of useful variation, deleterious effects, and relation to neofunctionalization, are discussed by surveying reported examples of evolving gene families. Emphasis is given toward understanding interactive effects of gene conversion and natural selection. http://www.mdpi.com/2073-4425/1/3/349/ Thu, 30 Sep 2010 00:00:00 CEST Genes 2010-09-30 1 3 Review 349 356 2073-4425 Gene Conversion and Evolution of Gene Families: An Overview 2010-09-30 doi: 10.3390/genes1030349 Tomoko Ohta http://www.mdpi.com/2073-4425/1/3/335/ Cell Division Autoantigen 1 (CDA1) was discovered following screening a human expression library with serum from a patient with Discoid Lupus Erythematosus. CDA1, encoded by TSPYL2 on the X chromosome, shares anti-proliferative and pro‑fibrotic properties with TGF-b. It inhibits cell growth through p53, pERK1/2 and p21‑mediated pathways and is implicated in tumorigenesis and the DNA damage response. Its pro-fibrotic property is mediated through cross-talk with TGF-b that results in upregulation of extracellular matrix proteins. The latter properties have identified a key role for CDA1 in diabetes associated atherosclerosis. These dual properties place CDA1 as an attractive molecular target for treating tumors and vascular fibrosis including atherosclerosis and other vascular disorders associated with enhanced TGF-β action and tissue scarring. http://www.mdpi.com/2073-4425/1/3/335/ Thu, 30 Sep 2010 00:00:00 CEST Genes 2010-09-30 1 3 Review 335 348 2073-4425 Role of Cell Division Autoantigen 1 (CDA1) in Cell Proliferation and Fibrosis 2010-09-30 doi: 10.3390/genes1030335 Ban-Hock Toh Yugang Tu Zemin Cao Mark E. Cooper Zhonglin Chai http://www.mdpi.com/2073-4425/1/2/317/ The recent arrival of ultra-high throughput, next generation sequencing (NGS) technologies has revolutionized the genetics and genomics fields by allowing rapid and inexpensive sequencing of billions of bases. The rapid deployment of NGS in a variety of sequencing-based experiments has resulted in fast accumulation of massive amounts of sequencing data. To process this new type of data, a torrent of increasingly sophisticated algorithms and software tools are emerging to help the analysis stage of the NGS applications. In this article, we strive to comprehensively identify the critical challenges that arise from all stages of NGS data analysis and provide an objective overview of what has been achieved in existing works. At the same time, we highlight selected areas that need much further research to improve our current capabilities to delineate the most information possible from NGS data. The article focuses on applications dealing with ChIP-Seq and RNA-Seq. http://www.mdpi.com/2073-4425/1/2/317/ Mon, 27 Sep 2010 00:00:00 CEST Genes 2010-09-27 1 2 Review 317 334 2073-4425 Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data 2010-09-27 doi: 10.3390/genes1020317 Debashis Ghosh Zhaohui S. Qin http://www.mdpi.com/2073-4425/1/2/308/ Spermatogenesis requires the concerted action of thousands of genes, all contributing to its efficiency to a different extent. The Y chromosome contains several testis-specific genes and among them the AZF region genes on the Yq and the TSPY1 array on the Yp are the most relevant candidates for spermatogenic function. TSPY1 was originally described as the putative gene for the gonadoblastoma locus on the Y (GBY) chromosome. Besides its oncogenic properties, expression analyses in the testis and in vitro and in vivo studies all converge on a physiological involvement of the TSPY1 protein in spermatogenesis as a pro-proliferative factor. The majority of TSPY1 copies are arranged in 20.4 kb of tandemly repeated units, with different copy numbers among individuals. Our recent study addressing the role of TSPY1 copy number variation in spermatogenesis reported that TSPY1 copy number influences spermatogenic efficiency and is positively correlated with sperm count. This finding provides further evidence for a role of TSPY1 in testicular germ cell proliferation and stimulates future research aimed at evaluating the relationship between the copy number and the protein expression level of the TSPY1 gene. http://www.mdpi.com/2073-4425/1/2/308/ Tue, 21 Sep 2010 00:00:00 CEST Genes 2010-09-21 1 2 Review 308 316 2073-4425 TSPY and Male Fertility 2010-09-21 doi: 10.3390/genes1020308 Csilla Krausz Claudia Giachini Gianni Forti http://www.mdpi.com/2073-4425/1/2/294/ The emergence of next-generation sequencing (NGS) platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow. http://www.mdpi.com/2073-4425/1/2/294/ Tue, 14 Sep 2010 00:00:00 CEST Genes 2010-09-14 1 2 Review 294 307 2073-4425 Bioinformatics for Next Generation Sequencing Data 2010-09-14 doi: 10.3390/genes1020294 Alberto Magi Matteo Benelli Alessia Gozzini Francesca Girolami Francesca Torricelli Maria Luisa Brandi http://www.mdpi.com/2073-4425/1/2/283/ TSPY is a Y-encoded gene that is expressed in normal testicular germ cells and various cancer types including germ cell tumor, melanoma, hepatocellular carcinoma, and prostate cancer. Currently, the correlation between TSPY expression and oncogenic development has not been established, particularly in somatic cancers. To establish such correlation, we analyzed the expression of TSPY, in reference to its interactive oncoprotein, EEF1A, tumor biomarker, AMACR, and normal basal cell biomarker, p63, in 41 cases of clinical prostate cancers (CPCa), 17 cases of latent prostate cancers (LPCa), and 19 cases of non-cancerous prostate (control) by immunohistochemistry. Our results show that TSPY was detected more frequently (78%) in the clinical prostate cancer specimens than those of latent prostate cancer (47%) and control (50%). In the latent cancer group, the levels of TSPY expression could be correlated with increasing Gleason grades. TSPY expression was detected in seven out of nine high-grade latent cancer samples (Gleason 7 and more). The expression of the TSPY binding partner EEF1A was detectable in all prostate specimens, but the levels were higher in cancer cells in clinical and latent prostate cancer specimens than normal prostatic cells. These observations suggest that expressions of TSPY and its binding partner EEF1A are associated with the development and progression of prostate cancer. http://www.mdpi.com/2073-4425/1/2/283/ Tue, 14 Sep 2010 00:00:00 CEST Genes 2010-09-14 1 2 Article 283 293 2073-4425 Expression of the Y-Encoded TSPY is Associated with Progression of Prostate Cancer 2010-09-14 doi: 10.3390/genes1020283 Tatsuo Kido Shingo Hatakeyama Chikara Ohyama Yun-Fai Chris Lau http://www.mdpi.com/2073-4425/1/2/263/ This study presents a new computer program for assessing the effects of different factors and sequencing strategies on de novo sequence assembly. The program uses reads from actual sequencing studies or from simulations with a reference genome that may also be real or simulated. The simulated reads can be created with our read simulator. They can be of differing length and coverage, consist of paired reads with varying distance, and include sequencing errors such as color space miscalls to imitate SOLiD data. The simulated or real reads are mapped to their reference genome and our assembly simulator is then used to obtain optimal assemblies that are limited only by the distribution of repeats. By way of this mapping, the assembly simulator determines which contigs are theoretically possible, or conversely (and perhaps more importantly), which are not. We illustrate the application and utility of our new simulation tools with several experiments that test the effects of genome complexity (repeats), read length and coverage, word size in De Bruijn graph assembly, and alternative sequencing strategies (e.g., BAC pooling) on sequence assemblies. These experiments highlight just some of the uses of our simulators in the experimental design of sequencing projects and in the further development of assembly algorithms. http://www.mdpi.com/2073-4425/1/2/263/ Mon, 13 Sep 2010 00:00:00 CEST Genes 2010-09-13 1 2 Article 263 282 2073-4425 A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly 2010-09-13 doi: 10.3390/genes1020263 Bjarne Knudsen Roald Forsberg Michael M. Miyamoto http://www.mdpi.com/2073-4425/1/2/244/ The TSPY gene, which encodes the testis-specific protein, Y-encoded, was first discovered and characterized in humans, but orthologous genes were subsequently identified on the Y chromosome of many other placental mammals. TSPY is expressed in the testis and to a much lesser extent in the prostate gland, and it is assumed that TSPY serves function in spermatogonial proliferation and/or differentiation. It is further supposed that TSPY is involved in male infertility and exerts oncogenic effects in gonadal and prostate tumor formation. As a member of the TSPY/SET/NAP protein family, TSPY is able to bind cyclin B types, and stimulates the cyclin B1-CDK1 kinase activity, thereby accelerating the G2/M phase transition of the cell cycle of target cells. Because the laboratory mouse carries only a nonfunctional Y-chromosomal Tspy-ps pseudogene, a knockout mouse model for functional research analyses is not a feasible approach. In the last decade, three classical transgenic mouse models have been developed to contribute to our understanding of TSPY regulation, expression and function. The different transgenic mouse approaches and their relevance for studying TSPY regulation, expression and function are discussed in this review. http://www.mdpi.com/2073-4425/1/2/244/ Wed, 18 Aug 2010 00:00:00 CEST Genes 2010-08-18 1 2 Review 244 262 2073-4425 Transgenic Mouse Studies to Understand the Regulation, Expression and Function of the Testis-Specific Protein Y-Encoded (TSPY) Gene 2010-08-18 doi: 10.3390/genes1020244 Stephanie Schubert Jörg Schmidtke http://www.mdpi.com/2073-4425/1/2/227/ The invention of next-generation-sequencing has revolutionized almost all fields of genetics, but few have profited from it as much as the field of ancient DNA research. From its beginnings as an interesting but rather marginal discipline, ancient DNA research is now on its way into the centre of evolutionary biology. In less than a year from its invention next-generation-sequencing had increased the amount of DNA sequence data available from extinct organisms by several orders of magnitude. Ancient DNA  research is now not only adding a temporal aspect to evolutionary studies and allowing for the observation of evolution in real time, it also provides important data to help understand the origins of our own species. Here we review progress that has been made in next-generation-sequencing of ancient DNA over the past five years and evaluate sequencing strategies and future directions. http://www.mdpi.com/2073-4425/1/2/227/ Wed, 28 Jul 2010 00:00:00 CEST Genes 2010-07-28 1 2 Review 227 243 2073-4425 Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives 2010-07-28 doi: 10.3390/genes1020227 Michael Knapp Michael Hofreiter http://www.mdpi.com/2073-4425/1/2/210/ Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases. http://www.mdpi.com/2073-4425/1/2/210/ Wed, 21 Jul 2010 00:00:00 CEST Genes 2010-07-21 1 2 Article 210 226 2073-4425 454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology 2010-07-21 doi: 10.3390/genes1020210 David J. Rooks Darren L. Smith James E. McDonald Martin J. Woodward Alan J. McCarthy Heather E. Allison http://www.mdpi.com/2073-4425/1/2/193/ In the house mouse there are numerous chromosomal races distinguished by different combinations of metacentric chromosomes. These may come into contact with each other and with the ancestral all-acrocentric race, and form hybrid zones. The chromosomal clines that make up these hybrid zones may be coincident or separated from each other (staggered). Such staggered hybrid zones are interesting because they may include populations of individuals homozygous for a mix of features of the hybridising races. We review the characteristics of four staggered hybrid zones in the house mouse and discuss whether they are examples of primary or secondary contact and whether they represent reticulate evolution or not. However, the most important aspect of staggered hybrid zones is that the homozygous populations within the zones have the potential to expand their distributions and become new races (a process termed ‘zonal raciation’). In this way they can add to the total ‘stock’ of chromosomal races in the species concerned. Speciation is an infrequent phenomenon that may involve an unusual set of circumstances. Each one of the products of zonal raciation has the potential to become a new species and by having more races increases the chance of a speciation event. http://www.mdpi.com/2073-4425/1/2/193/ Mon, 19 Jul 2010 00:00:00 CEST Genes 2010-07-19 1 2 Review 193 209 2073-4425 Staggered Chromosomal Hybrid Zones in the House Mouse: Relevance to Reticulate Evolution and Speciation 2010-07-19 doi: 10.3390/genes1020193 İslam Gündüz Christianne L. Pollock Mabel D. Giménez Daniel W. Förster Thomas A. White Maria A. Sans-Fuentes Heidi C. Hauffe Jacint Ventura María José López-Fuster Jeremy B. Searle http://www.mdpi.com/2073-4425/1/2/166/ The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants. http://www.mdpi.com/2073-4425/1/2/166/ Fri, 02 Jul 2010 00:00:00 CEST Genes 2010-07-02 1 2 Review 166 192 2073-4425 Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation) 2010-07-02 doi: 10.3390/genes1020166 Chester Leitch Soltis Soltis http://www.mdpi.com/2073-4425/1/2/143/ Epigenetic modifications play an important role in lymphoid malignancies. This has been evidenced by the large body of work published using microarray technologies to generate methylation profiles for numerous types and subtypes of lymphoma and leukemia. These studies have shown the importance of defining the epigenome so that we can better understand the biology of lymphoma. Recent advances in DNA sequencing technology have transformed the landscape of epigenomic analysis as we now have the ability to characterize the genome-wide distribution of chromatin modifications and DNA methylation using next-generation sequencing. To take full advantage of the throughput of next-generation sequencing, there are many methodologies that have been developed and many more that are currently being developed. Choosing the appropriate methodology is fundamental to the outcome of next-generation sequencing studies. In this review, published technologies and methodologies applicable to studying the methylome are presented. In addition, progress towards defining the methylome in lymphoma is discussed and prospective directions that have been made possible as a result of next-generation sequencing technology. Finally, methodologies are introduced that have not yet been published but that are being explored in the pursuit of defining the lymphoma methylome. http://www.mdpi.com/2073-4425/1/2/143/ Thu, 01 Jul 2010 00:00:00 CEST Genes 2010-07-01 1 2 Review 143 165 2073-4425 Next Generation Sequencing: Advances in Characterizing the Methylome 2010-07-01 doi: 10.3390/genes1020143 Taylor Shi Caldwell http://www.mdpi.com/2073-4425/1/1/124/ One common form of reticulate evolution arises as a consequence of secondary contact between previously allopatric populations. Using extensive coalescent simulations, we describe the conditions for, and extent of, the introgression of genetic material into the genome of a colonizing population from an endemic population. The simulated coalescent histories are sampled from models that describe the evolution of entire chromosomes, thereby allowing the expected length of introgressed haplotypes to be estimated. The results indicate that our ability to identify reticulate evolution from genetic data is highly variable and depends critically upon the duration of the period of allopatry, the timing of the secondary contact event, as well as the sizes of the populations at the time of contact. One particularly interesting result arises when secondary contact occurs close to the time of a severe founder event, in this case, genetic introgression can be substantially more difficult to detect. However, if secondary contact occurs after such a founding event, when the range of the colonizing population increases, introgression is more readily detectable across the genome. This result may have important implications for our ability to detect introgression between ancestrally bottlenecked modern human populations and archaic hominin species, such as Neanderthals. http://www.mdpi.com/2073-4425/1/1/124/ Fri, 25 Jun 2010 00:00:00 CEST Genes 2010-06-25 1 1 Article 124 142 2073-4425 Population Genomics of Secondary Contact 2010-06-25 doi: 10.3390/genes1010124 Geneva Garrigan http://www.mdpi.com/2073-4425/1/1/102/ Little attention has been given to the role that introgression and hybridization have played in the evolution of parasites. Most studies are host-centric and ask if the hybrid of a free-living species is more or less susceptible to parasite infection. Here we focus on what is known about how introgression and hybridization have influenced the evolution of protozoan and helminth parasites of animals. There are reports of genome or gene introgression from distantly related taxa into apicomplexans and filarial nematodes. Most common are genetic based reports of potential hybridization among congeneric taxa, but in several cases, more work is needed to definitively conclude current hybridization. In the medically important Trypanosoma it is clear that some clonal lineages are the product of past hybridization events. Similarly, strong evidence exists for current hybridization in human helminths such as Schistosoma and Ascaris. There remain topics that warrant further examination such as the potential hybrid origin of polyploid platyhelminths. Furthermore, little work has investigated the phenotype or fitness, and even less the epidemiological significance of hybrid parasites. http://www.mdpi.com/2073-4425/1/1/102/ Wed, 09 Jun 2010 00:00:00 CEST Genes 2010-06-09 1 1 Review 102 123 2073-4425 An Infectious Topic in Reticulate Evolution: Introgression and Hybridization in Animal Parasites 2010-06-09 doi: 10.3390/genes1010102 Detwiler Criscione http://www.mdpi.com/2073-4425/1/1/85/ DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states. http://www.mdpi.com/2073-4425/1/1/85/ Fri, 04 Jun 2010 00:00:00 CEST Genes 2010-06-04 1 1 Review 85 101 2073-4425 The Application of Next Generation Sequencing in DNA Methylation Analysis 2010-06-04 doi: 10.3390/genes1010085 Zhang Jeltsch http://www.mdpi.com/2073-4425/1/1/70/ miRNAs constitute a family of small RNA species that have been demonstrated to play a central role in regulating gene expression in many organisms. With the advent of next generation sequencing, new opportunities have arisen to identify and quantify miRNAs and elucidate their function. The unprecedented sequencing depth reached by next generation sequencing technologies makes it possible to get a comprehensive miRNA landscape but also poses new challenges for data analysis. We provide an overview of strategies used for miRNA sequencing, public miRNA resources, and useful methods and tools that are available for data analysis. http://www.mdpi.com/2073-4425/1/1/70/ Thu, 03 Jun 2010 00:00:00 CEST Genes 2010-06-03 1 1 Review 70 84 2073-4425 Next Generation Sequencing of miRNAs – Strategies, Resources and Methods 2010-06-03 doi: 10.3390/genes1010070 Motameny Wolters Nürnberg Schumacher http://www.mdpi.com/2073-4425/1/1/38/ In the years since the first complete human genome sequence was reported, there has been a rapid development of technologies to facilitate high-throughput sequence analysis of DNA (termed “next-generation” sequencing). These novel approaches to DNA sequencing offer the promise of complete genomic analysis at a cost feasible for routine clinical diagnostics. However, the ability to more thoroughly interrogate genomic sequence raises a number of important issues with regard to result interpretation, laboratory workflow, data storage, and ethical considerations. This review describes the current high-throughput sequencing platforms commercially available, and compares the inherent advantages and disadvantages of each. The potential applications for clinical diagnostics are considered, as well as the need for software and analysis tools to interpret the vast amount of data generated. Finally, we discuss the clinical and ethical implications of the wealth of genetic information generated by these methods. Despite the challenges, we anticipate that the evolution and refinement of high-throughput DNA sequencing technologies will catalyze a new era of personalized medicine based on individualized genomic analysis. http://www.mdpi.com/2073-4425/1/1/38/ Tue, 25 May 2010 00:00:00 CEST Genes 2010-05-25 1 1 Review 38 69 2073-4425 Next Generation DNA Sequencing and the Future of Genomic Medicine 2010-05-25 doi: 10.3390/genes1010038 Anderson Schrijver http://www.mdpi.com/2073-4425/1/1/23/ Chronic tinnitus is a highly prevalent and often incapacitating condition frequently associated with sensorineural hearing loss. While its etiology remains incompletely understood there is a growing awareness of genetic factors that predispose to, or aggravate chronic tinnitus. Candidate genes for the disorder include KCNE1, a potassium channel subunit gene that has been implicated in maturation defects of central vestibular neurons, in Menière\'s disease, and in noise-induced hearing loss. 201 Caucasian outpatients with a diagnosis of chronic tinnitus were systematically screened for mutations in the KCNE1 open reading frame and in the adjacent sequence by direct sequencing. Allele frequencies were determined for 46 known variants, plus two novel KCNE1 mutations. These comprised one missense substitution (V47I) in the highly conserved region encoding the KCNE1 transmembrane domain, and one rare variant in the gene\'s 3\'UTR. When genotypes were grouped assuming dominance of the minor alleles, no significant genotype or compound genotype effects were observed on tinnitus severity. The newly identified V47I substitution argues in favor of an enlarged spectrum of mutations in hearing disorders. However, with regard to allele frequencies in healthy control populations from earlier studies, more common KCNE1 variants are unlikely to play a major role in chronic tinnitus. Further investigations are invited to address variation in additional channel subunits as possible risk factors in tinnitus. http://www.mdpi.com/2073-4425/1/1/23/ Wed, 28 Apr 2010 00:00:00 CEST Genes 2010-04-28 1 1 Article 23 37 2073-4425 An Examination of KCNE1 Mutations and Common Variants in Chronic Tinnitus 2010-04-28 doi: 10.3390/genes1010023 Sand Luettich Kleinjung Hajak Langguth http://www.mdpi.com/2073-4425/1/1/9/ In this review, we discuss findings from studies carried out over the past 20+ years that document the occurrence of asymmetric introgressive hybridization in a plant clade. In particular, analyses of natural and experimental hybridization have demonstrated the consistent introgression of genes from Iris fulva into both Iris brevicaulis and Iris hexagona. Furthermore, our analyses have detected certain prezygotic and postzygotic barriers to reproduction that appear to contribute to the asymmetric introgression. Finally, our studies have determined that a portion of the genes transferred apparently affects adaptive traits. http://www.mdpi.com/2073-4425/1/1/9/ Mon, 15 Mar 2010 00:00:00 CET Genes 2010-03-15 1 1 Review 9 22 2073-4425 Asymmetric Introgressive Hybridization Among Louisiana Iris Species 2010-03-15 doi: 10.3390/genes1010009 Arnold Tang Knapp Martin http://www.mdpi.com/2073-4425/1/1/4/ Embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs) hold great promise for the therapeutic treatment of human diseases, but their functional similarity, their stability and especially the mechanism underlying their derivation are not yet clearly explained. [...] http://www.mdpi.com/2073-4425/1/1/4/ Tue, 09 Mar 2010 00:00:00 CET Genes 2010-03-09 1 1 Editorial 4 8 2073-4425 The Secret Lives of Pluripotent Cells: There and Back Again 2010-03-09 doi: 10.3390/genes1010004 Paolo Cinelli http://www.mdpi.com/2073-4425/1/1/1/ Genes have been in the scientific vocabulary for a hundred years. The term "gene" was proposed by the Danish plant scientist Wilhelm Johannsen in the first decade of the 20th century. For Johannsen, the gene remained an abstract concept, "free of any hypothesis" [1], but others were already pointing to chromosomes as the likely location of genes. The science of genetics was born at that time, and genes were rapidly connected with mutations, with patterns of inheritance, with development, with quantitative traits, with evolution and with biochemical pathways. All this was achieved without knowledge of the physical nature of genes, but this changed in mid-century with the discoveries of molecular biology. DNA was revealed as the genetic material, and the mechanisms were elucidated by which the information was encoded, and propagated, and linked to the phenotype. However, the concept of a "gene" did not become clearer. Quite the reverse, as the units of mutation, of recombination, of inheritance, of expression, of regulation, etc. did not necessarily coincide. [...] http://www.mdpi.com/2073-4425/1/1/1/ Mon, 02 Nov 2009 00:00:00 CET Genes 2009-11-02 1 1 Editorial 1 3 2073-4425 Genes: an Open Access Journal 2009-11-02 doi: 10.3390/genes1010001 J. Peter W. Young