http://www.mdpi.com/journal/biology Latest open access articles published in Biology at http://www.mdpi.com/journal/biology http://www.mdpi.com/2079-7737/2/2/784 Sixteen epilithic lichen samples (13 species), collected from seven locations in Northern and Southern Victoria Land in Antarctica, were investigated for the presence of black fungi. Thirteen fungal strains isolated were studied by both morphological and molecular methods. Nuclear ribosomal 18S gene sequences were used together with the most similar published and unpublished sequences of fungi from other sources, to reconstruct an ML tree. Most of the studied fungi could be grouped together with described or still unnamed rock-inhabiting species in lichen dominated Antarctic cryptoendolithic communities. At the edge of life, epilithic lichens withdraw inside the airspaces of rocks to find conditions still compatible with life; this study provides evidence, for the first time, that the same microbes associated to epilithic thalli also have the same fate and chose endolithic life. These results support the concept of lichens being complex symbiotic systems, which offer attractive and sheltered habitats for other microbes. Biology 2013-05-17 2 2 Article 10.3390/biology2020784 784 797 2079-7737 2013-05-17 doi: 10.3390/biology2020784 Laura Selbmann Martin Grube Silvano Onofri Daniela Isola Laura Zucconi http://www.mdpi.com/2079-7737/2/2/755 The bulk of Earth’s biosphere is cold (<5 °C) and inhabited by psychrophiles. Biocatalysts from psychrophilic organisms (psychrozymes) have attracted attention because of their application in the ongoing efforts to decrease energy consumption. Proteinases as a class represent the largest category of industrial enzymes. There has been an emphasis on employing cold-active proteases in detergents because this allows laundry operations at ambient temperatures. Proteases have been used in environmental bioremediation, food industry and molecular biology. In view of the present limited understanding and availability of cold-active proteases with diverse characteristics, it is essential to explore Earth’s surface more in search of an ideal cold-active protease. The understanding of molecular and mechanistic details of these proteases will open up new avenues to tailor proteases with the desired properties. A detailed account of the developments in the production and applications of cold-active proteases is presented in this review. Biology 2013-05-03 2 2 Review 10.3390/biology2020755 755 783 2079-7737 2013-05-03 doi: 10.3390/biology2020755 Swati Joshi Tulasi Satyanarayana http://www.mdpi.com/2079-7737/2/2/742 Using an 18-year dataset of arrival dates of 65 species of Maine migratory breeding birds, I take a deeper view of the data to ask questions about the shapes of the distribution. For each year, most species show a consistent right-skewed pattern of distribution, suggesting that selection is stronger against individuals that arrive too early compared to those that arrive later. Distributions are consistently leptokurtic, indicating a narrow window of optimal arrival dates. Species that arrive earlier in the spring show higher skewness and kurtosis values. Nectarivorous species showed more pronounced skewness. Wintering area did not explain patterns of skewness or kurtosis. Deviations from average temperatures and the North Atlantic Oscillation index explained little variation in skewness and kurtosis. When arrival date distributions are broken down into different medians (e.g., 5% median and 75% median), stronger correlations emerge for portions of the distribution that are adjacent, suggesting species fine-tune the progress of their migration. Interspecific correlations for birds arriving around the same time are stronger for earliest migrants (the 25% median) compared to the true median and the 75% median. Biology 2013-04-26 2 2 Article 10.3390/biology2020742 742 754 2079-7737 2013-04-26 doi: 10.3390/biology2020742 W. Wilson http://www.mdpi.com/2079-7737/2/2/719 Polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. Indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. Since the discovery that these ecosystems, contrary to what was initially expected, sustain a rather high density and broad diversity of living organisms, increasing efforts have been dedicated to the understanding of the molecular mechanisms involved in their successful adaptation to apparently unfavorable physical conditions. The first question that comes to mind is: How do these organisms compensate for the exponential decrease of reaction rate when temperature is lowered? As most of the chemical reactions that occur in living organisms are catalyzed by enzymes, the kinetic and thermodynamic properties of cold-adapted enzymes have been investigated. Presently, many crystallographic structures of these enzymes have been elucidated and allowed for a rather clear view of their adaptation to cold. They are characterized by a high specific activity at low and moderate temperatures and a rather low thermal stability, which induces a high flexibility that prevents the freezing effect of low temperatures on structure dynamics. These enzymes also display a low activation enthalpy that renders them less dependent on temperature fluctuations. This is accompanied by a larger negative value of the activation entropy, thus giving evidence of a more disordered ground state. Appropriate folding kinetics is apparently secured through a large expression of trigger factors and peptidyl–prolyl cis/trans-isomerases. Biology 2013-04-16 2 2 Review 10.3390/biology2020719 719 741 2079-7737 2013-04-16 doi: 10.3390/biology2020719 Charles Gerday http://www.mdpi.com/2079-7737/2/2/702 Streptococcus suis is an important swine pathogen associated with a variety of infections such as meningitis, arthritis and septicemia. The bacterium is zoonotic and has been found to cause meningitis especially in humans occupationally exposed to infected pigs. Since adhesion is a prerequisite for colonization and subsequent infection, anti-adhesion treatment seems a natural alternative to traditional treatment with antibiotics. In order to optimize the inhibitory potency a multivalency approach was taken in the inhibitor design. A synthetic tetravalent galabiose compound was chosen which had previously shown promising anti-adhesion effects with S. suis in vitro. The aim of this study was to evaluate the in vivo effects of the compound using an infection peritonitis mouse model. As such S. suis serotype 2 infection and treatment were tested in vivo and the effects were compared to the effect of treatment with penicillin. Biology 2013-04-08 2 2 Article 10.3390/biology2020702 702 718 2079-7737 2013-04-08 doi: 10.3390/biology2020702 Roland Pieters Hans-Christian Slotved Hanne Mortensen Lene Arler Jukka Finne Sauli Haataja John Joosten Hilbert Branderhorst Karen Krogfelt http://www.mdpi.com/2079-7737/2/2/693 Cyanobacteria and lichens living under sandstone surfaces in the McMurdo Dry Valleys require snow for moisture. Snow accumulated beyond a thin layer, however, is counterproductive, interfering with rock insolation, snow melting, and photosynthetic access to light. With this in mind, the facts that rock slope and direction control colonization, and that climate change results in regional extinctions, can be explained. Vertical cliffs, which lack snow cover and are perpetually dry, are devoid of organisms. Boulder tops and edges can trap snow, but gravity and wind prevent excessive buildup. There, the organisms flourish. In places where snow-thinning cannot occur and snow drifts collect, rocks may contain living or dead communities. In light of these observations, the possibility of finding extraterrestrial endolithic communities on Mars cannot be eliminated. Biology 2013-04-03 2 2 Article 10.3390/biology2020693 693 701 2079-7737 2013-04-03 doi: 10.3390/biology2020693 Henry Sun http://www.mdpi.com/2079-7737/2/2/651 Elevations in atmospheric carbon dioxide (CO2) are anticipated to acidify oceans because of fundamental changes in ocean chemistry created by CO2 absorption from the atmosphere. Over the next century, these elevated concentrations of atmospheric CO2 are expected to result in a reduction of the surface ocean waters from 8.1 to 7.7 units as well as a reduction in carbonate ion (CO32−) concentration. The potential impact that this change in ocean chemistry will have on marine and estuarine organisms and ecosystems is a growing concern for scientists worldwide. While species-specific responses to ocean acidification are widespread across a number of marine taxa, molluscs are one animal phylum with many species which are particularly vulnerable across a number of life-history stages. Molluscs make up the second largest animal phylum on earth with 30,000 species and are a major producer of CaCO3. Molluscs also provide essential ecosystem services including habitat structure and food for benthic organisms (i.e., mussel and oyster beds), purification of water through filtration and are economically valuable. Even sub lethal impacts on molluscs due to climate changed oceans will have serious consequences for global protein sources and marine ecosystems. Biology 2013-04-02 2 2 Review 10.3390/biology2020651 651 692 2079-7737 2013-04-02 doi: 10.3390/biology2020651 Laura Parker Pauline Ross Wayne O'Connor Hans Pörtner Elliot Scanes John Wright http://www.mdpi.com/2079-7737/2/2/629 Lake Vostok is the largest of the nearly 400 subglacial Antarctic lakes and has been continuously buried by glacial ice for 15 million years. Extreme cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier) and dissolved oxygen (delivered by melting meteoric ice), in addition to limited nutrients and complete darkness, combine to produce one of the most extreme environments on Earth. Metagenomic/metatranscriptomic analyses of ice that accreted over a shallow embayment and over the southern main lake basin indicate the presence of thousands of species of organisms (94% Bacteria, 6% Eukarya, and two Archaea). The predominant bacterial sequences were closest to those from species of Firmicutes, Proteobacteria and Actinobacteria, while the predominant eukaryotic sequences were most similar to those from species of ascomycetous and basidiomycetous Fungi. Based on the sequence data, the lake appears to contain a mixture of autotrophs and heterotrophs capable of performing nitrogen fixation, nitrogen cycling, carbon fixation and nutrient recycling. Sequences closest to those of psychrophiles and thermophiles indicate a cold lake with possible hydrothermal activity. Sequences most similar to those from marine and aquatic species suggest the presence of marine and freshwater regions. Biology 2013-03-28 2 2 Article 10.3390/biology2020629 629 650 2079-7737 2013-03-28 doi: 10.3390/biology2020629 Scott Rogers Yury Shtarkman Zeynep Koçer Robyn Edgar Ram Veerapaneni Tom D'Elia http://www.mdpi.com/2079-7737/2/2/603 Inherent to sea ice, like other high latitude environments, is the strong seasonality driven by changes in insolation throughout the year. Sea-ice organisms are exposed to shifting, sometimes limiting, conditions of temperature and salinity. An array of adaptations to survive these and other challenges has been acquired by those organisms that inhabit the ice. One key adaptive response is the production of extracellular polymeric substances (EPS), which play multiple roles in the entrapment, retention and survival of microorganisms in sea ice. In this concept paper we consider two main areas of sea-ice microbiology: the physico-chemical properties that define sea ice as a microbial habitat, imparting particular advantages and limits; and extracellular responses elicited in microbial inhabitants as they exploit or survive these conditions. Emphasis is placed on protective strategies used in the face of fluctuating and extreme environmental conditions in sea ice. Gaps in knowledge and testable hypotheses are identified for future research. Biology 2013-03-28 2 2 Review 10.3390/biology2020603 603 628 2079-7737 2013-03-28 doi: 10.3390/biology2020603 Marcela Ewert Jody Deming http://www.mdpi.com/2079-7737/2/2/587 Antitumor virotherapy consists of the use of replication-competent viruses to infect and kill tumor cells preferentially, without damaging healthy cells. Vaccine-attenuated strains of measles virus (MV) are good candidates for this approach. Attenuated MV uses the CD46 molecule as a major entry receptor into cells. This molecule negatively regulates the complement system and is frequently overexpressed by cancer cells to escape lysis by the complement system. MV exhibits oncolytic properties in many cancer types in vitro, and in mouse models. Phase I clinical trials using MV are currently underway. Here, we review the state of this therapeutic approach, with a focus on the effects of MV on the antitumor immune response. Biology 2013-03-28 2 2 Review 10.3390/biology2020587 587 602 2079-7737 2013-03-28 doi: 10.3390/biology2020587 Jean-Baptiste Guillerme Marc Gregoire Frédéric Tangy Jean-François Fonteneau http://www.mdpi.com/2079-7737/2/2/555 Myofibroblasts (MFBs) are smooth muscle-like cells that provide contractile force required for tissue repair during wound healing. The leading agonist for MFB differentiation is transforming growth factor β1 (TGFβ1) that induces transcription of genes encoding smooth muscle α-actin (SMαA) and interstitial collagen that are markers for MFB differentiation. TGFβ1 augments activation of Smad transcription factors, pro-survival Akt kinase, and p38 MAP kinase as well as Wingless/int (Wnt) developmental signaling. These actions conspire to activate β-catenin needed for expression of cyclin D, laminin, fibronectin, and metalloproteinases that aid in repairing epithelial cells and their associated basement membranes. Importantly, β-catenin also provides a feed-forward stimulus that amplifies local TGFβ1 autocrine/paracrine signaling causing transition of mesenchymal stromal cells, pericytes, and epithelial cells into contractile MFBs. Complex, mutually interactive mechanisms have evolved that permit several mammalian cell types to activate the SMαA promoter and undergo MFB differentiation. These molecular controls will be reviewed with an emphasis on the dynamic interplay between serum response factor, TGFβ1-activated Smads, Wnt-activated β-catenin, p38/calcium-activated NFAT protein, and the RNA-binding proteins, Purα, Purβ, and YB-1, in governing transcriptional and translational control of the SMαA gene in injury-activated MFBs. Biology 2013-03-28 2 2 Review 10.3390/biology2020555 555 586 2079-7737 2013-03-28 doi: 10.3390/biology2020555 Arthur Strauch Seethalakshmi Hariharan http://www.mdpi.com/2079-7737/2/2/533 Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants. Biology 2013-03-27 2 2 Review 10.3390/biology2020533 533 554 2079-7737 2013-03-27 doi: 10.3390/biology2020533 Terrence Bell Katrina Callender Lyle Whyte Charles Greer http://www.mdpi.com/2079-7737/2/2/514 The most familiar icy environments, seasonal lake and stream ice, have received little microbiological study. Bacteria and Eukarya dominated the microbial assemblage within the seasonal ice of Miquelon Lake, a shallow saline lake in Alberta, Canada. The bacterial assemblages were moderately diverse and did not vary with either ice depth or time. The closest relatives of the bacterial sequences from the ice included Actinobacteria, Bacteroidetes, Proteobacteria, Verrucomicrobia, and Cyanobacteria. The eukaryotic assemblages were less conserved and had very low diversity. Green algae relatives dominated the eukaryotic gene sequences; however, a copepod and cercozoan were also identified, possibly indicating the presence of complete microbial loop. The persistence of a chlorophyll a peak at 25–30 cm below the ice surface, despite ice migration and brine flushing, indicated possible biological activity within the ice. This is the first study of the composition, diversity, and stability of seasonal lake ice. Biology 2013-03-27 2 2 Article 10.3390/biology2020514 514 532 2079-7737 2013-03-27 doi: 10.3390/biology2020514 Anna Bramucci Sukkyun Han Justin Beckers Christian Haas Brian Lanoil http://www.mdpi.com/2079-7737/2/2/481 A general prediction of ecological theory is that climate change will favor invasive nonindigenous plant species (NIPS) over native species. However, the relative fitness advantage enjoyed by NIPS is often affected by resource limitation and potentially by extreme climatic events such as drought. Genetic constraints may also limit the ability of NIPS to adapt to changing climatic conditions. In this study, we investigated evidence for potential NIPS advantage under climate change in two sympatric perennial stipoid grasses from southeast Australia, the NIPS Nassella neesiana and the native Austrostipa bigeniculata. We compared the growth and reproduction of both species under current and year 2050 drought, temperature and CO2 regimes in a multifactor outdoor climate simulation experiment, hypothesizing that NIPS advantage would be higher under more favorable growing conditions. We also compared the quantitative variation and heritability of growth traits in populations of both species collected along a 200 km climatic transect. In contrast to our hypothesis we found that the NIPS N. neesiana was less responsive than A. bigeniculata to winter warming but maintained higher reproductive output during spring drought. However, overall tussock expansion was far more rapid in N. neesiana, and so it maintained an overall fitness advantage over A. bigeniculata in all climate regimes. N. neesiana also exhibited similar or lower quantitative variation and growth trait heritability than A. bigeniculata within populations but greater variability among populations, probably reflecting a complex past introduction history. We found some evidence that additional spring warmth increases the impact of drought on reproduction but not that elevated atmospheric CO2 ameliorates drought severity. Overall, we conclude that NIPS advantage under climate change may be limited by a lack of responsiveness to key climatic drivers, reduced genetic variability in range-edge populations, and complex drought-CO2 interactions. Biology 2013-03-27 2 2 Article 10.3390/biology2020481 481 513 2079-7737 2013-03-27 doi: 10.3390/biology2020481 Robert Godfree Bruce Robertson Washington Gapare Miloš Ivković David Marshall Brendan Lepschi Alexander Zwart http://www.mdpi.com/2079-7737/2/1/445 Intertidal wetlands are recognised for the provision of a range of valued ecosystem services. The two major categories of intertidal wetlands discussed in this contribution are saltmarshes and mangrove forests. Intertidal wetlands are under threat from a range of anthropogenic causes, some site-specific, others acting globally. Globally acting factors include climate change and its driving cause—the increasing atmospheric concentrations of greenhouse gases. One direct consequence of climate change will be global sea level rise due to thermal expansion of the oceans, and, in the longer term, the melting of ice caps and glaciers. The relative sea level rise experienced at any one locality will be affected by a range of factors, as will the response of intertidal wetlands to the change in sea level. If relative sea level is rising and sedimentation within intertidal wetlands does not keep pace, then there will be loss of intertidal wetlands from the seaward edge, with survival of the ecosystems only possible if they can retreat inland. When retreat is not possible, the wetland area will decline in response to the “squeeze” experienced. Any changes to intertidal wetland vegetation, as a consequence of climate change, will have flow on effects to biota, while changes to biota will affect intertidal vegetation. Wetland biota may respond to climate change by shifting in distribution and abundance landward, evolving or becoming extinct. In addition, impacts from ocean acidification and warming are predicted to affect the fertilisation, larval development, growth and survival of intertidal wetland biota including macroinvertebrates, such as molluscs and crabs, and vertebrates such as fish and potentially birds. The capacity of organisms to move and adapt will depend on their life history characteristics, phenotypic plasticity, genetic variability, inheritability of adaptive characteristics, and the predicted rates of environmental change. Biology 2013-03-19 2 1 Review 10.3390/biology2010445 445 480 2079-7737 2013-03-19 doi: 10.3390/biology2010445 Pauline Ross Paul Adam http://www.mdpi.com/2079-7737/2/1/419 Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. Biology 2013-03-13 2 1 Article 10.3390/biology2010419 419 444 2079-7737 2013-03-13 doi: 10.3390/biology2010419 Tamaki Yuri Rebecca Kimball John Harshman Rauri Bowie Michael Braun Jena Chojnowski Kin-Lan Han Shannon Hackett Christopher Huddleston William Moore Sushma Reddy Frederick Sheldon David Steadman Christopher Witt Edward Braun http://www.mdpi.com/2079-7737/2/1/399 The Class Amphibia is one of the most severely impacted taxa in an on-going global biodiversity crisis. Because amphibian reproduction is tightly associated with the presence of water, climatic changes that affect water availability pose a particularly menacing threat to both aquatic and terrestrial-breeding amphibians. We explore the impacts that one facet of climate change—that of extreme variation in precipitation—may have on amphibians. This variation is manifested principally as increases in the incidence and severity of both drought and major storm events. We stress the need to consider not only total precipitation amounts but also the pattern and timing of rainfall events. Such rainfall “pulses” are likely to become increasingly more influential on amphibians, especially in relation to seasonal reproduction. Changes in reproductive phenology can strongly influence the outcome of competitive and predatory interactions, thus potentially altering community dynamics in assemblages of co-existing species. We present a conceptual model to illustrate possible landscape and metapopulation consequences of alternative climate change scenarios for pond-breeding amphibians, using the Mole Salamander, Ambystoma talpoideum, as an example. Although amphibians have evolved a variety of life history strategies that enable them to cope with environmental uncertainty, it is unclear whether adaptations can keep pace with the escalating rate of climate change. Climate change, especially in combination with other stressors, is a daunting challenge for the persistence of amphibians and, thus, the conservation of global biodiversity. Biology 2013-03-11 2 1 Review 10.3390/biology2010399 399 418 2079-7737 2013-03-11 doi: 10.3390/biology2010399 Susan Walls William Barichivich Mary Brown http://www.mdpi.com/2079-7737/2/1/378 Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care. Biology 2013-03-01 2 1 Review 10.3390/biology2010378 378 398 2079-7737 2013-03-01 doi: 10.3390/biology2010378 Karen Frese Hugo Katus Benjamin Meder http://www.mdpi.com/2079-7737/2/1/356 Climate change is already altering the landscape at high latitudes. Permafrost is thawing, the growing season is starting earlier, and, as a result, certain regions in the Arctic may be subjected to an increased incidence of freeze-thaw events. The potential release of carbon and nutrients from soil microbial cells that have been lysed by freeze-thaw transitions could have significant impacts on the overall carbon balance of arctic ecosystems, and therefore on atmospheric CO2 concentrations. However, the impact of repeated freezing and thawing with the consequent growth and recrystallization of ice on microbial communities is still not well understood. Soil samples from three distinct sites, representing Canadian geographical low arctic, mid-arctic and high arctic soils were collected from Daring Lake, Alexandra Fjord and Cambridge Bay sampling sites, respectively. Laboratory-based experiments subjected the soils to multiple freeze-thaw cycles for 14 days based on field observations (0 °C to −10 °C for 12 h and −10 °C to 0 °C for 12 h) and the impact on the communities was assessed by phospholipid fatty acid (PLFA) methyl ester analysis and 16S ribosomal RNA gene sequencing. Both data sets indicated differences in composition and relative abundance between the three sites, as expected. However, there was also a strong variation within the two high latitude sites in the effects of the freeze-thaw treatment on individual PLFA and 16S-based phylotypes. These site-based heterogeneities suggest that the impact of climate change on soil microbial communities may not be predictable a priori; minor differential susceptibilities to freeze-thaw stress could lead to a “butterfly effect” as described by chaos theory, resulting in subsequent substantive differences in microbial assemblages. This perspectives article suggests that this is an unwelcome finding since it will make future predictions for the impact of on-going climate change on soil microbial communities in arctic regions all but impossible. Biology 2013-02-28 2 1 Article 10.3390/biology2010356 356 377 2079-7737 2013-02-28 doi: 10.3390/biology2010356 Niraj Kumar Paul Grogan Haiyan Chu Casper Christiansen Virginia Walker http://www.mdpi.com/2079-7737/2/1/341 Almost all transfection protocols for mammalian cells use a drug resistance gene for the selection of transfected cells. However, it always requires the characterization of each isolated clone regarding transgene expression, which is time-consuming and labor-intensive. In the current study, we developed a novel method to selectively isolate clones with high transgene expression without drug selection. Porcine embryonic fibroblasts were transfected with pCEIEnd, an expression vector that simultaneously expresses enhanced green fluorescent protein (EGFP) and endo-b-galactosidase C(EndoGalC; an enzyme capable of digesting cell surface a-Gal epitope) upon transfection. After transfection, the surviving cells were briefly treated with IB4SAP (a-Gal epitope-specific BS-I-B4 lectin conjugated with a toxin saporin). The treated cells were then allowed to grow in normal medium, during which only cells strongly expressing EndoGalC and EGFP would survive because of the absence of a-Gal epitopes on their cell surface. Almost all the surviving colonies after IB4SAP treatment were in fact negative for BS-I-B4 staining, and also strongly expressed EGFP. This system would be particularly valuable for researchers who wish to perform large-scale production of therapeutically important recombinant proteins. Biology 2013-02-28 2 1 Article 10.3390/biology2010341 341 355 2079-7737 2013-02-28 doi: 10.3390/biology2010341 Masahiro Sato Eri Akasaka Issei Saitoh Masato Ohtsuka Shingo Nakamura Takayuki Sakurai Satoshi Watanabe http://www.mdpi.com/2079-7737/2/1/331 The discovery of extensive and complex hypolithic communities in both cold and hot deserts has raised many questions regarding their ecology, biodiversity and relevance in terms of regional productivity. However, most hypolithic research has focused on the bacterial elements of the community. This study represents the first investigation of micro-eukaryotic communities in all three hypolith types. Here we show that Antarctic hypoliths support extensive populations of novel uncharacterized bryophyta, fungi and protists and suggest that well known producer-decomposer-predator interactions may create the necessary conditions for hypolithic productivity in Antarctic deserts. Biology 2013-02-22 2 1 Communication 10.3390/biology2010331 331 340 2079-7737 2013-02-22 doi: 10.3390/biology2010331 Jarishma Gokul Angel Valverde Marla Tuffin Stephen Cary Don Cowan http://www.mdpi.com/2079-7737/2/1/317 The Arctic environment is undergoing changes due to climate shifts, receiving contaminants from distant sources and experiencing increased human activity. Climate change may alter microbial functioning by increasing growth rates and substrate use due to increased temperature. This may lead to changes of process rates and shifts in the structure of microbial communities. Biodiversity may increase as the Arctic warms and population shifts occur as psychrophilic/psychrotolerant species disappear in favor of more mesophylic ones. In order to predict how ecological processes will evolve as a function of global change, it is essential to identify which populations participate in each process, how they vary physiologically, and how the relative abundance, activity and community structure will change under altered environmental conditions. This review covers aspects of the importance and implication of snowpack in microbial ecology emphasizing the diversity and activity of these critical members of cold zone ecosystems. Biology 2013-02-05 2 1 Review 10.3390/biology2010317 317 330 2079-7737 2013-02-05 doi: 10.3390/biology2010317 Catherine Larose Aurélien Dommergue Timothy Vogel http://www.mdpi.com/2079-7737/2/1/304 Hepatitis C virus (HCV), a hepatotropic virus, is a single stranded-positive RNA virus of ~9,600 nt. length belonging to the Flaviviridae family. HCV infection causes acute hepatitis, chronic hepatitis, cirrhosis and hepatocellular carcinoma (HCC). It has been reported that HCV-coding proteins interact with host-cell factors that are involved in cell cycle regulation, transcriptional regulation, cell proliferation and apoptosis. Severe inflammation and advanced liver fibrosis in the liver background are also associated with the incidence of HCV-related HCC. In this review, we discuss the mechanism of hepatocarcinogenesis in HCV-related liver diseases. Biology 2013-01-30 2 1 Review 10.3390/biology2010304 304 316 2079-7737 2013-01-30 doi: 10.3390/biology2010304 Tatsuo Kanda Osamu Yokosuka Masao Omata http://www.mdpi.com/2079-7737/2/1/284 Transcriptional regulation of genes involved in fatty acid metabolism is considered the major long-term regulatory mechanism controlling lipid homeostasis. By means of this mechanism, transcription factors, nutrients, hormones and epigenetics control not only fatty acid metabolism, but also many metabolic pathways and cellular functions at the molecular level. The regulation of the expression of many genes at the level of their transcription has already been analyzed. This review focuses on the transcriptional control of two genes involved in fatty acid biosynthesis and oxidation: the citrate carrier (CIC) and the carnitine/ acylcarnitine/carrier (CAC), which are members of the mitochondrial carrier gene family, SLC25. The contribution of tissue-specific and less tissue-specific transcription factors in activating or repressing CIC and CAC gene expression is discussed. The interaction with drugs of some transcription factors, such as PPAR and FOXA1, and how this interaction can be an attractive therapeutic approach, has also been evaluated. Moreover, the mechanism by which the expression of the CIC and CAC genes is modulated by coordinated responses to hormonal and nutritional changes and to epigenetics is highlighted. Biology 2013-01-29 2 1 Review 10.3390/biology2010284 284 303 2079-7737 2013-01-29 doi: 10.3390/biology2010284 Vito Iacobazzi Vittoria Infantino Ferdinando Palmieri http://www.mdpi.com/2079-7737/2/1/233 The Natural resistance-associated macrophage protein 1 (Nramp1 or Solute carrier 11 member 1, Slc11a1) transports divalent metals across the membrane of late endosomes and lysosomes in professional phagocytes. Nramp1 represents an ancient eukaryotic cell-autonomous defense whereas the gene duplication that yielded Nramp1 and Nramp2 predated the origin of Sarcopterygians (lobe-finned fishes and tetrapods). SLC11A1 genetic polymorphisms associated with human resistance to tuberculosis consist of potential regulatory variants. Herein, current knowledge of the regulation of SLC11A1 gene expression is reviewed and comprehensive analysis of ENCODE data available for hematopoietic cell-types suggests a hypothesis for the regulation of SLC11A1 expression during myeloid development and phagocyte functional polarization. SLC11A1 is part of a 34.6 kb CTCF-insulated locus scattered with predicted regulatory elements: a 3' enhancer, a large 5' enhancer domain and four elements spread around the transcription start site (TSS), including several C/EBP and PU.1 sites. SLC11A1 locus ends appear mobilized by ETS-related factors early during myelopoiesis; activation of both 5' and 3' enhancers in myelo-monocytic cells correlate with transcription factor binding at the TSS. Characterizing the corresponding cis/trans determinants functionally will establish the mechanisms involved and possibly reveal genetic variation that impacts susceptibility to infectious or immune diseases. Biology 2013-01-25 2 1 Article 10.3390/biology2010233 233 283 2079-7737 2013-01-25 doi: 10.3390/biology2010233 Mathieu Cellier http://www.mdpi.com/2079-7737/2/1/206 Ice deposited in Greenland and Antarctica entraps viable and nonviable microbes, as well as biomolecules, that become temporal atmospheric records. Five sections (estimated to be 500, 10,500, 57,000, 105,000 and 157,000 years before present, ybp) from the GISP2D (Greenland) ice core, three sections (500, 30,000 and 70,000 ybp) from the Byrd ice core, and four sections from the Vostok 5G (Antarctica) ice core (10,500, 57,000, 105,000 and 105,000 ybp) were studied by scanning electron microscopy, cultivation and rRNA gene sequencing. Bacterial and fungal isolates were recovered from 10 of the 12 sections. The highest numbers of isolates were found in ice core sections that were deposited during times of low atmospheric CO2, low global temperatures and low levels of atmospheric dust. Two of the sections (GISP2D at 10,500 and 157,000 ybp) also were examined using metagenomic/metatranscriptomic methods. These results indicated that sequences from microbes common to arid and saline soils were deposited in the ice during a time of low temperature, low atmospheric CO2 and high dust levels. Members of Firmicutes and Cyanobacteria were the most prevalent bacteria, while Rhodotorula species were the most common eukaryotic representatives. Isolates of Bacillus, Rhodotorula, Alternaria and members of the Davidiellaceae were isolated from both Greenland and Antarctica sections of the same age, although the sequences differed between the two polar regions. Biology 2013-01-25 2 1 Article 10.3390/biology2010206 206 232 2079-7737 2013-01-25 doi: 10.3390/biology2010206 Caitlin Knowlton Ram Veerapaneni Tom D'Elia Scott Rogers http://www.mdpi.com/2079-7737/2/1/189 MicroRNAs (miRNAs) are small non-coding RNA molecules of 21–23 nucleotides that control gene expression at the post-transcriptional level. They have been shown to play a vital role in a wide variety of biological processes and dysregulated expression of miRNAs is observed in many pathologies. Understanding the mechanism of action and identifying functionally important mRNA targets of a specific miRNA are essential to unravelling its biological function and to assist miRNA-based drug development. This review summarizes the current understanding of the mechanistic aspects of miRNA-mediated gene repression and focuses on the different approaches for miRNA target identification that have been proposed in recent years. Biology 2013-01-25 2 1 Review 10.3390/biology2010189 189 205 2079-7737 2013-01-25 doi: 10.3390/biology2010189 Aida Martinez-Sanchez Chris Murphy http://www.mdpi.com/2079-7737/2/1/177 An Antarctic soil metagenomic library was screened for lipolytic enzymes and allowed for the isolation of a new cytosolic esterase from the a/b hydrolase family 6, named MHlip. This enzyme is related to hypothetical genes coding esterases, aryl-esterases and peroxydases, among others. MHlip was produced, purified and its activity was determined. The substrate profile of MHlip reveals a high specificity for short p-nitrophenyl-esters. The apparent optimal activity of MHlip was measured for p-nitrophenyl-acetate, at 33 °C, in the pH range of 6–9. The MHlip thermal unfolding was investigated by spectrophotometric methods, highlighting a transition (Tm) at 50 °C. The biochemical characterization of this enzyme showed its adaptation to cold temperatures, even when it did not present evident signatures associated with cold-adapted proteins. Thus, MHlip adaptation to cold probably results from many discrete structural modifications, allowing the protein to remain active at low temperatures. Functional metagenomics is a powerful approach to isolate new enzymes with tailored biophysical properties (e.g., cold adaptation). In addition, beside the ever growing amount of sequenced DNA, the functional characterization of new catalysts derived from environment is still required, especially for poorly characterized protein families like α/b hydrolases. Biology 2013-01-25 2 1 Article 10.3390/biology2010177 177 188 2079-7737 2013-01-25 doi: 10.3390/biology2010177 Renaud Berlemont Olivier Jacquin Maud Delsaute Marcello La Salla Jacques Georis Fabienne Verté Moreno Galleni Pablo Power http://www.mdpi.com/2079-7737/2/1/151 Lake Vanda is a perennially ice-covered, closed-basin lake in the McMurdo Dry Valleys, Antarctica. Laminated photosynthetic microbial mats cover the floor of the lake from below the ice cover to >40 m depth. In recent decades, the water level of Lake Vanda has been rising, creating a “natural experiment” on development of mat communities on newly flooded substrates and the response of deeper mats to declining irradiance. Mats in recently flooded depths accumulate one lamina (~0.3 mm) per year and accrue ~0.18 µg chlorophyll-a cm−2 y−1. As they increase in thickness, vertical zonation becomes evident, with the upper 2-4 laminae forming an orange-brown zone, rich in myxoxanthophyll and dominated by intertwined Leptolyngbya trichomes. Below this, up to six phycobilin-rich green/pink-pigmented laminae form a subsurface zone, inhabited by Leptolyngbya, Oscillatoria and Phormidium morphotypes. Laminae continued to increase in thickness for several years after burial, and PAM fluorometry indicated photosynthetic potential in all pigmented laminae. At depths that have been submerged for >40 years, mats showed similar internal zonation and formed complex pinnacle structures that were only beginning to appear in shallower mats. Chlorophyll-a did not change over time and these mats appear to represent resource-limited “climax” communities. Acclimation of microbial mats to changing environmental conditions is a slow process, and our data show how legacy effects of past change persist into the modern community structure. Biology 2013-01-25 2 1 Article 10.3390/biology2010151 151 176 2079-7737 2013-01-25 doi: 10.3390/biology2010151 Ian Hawes Dawn Sumner Dale Andersen Anne Jungblut Tyler Mackey http://www.mdpi.com/2079-7737/2/1/142 Three psychrophilic protein pheromones (En-1, En-2 and En-6) from the polar ciliate, Euplotes nobilii, and six mesophilic pheromones (Er-1, Er-2, Er-10, Er-11, Er-22 and Er-23) from the temperate-water sister species, Euplotes raikovi, were studied in aqueous solution for their thermal unfolding and refolding based on the temperature dependence of their circular dichroism (CD) spectra. The three psychrophilic proteins showed thermal unfolding with mid points in the temperature range 55–70 °C. In contrast, no unfolding was observed for any of the six mesophilic proteins and their regular secondary structures were maintained up to 95 °C. Possible causes of these differences are discussed based on comparisons of the NMR structures of the nine proteins. Biology 2013-01-14 2 1 Article 10.3390/biology2010142 142 150 2079-7737 2013-01-14 doi: 10.3390/biology2010142 Michael Geralt Claudio Alimenti Adriana Vallesi Pierangelo Luporini Kurt Wüthrich http://www.mdpi.com/2079-7737/2/1/107 PRDM (PRDI-BF1 and RIZ homology domain containing) protein family members are characterized by the presence of a PR domain and a variable number of Zn-finger repeats. Experimental evidence has shown that the PRDM proteins play an important role in gene expression regulation, modifying the chromatin structure either directly, through the intrinsic methyltransferase activity, or indirectly through the recruitment of chromatin remodeling complexes. PRDM proteins have a dual action: they mediate the effect induced by different cell signals like steroid hormones and control the expression of growth factors. PRDM proteins therefore have a pivotal role in the transduction of signals that control cell proliferation and differentiation and consequently neoplastic transformation. In this review, we describe pathways in which PRDM proteins are involved and the molecular mechanism of their transcriptional regulation. Biology 2013-01-14 2 1 Review 10.3390/biology2010107 107 141 2079-7737 2013-01-14 doi: 10.3390/biology2010107 Erika Di Zazzo Caterina De Rosa Ciro Abbondanza Bruno Moncharmont http://www.mdpi.com/2079-7737/2/1/85 In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of phospolipid fatty acids (PLFA) demonstrated the dominance of bacteria over fungi; the analysis of fatty acids specific for Gram-positive and Gram-negative bacteria revealed an approximately twofold higher amount of Gram-negative bacteria compared to Gram-positive bacteria. Direct microbial counts after natural permafrost enrichment showed the presence of (4.7 ± 1.5) × 108 cells g−1 sediment dry mass. Viable heterotrophic bacteria were found at 0 °C, 10 °C and 25 °C, but not at 37 °C. Spore-forming bacteria were not detected. Numbers of viable fungi were low and were only detected at 0 °C and 10 °C. Selected culturable bacterial isolates were identified as representatives of Arthrobacter phenanthrenivorans, Subtercola frigoramans and Glaciimonas immobilis. Representatives of each of these species were characterized with regard to their growth temperature range, their ability to grow on different media, to produce enzymes, to grow in the presence of NaCl, antibiotics, and heavy metals, and to degrade hydrocarbons. All strains could grow at −5 °C; the upper temperature limit for growth in liquid culture was 25 °C or 30 °C. Sensitivity to rich media, antibiotics, heavy metals, and salt increased when temperature decreased (20 °C > 10 °C > 1 °C). In spite of the ligninolytic activity of some strains, no biodegradation activity was detected. Biology 2013-01-10 2 1 Article 10.3390/biology2010085 85 106 2079-7737 2013-01-10 doi: 10.3390/biology2010085 De-Chao Zhang Anatoli Brouchkov Gennady Griva Franz Schinner Rosa Margesin http://www.mdpi.com/2079-7737/2/1/64 Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs) that are required to respond to signal transduction cues that direct cell specific gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter their responses to signal transduction cues. However, identification of CRSs, and the effects of allelic variation on their ability to respond to signal transduction cues, is still at an early stage. In the current review we describe the use of comparative genomics and experimental techniques that allow for the identification of CRSs building on recent advances by the ENCODE consortium. In addition we describe techniques that allow for the analysis of the effects of allelic variation and epigenetic modification on CRS responses to signal transduction cues. Using specific examples we show that the interactions driving these elements are highly complex and the effects of disease associated polymorphisms often subtle. It is clear that gaining an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is essential to understanding the genetic basis of human disease and stratification whilst providing novel directions for the development of personalised medicine. Biology 2013-01-09 2 1 Review 10.3390/biology2010064 64 84 2079-7737 2013-01-09 doi: 10.3390/biology2010064 Philip Cowie Ruth Ross Alasdair MacKenzie http://www.mdpi.com/2079-7737/2/1/40 BRCA1 is a large multi-domain protein with a pivotal role in maintaining genome stability and cell cycle progression. Germline mutations in the BRCA1 gene confer an estimated lifetime risk of 60%–80% for breast cancer and 15%–60% for ovarian cancer. Many of the germline mutations associated with cancer development are concentrated in the amino terminal RING domain and the carboxyl terminal BRCT motifs of BRCA1, which are the most well-characterized regions of the protein. The function of BRCA1 in DNA repair, transcription and cell cycle control through the DNA damage response is orchestrated through its association with an impressive repertoire of protein complexes. The association of BRCA1 with ATM/ATR, CHK2 and Aurora A protein kinases regulates cell cycle progression, whilst its association with RAD51 has a direct impact on the repair of double strand DNA breaks (DSBs) by homologous recombination (HR). BRCA1 interactions with the MRN complex of proteins, with the BRCC complex of proteins that exhibit E3 ligase activity and with the phosphor proteins CtIP, BACH1 (BRIP1) and Abraxas (CCDC98) are also implicated in DNA repair mechanisms and cell cycle checkpoint control. BRCA1 through its association with specific proteins and multi-protein complexes is a sentinel of the normal cell cycle control and DNA repair. Biology 2013-01-02 2 1 Review 10.3390/biology2010040 40 63 2079-7737 2013-01-02 doi: 10.3390/biology2010040 Charita Christou Kyriacos Kyriacou http://www.mdpi.com/2079-7737/2/1/26 Adrenocortical tumors are frequently found in the general population, and may be benign adrenocortical adenomas or malignant adrenocortical carcinomas. Unfortunately the clinical, biochemical and histopathological distinction between benign and malignant adrenocortical tumors may be difficult in the absence of widely invasive or metastatic disease, and hence attention has turned towards a search for molecular markers. The study of rare genetic diseases that are associated with the development of adrenocortical carcinomas has contributed to our understanding of adrenocortical tumorigenesis. In addition, comprehensive genomic hybridization, methylation profiling, and genome wide mRNA and miRNA profiling have led to improvements in our understanding, as well as demonstrated several genes and pathways that may serve as diagnostic or prognostic markers. Biology 2012-12-27 2 1 Review 10.3390/biology2010026 26 39 2079-7737 2012-12-27 doi: 10.3390/biology2010026 Annabelle Fonseca James Healy John Kunstman Reju Korah Tobias Carling http://www.mdpi.com/2079-7737/2/1/1 Assisted colonization—the deliberate translocation of species from unsuitable to suitable regions—is a controversial management tool that aims to prevent the extinction of populations that are unable to migrate in response to climate change or to survive in situ. The identification of suitable translocation sites is therefore a pressing issue. Correlative species distribution models, which are based on occurrence data, are of limited use for site selection for species with historically restricted distributions. In contrast, mechanistic species distribution models hold considerable promise in selecting translocation sites. Here we integrate ecoenergetic and hydrological models to assess the longer-term suitability of the current habitat of one of the world’s rarest chelonians, the Critically Endangered Western Swamp Tortoise (Psuedemydura umbrina). Our coupled model allows us to understand the interaction between thermal and hydric constraints on the foraging window of tortoises, based on hydrological projections of its current habitat. The process can then be repeated across a range of future climates to identify regions that would fall within the tortoise’s thermodynamic niche. The predictions indicate that climate change will result in reduced hydroperiods for the tortoises. However, under some climate change scenarios, habitat suitability may remain stable or even improve due to increases in the heat budget. We discuss how our predictions can be integrated with energy budget models that can capture the consequences of these biophysical constraints on growth, reproduction and body condition. Biology 2012-12-27 2 1 Article 10.3390/biology2010001 1 25 2079-7737 2012-12-27 doi: 10.3390/biology2010001 Nicola Mitchell Matthew Hipsey Sophie Arnall Gavan McGrath Hasnein Tareque Gerald Kuchling Ryan Vogwill Murugesu Sivapalan Warren Porter Michael Kearney http://www.mdpi.com/2079-7737/1/3/906 The possible loss of whole branches from the tree of life is a dramatic, but under-studied, biological implication of climate change. The tree of life represents an evolutionary heritage providing both present and future benefits to humanity, often in unanticipated ways. Losses in this evolutionary (evo) life-support system represent losses in “evosystem” services, and are quantified using the phylogenetic diversity (PD) measure. High species-level biodiversity losses may or may not correspond to high PD losses. If climate change impacts are clumped on the phylogeny, then loss of deeper phylogenetic branches can mean disproportionately large PD loss for a given degree of species loss. Over time, successive species extinctions within a clade each may imply only a moderate loss of PD, until the last species within that clade goes extinct, and PD drops precipitously. Emerging methods of “phylogenetic risk analysis” address such phylogenetic tipping points by adjusting conservation priorities to better reflect risk of such worst-case losses. We have further developed and explored this approach for one of the most threatened taxonomic groups, corals. Based on a phylogenetic tree for the corals genus Acropora, we identify cases where worst-case PD losses may be avoided by designing risk-averse conservation priorities. We also propose spatial heterogeneity measures changes to assess possible changes in the geographic distribution of corals PD. Biology 2012-12-14 1 3 Article 10.3390/biology1030906 906 932 2079-7737 2012-12-14 doi: 10.3390/biology1030906 Daniel Faith Zoe Richards http://www.mdpi.com/2079-7737/1/3/895 Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/. Biology 2012-12-14 1 3 Article 10.3390/biology1030895 895 905 2079-7737 2012-12-14 doi: 10.3390/biology1030895 Matthias Dodt Johannes Roehr Rina Ahmed Christoph Dieterich http://www.mdpi.com/2079-7737/1/3/880 Changes in the potential habitat of five allopatric species of threatened Macrozamia cycads under scenarios of increased ambient temperature were examined. A lack of seed dispersal, poor recruitment, low seedling survival, obligate pollinator mutualisms and continued habitat loss have led to extant populations being largely restricted to refugia. Models predict that the area of suitable habitat will further contract and move upslope, resulting in a reduced incidence within protected areas with increasing annual mean temperature. Areas of potential habitat for all five species are also predicted to become increasingly isolated from one another, further reducing the exchange between metapopulations and subpopulations, exacerbating existing threatening processes. Biology 2012-12-14 1 3 Article 10.3390/biology1030880 880 894 2079-7737 2012-12-14 doi: 10.3390/biology1030880 Melinda Laidlaw Paul Forster http://www.mdpi.com/2079-7737/1/3/869 The chemokine receptor CCR5 regulates trafficking of immune cells of the lymphoid and the myeloid lineage (such as monocytes, macrophages and immature dendritic cells) and microglia. Because of this, there is an increasing recognition of the important role of CCR5 in the pathology of (neuro-) inflammatory diseases such as atherosclerosis and multiple sclerosis. Expression of CCR5 is under the control of a complexly organized promoter region upstream of the gene. The transcription factor cAMP-responsive element binding protein 1 (CREB-1) transactivates the CCR5 P1 promoter. The cell-specific expression of CCR5 however is realized by using various epigenetic marks providing a multivalent chromatin state particularly in monocytes. Here we discuss the transcriptional regulation of CCR5 with a focus on the epigenetic peculiarities of CCR5 transcription. Biology 2012-12-13 1 3 Review 10.3390/biology1030869 869 879 2079-7737 2012-12-13 doi: 10.3390/biology1030869 Rutger Wierda Peter van den Elsen http://www.mdpi.com/2079-7737/1/3/857 An understanding of the climate conditions governing spatial variation in the reproductive performance of plants can provide important information about the factors characterizing plant community structure, especially in the context of climate change. This study focuses on the effect of climate on the sexual reproductive output of Dactylis glomerata L., a perennial grass species widely distributed throughout temperate regions. An indirect space-for-time substitution procedure was used. Sixty mountain populations of the same target species were surveyed along an elevation gradient, and then, a relevant climate model was used to infer a potential response to climate change over time. Within each population, information on the number of stems, seed number and seed mass were collected. Resource investment in reproduction (RIR) was quantified as seed number × seed mass. A clear variation was found in the reproductive performance of D. glomerata along the elevational gradient: RIR improved with increasing temperature. The best model included only one term: the maximum temperature of the warmest month. This study demonstrates that mountain ecosystems offer particularly good opportunities to study climate effects over relatively short distances and suggests that warming will enhance D. glomerata’s reproductive output throughout its elevational range. Furthermore, it can be hypothesized that a potential migration of D. glomerata toward higher altitudes may occur in response to accelerated climate change. Biology 2012-12-13 1 3 Article 10.3390/biology1030857 857 868 2079-7737 2012-12-13 doi: 10.3390/biology1030857 Matteo Dainese http://www.mdpi.com/2079-7737/1/3/794 Large tracts of lowlands have been drained to expand extensive agriculture into areas that were historically categorized as wasteland. This expansion in agriculture necessarily coincided with changes in ecosystem structure, biodiversity, and nutrient cycling. These changes have impacted not only the landscapes in which they occurred, but also larger water bodies receiving runoff from drained land. New approaches must append current efforts toward land conservation and restoration, as the continuing impacts to receiving waters is an issue of major environmental concern. One of these approaches is agricultural drainage management. This article reviews how this approach differs from traditional conservation efforts, the specific practices of drainage management and the current state of knowledge on the ecology of drainage ditches. A bottom-up approach is utilized, examining the effects of stochastic hydrology and anthropogenic disturbance on primary production and diversity of primary producers, with special regard given to how management can affect establishment of macrophytes and how macrophytes in agricultural landscapes alter their environment in ways that can serve to mitigate non-point source pollution and promote biodiversity in receiving waters. Biology 2012-12-10 1 3 Review 10.3390/biology1030794 794 856 2079-7737 2012-12-10 doi: 10.3390/biology1030794 Samuel Pierce Robert Kröger Reza Pezeshki http://www.mdpi.com/2079-7737/1/3/778 Enhancer elements regulate the tissue- and developmental-stage-specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we provide an overview of enhancer function and discuss how transcription of enhancers or enhancer-generated transcripts could contribute to the regulation of gene expression during development and differentiation. Biology 2012-12-05 1 3 Review 10.3390/biology1030778 778 793 2079-7737 2012-12-05 doi: 10.3390/biology1030778 Jared Stees Fred Varn Suming Huang John Strouboulis Jörg Bungert http://www.mdpi.com/2079-7737/1/3/766 Forward genetic screens in Drosophila melanogaster using ethyl methanesulfonate (EMS) mutagenesis are a powerful approach for identifying genes that modulate specific biological processes in an in vivo setting. The mapping of genes that contain randomly-induced point mutations has become more efficient in Drosophila thanks to the maturation and availability of many types of genetic tools. However, classic approaches to gene mapping are relatively slow and ultimately require extensive Sanger sequencing of candidate chromosomal loci. With the advent of new high-throughput sequencing techniques, it is increasingly efficient to directly re-sequence the whole genome of model organisms. This approach, in combination with traditional chromosomal mapping, has the potential to greatly simplify and accelerate mutation identification in mutants generated in EMS screens. Here we show that next-generation sequencing (NGS) is an accurate and efficient tool for high-throughput sequencing and mutation discovery in Drosophila melanogaster. As a test case, mutant strains of Drosophila that exhibited long-term survival of severed peripheral axons were identified in a forward EMS mutagenesis. All mutants were recessive and fell into a single lethal complementation group, which suggested that a single gene was responsible for the protective axon degenerative phenotype. Whole genome sequencing of these genomes identified the underlying gene ect4. To improve the process of genome wide mutation identification, we developed Genomes Management Application (GEM.app, https://genomics.med.miami.edu), a graphical online user interface to a custom query framework. Using a custom GEM.app query, we were able to identify that each mutant carried a unique non-sense mutation in the gene ect4 (dSarm), which was recently shown by Osterloh et al. to be essential for the activation of axonal degeneration. Our results demonstrate the current advantages and limitations of NGS in Drosophila and we introduce GEM.app as a simple yet powerful genomics analysis tool for the Drosophila community. At a current cost of <$1,000 per genome, NGS should thus become a standard gene discovery tool in EMS induced genetic forward screens. Biology 2012-12-05 1 3 Article 10.3390/biology1030766 766 777 2079-7737 2012-12-05 doi: 10.3390/biology1030766 Michael Gonzalez Derek Van Booven William Hulme Rick Ulloa Rafael Lebrigio Jeannette Osterloh Mary Logan Marc Freeman Stephan Zuchner http://www.mdpi.com/2079-7737/1/3/736 Species endemic to mountains on oceanic islands are subject to a number of existing threats (in particular, invasive species) along with the impacts of a rapidly changing climate. The Lord Howe Island endemic palm Hedyscepe canterburyana is restricted to two mountains above 300 m altitude. Predation by the introduced Black Rat (Rattus rattus) is known to significantly reduce seedling recruitment. We examined the variation in Hedyscepe in terms of genetic variation, morphology, reproductive output and demographic structure, across an altitudinal gradient. We used demographic data to model population persistence under climate change predictions of upward range contraction incorporating long-term climatic records for Lord Howe Island. We also accounted for alternative levels of rat predation into the model to reflect management options for control. We found that Lord Howe Island is getting warmer and drier and quantified the degree of temperature change with altitude (0.9 °C per 100 m). For H. canterburyana, differences in development rates, population structure, reproductive output and population growth rate were identified between altitudes. In contrast, genetic variation was high and did not vary with altitude. There is no evidence of an upward range contraction as was predicted and recruitment was greatest at lower altitudes. Our models predicted slow population decline in the species and that the highest altitude populations are under greatest threat of extinction. Removal of rat predation would significantly enhance future persistence of this species. Biology 2012-11-23 1 3 Article 10.3390/biology1030736 736 765 2079-7737 2012-11-23 doi: 10.3390/biology1030736 Catherine Simmons Tony Auld Ian Hutton William Baker Alison Shapcott http://www.mdpi.com/2079-7737/1/3/714 Development of neural and sensory primordia at the early stages of embryogenesis depends on the activity of two B1 Sox transcription factors, Sox2 and Sox3. The embryonic expression patterns of the Sox2 and Sox3 genes are similar, yet they show gene-unique features. We screened for enhancers of the 231-kb genomic region encompassing Sox3 of chicken, and identified 13 new enhancers that showed activity in different domains of the neuro-sensory primordia. Combined with the three Sox3-proximal enhancers determined previously, at least 16 enhancers were involved in Sox3 regulation. Starting from the NP1 enhancer, more enhancers with different specificities are activated in sequence, resulting in complex overlapping patterns of enhancer activities. NP1 was activated in the caudal lateral epiblast adjacent to the posterior growing end of neural plate, and by the combined action of Wnt and Fgf signaling, similar to the Sox2 N1 enhancer involved in neural/mesodermal dichotomous cell lineage segregation. The Sox3 D5 enhancer and Sox2 N3 enhancer were also activated similarly in the diencephalon, optic vesicle and lens placode, suggesting analogies in their regulation. In general, however, the specificities of the enhancers were not identical between Sox3 and Sox2, including the cases of the NP1 and D5 enhancers. Biology 2012-11-22 1 3 Article 10.3390/biology1030714 714 735 2079-7737 2012-11-22 doi: 10.3390/biology1030714 Naoko Nishimura Yoshifumi Kamimura Yoshiko Ishida Tatsuya Takemoto Hisato Kondoh Masanori Uchikawa http://www.mdpi.com/2079-7737/1/3/698 Bone is a complex connective tissue characterized by a calcified extracellular matrix. This mineralized matrix is constantly being formed and resorbed throughout life, allowing the bone to adapt to daily mechanical loads and maintain skeletal properties and composition. The imbalance between bone formation and bone resorption leads to changes in bone mass. This is the case of osteoporosis and osteoarthritis, two common skeletal disorders. While osteoporosis is characterized by a decreased bone mass and, consequently, higher susceptibly to fractures, bone mass tends to be higher in patients with osteoarthritis, especially in the subchondral bone region. It is known that these diseases are influenced by heritable factors. However, the DNA polymorphisms identified so far in GWAS explain less than 10% of the genetic risk, suggesting that other factors, and specifically epigenetic mechanisms, are involved in the pathogenesis of these disorders. This review summarizes current knowledge about the influence of epigenetic marks on bone homeostasis, paying special attention to the role of DNA methylation in the onset and progression of osteoporosis and osteoarthritis. Biology 2012-11-22 1 3 Review 10.3390/biology1030698 698 713 2079-7737 2012-11-22 doi: 10.3390/biology1030698 Jesús Delgado-Calle José Riancho http://www.mdpi.com/2079-7737/1/3/668 After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replication. Basal transcription from the integrated HIV promoter is very low in the absence of the HIV transactivator of transcription (Tat) protein and is solely dependent on cellular transcription factors. The 5' terminal region (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loop structure called the Transactivation Responsive (TAR) element. Once Tat is made, it binds to TAR and drastically activates transcription from the HIV LTR promoter. Mutations in either the Tat protein or TAR sequence usually affect HIV replication, indicating a strong requirement for their conservation. The necessity of the Tat-mediated transactivation cascade for robust HIV replication renders Tat one of the most desirable targets for transcriptional therapy against HIV replication. Screening based on inhibition of the Tat-TAR interaction has identified a number of potential compounds, but none of them are currently used as therapeutics, partly because these agents are not easily delivered for an efficient therapy, emphasizing the need for small molecule compounds. Here we will give an overview of the different strategies used to inhibit HIV transcription and review the current repertoire of small molecular weight compounds that target HIV transcription. Biology 2012-11-19 1 3 Review 10.3390/biology1030668 668 697 2079-7737 2012-11-19 doi: 10.3390/biology1030668 Guillaume Mousseau Susana Valente http://www.mdpi.com/2079-7737/1/3/658 RNA-sequencing (RNA-seq) has become the tool of choice for transcriptomics. Several recent studies demonstrate its successful adaption to single cell analysis. This allows new biological insights into cell differentiation, cell-to-cell variation and gene regulation, and how these aspects depend on each other. Here, I review the current single cell RNA-seq (scRNA-seq) efforts and discuss experimental protocols, challenges and potentials. Biology 2012-11-16 1 3 Article 10.3390/biology1030658 658 667 2079-7737 2012-11-16 doi: 10.3390/biology1030658 Daniel Hebenstreit http://www.mdpi.com/2079-7737/1/3/639 Many migratory birds have changed their timing of arrival at breeding grounds in response to recent climate change. Understanding the adaptive value and the demographic consequences of these shifts are key challenges. To address these questions we extend previous models of phenological adaptation to climate change under territory competition to include feedback from population dynamics, winter survival and habitat productivity. We study effects of improved pre-breeding survival and of earlier food abundance peak. We show that phenological responses depend strongly on equilibrium population density via effects on territory competition. When density is high, improved pre-breeding survival affects selection pressures more than shifts of the resource peak. Under certain conditions, an advanced food peak can even select for later arrival due to competitive release. Improved pre-breeding survival has positive effects on population density that in many cases is stronger than negative effects of an advanced food peak. The fraction of young in the population decreases in all scenarios of change, but food peak shifts only affect population structure marginally unless population density is low. This work thus provides several missing links between phenological adaptation and demographic responses, and augments the toolbox for interpreting ongoing phenological shifts in migratory birds. We illustrate the utility of our model by explaining different patterns in demographic trends and phenological shifts in populations of Pied flycatchers (Ficedula hypoleuca) across Western Europe. Biology 2012-11-14 1 3 Article 10.3390/biology1030639 639 657 2079-7737 2012-11-14 doi: 10.3390/biology1030639 Jacob Johansson Isabel M. Smallegange Niclas Jonzén http://www.mdpi.com/2079-7737/1/3/617 Intertidal mangrove ecosystems are sensitive to climate change impacts, particularly to associated relative sea level rise. Human stressors and low tidal range add to vulnerability, both characteristics of the Doula Estuary, Cameroon. To investigate vulnerability, spatial techniques were combined with ground surveys to map distributions of mangrove zones, and compare with historical spatial records to quantify change over the last few decades. Low technology techniques were used to establish the tidal range and relative elevation of the mapped mangrove area. Stratigraphic coring and palaeobiological reconstruction were used to show the longer term biological history of mangroves and net sedimentation rate, and oral history surveys of local communities were used to provide evidence of recent change and identify possible causes. Results showed that the seaward edge of mangroves had over two thirds of the shoreline experienced dieback at up to 3 m per year over the last three decades, and an offshore mangrove island had suffered 89% loss. Results also showed low net sedimentation rates under seaward edge mangroves, and restricted intertidal elevation habitats of all mangroves, and Avicennia and Laguncularia in particular. To reduce vulnerability, adaptation planning can be improved by reducing the non-climate stressors on the mangrove area, particularly those resulting from human impacts. Other priorities for adaptation planning in mangrove areas that are located in such low tidal range regions are to plan inland migration areas and strategic protected areas for mangroves, and to undertake management activities that enhance accretion within the mangroves. Biology 2012-11-06 1 3 Article 10.3390/biology1030617 617 638 2079-7737 2012-11-06 doi: 10.3390/biology1030617 Joanna Ellison Isabella Zouh http://www.mdpi.com/2079-7737/1/3/597 In many European estuaries, extensive areas of intertidal habitats consist of bare mudflats and sandflats that harbour a very high abundance and biomass of macrobenthic invertebrates. The high stocks of macrobenthos in turn provide important food sources for the higher trophic levels such as fish and shorebirds. Climate change and associated sea-level rise will have potential to cause changes in coastal and estuarine physical properties in a number of ways and thereby influence the ecology of estuarine dependent organisms. Although the mechanisms involved in biological responses resulting from such environmental changes are complex, the ecological effects are likely to be significant for the estuarine benthic macrofauna and hence the consumers they support. This paper reviews the utilisation patterns of estuarine intertidal habitats by shorebirds, fish and crustaceans, as well as factors affecting the distribution, abundance and biomass of estuarine macrobenthos that is known to be important food source for these estuarine predators. This study also provides simple conceptual models of the likely impacts of sea-level rise on the physical and biological elements of estuarine intertidal habitats, and implications of these results are discussed in the context of sustainable long term flood and coastal management in estuarine environments. Biology 2012-11-05 1 3 Review 10.3390/biology1030597 597 616 2079-7737 2012-11-05 doi: 10.3390/biology1030597 Toyonobu Fujii http://www.mdpi.com/2079-7737/1/3/575 Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha) and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio) and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity pi). We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence. Biology 2012-10-25 1 3 Article 10.3390/biology1030575 575 596 2079-7737 2012-10-25 doi: 10.3390/biology1030575 Sébastien Renaut Christopher J. Grassa Brook T. Moyers Nolan C. Kane Loren H. Rieseberg http://www.mdpi.com/2079-7737/1/3/557 How have animals evolved new body designs (morphological evolution)? This requires explanations both for simple morphological changes, such as differences in pigmentation and hair patterns between different Drosophila populations and species, and also for more complex changes, such as differences in the forelimbs of mice and bats, and the necks of amphibians and reptiles. The genetic changes and pathways involved in these evolutionary steps require identification. Many, though not all, of these events occur by changes in cis-regulatory (enhancer) elements within developmental genes. Enhancers are modular, each affecting expression in only one or a few tissues. Therefore it is possible to add, remove or alter an enhancer without producing changes in multiple tissues, and thereby avoid widespread (pleiotropic) deleterious effects. Ideally, for a given step in morphological evolution it is necessary to identify (i) the change in phenotype, (ii) the changes in gene expression, (iii) the DNA region, enhancer or otherwise, affected, (iv) the mutation involved, (v) the nature of the transcription or other factors that bind to this site. In practice these data are incomplete for most of the published studies upon morphological evolution. Here, the investigations are categorized according to how far these analyses have proceeded. Biology 2012-10-25 1 3 Review 10.3390/biology1030557 557 574 2079-7737 2012-10-25 doi: 10.3390/biology1030557 Stephen Gaunt Yu-Lee Paul http://www.mdpi.com/2079-7737/1/3/542 Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the bioenergetics of polar marine ecosystems is unknown. In this minireview, we discuss recent advances in our understanding of phototrophic bacteria and highlight the need for future research. Biology 2012-10-22 1 3 Review 10.3390/biology1030542 542 556 2079-7737 2012-10-22 doi: 10.3390/biology1030542 Eileen Y. Koh Andrew R. Martin Andrew McMinn Ken G. Ryan http://www.mdpi.com/2079-7737/1/3/521 HIV-1 enzyme reverse transcriptase (RT) is a major target for antiviral drug development, with over half of current FDA-approved therapeutics against HIV infection targeting the DNA polymerase activity of this enzyme. HIV-1 RT is a multifunctional enzyme that has RNA and DNA dependent polymerase activity, along with ribonuclease H (RNase H) activity. The latter is responsible for degradation of the viral genomic RNA template during first strand DNA synthesis to allow completion of reverse transcription and the viral dsDNA. While the RNase H activity of RT has been shown to be essential for virus infectivity, all currently used drugs directed at RT inhibit the polymerase activity of the enzyme; none target RNase H. In the last decade, the increasing prevalence of HIV variants resistant to clinically used antiretrovirals has stimulated the search for inhibitors directed at stages of HIV replication different than those targeted by current drugs. HIV RNase H is one such novel target and, over the past few years, significant progress has been made in identifying and characterizing new RNase H inhibitor pharmacophores. In this review we focus mainly on the most potent low micromolar potency compounds, as these provide logical bases for further development. We also discuss why HIV RNase H has been a difficult target for antiretroviral drug development. Biology 2012-10-19 1 3 Review 10.3390/biology1030521 521 541 2079-7737 2012-10-19 doi: 10.3390/biology1030521 Tatiana Ilina Krystal LaBarge Stefan G. Sarafianos Rieko Ishima Michael A. Parniak http://www.mdpi.com/2079-7737/1/3/508 Unravelling the role of neuromessenger processes in learning and memory has long interested researchers. We investigated the effects of an acetylcholinesterase blocker, Methyl Parathion (MeP), on honeybee learning. We used visual and olfactory tasks to test whether MeP had a detrimental effect on the acquisition of new knowledge when this new knowledge contradicts previously acquired one. Our results indicate that treatment with MeP prior to conditioning was significantly detrimental to the acquisition of incongruous (but not irrelevant or congruous) new knowledge due to improved recall. The neurobiological and ecotoxicological consequences of these results are discussed. Biology 2012-10-16 1 3 Article 10.3390/biology1030508 508 520 2079-7737 2012-10-16 doi: 10.3390/biology1030508 David Guez Hong Zhu Shao-Wu Zhang http://www.mdpi.com/2079-7737/1/3/495 Genome Walking (GW) comprises a number of PCR-based methods for the identification of nucleotide sequences flanking known regions. The different methods have been used for several purposes: from de novo sequencing, useful for the identification of unknown regions, to the characterization of insertion sites for viruses and transposons. In the latter cases Genome Walking methods have been recently boosted by coupling to Next Generation Sequencing technologies. This review will focus on the development of several protocols for the application of Next Generation Sequencing (NGS) technologies to GW, which have been developed in the course of analysis of insertional libraries. These analyses find broad application in protocols for functional genomics and gene therapy. Thanks to the application of NGS technologies, the original vision of GW as a procedure for walking along an unknown genome is now changing into the possibility of observing the parallel marching of hundreds of thousands of primers across the borders of inserted DNA molecules in host genomes. Biology 2012-10-01 1 3 Review 10.3390/biology1030495 495 507 2079-7737 2012-10-01 doi: 10.3390/biology1030495 Mariateresa Volpicella Claudia Leoni Alessandra Costanza Immacolata Fanizza Antonio Placido Luigi R. Ceci http://www.mdpi.com/2079-7737/1/3/484 The TLRs and IL-1 receptors have evolved to coordinate the innate immune response following pathogen invasion. Receptors and signalling intermediates of these systems are generally characterised by a high level of evolutionary conservation. The recently described IL-1R1 co-receptor TILRR is a transcriptional variant of the FREM1 gene. Here we investigate whether innate co-receptor differences between teleosts and mammals extend to the expression of the TILRR isoform of FREM1. Bioinformatic and phylogenetic approaches were used to analyse the genome sequences of FREM1 from eukaryotic organisms including 37 tetrapods and five teleost fish. The TILRR consensus peptide sequence was present in the FREM1 gene of the tetrapods, but not in fish orthologs of FREM1, and neither FREM1 nor TILRR were present in invertebrates. The TILRR gene appears to have arisen via incorporation of adjacent non-coding DNA with a contiguous exonic sequence after the teleost divergence. Comparing co-receptors in other systems, points to their origin during the same stages of evolution. Our results show that modern teleost fish do not possess the IL-1RI co-receptor TILRR, but that this is maintained in tetrapods as early as amphibians. Further, they are consistent with data showing that co-receptors are recent additions to these regulatory systems and suggest this may underlie differences in innate immune responses between mammals and fish. Biology 2012-09-25 1 3 Article 10.3390/biology1030484 484 494 2079-7737 2012-09-25 doi: 10.3390/biology1030484 Richard C. Hudson Caroline Gray Endre Kiss-Toth Timothy J. A. Chico Eva E. Qwarnstrom http://www.mdpi.com/2079-7737/1/3/460 The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application. Biology 2012-09-25 1 3 Review 10.3390/biology1030460 460 483 2079-7737 2012-09-25 doi: 10.3390/biology1030460 Stéphane Deschamps Victor Llaca Gregory D. May http://www.mdpi.com/2079-7737/1/2/439 In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed. Biology 2012-09-18 1 2 Review 10.3390/biology1020439 439 459 2079-7737 2012-09-18 doi: 10.3390/biology1020439 Manuel Gonzalo Claros Rocío Bautista Darío Guerrero-Fernández Hicham Benzerki Pedro Seoane Noé Fernández-Pozo http://www.mdpi.com/2079-7737/1/2/411 It is now generally acknowledged that climate change has wide-ranging biological consequences, potentially leading to impacts on biodiversity. Environmental factors can have diverse and often strong effects on reproduction, with obvious ramifications for population fitness. Nevertheless, reproductive traits are often neglected in conservation considerations. Focusing on animals, recent progress in sexual selection and sexual conflict research suggests that reproductive costs may pose an underestimated hurdle during rapid climate change, potentially lowering adaptive potential and increasing extinction risk of certain populations. Nevertheless, regime shifts may have both negative and positive effects on reproduction, so it is important to acquire detailed experimental data. We hence present an overview of the literature reporting short-term reproductive consequences of exposure to different environmental factors. From the enormous diversity of findings, we conclude that climate change research could benefit greatly from more coordinated efforts incorporating evolutionary approaches in order to obtain cross-comparable data on how individual and population reproductive fitness respond in the long term. Therefore, we propose ideas and methods concerning future efforts dealing with reproductive consequences of climate change, in particular by highlighting the advantages of multi-generational experimental evolution experiments. Biology 2012-09-13 1 2 Review 10.3390/biology1020411 411 438 2079-7737 2012-09-13 doi: 10.3390/biology1020411 Vera M. Grazer Oliver Y. Martin http://www.mdpi.com/2079-7737/1/2/395 Transposable elements (TEs) are common mobile DNA elements present in nearly all genomes. Since the movement of TEs within a genome can sometimes have phenotypic consequences, an accurate report of TE actions is desirable. To this end, we developed TE-Locate, a computational tool that uses paired-end reads to identify the novel locations of known TEs. TE-Locate can utilize either a database of TE sequences, or annotated TEs within the reference sequence of interest. This makes TE-Locate useful in the search for any mobile sequence, including retrotransposed gene copies. One major concern is to act on the correct hierarchy level, thereby avoiding an incorrect calling of a single insertion as multiple events of TEs with high sequence similarity. We used the (super)family level, but TE-Locate can also use any other level, right down to the individual transposable element. As an example of analysis with TE-Locate, we used the Swedish population in the 1,001 Arabidopsis genomes project, and presented the biological insights gained from the novel TEs, inducing the association between different TE superfamilies. The program is freely available, and the URL is provided in the end of the paper. Biology 2012-09-12 1 2 Article 10.3390/biology1020395 395 410 2079-7737 2012-09-12 doi: 10.3390/biology1020395 Alexander Platzer Viktoria Nizhynska Quan Long http://www.mdpi.com/2079-7737/1/2/383 Hepatocellular Carcinoma (HCC) is the third most deadly malignancy worldwide characterized by phenotypic and molecular heterogeneity. In the past two decades, advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. More recently, improvements of sophisticated next-generation sequencing (NGS) technologies have enabled complete and cost-efficient analyses of cancer genomes at a single nucleotide resolution and advanced into valuable tools in translational medicine. Although the use of NGS in human liver cancer is still in its infancy, great promise rests in the systematic integration of different molecular analyses obtained by these methodologies, i.e., genomics, transcriptomics and epigenomics. This strategy is likely to be helpful in identifying relevant and recurrent pathophysiological hallmarks thereby elucidating our limited understanding of liver cancer. Beside tumor heterogeneity, progress in translational oncology is challenged by the amount of biological information and considerable “noise” in the data obtained from different NGS platforms. Nevertheless, the following review aims to provide an overview of the current status of next-generation approaches in liver cancer, and outline the prospects of these technologies in diagnosis, patient classification, and prediction of outcome. Further, the potential of NGS to identify novel applications for concept clinical trials and to accelerate the development of new cancer therapies will be summarized. Biology 2012-08-31 1 2 Review 10.3390/biology1020383 383 394 2079-7737 2012-08-31 doi: 10.3390/biology1020383 Jens U. Marquardt Jesper B. Andersen http://www.mdpi.com/2079-7737/1/2/370 Single nucleotide polymorphisms (SNPs) are becoming the dominant form of molecular marker for genetic and genomic analysis. The advances in second generation DNA sequencing provide opportunities to identify very large numbers of SNPs in a range of species. However, SNP identification remains a challenge for large and polyploid genomes due to their size and complexity. We have developed a pipeline for the robust identification of SNPs in large and complex genomes using Illumina second generation DNA sequence data and demonstrated this by the discovery of SNPs in the hexaploid wheat genome. We have developed a SNP discovery pipeline called SGSautoSNP (Second-Generation Sequencing AutoSNP) and applied this to discover more than 800,000 SNPs between four hexaploid wheat cultivars across chromosomes 7A, 7B and 7D. All SNPs are presented for download and viewing within a public GBrowse database. Validation suggests an accuracy of greater than 93% of SNPs represent polymorphisms between wheat cultivars and hence are valuable for detailed diversity analysis, marker assisted selection and genotyping by sequencing. The pipeline produces output in GFF3, VCF, Flapjack or Illumina Infinium design format for further genotyping diverse populations. As well as providing an unprecedented resource for wheat diversity analysis, the method establishes a foundation for high resolution SNP discovery in other large and complex genomes. Biology 2012-08-27 1 2 Article 10.3390/biology1020370 370 382 2079-7737 2012-08-27 doi: 10.3390/biology1020370 Michał T. Lorenc Satomi Hayashi Jiri Stiller Hong Lee Sahana Manoli Pradeep Ruperao Paul Visendi Paul J. Berkman Kaitao Lai Jacqueline Batley David Edwards http://www.mdpi.com/2079-7737/1/2/339 Gene silencing via non-coding RNA, such as siRNA and miRNA, can occur at the transcriptional, post-transcriptional, and translational stages of expression. Transcriptional gene silencing (TGS) involving the RNAi machinery generally occurs through DNA methylation, as well as histone post-translational modifications, and corresponding remodeling of chromatin around the target gene into a heterochromatic state. The mechanism by which mammalian TGS occurs includes the recruitment of RNA-induced initiation of transcriptional gene silencing (RITS) complexes, DNA methyltransferases (DNMTs), and other chromatin remodelers. Additionally, virally infected cells encoding miRNAs have also been shown to manipulate the host cell RNAi machinery to induce TGS at the viral genome, thereby establishing latency. Furthermore, the introduction of exogenous siRNA and shRNA into infected cells that target integrated viral promoters can greatly suppress viral transcription via TGS. Here we examine the latest findings regarding mammalian TGS, specifically focusing on HIV-1 infected cells, and discuss future avenues of exploration in this field. Biology 2012-08-24 1 2 Review 10.3390/biology1020339 339 369 2079-7737 2012-08-24 doi: 10.3390/biology1020339 Gavin C. Sampey Irene Guendel Ravi Das Elizabeth Jaworski Zachary Klase Aarthi Narayanan Kylene Kehn-Hall Fatah Kashanchi http://www.mdpi.com/2079-7737/1/2/311 Virus-cell fusion is the primary means by which the human immunodeficiency virus-1 (HIV) delivers its genetic material into the human T-cell host. Fusion is mediated in large part by the viral glycoprotein 41 (gp41) which advances through four distinct conformational states: (i) native, (ii) pre-hairpin intermediate, (iii) fusion active (fusogenic), and (iv) post-fusion. The pre-hairpin intermediate is a particularly attractive step for therapeutic intervention given that gp41 N-terminal heptad repeat (NHR) and C‑terminal heptad repeat (CHR) domains are transiently exposed prior to the formation of a six-helix bundle required for fusion. Most peptide-based inhibitors, including the FDA‑approved drug T20, target the intermediate and there are significant efforts to develop small molecule alternatives. Here, we review current approaches to studying interactions of inhibitors with gp41 with an emphasis on atomic-level computer modeling methods including molecular dynamics, free energy analysis, and docking. Atomistic modeling yields a unique level of structural and energetic detail, complementary to experimental approaches, which will be important for the design of improved next generation anti-HIV drugs. Biology 2012-08-20 1 2 Review 10.3390/biology1020311 311 338 2079-7737 2012-08-20 doi: 10.3390/biology1020311 William J. Allen Robert C. Rizzo http://www.mdpi.com/2079-7737/1/2/297 MicroRNAs (miRNAs) are 20- to 24-nucleotide endogenous small RNA molecules emerging as an important class of sequence-specific, trans-acting regulators for modulating gene expression at the post-transcription level. There has been a surge of interest in the past decade in identifying miRNAs and profiling their expression pattern using various experimental approaches. In particular, ultra-deep sampling of specifically prepared low-molecular-weight RNA libraries based on next-generation sequencing technologies has been used successfully in diverse species. The challenge now is to effectively deconvolute the complex sequencing data to provide comprehensive and reliable information on the miRNAs, miRNA precursors, and expression profile of miRNA genes. Here we review the recently developed computational tools and their applications in profiling the miRNA transcriptomes, with an emphasis on the model plant Arabidopsis thaliana. Highlighted is also progress and insight into miRNA biology derived from analyzing available deep sequencing data. Biology 2012-08-15 1 2 Review 10.3390/biology1020297 297 310 2079-7737 2012-08-15 doi: 10.3390/biology1020297 Xiaozeng Yang Lei Li http://www.mdpi.com/2079-7737/1/2/277 The binding between the HIV-1 trans-activator of transcription (Tat) and p300/(CREB-binding protein)-associated factor (PCAF) bromodomain is a crucial step in the HIV-1 life cycle. However, the structure of the full length acetylated Tat bound to PCAF has not been yet determined experimentally. Acetylation of Tat residues can play a critical role in enhancing HIV-1 transcriptional activation. Here, we have combined a fully flexible protein-protein docking approach with molecular dynamics simulations to predict the structural determinants of the complex for the common HIV-1BRU variant. This model reproduces all the crucial contacts between the Tat peptide 46SYGR(AcK)KRRQRC56 and the PCAF bromodomain previously reported by NMR spectroscopy. Additionally, inclusion of the entire Tat protein results in additional contact points at the protein-protein interface. The model is consistent with the available experimental data reported and adds novel information to our previous structural predictions of the PCAF bromodomain in complex with the rare HIVZ2 variant, which was obtained with a less accurate computational method. This improved characterization of Tat.PCAF bromodomain binding may help in defining the structural determinants of other protein interactions involving lysine acetylation. Biology 2012-08-13 1 2 Article 10.3390/biology1020277 277 296 2079-7737 2012-08-13 doi: 10.3390/biology1020277 Vo Cam Quy Sergio Pantano Giulia Rossetti Mauro Giacca Paolo Carloni http://www.mdpi.com/2079-7737/1/2/260 APOBEC3G is the best known of several DNA cytosine deaminases that function to inhibit the replication of parasitic genetic elements including the lentivirus HIV. Several high-resolution structures of the APOBEC3G catalytic domain have been generated, but none reveal how this enzyme binds to substrate single-stranded DNA. Here, we constructed a panel of APOBEC3G amino acid substitution mutants and performed a series of biochemical, genetic, and structural assays to distinguish between “Brim” and “Kink” models for single-strand DNA binding. Each model predicts distinct sets of interactions between surface arginines and negatively charged phosphates in the DNA backbone. Concordant with both models, changing the conserved arginine at position 313 to glutamate abolished both catalytic and restriction activities. In support of the Brim model, arginine to glutamate substitutions at positions 213, 215, and 320 also compromised these APOBEC3G activities. Arginine to glutamate substitutions at Kink model residues 374 and 376 had smaller effects. These observations were supported by A3G catalytic domain-ssDNA chemical shift perturbation experiments. The overall data set is most consistent with the Brim model for single-stranded DNA binding by APOBEC3G. Biology 2012-08-02 1 2 Article 10.3390/biology1020260 260 276 2079-7737 2012-08-02 doi: 10.3390/biology1020260 Keisuke Shindo Ming Li Phillip J. Gross William L. Brown Elena Harjes Yongjian Lu Hiroshi Matsuo Reuben S. Harris http://www.mdpi.com/2079-7737/1/2/245 The human APOBEC3G protein (A3G) is a single-stranded DNA deaminase that inhibits the replication of retrotransposons and retroviruses, including HIV-1. Atomic details of A3G’s catalytic mechanism have started to emerge, as the structure of its catalytic domain (A3Gctd) has been revealed by NMR and X-ray crystallography. The NMR and crystal structures are similar overall; however, differences are apparent for β2 strand (β2) and loops close to the catalytic site. To add some insight into these differences and to better characterize A3Gctd dynamics, we calculated its free energy profile by using the Generalized-Born surface area (GBSA) method accompanied with a molecular dynamics simulation. The GBSA method yielded an enthalpy term for A3Gctd’s free energy, and we developed a new method that takes into account the distribution of the protein’s dihedral angles to calculate its entropy term. The structure solved by NMR was found to have a lower energy than that of the crystal structure, suggesting that this conformation is dominant in solution. In addition, β2-loop-β2’ configuration was stable throughout a 20-ns molecular dynamics (MD) simulation. This finding suggests that in solution A3Gctd is not likely to adopt the continuous β2 strand configuration present in the APOBEC2 crystal structure. In the NMR structure, the solvent water accessibility of the catalytic Zn2+ was limited throughout the 20-ns MD simulation. This result explains previous observations in which A3G did not bind or catalyze single cytosine nucleotide, even when at excessive concentrations. Biology 2012-07-26 1 2 Article 10.3390/biology1020245 245 259 2079-7737 2012-07-26 doi: 10.3390/biology1020245 Yoshifumi Fukunishi Saki Hongo Masami Lintuluoto Hiroshi Matsuo http://www.mdpi.com/2079-7737/1/2/222 HIV-1 Reverse Transcriptase (RT) is a multifunctional enzyme responsible for the transcription of the RNA genome of the HIV virus into DNA suitable for incorporation within the DNA of human host cells. Its crucial role in the viral life cycle has made it one of the major targets for antiretroviral drug therapy. The Non-Nucleoside RT Inhibitor (NNRTI) class of drugs binds allosterically to the enzyme, affecting many aspects of its activity. We use both coarse grained network models and atomistic molecular dynamics to explore the changes in protein dynamics induced by NNRTI binding. We identify changes in the flexibility and conformation of residue Glu396 in the RNaseH primer grip which could provide an explanation for the acceleration in RNaseH cleavage rate observed experimentally in NNRTI bound HIV-1 RT. We further suggest a plausible path for conformational and dynamic changes to be communicated from the vicinity of the NNRTI binding pocket to the RNaseH at the other end of the enzyme. Biology 2012-07-26 1 2 Article 10.3390/biology1020222 222 244 2079-7737 2012-07-26 doi: 10.3390/biology1020222 David W. Wright Benjamin A. Hall Paul Kellam Peter V. Coveney http://www.mdpi.com/2079-7737/1/2/196 Soil flooding in wetlands is accompanied by changes in soil physical and chemical characteristics. These changes include the lowering of soil redox potential (Eh) leading to increasing demand for oxygen within the soil profile as well as production of soil phytotoxins that are by-products of soil reduction and thus, imposing potentially severe stress on plant roots. Various methods are utilized for quantifying plant responses to reducing soil conditions that include measurement of radial oxygen transport, plant enzymatic responses, and assessment of anatomical/morphological changes. However, the chemical properties and reducing nature of soil environment in which plant roots are grown, including oxygen demand, and other associated processes that occur in wetland soils, pose a challenge to evaluation and comparison of plant responses that are reported in the literature. This review emphasizes soil-plant interactions in wetlands, drawing attention to the importance of quantifying the intensity and capacity of soil reduction for proper evaluation of wetland plant responses, particularly at the process and whole-plant levels. Furthermore, while root oxygen-deficiency may partially account for plant stress responses, the importance of soil phytotoxins, produced as by-products of low soil Eh conditions, is discussed and the need for development of methods to allow differentiation of plant responses to reduced or anaerobic soil conditions vs. soil phytotoxins is emphasized. Biology 2012-07-26 1 2 Review 10.3390/biology1020196 196 221 2079-7737 2012-07-26 doi: 10.3390/biology1020196 S. R. Pezeshki R. D. DeLaune http://www.mdpi.com/2079-7737/1/2/175 A major challenge in studies of human diseases involving macrophages is low yield and heterogeneity of the primary cells and limited ability of these cells for transfections and genetic manipulations. To address this issue, we developed a simple and efficient three steps method for somatic 293T cells reprogramming into monocytes and macrophage-like cells. First, 293T cells were reprogrammed into induced pluripotent stem cells (iPSCs) through a transfection-mediated expression of two factors, Oct-4 and Sox2, resulting in a high yield of iPSC. Second, the obtained iPSC were differentiated into monocytes using IL-3 and M-CSF treatment. And third, monocytes were differentiated into macrophage-like cells in the presence of M-CSF. As an example, we developed HIV-1-resistant macrophage-like cells from 293T cells with knockdown of CDK2, a factor critical for HIV-1 transcription. Our study provides a proof-of-principle approach that can be used to study the role of host cell factors in HIV-1 infection of human macrophages. Biology 2012-07-26 1 2 Article 10.3390/biology1020175 175 195 2079-7737 2012-07-26 doi: 10.3390/biology1020175 Marina Jerebtsova Namita Kumari Min Xu Gustavo Brito Alvim de Melo Xiaomei Niu Kuan-Teh Jeang Sergei Nekhai http://www.mdpi.com/2079-7737/1/2/165 Post-transcriptional regulation of HIV-1 gene expression is largely governed by the activities of the viral Rev protein. In this minireview, the multiple post-transcriptional activities of Rev in the export of partially spliced and unspliced HIV-1 RNAs from the nucleus to the cytoplasm, in the translation of HIV-1 transcripts, and in the packaging of viral genomic RNAs are reviewed in brief. Biology 2012-07-23 1 2 Review 10.3390/biology1020165 165 174 2079-7737 2012-07-23 doi: 10.3390/biology1020165 Kuan-Teh Jeang http://www.mdpi.com/2079-7737/1/2/134 The development of an animal model of human immunodeficiency virus type 1 (HIV-1)/AIDS that is suitable for preclinical testing of antiretroviral therapy, vaccines, curative strategies, and studies of pathogenesis has been hampered by the human-specific tropism of HIV-1. Although simian immunodeficiency virus (SIV) or HIV-1/SIV chimeric viruses (SHIVs)-rhesus macaque models are excellent surrogates for AIDS research, the genetic differences between SIV or SHIV and HIV-1 limit their utility as model systems. The identification of innate retroviral restriction factors has increased our understanding about blockades to HIV-1 replication in macaques and provided a guide for the construction of macaque-tropic HIV-1 clones. However, while these viruses replicate in macaque cells in vitro, they are easily controlled and have not caused AIDS in host animals, indicating that we may not fully understand the restrictive barriers of innate immunity. In this review, we discuss recent findings regarding HIV-1 restriction factors, particularly as they apply to cross-species transmission of primate lentiviruses and the development of a macaque model of HIV-1/AIDS. Biology 2012-07-05 1 2 Review 10.3390/biology1020134 134 164 2079-7737 2012-07-05 doi: 10.3390/biology1020134 Rajesh Thippeshappa Hongmei Ruan Jason T. Kimata http://www.mdpi.com/2079-7737/1/2/116 Gene expression of the human immunodeficiency virus type 1 (HIV-1) is a highly regulated process. Basal transcription of the integrated provirus generates early transcripts that encode for the viral products Tat and Rev. Tat promotes the elongation of RNA polymerase while Rev mediates the nuclear export of viral RNAs that contain the Rev-responsive RNA element (RRE). These RNAs are exported from the nucleus to allow expression of Gag-Pol and Env proteins and for the production of full-length genomic RNAs. A balance exists between completely processed mRNAs and RRE-containing RNAs. Rev functions as an adaptor that recruits cellular factors to re-direct singly spliced and unspliced viral RNAs to nuclear export. The aim of this review is to address the dynamic regulation of this post-transcriptional pathway in light of recent findings that implicate several novel cellular cofactors of Rev function. Biology 2012-07-03 1 2 Review 10.3390/biology1020116 116 133 2079-7737 2012-07-03 doi: 10.3390/biology1020116 Anna Kula Alessandro Marcello http://www.mdpi.com/2079-7737/1/1/94 Productive transcription of the integrated HIV-1 provirus is restricted by cellular factors that inhibit RNA polymerase II elongation. The viral Tat protein overcomes this by recruiting a general elongation factor, P-TEFb, to the TAR RNA element that forms at the 5’ end of nascent viral transcripts. P-TEFb exists in multiple complexes in cells, and its core consists of a kinase, Cdk9, and a regulatory subunit, either Cyclin T1 or Cyclin T2. Tat binds directly to Cyclin T1 and thereby targets the Cyclin T1/P-TEFb complex that phosphorylates the CTD of RNA polymerase II and the negative factors that inhibit elongation, resulting in efficient transcriptional elongation. P-TEFb is tightly regulated in cells infected by HIV-1—CD4+ T lymphocytes and monocytes/macrophages. A number of mechanisms have been identified that inhibit P-TEFb in resting CD4+ T lymphocytes and monocytes, including miRNAs that repress Cyclin T1 protein expression and dephosphorylation of residue Thr186 in the Cdk9 T-loop. These repressive mechanisms are overcome upon T cell activation and macrophage differentiation when the permissivity for HIV-1 replication is greatly increased. This review will summarize what is currently known about mechanisms that regulate P-TEFb and how this regulation impacts HIV-1 replication and latency. Biology 2012-06-15 1 1 Review 10.3390/biology1010094 94 115 2079-7737 2012-06-15 doi: 10.3390/biology1010094 Rajesh Ramakrishnan Karen Chiang Hongbing Liu Sona Budhiraja Hart Donahue Andrew P. Rice http://www.mdpi.com/2079-7737/1/1/81 Designing HIV-1 protease inhibitors that overcome drug-resistance is still a challenging task. In this study, four clinical isolates of multi-drug resistant HIV-1 proteases that exhibit resistance to all the US FDA-approved HIV-1 protease inhibitors and also reduce the substrate recognition ability were examined. A multi-drug resistant HIV-1 protease isolate, MDR 769, was co-crystallized with the p2/NC substrate and the mutated CA/p2 substrate, CA/p2 P1’F. Both substrates display different levels of molecular recognition by the wild-type and multi-drug resistant HIV-1 protease. From the crystal structures, only limited differences can be identified between the wild-type and multi-drug resistant protease. Therefore, a wild-type HIV-1 protease and four multi-drug resistant HIV-1 proteases in complex with the two peptides were modeled based on the crystal structures and examined during a 10 ns-molecular dynamics simulation. The simulation results reveal that the multi-drug resistant HIV-1 proteases require higher desolvation energy to form complexes with the peptides. This result suggests that the desolvation of the HIV-1 protease active site is an important step of protease-ligand complex formation as well as drug resistance. Therefore, desolvation energy could be considered as a parameter in the evaluation of future HIV-1 protease inhibitor candidates. Biology 2012-05-31 1 1 Article 10.3390/biology1010081 81 93 2079-7737 2012-05-31 doi: 10.3390/biology1010081 Yong Wang Tamaria G. Dewdney Zhigang Liu Samuel J. Reiter Joseph S. Brunzelle Iulia A. Kovari Ladislau C. Kovari http://www.mdpi.com/2079-7737/1/1/58 Despite its discovery over 30 years ago, human immunodeficiency virus (HIV) continues to threaten public health worldwide. Semen is the principal vehicle for the transmission of this retrovirus and several endogenous peptides in semen, including fragments of prostatic acid phosphatase (PAP248-286 and PAP85-120) and semenogelins (SEM1 and SEM2), assemble into amyloid fibrils that promote HIV infection. For example, PAP248-286 fibrils, termed SEVI (Semen derived Enhancer of Viral Infection), potentiate HIV infection by up to 105-fold. Fibrils enhance infectivity by facilitating virion attachment and fusion to target cells, whereas soluble peptides have no effect. Importantly, the stimulatory effect is greatest at low viral titers, which mimics mucosal transmission of HIV, where relatively few virions traverse the mucosal barrier. Devising a method to rapidly reverse fibril formation (rather than simply inhibit it) would provide an innovative and urgently needed preventative strategy for reducing HIV infection via the sexual route. Targeting a host-encoded protein conformer represents a departure from traditional microbicidal approaches that target the viral machinery, and could synergize with direct antiviral approaches. Here, we review the identification of these amyloidogenic peptides, their mechanism of action, and various strategies for inhibiting their HIV-enhancing effects. Biology 2012-05-29 1 1 Review 10.3390/biology1010058 58 80 2079-7737 2012-05-29 doi: 10.3390/biology1010058 Laura M. Castellano James Shorter http://www.mdpi.com/2079-7737/1/1/43 Development of the atherosclerotic plaque involves a complex interplay between a number of cell types and an extensive inter-cellular communication via cell bound as well as soluble mediators. The family of tribbles proteins has recently been identified as novel controllers of pro-inflammatory signal transduction. The objective of this study was to address the expression pattern of all three tribbles proteins in atherosclerotic plaques from a mouse model of atherosclerosis. Each tribbles were expressed in vascular smooth muscle cells, endothelial cells as well as in resident macrophages of mouse atherosclerotic plaques. The role of IL-1 mediated inflammatory events in controlling tribbles expression was also addressed by inducing experimental atherosclerosis in ApoE−/−IL1R1−/− (double knockout) mice. Immunohistochemical analysis of these mice showed a selective decrease in the percentage of trb-1 expressing macrophages, compared to the ApoE−/− cohort (14.7% ± 1.55 vs. 26.3% ± 1.19). The biological significance of this finding was verified in vitro where overexpression of trb-1 in macrophages led to a significant attenuation (~70%) of IL-6 production as well as a suppressed IL-12 expression induced by a proinflammatory stimulus. In this in vitro setting, expression of truncated trb-1 mutants suggests that the kinase domain of this protein is sufficient to exert this inhibitory action. Biology 2012-04-10 1 1 Article 10.3390/biology1010043 43 57 2079-7737 2012-04-10 doi: 10.3390/biology1010043 Hye Youn Sung Sheila E. Francis Nadine D. Arnold Karen Holland Vanessa Ernst Adrienn Angyal Endre Kiss-Toth http://www.mdpi.com/2079-7737/1/1/18 Due to a mutation in the Foxp3 transcription factor, Scurfy mice lack regulatory T-cells that maintain self-tolerance of the immune system. They develop multi-organ inflammation (MOI) and die around four weeks old. The affected organs are skin, tail, lungs and liver. In humans, endocrine and gastrointestinal inflammation are also observed, hence the disease is termed IPEX (Immunodysregulation, Polyendocrinopathy, Enteropathy, X-linked) syndrome. The three week period of fatal MOI offers a useful autoimmune model in which the controls by genetics, T-cell subsets, cytokines, and effector mechanisms could be efficiently investigated. In this report, we will review published work, summarize our recent studies of Scurfy double mutants lacking specific autoimmune-related genes, discuss the cellular and cytokine controls by these genes on MOI, the organ-specificities of the MOI controlled by environments, and the effector mechanisms regulated by specific Th cytokines, including several newly identified control mechanisms for organ-specific autoimmune response. Biology 2012-04-04 1 1 Article 10.3390/biology1010018 18 42 2079-7737 2012-04-04 doi: 10.3390/biology1010018 Shyr-Te Ju Rahul Sharma Felicia Gaskin John T. Kung Shu Man Fu http://www.mdpi.com/2079-7737/1/1/5 Discovery of prognostic and diagnostic biomarker gene signatures for diseases, such as cancer, is seen as a major step towards a better personalized medicine. During the last decade various methods, mainly coming from the machine learning or statistical domain, have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinical diagnosis is the typical low reproducibility of these signatures combined with the difficulty to achieve a clear biological interpretation. For that purpose in the last years there has been a growing interest in approaches that try to integrate information from molecular interaction networks. Here we review the current state of research in this field by giving an overview about so-far proposed approaches. Biology 2012-02-27 1 1 Review 10.3390/biology1010005 5 17 2079-7737 2012-02-27 doi: 10.3390/biology1010005 Yupeng Cun Holger Fröhlich http://www.mdpi.com/2079-7737/1/1/1 There has never been a more exciting time to study the science of living systems. Contemporary biology is a vibrant field which grows stronger year on year. Biological scientists have access to powerful new tools and techniques that even recently would have seemed like science fiction. We are enjoying ‘a wellspring of technical advancements’ [1]. The consequence is a deeper and wider understanding of living systems. Older approaches remain important and often essential, but new unbiased and often fast approaches are helping us to deploy our traditional approaches more rationally. The result of this synergy of old and new is an explosion in the field of biological sciences. It may seem daunting to consider what lies ahead and the challenges will be great, but the pace of discovery is increasingly rapid.[...] Biology 2011-09-01 1 1 Editorial 10.3390/biology1010001 1 4 2079-7737 2011-09-01 doi: 10.3390/biology1010001 Christopher A. O’Callaghan