Genes

17 pages, 3141 KiB

Open AccessArticle

CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads

by Dongmei Ai^1,*, Hongfei Pan¹, Ruocheng Huang² and Li C. Xia^3,*

¹ School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China

² Sinotech Genomics, Shanghai 200120, China

³ Department of Medicine, Stanford University School of Medicine, 269 Campus Dr., Stanford, CA 94305, USA

Genes 2018, 9(6), 313; https://doi.org/10.3390/genes9060313 - 20 Jun 2018

Cited by 2 | Viewed by 4474

Abstract

With the rapid development of high-throughput sequencing technology, the analysis of metagenomic sequencing data and the accurate and efficient estimation of relative microbial abundance have become important ways to explore the microbial composition and function of microbes. In addition, the accuracy and efficiency [...] Read more.

With the rapid development of high-throughput sequencing technology, the analysis of metagenomic sequencing data and the accurate and efficient estimation of relative microbial abundance have become important ways to explore the microbial composition and function of microbes. In addition, the accuracy and efficiency of the relative microbial abundance estimation are closely related to the algorithm and the selection of the reference sequence for sequence alignment. We introduced the microbial core genome as the reference sequence for potential microbes in a metagenomic sample, and we constructed a finite mixture and latent Dirichlet models and used the Gibbs sampling algorithm to estimate the relative abundance of microorganisms. The simulation results showed that our approach can improve the efficiency while maintaining high accuracy and is more suitable for high-throughput metagenomic data. The new approach was implemented in our CoreProbe package which provides a pipeline for an accurate and efficient estimation of the relative abundance of microbes in a community. This tool is available free of charge from the CoreProbe’s website: Access the Docker image with the following instruction: sudo docker pull panhongfei/coreprobe:1.0. Full article

(This article belongs to the Section Technologies and Resources for Genetics)

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Graphical abstract

8 pages, 857 KiB

Open AccessCommunication

The Case of X and Y Localization of Nucleolus Organizer Regions (NORs) in Tragulus javanicus (Cetartiodactyla, Mammalia)

by Anastasia A. Proskuryakova^1,2,*

, Anastasia I. Kulemzina¹, Polina L. Perelman^1,2, Natalia A. Serdukova¹, Oliver A. Ryder³

and Alexander S. Graphodatsky^1,2

¹ Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev ave 8/2, Novosibirsk 630090, Russia

² Novosibirsk State University, Pirogova str. 1, Novosibirsk 630090, Russia

³ San Diego Zoo Institute for Conservation Research, San Pasqual Valley Rd 15600, Escondido, CA 92027, USA

Genes 2018, 9(6), 312; https://doi.org/10.3390/genes9060312 - 20 Jun 2018

Cited by 6 | Viewed by 4126

Abstract

There are differences in number and localization of nucleolus organizer regions (NORs) in genomes. In mammalian genomes, NORs are located on autosomes, which are often situated on short arms of acrocentric chromosomes and more rarely in telomeric, pericentromeric, or interstitial regions. In this [...] Read more.

There are differences in number and localization of nucleolus organizer regions (NORs) in genomes. In mammalian genomes, NORs are located on autosomes, which are often situated on short arms of acrocentric chromosomes and more rarely in telomeric, pericentromeric, or interstitial regions. In this work, we report the unique case of active NORs located on gonоsomes of a eutherian mammal, the Javan mouse-deer (Tragulus javanicus). We have investigated the position of NORs by FISH experiments with ribosomal DNA (rDNA) sequences (18S, 5.8S, and 28S) and show the presence of a single NOR site on the X and Y chromosomes. The NOR is localized interstitially on the p-arm of the X chromosome in close proximity with prominent C-positive heterochromatin blocks and in the pericentromeric area of mostly heterochromatic Y. The NOR sites are active on both the X and Y chromosomes in the studied individual and surrounded by GC enriched heterochromatin. We hypothesize that the surrounding heterochromatin might have played a role in the transfer of NORs from autosomes to sex chromosomes during the karyotype evolution of the Javan mouse-deer. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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13 pages, 2715 KiB

Open AccessArticle

Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia

by Jinxing Wang, Jing Lin^*, Jialiang Kan, Hong Wang, Xiaogang Li, Qingsong Yang, Hui Li and Youhong Chang

Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China

Genes 2018, 9(6), 311; https://doi.org/10.3390/genes9060311 - 20 Jun 2018

Cited by 27 | Viewed by 4566

Abstract

Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome [...] Read more.

Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome of P. betulifolia under drought stress was analyzed to identify lncRNAs. A total of 14,478 lncRNAs were identified, of which 251 were found to be drought-responsive. The putative target genes of these differentially expressed lncRNAs were significantly enriched in metabolic processes, organic substance metabolic processes, macromolecule metabolic processes, and heterocyclic compound binding. Real-time quantitative polymerase chain reaction validation suggested that the results of the RNA sequencing data analysis were reliable. This study will provide genetic resources for pear breeding and provide reference to other pomological studies. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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19 pages, 1466 KiB

Open AccessReview

H1.0 Linker Histone as an Epigenetic Regulator of Cell Proliferation and Differentiation

by Carlo Maria Di Liegro¹, Gabriella Schiera¹

and Italia Di Liegro^2,*

¹ Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo (UNIPA), I-90128 Palermo, Italy

² Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo, I-90127 Palermo, Italy

Genes 2018, 9(6), 310; https://doi.org/10.3390/genes9060310 - 20 Jun 2018

Cited by 24 | Viewed by 6460

Abstract

H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having [...] Read more.

H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having a general structural role, H1 histones also have additional epigenetic functions related to DNA replication and repair, genome stability, and gene-specific expression regulation. Synthesis of the H1 subtypes is differentially regulated both in development and adult cells, thus suggesting that each protein has a more or less specific function. The somatic variant H1.0 is a linker histone that was recognized since long ago to be involved in cell differentiation. Moreover, it has been recently found to affect generation of epigenetic and functional intra-tumor heterogeneity. Interestingly, H1.0 or post-translational forms of it have been also found in extracellular vesicles (EVs) released from cancer cells in culture, thus suggesting that these cells may escape differentiation at least in part by discarding H1.0 through the EV route. In this review we will discuss the role of H1.0 in development, differentiation, and stem cell maintenance, also in relation with tumorigenesis, and EV production. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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22 pages, 1822 KiB

Open AccessReview

Production of Plant Secondary Metabolites: Examples, Tips and Suggestions for Biotechnologists

by Gea Guerriero^1,*

, Roberto Berni^2,3, J. Armando Muñoz-Sanchez⁴, Fabio Apone⁵, Eslam M. Abdel-Salam⁶

, Ahmad A. Qahtan⁶, Abdulrahman A. Alatar⁶, Claudio Cantini³

, Giampiero Cai²

, Jean-Francois Hausman¹

, Khawar Sohail Siddiqui⁷, S. M. Teresa Hernández-Sotomayor⁴ and Mohammad Faisal^6,*

¹ Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg

² Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy

³ Trees and timber institute-National research council of Italy (CNR-IVALSA), via Aurelia 49, 58022 Follonica (GR), Italy

⁴ Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43 # 130 X 32 y 34, Col. Chuburná de Hidalgo, Mérida, Yucatán 97205, Mexico

⁵ Arterra Biosciences srl/Vitalab srl, via B. Brin 69, 80142 Naples, Italy

⁶ Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia

⁷ Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), 31261 Dhahran, Saudi Arabia

Genes 2018, 9(6), 309; https://doi.org/10.3390/genes9060309 - 20 Jun 2018

Cited by 303 | Viewed by 30790

Abstract

Plants are sessile organisms and, in order to defend themselves against exogenous (a)biotic constraints, they synthesize an array of secondary metabolites which have important physiological and ecological effects. Plant secondary metabolites can be classified into four major classes: terpenoids, phenolic compounds, alkaloids and [...] Read more.

Plants are sessile organisms and, in order to defend themselves against exogenous (a)biotic constraints, they synthesize an array of secondary metabolites which have important physiological and ecological effects. Plant secondary metabolites can be classified into four major classes: terpenoids, phenolic compounds, alkaloids and sulphur-containing compounds. These phytochemicals can be antimicrobial, act as attractants/repellents, or as deterrents against herbivores. The synthesis of such a rich variety of phytochemicals is also observed in undifferentiated plant cells under laboratory conditions and can be further induced with elicitors or by feeding precursors. In this review, we discuss the recent literature on the production of representatives of three plant secondary metabolite classes: artemisinin (a sesquiterpene), lignans (phenolic compounds) and caffeine (an alkaloid). Their respective production in well-known plants, i.e., Artemisia, Coffea arabica L., as well as neglected species, like the fibre-producing plant Urtica dioica L., will be surveyed. The production of artemisinin and caffeine in heterologous hosts will also be discussed. Additionally, metabolic engineering strategies to increase the bioactivity and stability of plant secondary metabolites will be surveyed, by focusing on glycosyltransferases (GTs). We end our review by proposing strategies to enhance the production of plant secondary metabolites in cell cultures by inducing cell wall modifications with chemicals/drugs, or with altered concentrations of the micronutrient boron and the quasi-essential element silicon. Full article

(This article belongs to the Special Issue Plant Metabolic Engineering of High Value Bioactive Products)

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21 pages, 2604 KiB

Open AccessArticle

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly

by Halie M. Rando^1,2

, Marta Farré³

, Michael P. Robson⁴, Naomi B. Won², Jennifer L. Johnson², Ronak Buch⁴

, Estelle R. Bastounes², Xueyan Xiang⁵, Shaohong Feng⁵, Shiping Liu⁵, Zijun Xiong⁵, Jaebum Kim⁶, Guojie Zhang^5,7,8, Lyudmila N. Trut⁹, Denis M. Larkin³ and Anna V. Kukekova^2,*

¹ Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

² Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

³ Department of Comparative Biomedical Science, Royal Veterinary College, London NW1 0TU, UK

⁴ Department of Computer Science, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

⁵ China National Genebank, BGI -Shenzhen, Shenzhen 518083, Guangdong, China

⁶ Department of Stem Cell and Regenerative Biology, Konkuk University, Seoul 05029, Korea

⁷ Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark

⁸ State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

⁹ Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia

Genes 2018, 9(6), 308; https://doi.org/10.3390/genes9060308 - 20 Jun 2018

Cited by 10 | Viewed by 7640

Abstract

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of [...] Read more.

The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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14 pages, 1371 KiB

Open AccessArticle

The Quorum Sensing System of Yersinia enterocolitica 8081 Regulates Swimming Motility, Host Cell Attachment, and Virulence Plasmid Maintenance

by Yen-Kuan Ng¹, Marco Grasso¹, Victoria Wright², Vanina Garcia¹, Paul Williams¹ and Steve Atkinson^1,*

¹ Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK

² Deep Seq, Centre for Genetics and Genomics, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK

Genes 2018, 9(6), 307; https://doi.org/10.3390/genes9060307 - 20 Jun 2018

Cited by 19 | Viewed by 5071

Abstract

Although Yersinia enterocolitica genomes are highly heterogeneous, they contain a conserved N-acylhomoserine lactone-dependent (AHL) quorum sensing (QS) system consisting of the luxR and luxI orthologs yenR and yenI respectively. Certain hypervirulent strains also contain a putative orphan luxR gene, ycoR, that [...] Read more.

Although Yersinia enterocolitica genomes are highly heterogeneous, they contain a conserved N-acylhomoserine lactone-dependent (AHL) quorum sensing (QS) system consisting of the luxR and luxI orthologs yenR and yenI respectively. Certain hypervirulent strains also contain a putative orphan luxR gene, ycoR, that is not linked to an AHL synthase. To explore the contribution of yenR/yenI/ycoR to QS-dependent phenotypes in Yersinia enterocolitica strain 8081, single and multiple mutants were constructed. AHL profiling identified N-(3-oxohexanoyl) homoserine lactone, N-hexanoylhomoserine lactone, and N-(3-oxoseptanoyl) homoserine lactone as the most abundant. The AHL profiles of the yenR, ycoR and yenR/ycoR mutants were similar to the parent suggesting that the two LuxR homologues do not regulate AHL production while the yenI mutants were AHL-negative. A role for QS in swimming motility and cell attachment was demonstrated. Down-regulation of the virulence plasmid partition gene, spyA, in yenI and yenI/yenR/ycoR mutants is consistent with the greater loss of the Y. enterocolitica pYVe virulence plasmid in the yenI mutant during serial passage at 37 °C but not at 22 °C. A role for QS-regulated spyA in virulence plasmid maintenance is suggested. Full article

(This article belongs to the Special Issue Genetic Networks and Gene Regulation Mechanisms for Quorum Sensing and Quorum Quenching in Bacteria)

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21 pages, 4979 KiB

Open AccessArticle

From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes)

by Felipe Faix Barby¹, Petr Ráb², Sébastien Lavoué³, Tariq Ezaz⁴

, Luiz Antônio Carlos Bertollo¹, Andrzej Kilian⁵, Sandra Regina Maruyama¹

, Ezequiel Aguiar de Oliveira¹

, Roberto Ferreira Artoni⁶, Mateus Henrique Santos⁶, Oladele Ilesanmi Jegede⁷, Terumi Hatanaka¹, Alongklod Tanomtong⁸, Thomas Liehr⁹

and Marcelo De Bello Cioffi^1,*

¹ Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP 13565-905, Brazil

² Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic

³ Institute of Oceanography, National Taiwan University, Roosevelt Road, Taipei 10617, Taiwan

⁴ Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia

⁵ Diversity Arrays Technology, University of Canberra, Bruce, Australian Capital Territory, Canberra, ACT 2617, Australia

⁶ Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR 84030-900 Brazil

⁷ Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25 Mubi. Adamawa State, Nigeria

⁸ Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen 40002, Thailand

⁹ Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany

Genes 2018, 9(6), 306; https://doi.org/10.3390/genes9060306 - 19 Jun 2018

Cited by 21 | Viewed by 7008

Abstract

In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the [...] Read more.

In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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12 pages, 1967 KiB

Open AccessArticle

MiRAR—miRNA Activity Reporter for Living Cells

by Matthew A. Turk¹, Christina Z. Chung¹, Emad Manni¹, Stephanie A. Zukowski¹, Anish Engineer², Yasaman Badakhshi¹, Yumin Bi¹ and Ilka U. Heinemann^1,*

¹ Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada

² Department of Physiology and Pharmacology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada

Genes 2018, 9(6), 305; https://doi.org/10.3390/genes9060305 - 19 Jun 2018

Cited by 11 | Viewed by 5864

Abstract

microRNA (miRNA) activity and regulation are of increasing interest as new therapeutic targets. Traditional approaches to assess miRNA levels in cells rely on RNA sequencing or quantitative PCR. While useful, these approaches are based on RNA extraction and cannot be applied in real-time [...] Read more.

microRNA (miRNA) activity and regulation are of increasing interest as new therapeutic targets. Traditional approaches to assess miRNA levels in cells rely on RNA sequencing or quantitative PCR. While useful, these approaches are based on RNA extraction and cannot be applied in real-time to observe miRNA activity with single-cell resolution. We developed a green fluorescence protein (GFP)-based reporter system that allows for a direct, real-time readout of changes in miRNA activity in live cells. The miRNA activity reporter (MiRAR) consists of GFP fused to a 3′ untranslated region containing specific miRNA binding sites, resulting in miRNA activity-dependent GFP expression. Using qPCR, we verified the inverse relationship of GFP fluorescence and miRNA levels. We demonstrated that this novel optogenetic reporter system quantifies cellular levels of the tumor suppressor miRNA let-7 in real-time in single Human embryonic kidney 293 (HEK 293) cells. Our data shows that the MiRAR can be applied to detect changes in miRNA levels upon disruption of miRNA degradation pathways. We further show that the reporter could be adapted to monitor another disease-relevant miRNA, miR-122. With trivial modifications, this approach could be applied across the miRNome for quantification of many specific miRNA in cell cultures, tissues, or transgenic animal models. Full article

(This article belongs to the Special Issue Synthetic DNA and RNA Programming)

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18 pages, 1144 KiB

Open AccessReview

Membrane Proteins in Trypanosomatids Involved in Ca²⁺ Homeostasis and Signaling

by Srinivasan Ramakrishnan¹ and Roberto Docampo^1,2,*

¹ Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA

² Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA

Genes 2018, 9(6), 304; https://doi.org/10.3390/genes9060304 - 19 Jun 2018

Cited by 25 | Viewed by 5338

Abstract

Calcium ion (Ca²⁺) serves as a second messenger for a variety of cell functions in trypanosomes. Several proteins in the plasma membrane, acidocalcisomes, endoplasmic reticulum, and mitochondria are involved in its homeostasis and in cell signaling roles. The plasma membrane has [...] Read more.

Calcium ion (Ca²⁺) serves as a second messenger for a variety of cell functions in trypanosomes. Several proteins in the plasma membrane, acidocalcisomes, endoplasmic reticulum, and mitochondria are involved in its homeostasis and in cell signaling roles. The plasma membrane has a Ca²⁺ channel for its uptake and a plasma membrane-type Ca²⁺-ATPase (PMCA) for its efflux. A similar PMCA is also located in acidocalcisomes, acidic organelles that are the primary Ca²⁺ store and that possess an inositol 1,4,5-trisphosphate receptor (IP₃R) for Ca²⁺ efflux. Their mitochondria possess a mitochondrial calcium uniporter complex (MCUC) for Ca²⁺ uptake and a Ca²⁺/H⁺ exchanger for Ca²⁺ release. The endoplasmic reticulum has a sarcoplasmic-endoplasmic reticulum-type Ca²⁺-ATPase (SERCA) for Ca²⁺ uptake but no Ca²⁺ release mechanism has been identified. Additionally, the trypanosomatid genomes contain other membrane proteins that could potentially bind calcium and await further characterization. Full article

(This article belongs to the Special Issue Membrane Proteins in Parasitic Protozoa)

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17 pages, 2508 KiB

Open AccessArticle

Integrative Analysis of Dysregulated lncRNA-Associated ceRNA Network Reveals Functional lncRNAs in Gastric Cancer

by Haiming Liu^1,2,†

, Zhe Zhang^3,†, Nan Wu^3,4,†, Hao Guo³

, Hao Zhang^1,2

, Daiming Fan³, Yongzhan Nie^3,* and Yuanning Liu^1,2,*

¹ College of Computer Science and Technology, Jilin University, Changchun 130012, Jilin, China

² Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, Jilin University, Changchun 130012, Jilin, China

³ State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an 710032, Shaanxi, China

⁴ College of Life Sciences, Northwest University, Xi’an 710032, Shaanxi, China

^† These authors contributed equally to this work.

Genes 2018, 9(6), 303; https://doi.org/10.3390/genes9060303 - 18 Jun 2018

Cited by 61 | Viewed by 6177

Abstract

Mounting evidence suggests that long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA as ceRNA in gastric cancer (GC) are not fully understood. Here, we first [...] Read more.

Mounting evidence suggests that long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA as ceRNA in gastric cancer (GC) are not fully understood. Here, we first constructed a dysregulated lncRNA-associated ceRNA network by integrating analysis of gene expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs). Then, we determined three lncRNAs (RP5-1120P11, DLEU2, and DDX11-AS1) as hub lncRNAs, in which associated ceRNA subnetworks were involved in cell cycle-related processes and cancer-related pathways. Furthermore, we confirmed that the two lncRNAs (DLEU2 and DDX11-AS1) were significantly upregulated in GC tissues, promote GC cell proliferation, and negatively regulate miRNA expression, respectively. The hub lncRNAs (DLEU2 and DDX11-AS1) could have oncogenic functions, and act as potential ceRNAs to sponge miRNA. Our findings not only provide novel insights on ceRNA regulation in GC, but can also provide opportunities for the functional characterization of lncRNAs in future studies. Full article

(This article belongs to the Special Issue Selected Papers from the Bioinformatics and Intelligent Information Processing Conference (BIIP2018))

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9 pages, 224 KiB

Open AccessReview

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes

by Dmitri D. Pervouchine^1,2,3

¹ Skolkovo Institute for Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia

² The Faculty of Bioengineering and Bioinformatics, Moscow State University 1-73, Moscow 119899, Russia

³ Faculty of Computer Science, Higher School of Economics, Kochnovskiy Proyezd 3, Moscow 125319, Russia

Genes 2018, 9(6), 302; https://doi.org/10.3390/genes9060302 - 15 Jun 2018

Cited by 19 | Viewed by 4997

Abstract

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and [...] Read more.

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA–RNA interactions across the transcriptome. Full article

(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)

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13 pages, 1110 KiB

Open AccessArticle

Decision Variants for the Automatic Determination of Optimal Feature Subset in RF-RFE

by Qi Chen^1,2, Zhaopeng Meng^1,3, Xinyi Liu¹, Qianguo Jin¹ and Ran Su^1,4,*

¹ School of Computer Software, Tianjin University, Tianjin 300350, China

² The Military Transportation Command Department, Army Military Transportation University, Tianjin 300361, China

³ Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China

⁴ State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300074, China

Genes 2018, 9(6), 301; https://doi.org/10.3390/genes9060301 - 15 Jun 2018

Cited by 117 | Viewed by 7172

Abstract

Feature selection, which identifies a set of most informative features from the original feature space, has been widely used to simplify the predictor. Recursive feature elimination (RFE), as one of the most popular feature selection approaches, is effective in data dimension reduction and [...] Read more.

Feature selection, which identifies a set of most informative features from the original feature space, has been widely used to simplify the predictor. Recursive feature elimination (RFE), as one of the most popular feature selection approaches, is effective in data dimension reduction and efficiency increase. A ranking of features, as well as candidate subsets with the corresponding accuracy, is produced through RFE. The subset with highest accuracy (HA) or a preset number of features (PreNum) are often used as the final subset. However, this may lead to a large number of features being selected, or if there is no prior knowledge about this preset number, it is often ambiguous and subjective regarding final subset selection. A proper decision variant is in high demand to automatically determine the optimal subset. In this study, we conduct pioneering work to explore the decision variant after obtaining a list of candidate subsets from RFE. We provide a detailed analysis and comparison of several decision variants to automatically select the optimal feature subset. Random forest (RF)-recursive feature elimination (RF-RFE) algorithm and a voting strategy are introduced. We validated the variants on two totally different molecular biology datasets, one for a toxicogenomic study and the other one for protein sequence analysis. The study provides an automated way to determine the optimal feature subset when using RF-RFE. Full article

(This article belongs to the Special Issue Selected Papers from the Bioinformatics and Intelligent Information Processing Conference (BIIP2018))

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24 pages, 1440 KiB

Open AccessArticle

Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures

by Pierce Radecki^†, Mirko Ledda^†

and Sharon Aviran^*

¹ Biomedical Engineering Department and Genome Center, University of California Davis, Davis, CA 95616, USA

^† These authors contributed equally to this work.

Genes 2018, 9(6), 300; https://doi.org/10.3390/genes9060300 - 14 Jun 2018

Cited by 7 | Viewed by 5062

Abstract

High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA, an algorithm for rapidly [...] Read more.

High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA, an algorithm for rapidly mining SP data for patterns characteristic of such motifs. This work provided a proof-of-concept for the detection of motifs and the capability of distinguishing structures displaying pronounced conformational changes. Here, we describe several improvements and automation routines to patteRNA. We then consider more elaborate biological situations starting with the comparison or integration of results from searches for distinct motifs and across datasets. To facilitate such analyses, we characterize patteRNA’s outputs and describe a normalization framework that regularizes results. We then demonstrate that our algorithm successfully discerns between highly similar structural variants of the human immunodeficiency virus type 1 (HIV-1) Rev response element (RRE) and readily identifies its exact location in whole-genome structure profiles of HIV-1. This work highlights the breadth of information that can be gleaned from SP data and broadens the utility of data-driven methods as tools for the detection of novel RNA elements. Full article

(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)

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8 pages, 1425 KiB

Open AccessCommunication

Cytogenetics in Arctica islandica (Bivalvia, Arctidae): the Longest Lived Non-Colonial Metazoan

by Daniel García-Souto^1,2

and Juan J. Pasantes^1,*

¹ Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain

² CIMUS Biomedical Research Institute, University of Santiago de Compostela, E-15706 Santiago de Compostela, Spain

Genes 2018, 9(6), 299; https://doi.org/10.3390/genes9060299 - 13 Jun 2018

Cited by 3 | Viewed by 4140

Abstract

Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic [...] Read more.

Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects but nothing is known about their chromosomes. In this work, the chromosomes of the ocean quahog Arctica islandica were analysed by means of 4′,6-diamidino-2-phenylindole (DAPI)/propidium iodide (PI) staining and fluorescent in situ hybridization (FISH) with rDNA, histone gene and telomeric probes. Whilst both 5S rDNA and 45S rDNA were clustered at single subcentromeric locations on the long arms of chromosome pairs 2 and 12, respectively, histone gene clusters located on the short arms of chromosome pairs 7, 10 and 17. As happens with most bivalves, the location of the vertebrate type telomeric sequence clusters was restricted to chromosome ends. The knowledge of the karyotype can facilitate the anchoring of genomic sequences to specific chromosome pairs in this species. Full article

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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16 pages, 1897 KiB

Open AccessPerspective

Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence

by Marius Roesti

Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

Genes 2018, 9(6), 298; https://doi.org/10.3390/genes9060298 - 13 Jun 2018

Cited by 12 | Viewed by 6234

Abstract

Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally [...] Read more.

Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally adaptive alleles at fortuitously co-localized loci within a genome, thereby facilitating local adaptation with gene flow (‘allele-only clustering’). On the other hand, the selective pressure to link adaptive alleles may drive co-localization of the actual loci relevant for local adaptation within a genome through structural genome changes or an evolving intra-genomic crossover rate (‘locus clustering’). While the expected outcome is, in both cases, a higher frequency of locally adaptive alleles in some genome regions than others, the molecular units evolving in response to gene flow differ (i.e., alleles versus loci). I argue that, although making this distinction is important, we commonly lack the critical empirical evidence to do so. This is mainly because many current approaches are biased towards detecting local adaptation in genome regions with low crossover rates. The importance of low-crossover genome regions for adaptation with gene flow, such as in co-localizing relevant loci within a genome, thus remains unclear. Future empirical investigations should address these questions by making use of comparative genomics, where multiple de novo genome assemblies from species evolved under different degrees of genetic exchange are compared. This research promises to advance our understanding of how a genome adapts to maladaptive gene flow, thereby promoting adaptive divergence and reproductive isolation. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Reproductive Isolation)

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32 pages, 6989 KiB

Open AccessArticle

Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis

by Julian Lange¹, Eugenia Münch¹, Jan Müller¹

, Tobias Busche^2,3, Jörn Kalinowski²

, Ralf Takors¹ and Bastian Blombach^1,*

¹ Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany

² Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany

³ Institute for Biology-Microbiology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany

Genes 2018, 9(6), 297; https://doi.org/10.3390/genes9060297 - 13 Jun 2018

Cited by 17 | Viewed by 6868

Abstract

Zero-growth processes are a promising strategy for the production of reduced molecules and depict a steady transition from aerobic to anaerobic conditions. To investigate the adaptation of Corynebacterium glutamicum to altering oxygen availabilities, we conceived a triple-phase fermentation process that describes a gradual [...] Read more.

Zero-growth processes are a promising strategy for the production of reduced molecules and depict a steady transition from aerobic to anaerobic conditions. To investigate the adaptation of Corynebacterium glutamicum to altering oxygen availabilities, we conceived a triple-phase fermentation process that describes a gradual reduction of dissolved oxygen with a shift from aerobiosis via microaerobiosis to anaerobiosis. The distinct process phases were clearly bordered by the bacteria’s physiologic response such as reduced growth rate, biomass substrate yield and altered yield of fermentation products. During the process, sequential samples were drawn at six points and analyzed via RNA-sequencing, for metabolite concentrations and for enzyme activities. We found transcriptional alterations of almost 50% (1421 genes) of the entire protein coding genes and observed an upregulation of fermentative pathways, a rearrangement of respiration, and mitigation of the basic cellular mechanisms such as transcription, translation and replication as a transient response related to the installed oxygen dependent process phases. To investigate the regulatory regime, 18 transcriptionally altered (putative) transcriptional regulators were deleted, but none of the deletion strains showed noticeable growth kinetics under an oxygen restricted environment. However, the described transcriptional adaptation of C. glutamicum resolved to varying oxygen availabilities provides a useful basis for future process and strain engineering. Full article

(This article belongs to the Special Issue Microbial Metabolic Engineering)

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13 pages, 1359 KiB

Open AccessFeature PaperArticle

Efficient Knock-in of a Point Mutation in Porcine Fibroblasts Using the CRISPR/Cas9-GMNN Fusion Gene

by Max Gerlach¹, Theresia Kraft¹, Bernhard Brenner^1,†, Björn Petersen²

, Heiner Niemann² and Judith Montag^1,*

¹ Institute for Molecular and Cell Physiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany

² Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystrasse 10, Mariensee, 31535 Neustadt, Germany

^† Deceased.

Genes 2018, 9(6), 296; https://doi.org/10.3390/genes9060296 - 13 Jun 2018

Cited by 21 | Viewed by 6155

Abstract

During CRISPR/Cas9 mediated genome editing, site-specific double strand breaks are introduced and repaired either unspecific by non-homologous end joining (NHEJ) or sequence dependent by homology directed repair (HDR). Whereas NHEJ-based generation of gene knock-out is widely performed, the HDR-based knock-in of specific mutations [...] Read more.

During CRISPR/Cas9 mediated genome editing, site-specific double strand breaks are introduced and repaired either unspecific by non-homologous end joining (NHEJ) or sequence dependent by homology directed repair (HDR). Whereas NHEJ-based generation of gene knock-out is widely performed, the HDR-based knock-in of specific mutations remains a bottleneck. Especially in primary cell lines that are essential for the generation of cell culture and animal models of inherited human diseases, knock-in efficacy is insufficient and needs significant improvement. Here, we tested two different approaches to increase the knock-in frequency of a specific point mutation into the MYH7-gene in porcine fetal fibroblasts. We added a small molecule inhibitor of NHEJ, SCR7 (5,6-bis((E)-benzylideneamino)-2-mercaptopyrimidin-4-ol), during genome editing and screened cell cultures for the point mutation. However, this approach did not yield increased knock-in rates. In an alternative approach, we fused humanized Cas9 (hCas9) to the N-terminal peptide of the Geminin gene (GMNN). The fusion protein is degraded in NHEJ-dominated cell cycle phases, which should increase HDR-rates. Using hCas9-GMNN and point mutation-specific real time PCR screening, we found a two-fold increase in genome edited cell cultures. This increase of HDR by hCas9-GMNN provides a promising way to enrich specific knock-in in porcine fibroblast cultures for somatic cloning approaches. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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14 pages, 3473 KiB

Open AccessArticle

C/EBPβ Promotes STAT3 Expression and Affects Cell Apoptosis and Proliferation in Porcine Ovarian Granulosa Cells

by Xiaolong Yuan^1,†, Xiaofeng Zhou^1,†, Yingting He¹

, Yuyi Zhong¹

, Ailing Zhang², Zhe Zhang¹

, Hao Zhang¹ and Jiaqi Li^1,*

¹ Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China

² College of Biological and Food Engineering, Guangdong University of Education, Guangzhou 510303, China

^† These authors contributed equally to this work.

Genes 2018, 9(6), 295; https://doi.org/10.3390/genes9060295 - 13 Jun 2018

Cited by 12 | Viewed by 3809

Abstract

Previous studies suggest that signal transducer and activator of transcription 3 (STAT3) and CCAAT/enhancer binding protein beta (C/EBPβ) play an essential role in ovarian granulosa cells (GCs) for mammalian follicular development. Several C/EBPβ putative binding sites were previously predicted on the STAT3 promoter [...] Read more.

Previous studies suggest that signal transducer and activator of transcription 3 (STAT3) and CCAAT/enhancer binding protein beta (C/EBPβ) play an essential role in ovarian granulosa cells (GCs) for mammalian follicular development. Several C/EBPβ putative binding sites were previously predicted on the STAT3 promoter in mammals. However, the molecular regulation of C/EBPβ on STAT3 and their effects on cell proliferation and apoptosis remain virtually unexplored in GCs. Using porcine GCs as a model, the 5′-deletion, luciferase report assay, mutation, chromatin immunoprecipitation, Annexin-V/PI staining and EdU assays were applied to investigate the molecular mechanism for C/EBPβ regulating the expression of STAT3 and their effects on the cell proliferation and apoptosis ability. We found that over and interfering with the expression of C/EBPβ significantly increased and decreased the messenger RNA (mRNA) and protein levels of STAT3, respectively. The dual luciferase reporter assay showed that C/EBPβ directly bound at −1397/−1387 of STAT3 to positively regulate the mRNA and protein expressions of STAT3. Both C/EBPβ and STAT3 were observed to inhibit cell apoptosis and promote cell proliferation. Furthermore, C/EBPβ might enhance the antiapoptotic and pro-proliferative effects of STAT3. These results would be of great insight in further exploring the molecular mechanism of C/EBPβ and STAT3 on the function of GCs and the development of ovarian follicles in mammals. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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24 pages, 3892 KiB

Open AccessArticle

Tissue Specificity and Dynamics of Sex-Biased Gene Expression in a Common Frog Population with Differentiated, Yet Homomorphic, Sex Chromosomes

by Wen-Juan Ma^1,*,†

, Paris Veltsos^1,2,†

, Melissa A. Toups^1,3,†, Nicolas Rodrigues¹, Roberto Sermier¹, Daniel L. Jeffries¹ and Nicolas Perrin¹

¹ Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland

² Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, IN 47405, USA

³ Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria

^† Co-first authors.

Genes 2018, 9(6), 294; https://doi.org/10.3390/genes9060294 - 12 Jun 2018

Cited by 18 | Viewed by 6065

Abstract

Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained [...] Read more.

Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage- or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes. Full article

(This article belongs to the Special Issue The Evolutionary Life Cycle of Sex Chromosomes)

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14 pages, 1889 KiB

Open AccessArticle

Long-Term Follow-Up of Acute Hepatitis B: New Insights in Its Natural History and Implications for Antiviral Treatment

by Stefano Menzo^1,*

, Claudia Minosse²

, Donatella Vincenti²

, Laura Vincenzi³, Fabio Iacomi³, Paola Zaccaro², Gianpiero D’Offizi³ and Maria R. Capobianchi²

¹ Department of Biomedical Sciences and Public Medicine, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy

² Virology Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”, via Portuense 292, 00149 Rome, Italy

³ Infectious Diseases and Hepatology Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”, via Portuense 292, 00149 Rome, Italy

Genes 2018, 9(6), 293; https://doi.org/10.3390/genes9060293 - 12 Jun 2018

Cited by 9 | Viewed by 4517

Abstract

Acute hepatitis B infection (AHB) is still a common viral acute hepatitis worldwide. As vaccination, antiviral treatment, and immigration are bound to affect the epidemiological landscape of HBV infections, and some of its aspects need to be investigated: (1) the circulation of vaccine [...] Read more.

Acute hepatitis B infection (AHB) is still a common viral acute hepatitis worldwide. As vaccination, antiviral treatment, and immigration are bound to affect the epidemiological landscape of HBV infections, and some of its aspects need to be investigated: (1) the circulation of vaccine escape mutants and of primary drug resistant strains; (2) the change in HBV genotype prevalence; and (3) the clinical implications of AHB and the probability of chronification. The serological, virological, and clinical parameters of 75 patients, acutely infected by HBV, were gathered for a retrospective study. Long-term follow up, either to complete seroconversion or for up to five years, was possible for 44 patients. Sequence analysis of the reverse transcriptase/HBsAg and precore regions was performed to investigate the molecular epidemiology and pathogenesis of recent infections by HBV. Genotype distribution in AHB in Italian patients was radically different from that of chronic infections, with a dramatic increase of extra-European genotypes (A1, F), suggesting that a proportion of AHBs are currently related to imported strains. None of the documented infections occurred in vaccinated individuals, while HBsAg variants (potentially vaccine escape variants) were rare and less prevalent than in chronic infections. No drug resistant strains were observed. Spontaneous viral clearance occurred in all but three cases. Time to viral clearance was inversely proportional to liver damage, but HBsAg titer on day 28 and, better still, HBsAg decay from day 0 to day 28 after admission, were the best predictors of chronification. They are, thus, potentially useful to guide antiviral treatment to prevent chronic evolution. Full article

(This article belongs to the Special Issue Hepatitis B Virus Infection: An Update on Epidemiology, Diagnosis, Treatment and Prevention)

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22 pages, 5042 KiB

Open AccessArticle

LTBSG1, a New Allele of BRD2, Regulates Panicle and Grain Development in Rice by Brassinosteroid Biosynthetic Pathway

by Ran Qin¹, Dongdong Zeng¹, Chengcong Yang¹, Delara Akhter^1,2, Md. Alamin¹

, Xiaoli Jin¹ and Chunhai Shi^1,*

¹ Department of Agronomy, Zhejiang University, Hangzhou 310058, China

² Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet 3100, Bangladesh

Genes 2018, 9(6), 292; https://doi.org/10.3390/genes9060292 - 11 Jun 2018

Cited by 26 | Viewed by 6206

Abstract

Panicle architecture and grain size are two important agronomic traits which determine grain yield directly in rice. In the present study, a mutant named ltbsg1 (longer top branch and shorter grain 1) was isolated from the cultivar “Zhenong 34” (Oryza [...] Read more.

Panicle architecture and grain size are two important agronomic traits which determine grain yield directly in rice. In the present study, a mutant named ltbsg1 (longer top branch and shorter grain 1) was isolated from the cultivar “Zhenong 34” (Oryza sativa L. ssp. indica) by ethyl methane sulfonate (EMS) mutagenesis. The target gene was studied through phenotype observation, genetic analysis, map-based cloning and functional analysis. The histocytological analysis indicated that the elongated top branch and shorter grain of mutant ltbsg1 were caused from the defects of cell elongation. The ltbsg1 gene in mutant revealed a single nucleotide substitution (G-A) in the exon 2 of LOC_Os10g25780, causing an amino acid variation (Glycine-Arginine) in the FAD (Flavin-adenine dinucleotide)-binding domain of delta (24)-sterol reductase, which was involved in the brassinosteroid (BR) biosynthesis. LTBSG1 was constitutively expressed and the protein was widely localized in chloroplast, nucleus and cytomembrane. The ltbsg1 seedlings had a lower endogenous BR level and could be restored to the phenotype of wild type by exogenous BR. The LTBSG1 knock-out lines showed similar phenotype defects as mutant ltbsg1, which confirmed that LTBSG1 was responsible for top branch elongation and grain size reduction. Furthermore, LTBSG1 along with other BR-related genes were feedback-regulated due to their obvious altered expression in mutant ltbsg1. This study demonstrated that LTBSG1 could play a new role in regulating panicle and grain development by BR biosynthetic pathway. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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27 pages, 2213 KiB

Open AccessReview

What Does the Future Hold for Yellow Fever Virus? (I)

by Raphaëlle Klitting^1,*

, Ernest A. Gould¹, Christophe Paupy² and Xavier De Lamballerie¹

¹ Unité des Virus Émergents (UVE: Aix-Marseille Université, IRD 190, Inserm 1207, IHU Méditerranée Infection), 13385 Marseille Cedex 05, France

² UMR Maladies Infectieuses et Vecteurs: Écologie, Génétique Évolution et Contrôle (MIVEGEC: IRD, CNRS, Université Montpellier), 34394 Montpellier, France

Genes 2018, 9(6), 291; https://doi.org/10.3390/genes9060291 - 8 Jun 2018

Cited by 40 | Viewed by 9705

Abstract

The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. Yellow fever virus had been a human plague for centuries prior to the identification of its [...] Read more.

The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. Yellow fever virus had been a human plague for centuries prior to the identification of its urban transmission vector, the Aedes (Stegomyia) aegypti (Linnaeus) mosquito species, and the development of an efficient live-attenuated vaccine, the YF-17D strain. The combination of vector-control measures and vaccination campaigns drastically reduced YFV incidence in humans on many occasions, but the virus never ceased to circulate in the forest, through its sylvatic invertebrate vector(s) and vertebrate host(s). Outbreaks recently reported in Central Africa (2015–2016) and Brazil (since late 2016), reached considerable proportions in terms of spatial distribution and total numbers of cases, with multiple exports, including to China. In turn, questions about the likeliness of occurrence of large urban YFV outbreaks in the Americas or of a successful import of YFV to Asia are currently resurfacing. This two-part review describes the current state of knowledge and gaps regarding the molecular biology and transmission dynamics of YFV, along with an overview of the tools that can be used to manage the disease at individual, local and global levels. Full article

(This article belongs to the Special Issue Emerging and re-Emerging Arboviruses in Human Health)

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18 pages, 1181 KiB

Open AccessArticle

Investigating the Molecular Genetic Basis of Cytoplasmic Sex Determination Caused by Wolbachia Endosymbionts in Terrestrial Isopods

by Myriam Badawi

, Bouziane Moumen, Isabelle Giraud, Pierre Grève and Richard Cordaux^*

Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Université de Poitiers, UMR CNRS 7267, Bât. B8, 5 rue Albert Turpin, TSA 51106, 86073 Poitiers CEDEX 9, France

Genes 2018, 9(6), 290; https://doi.org/10.3390/genes9060290 - 8 Jun 2018

Cited by 13 | Viewed by 6041

Abstract

In animals, sexual differences between males and females are usually determined by sex chromosomes. Alternatively, sex may also be determined by vertically transmitted intracellular microbial endosymbionts. The best known cytoplasmic sex manipulative endosymbiont is Wolbachia which can, for instance, feminize genetic males into [...] Read more.

In animals, sexual differences between males and females are usually determined by sex chromosomes. Alternatively, sex may also be determined by vertically transmitted intracellular microbial endosymbionts. The best known cytoplasmic sex manipulative endosymbiont is Wolbachia which can, for instance, feminize genetic males into phenotypic females in the terrestrial isopod Armadillidium vulgare. However, the molecular genetic basis of cytoplasmic sex determination is unknown. To identify candidate genes of feminization induced by Wolbachia strain wVulC from A. vulgare, we sequenced the genome of Wolbachia strain wCon from Cylisticus convexus, the most closely related known Wolbachia strain to wVulC that does not induce feminization, and compared it to the wVulC genome. Then, we performed gene expression profiling of the 216 resulting wVulC candidate genes throughout host developmental stages in A. vulgare and the heterologous host C. convexus. We identified a set of 35 feminization candidate genes showing differential expression during host sexual development. Interestingly, 27 of the 35 genes are present in the f element, which is a piece of a feminizing Wolbachia genome horizontally transferred into the nuclear genome of A. vulgare and involved in female sex determination. Assuming that the molecular genetic basis of feminization by Wolbachia and the f element is the same, the 27 genes are candidates for acting as master sex determination genes in A. vulgare females carrying the f element. Full article

(This article belongs to the Special Issue The Evolutionary Life Cycle of Sex Chromosomes)

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21 pages, 1582 KiB

Open AccessReview

Decoding the Heart through Next Generation Sequencing Approaches

by Michal Pawlak^1,†, Katarzyna Niescierowicz^1,† and Cecilia Lanny Winata^1,2,*

¹ International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland

² Max-Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany

^† These authors contributed equally.

Genes 2018, 9(6), 289; https://doi.org/10.3390/genes9060289 - 7 Jun 2018

Cited by 14 | Viewed by 7727

Abstract

Vertebrate organs develop through a complex process which involves interaction between multiple signaling pathways at the molecular, cell, and tissue levels. Heart development is an example of such complex process which, when disrupted, results in congenital heart disease (CHD). This complexity necessitates a [...] Read more.

Vertebrate organs develop through a complex process which involves interaction between multiple signaling pathways at the molecular, cell, and tissue levels. Heart development is an example of such complex process which, when disrupted, results in congenital heart disease (CHD). This complexity necessitates a holistic approach which allows the visualization of genome-wide interaction networks, as opposed to assessment of limited subsets of factors. Genomics offers a powerful solution to address the problem of biological complexity by enabling the observation of molecular processes at a genome-wide scale. The emergence of next generation sequencing (NGS) technology has facilitated the expansion of genomics, increasing its output capacity and applicability in various biological disciplines. The application of NGS in various aspects of heart biology has resulted in new discoveries, generating novel insights into this field of study. Here we review the contributions of NGS technology into the understanding of heart development and its disruption reflected in CHD and discuss how emerging NGS based methodologies can contribute to the further understanding of heart repair. Full article

(This article belongs to the Special Issue Emerging Applications for Next Generation Sequencing)

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9 pages, 510 KiB

Open AccessReview

Hyperphagia and Obesity in Prader–Willi Syndrome: PCSK1 Deficiency and Beyond?

by Bruno Ramos-Molina^1,†

, María Molina-Vega^2,†, José C. Fernández-García^1,2,3,*

and John W. Creemers⁴

¹ Laboratory of Cellular and Molecular Endocrinology, Institute of Biomedical Research in Malaga (IBIMA), Virgen de la Victoria University Hospital, 29010 Malaga, Spain

² Department of Endocrinology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain

³ CIBER Fisiopatología de la Obesidad y Nutrición (CIBERObn CB06/003), Instituto de Salud Carlos III, 28029 Madrid, Spain

⁴ Laboratory of Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium

^† These authors contributed equally.

Genes 2018, 9(6), 288; https://doi.org/10.3390/genes9060288 - 7 Jun 2018

Cited by 9 | Viewed by 6744

Abstract

Prader–Willi syndrome (PWS) is a complex genetic disorder that, besides cognitive impairments, is characterized by hyperphagia, obesity, hypogonadism, and growth impairment. Proprotein convertase subtilisin/kexin type 1 (PCSK1) deficiency, a rare recessive congenital disorder, partially overlaps phenotypically with PWS, but both genetic [...] Read more.

Prader–Willi syndrome (PWS) is a complex genetic disorder that, besides cognitive impairments, is characterized by hyperphagia, obesity, hypogonadism, and growth impairment. Proprotein convertase subtilisin/kexin type 1 (PCSK1) deficiency, a rare recessive congenital disorder, partially overlaps phenotypically with PWS, but both genetic disorders show clear dissimilarities as well. The recent observation that PCSK1 is downregulated in a model of human PWS suggests that overlapping pathways are affected. In this review we will not only discuss the mechanisms by which PWS and PCSK1 deficiency could lead to hyperphagia but also the therapeutic interventions to treat obesity in both genetic disorders. Full article

(This article belongs to the Special Issue Advances in Genetics of Regeneration in Metabesity)

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11 pages, 818 KiB

Open AccessCase Report

Prenatal Diagnosis of Fragile X Syndrome in a Twin Pregnancy Complicated by a Complete Retraction

by Yael Prawer^1,2,*

, Matthew Hunter^1,2

, Sara Cronin³, Ling Ling³, Solange Aliaga Vera³, Michael Fahey¹, Nikki Gelfand^1,2, Ralph Oertel³, Essra Bartlett³, David Francis³ and David Godler^3,4

¹ Monash Genetics, Monash Health, Clayton, 3168 Victoria, Australia

² Department of Paediatrics, Monash University, Clayton, 3168 Victoria, Australia

³ Cyto-Molecular Diagnostic Research Laboratory, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, 3052 Victoria, Australia

⁴ Dentistry and Health Sciences, Department of Paediatrics, Faculty of Medicine, University of Melbourne, Parkville, 3052 Victoria, Australia

Genes 2018, 9(6), 287; https://doi.org/10.3390/genes9060287 - 7 Jun 2018

Cited by 9 | Viewed by 5496

Abstract

Fragile X syndrome (FXS) is usually associated with a CGG repeat expansion >200 repeats within the FMR1 gene, known as a full mutation (FM). FM alleles produce abnormal methylation of the FMR1 promoter with reduction or silencing of FMR1 gene expression. Furthermore, premutation [...] Read more.

Fragile X syndrome (FXS) is usually associated with a CGG repeat expansion >200 repeats within the FMR1 gene, known as a full mutation (FM). FM alleles produce abnormal methylation of the FMR1 promoter with reduction or silencing of FMR1 gene expression. Furthermore, premutation (PM: 55–199 CGGs) and full mutation alleles usually expand in size when maternally transmitted to progeny. This study describes a PM allele carried by the mother decreasing to a normal sized allele in a male from a dichorionic diamniotic (DCDA) twin pregnancy, with the female twin inheriting FM (200–790 CGGs), PM (130 CGGs) and normal-sized (39 CGGs) alleles. Further evidence of instability of the maternal PM allele was shown by a male proband (older brother) mosaic for PM (CGG 78 and 150 CGGs) and FM (200–813 CGGs), and a high level of FMR1 promoter methylation, between 50 and 70%, in multiple tissues. The fully-retracted, normal-sized allele was identified by PCR CGG sizing in the male twin, with no evidence of a FM allele identified using Southern blot analysis in multiple tissues collected postnatally and prenatally. Consistent with this, prenatal PCR sizing (35 CGGs) showed inconsistent inheritance of the maternal normal allele (30 CGGs), with single-nucleotide polymorphism (SNP) linkage analysis confirming that the abnormal FMR1 chromosome had been inherited from the mother’s PM chromosome. Importantly, the male twin showed no significant hypermethylation of the FMR1 promoter in all pre and postnatal tissues tested, as well as normal levels of FMR1 mRNA in blood. In summary, this report demonstrates the first postnatal follow up of a prenatal case in which FMR1 mRNA levels were approaching normal, with normal levels of FMR1 promoter methylation and normal CGG size in multiple pre and postnatally collected tissues. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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18 pages, 1118 KiB

Open AccessArticle

Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus

by Komlan Avia^1,2,*,†

, Agnieszka P. Lipinska^1,†, Laure Mignerot¹, Alejandro E. Montecinos^2,3, Mahwash Jamy¹, Sophia Ahmed¹, Myriam Valero²

, Akira F. Peters⁴

, J. Mark Cock¹

, Denis Roze² and Susana M. Coelho¹

¹ Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France

² Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France

³ Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile

⁴ Bezhin Rosko, 29250 Santec, France

^† These authors contributed equally to this work.

Genes 2018, 9(6), 286; https://doi.org/10.3390/genes9060286 - 6 Jun 2018

Cited by 15 | Viewed by 7188

Abstract

Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a [...] Read more.

Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes. Full article

(This article belongs to the Special Issue The Evolutionary Life Cycle of Sex Chromosomes)

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29 pages, 3041 KiB

Open AccessReview

Development of Microplatforms to Mimic the In Vivo Architecture of CNS and PNS Physiology and Their Diseases

by John Saliba¹, Arij Daou¹, Samar Damiati²

, Jessica Saliba³

, Marwan El-Sabban⁴ and Rami Mhanna^1,*

¹ Biomedical Engineering Program, American University of Beirut (AUB), Beirut 1107 2020, Lebanon

² Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia

³ Department of Biology, Faculty of Science, Lebanese University, Beirut 6573/14, Lebanon

⁴ Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut (AUB), Beirut 1107 2020, Lebanon

Genes 2018, 9(6), 285; https://doi.org/10.3390/genes9060285 - 6 Jun 2018

Cited by 28 | Viewed by 7051

Abstract

Understanding the mechanisms that govern nervous tissues function remains a challenge. In vitro two-dimensional (2D) cell culture systems provide a simplistic platform to evaluate systematic investigations but often result in unreliable responses that cannot be translated to pathophysiological settings. Recently, microplatforms have emerged [...] Read more.

Understanding the mechanisms that govern nervous tissues function remains a challenge. In vitro two-dimensional (2D) cell culture systems provide a simplistic platform to evaluate systematic investigations but often result in unreliable responses that cannot be translated to pathophysiological settings. Recently, microplatforms have emerged to provide a better approximation of the in vivo scenario with better control over the microenvironment, stimuli and structure. Advances in biomaterials enable the construction of three-dimensional (3D) scaffolds, which combined with microfabrication, allow enhanced biomimicry through precise control of the architecture, cell positioning, fluid flows and electrochemical stimuli. This manuscript reviews, compares and contrasts advances in nervous tissues-on-a-chip models and their applications in neural physiology and disease. Microplatforms used for neuro-glia interactions, neuromuscular junctions (NMJs), blood-brain barrier (BBB) and studies on brain cancer, metastasis and neurodegenerative diseases are addressed. Finally, we highlight challenges that can be addressed with interdisciplinary efforts to achieve a higher degree of biomimicry. Nervous tissue microplatforms provide a powerful tool that is destined to provide a better understanding of neural health and disease. Full article

(This article belongs to the Special Issue From the Lab-on-a-Chip to the Organ-on-a-Chip)

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13 pages, 1284 KiB

Open AccessArticle

In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

by Gökhan Karakülah^1,2

and Athanasia Pavlopoulou^1,*

¹ Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey

² Izmir International Biomedicine and Genome Center (IBG), Izmir 35340, Turkey

Genes 2018, 9(6), 284; https://doi.org/10.3390/genes9060284 - 6 Jun 2018

Cited by 10 | Viewed by 5634

Abstract

Transposable elements of the hAT family exhibit a cross-kingdom distribution. The plant hAT transposons are proposed to play a critical role in plant adaptive evolution and DNA damage repair. The sequencing of an increasing number of plant genomes has facilitated the discovery of [...] Read more.

Transposable elements of the hAT family exhibit a cross-kingdom distribution. The plant hAT transposons are proposed to play a critical role in plant adaptive evolution and DNA damage repair. The sequencing of an increasing number of plant genomes has facilitated the discovery of a plethora of hAT elements. This enabled us to perform an in-depth phylogenetic analysis of consensus hAT sequences in the fully-sequenced genomes of 11 plant species that represent diverse taxonomic divisions. Four putative nucleotide sequences were detected in cottonwood that were similar to the corresponding animal hAT elements, which are possibly sequence artifacts. Phylogenetic trees were constructed based both on the known and putative hAT sequences, by employing two different methods of phylogenetic inference. On the basis of the reconstructed phylogeny, plant hAT elements have rather evolved through kingdom-specific vertical gene transfer and gene amplifications within eudicotyledons, monocotyledons, and chlorophytes. Furthermore, the plant hAT sequences were searched for conserved DNA and amino acid sequence features. In this way, diagnostic sequence patterns were detected which allowed us to assign functional annotations to the plant hAT sequences. Full article

(This article belongs to the Special Issue DNA Damage Responses in Plants)

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