BioMed Research International: Evolutionary Biology The latest articles from Hindawi Publishing Corporation © 2016 , Hindawi Publishing Corporation . All rights reserved. Zebrafish: A Versatile Animal Model for Fertility Research Sun, 31 Jul 2016 10:20:58 +0000 The utilization of zebrafish in biomedical research is very common in the research world nowadays. Today, it has emerged as a favored vertebrate organism for the research in science of reproduction. There is a significant growth in amount numbers of scientific literature pertaining to research discoveries in reproductive sciences in zebrafish. It has implied the importance of zebrafish in this particular field of research. In essence, the current available literature has covered from the very specific brain region or neurons of zebrafish, which are responsible for reproductive regulation, until the gonadal level of the animal. The discoveries and findings have proven that this small animal is sharing a very close/similar reproductive system with mammals. More interestingly, the behavioral characteristics and along with the establishment of animal courtship behavior categorization in zebrafish have laid an even stronger foundation and firmer reason on the suitability of zebrafish utilization in research of reproductive sciences. In view of the immense importance of this small animal for the development of reproductive sciences, this review aimed at compiling and describing the proximate close similarity of reproductive regulation on zebrafish and human along with factors contributing to the infertility, showing its versatility and its potential usage for fertility research. Jing Ying Hoo, Yatinesh Kumari, Mohd Farooq Shaikh, Seow Mun Hue, and Bey Hing Goh Copyright © 2016 Jing Ying Hoo et al. All rights reserved. Signal Transduction and Regulation: Insights into Evolution Wed, 20 Jul 2016 08:11:57 +0000 Song Yi, Sidi Chen, Luoying Zhang, and Nidhi Sahni Copyright © 2016 Song Yi et al. All rights reserved. Corrigendum to “Circadian Control of Global Transcription” Tue, 19 Jul 2016 11:43:25 +0000 Shujing Li and Luoying Zhang Copyright © 2016 Shujing Li and Luoying Zhang. All rights reserved. Fermentation Quality and Additives: A Case of Rice Straw Silage Mon, 27 Jun 2016 12:25:20 +0000 Rice cultivation generates large amount of crop residues of which only 20% are utilized for industrial and domestic purposes. In most developing countries especially southeast Asia, rice straw is used as part of feeding ingredients for the ruminants. However, due to its low protein content and high level of lignin and silica, there is limitation to its digestibility and nutritional value. To utilize this crop residue judiciously, there is a need for improvement of its nutritive value to promote its utilization through ensiling. Understanding the fundamental principle of ensiling is a prerequisite for successful silage product. Prominent factors influencing quality of silage product include water soluble carbohydrates, natural microbial population, and harvesting conditions of the forage. Additives are used to control the fermentation processes to enhance nutrient recovery and improve silage stability. This review emphasizes some practical aspects of silage processing and the use of additives for improvement of fermentation quality of rice straw. Yusuff Oladosu, Mohd Y. Rafii, Norhani Abdullah, Usman Magaji, Ghazali Hussin, Asfaliza Ramli, and Gous Miah Copyright © 2016 Yusuff Oladosu et al. All rights reserved. Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks Tue, 14 Jun 2016 08:28:00 +0000 The advent of the human genome sequence and the resulting ~20,000 genes provide a crucial framework for a transition from traditional biology to an integrative “OMICs” arena (Lander et al., 2001; Venter et al., 2001; Kitano, 2002). This brings in a revolution for cancer research, which now enters a big data era. In the past decade, with the facilitation by next-generation sequencing, there have been a huge number of large-scale sequencing efforts, such as The Cancer Genome Atlas (TCGA), the HapMap, and the 1000 genomes project. As a result, a deluge of genomic information becomes available from patients stricken by a variety of cancer types. The list of cancer-associated genes is ever expanding. New discoveries are made on how frequent and highly penetrant mutations, such as those in the telomerase reverse transcriptase (TERT) and TP53, function in cancer initiation, progression, and metastasis. Most genes with relatively frequent but weakly penetrant cancer mutations still remain to be characterized. In addition, genes that harbor rare but highly penetrant cancer-associated mutations continue to emerge. Here, we review recent advances related to cancer genomics, proteomics, and systems biology and suggest new perspectives in targeted therapy and precision medicine. Shengda Lin, Yi A. Yin, Xiaoqian Jiang, Nidhi Sahni, and Song Yi Copyright © 2016 Shengda Lin et al. All rights reserved. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks Mon, 28 Mar 2016 11:24:37 +0000 Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins) are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons) tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another. Sandip Chakraborty and David Alvarez-Ponce Copyright © 2016 Sandip Chakraborty and David Alvarez-Ponce. All rights reserved. Identification and Evolutionary Analysis of Potential Candidate Genes in a Human Eating Disorder Mon, 21 Mar 2016 09:46:51 +0000 The purpose of this study was to find genes linked with eating disorders and associated with both metabolic and neural systems. Our operating hypothesis was that there are genetic factors underlying some eating disorders resting in both those pathways. Specifically, we are interested in disorders that may rest in both sleep and metabolic function, generally called Night Eating Syndrome (NES). A meta-analysis of the Gene Expression Omnibus targeting the mammalian nervous system, sleep, and obesity studies was performed, yielding numerous genes of interest. Through a text-based analysis of the results, a number of potential candidate genes were identified. VGF, in particular, appeared to be relevant both to obesity and, broadly, to brain or neural development. VGF is a highly connected protein that interacts with numerous targets via proteolytically digested peptides. We examined VGF from an evolutionary perspective to determine whether other available evidence supported a role for the gene in human disease. We conclude that some of the already identified variants in VGF from human polymorphism studies may contribute to eating disorders and obesity. Our data suggest that there is enough evidence to warrant eGWAS and GWAS analysis of these genes in NES patients in a case-control study. Ubadah Sabbagh, Saman Mullegama, and Gerald J. Wyckoff Copyright © 2016 Ubadah Sabbagh et al. All rights reserved. Neurotrophin, p75, and Trk Signaling Module in the Developing Nervous System of the Marine Annelid Platynereis dumerilii Wed, 16 Mar 2016 13:46:29 +0000 In vertebrates, neurotrophic signaling plays an important role in neuronal development, neural circuit formation, and neuronal plasticity, but its evolutionary origin remains obscure. We found and validated nucleotide sequences encoding putative neurotrophic ligands (neurotrophin, NT) and receptors (Trk and p75) in two annelids, Platynereis dumerilii (Errantia) and Capitella teleta (Sedentaria, for which some sequences were found recently by Wilson, 2009). Predicted protein sequences and structures of Platynereis neurotrophic molecules reveal a high degree of conservation with the vertebrate counterparts; some amino acids signatures present in the annelid Trk sequences are absent in the basal chordate amphioxus, reflecting secondary loss in the cephalochordate lineage. In addition, expression analysis of NT, Trk, and p75 during Platynereis development by whole-mount mRNA in situ hybridization supports a role of these molecules in nervous system and circuit development. These annelid data corroborate the hypothesis that the neurotrophic signaling and its involvement in shaping neural networks predate the protostome-deuterostome split and were present in bilaterian ancestors. Antonella Lauri, Paola Bertucci, and Detlev Arendt Copyright © 2016 Antonella Lauri et al. All rights reserved. A CRISPR-Based Toolbox for Studying T Cell Signal Transduction Mon, 01 Feb 2016 13:03:59 +0000 CRISPR/Cas9 system is a powerful technology to perform genome editing in a variety of cell types. To facilitate the application of Cas9 in mapping T cell signaling pathways, we generated a toolbox for large-scale genetic screens in human Jurkat T cells. The toolbox has three different Jurkat cell lines expressing distinct Cas9 variants, including wild-type Cas9, dCas9-KRAB, and sunCas9. We demonstrated that the toolbox allows us to rapidly disrupt endogenous gene expression at the DNA level and to efficiently repress or activate gene expression at the transcriptional level. The toolbox, in combination with multiple currently existing genome-wide sgRNA libraries, will be useful to systematically investigate T cell signal transduction using both loss-of-function and gain-of-function genetic screens. Shen Chi, Arthur Weiss, and Haopeng Wang Copyright © 2016 Shen Chi et al. All rights reserved. Computational Analysis of the Binding Specificities of PH Domains Thu, 31 Dec 2015 08:57:49 +0000 Pleckstrin homology (PH) domains share low sequence identities but extremely conserved structures. They have been found in many proteins for cellular signal-dependent membrane targeting by binding inositol phosphates to perform different physiological functions. In order to understand the sequence-structure relationship and binding specificities of PH domains, quantum mechanical (QM) calculations and sequence-based combined with structure-based binding analysis were employed in our research. In the structural aspect, the binding specificities were shown to correlate with the hydropathy characteristics of PH domains and electrostatic properties of the bound inositol phosphates. By comparing these structure properties with sequence-based profiles of physicochemical properties, PH domains can be classified into four functional subgroups according to their binding specificities and affinities to inositol phosphates. The method not only provides a simple and practical paradigm to predict binding specificities for functional genomic research but also gives new insight into the understanding of the basis of diseases with respect to PH domain structures. Zhi Jiang, Zhongjie Liang, Bairong Shen, and Guang Hu Copyright © 2015 Zhi Jiang et al. All rights reserved. SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq) Data Tue, 29 Dec 2015 13:10:04 +0000 The performance evaluation of fusion detection algorithms from high-throughput sequencing data crucially relies on the availability of data with known positive and negative cases of gene rearrangements. The use of simulated data circumvents some shortcomings of real data by generation of an unlimited number of true and false positive events, and the consequent robust estimation of accuracy measures, such as precision and recall. Although a few simulated fusion datasets from RNA Sequencing (RNA-Seq) are available, they are of limited sample size. This makes it difficult to systematically evaluate the performance of RNA-Seq based fusion-detection algorithms. Here, we present SimFuse to address this problem. SimFuse utilizes real sequencing data as the fusions’ background to closely approximate the distribution of reads from a real sequencing library and uses a reference genome as the template from which to simulate fusions’ supporting reads. To assess the supporting read-specific performance, SimFuse generates multiple datasets with various numbers of fusion supporting reads. Compared to an extant simulated dataset, SimFuse gives users control over the supporting read features and the sample size of the simulated library, based on which the performance metrics needed for the validation and comparison of alternative fusion-detection algorithms can be rigorously estimated. Yuxiang Tan, Yann Tambouret, and Stefano Monti Copyright © 2015 Yuxiang Tan et al. All rights reserved. Circadian Control of Global Transcription Mon, 23 Nov 2015 12:40:03 +0000 Circadian rhythms exist in most if not all organisms on the Earth and manifest in various aspects of physiology and behavior. These rhythmic processes are believed to be driven by endogenous molecular clocks that regulate rhythmic expression of clock-controlled genes (CCGs). CCGs consist of a significant portion of the genome and are involved in diverse biological pathways. The transcription of CCGs is tuned by rhythmic actions of transcription factors and circadian alterations in chromatin. Here, we review the circadian control of CCG transcription in five model organisms that are widely used, including cyanobacterium, fungus, plant, fruit fly, and mouse. Comparing the similarity and differences in the five organisms could help us better understand the function of the circadian clock, as well as its output mechanisms adapted to meet the demands of diverse environmental conditions. Shujing Li and Luoying Zhang Copyright © 2015 Shujing Li and Luoying Zhang. All rights reserved. Molecular Characterization of Candida africana in Genital Specimens in Shanghai, China Thu, 19 Nov 2015 12:15:06 +0000 Candida africana, an emerging yeast pathogen, is closely related to Candida albicans and most commonly involved in vulvovaginal candidiasis (VVC). However, its prevalence in candidal balanoposthitis is still unclear. In this study, the prevalence of C. africana in both candidal balanoposthitis and VVC in a sexually transmitted diseases (STD) clinic in Shanghai, China, was analyzed, and the molecular characterization and susceptible profiles of C. africana isolates were investigated. As results, C. africana was only isolated in 5 out of 79 (6.3%) cases of candidal balanoposthitis rather than cases with vulvovaginal candidiasis. Among them, 4 out of 5 isolates share the same genotype of DST 782 with an isolate from vaginal swab in Japan published previously. All C. africana isolates were susceptible to amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole, posaconazole, caspofungin, and micafungin. Yang Hu, Aihua Yu, Xiangming Chen, Guojiang Wang, and Xiaobo Feng Copyright © 2015 Yang Hu et al. All rights reserved. Roles of Hsp70s in Stress Responses of Microorganisms, Plants, and Animals Mon, 16 Nov 2015 09:31:26 +0000 Hsp70s (heat shock protein 70s) are a class of molecular chaperones that are highly conserved and ubiquitous in organisms ranging from microorganisms to plants and humans. Most research on Hsp70s has focused on the mechanisms of their functions as molecular chaperones, but recently, studies on stress responses are coming to the forefront. Hsp70s play key roles in cellular development and protecting living organisms from environmental stresses such as heat, drought, salinity, acidity, and cold. Moreover, functions of human Hsp70s are related to diseases including neurological disorders, cancer, and virus infection. In this review, we provide an overview of the specific roles of Hsp70s in response to stress, particularly abiotic stress, in all living organisms. Anmin Yu, Ping Li, Ting Tang, Jiancai Wang, Yuan Chen, and Li Liu Copyright © 2015 Anmin Yu et al. All rights reserved. Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013 Mon, 02 Nov 2015 11:14:17 +0000 Since H9N2 avian influenza virus (AIV) was first isolated in Guangdong province of China, the virus has been circulating in chicken flocks in mainland China. However, a systematic phylogenetic analysis of H9N2 AIV from chickens in Shandong of China has not been conducted. Based on hemagglutinin (HA) gene sequences of H9N2 AIVs isolated from chickens in Shandong of China between 1998 and 2013, genetic evolution of 35 HA gene sequences was systematically analyzed in this study. Our findings showed that the majority of H9N2 AIVs (21 out of 35) belonged to the lineage h9.4.2.5. Most of isolates (33 out of 35) had a PSRSSR↓GLF motif in HA cleavage site. Importantly, 29 out of these 35 isolates had an amino acid exchange (Q226L) in the receptor-binding site. The substitution showed that H9N2 AIVs had the potential affinity to bind to human-like receptor. The currently prevalent H9N2 AIVs in Shandong belonged to the lineage h9.4.2.5 which are different from the vaccine strain SS/94 clade h9.4.2.3. Therefore, the long-term surveillance of H9N2 AIVs is of significance to combat the possible H9N2 AIV outbreaks. Yuxin Zhao, Song Li, Yufa Zhou, Wengang Song, Yujing Tang, Quanhai Pang, and Zengmin Miao Copyright © 2015 Yuxin Zhao et al. All rights reserved. Loss of flfl Triggers JNK-Dependent Cell Death in Drosophila Sun, 25 Oct 2015 11:08:55 +0000 falafel (flfl) encodes a Drosophila homolog of human SMEK whose in vivo functions remain elusive. In this study, we performed gain-of-function and loss-of-function analysis in Drosophila and identified flfl as a negative regulator of JNK pathway-mediated cell death. While ectopic expression of flfl suppresses TNF-triggered JNK-dependent cell death, loss of flfl promotes JNK activation and cell death in the developing eye and wing. These data report for the first time an essential physiological function of flfl in maintaining tissue homeostasis and organ development. As the JNK signaling pathway has been evolutionary conserved from fly to human, a similar role of PP4R3 in JNK-mediated physiological process is speculated. Jiuhong Huang and Lei Xue Copyright © 2015 Jiuhong Huang and Lei Xue. All rights reserved. Lost Polarization of Aquaporin4 and Dystroglycan in the Core Lesion after Traumatic Brain Injury Suggests Functional Divergence in Evolution Sun, 25 Oct 2015 09:25:59 +0000 Objective. To understand how aquaporin4 (AQP4) and dystroglycan (DG) polarized distribution change and their roles in brain edema formation after traumatic brain injury (TBI). Methods. Brain water content, Evans blue detection, real-time PCR, western blot, and immunofluorescence were used. Results. At an early stage of TBI, AQP4 and DG maintained vessel-like pattern in perivascular endfeet; M1, M23, and M1/M23 were increased in the core lesion. At a later stage of TBI, DG expression was lost in perivascular area, accompanied with similar but delayed change of AQP4 expression; expression of M1, M23, and DG and the ratio of M1/M2 were increased. Conclusion. At an early stage, AQP4 and DG maintained the polarized distribution. Upregulated M1 and M23 could retard the cytotoxic edema formation. At a later stage AQP4 and DG polarized expression were lost from perivascular endfeet and induced the worst cytotoxic brain edema. The alteration of DG expression could regulate that of AQP4 expression after TBI. Hui Liu, Gou ping Qiu, Fei Zhuo, Wei hua Yu, Shan quan Sun, Fen hong Li, and Mei Yang Copyright © 2015 Hui Liu et al. All rights reserved. Clinical End-Points Associated with Mycobacterium tuberculosis and Lung Cancer: Implications into Host-Pathogen Interaction and Coevolution Sun, 25 Oct 2015 09:04:13 +0000 There is a recent emerging theory that suggests a cross-link between pathogens and cancer. In this context, we examined the association between the Mycobacterium tuberculosis (MTB) with its L-forms (MTB-L) and lung cancer. In the present study, we have optimized and applied a highly sensitive assay to detect the presence of MTB and MTB-L in 187 lung cancer samples and 39 samples of other cancer origins. By carefully controlling confounding factors, we have found that 62% of the lung cancer samples are MTB-L positive, while only 5.1% of the other cancer samples are MTB-L positive. Through generalized linear models and random forest models, we have further identified a set of clinical end-points that are strongly associated with MTB-L presence. Our finding provides the basis for future studies to investigate the underlying mechanism linking MTB-L infection to lung cancer development. Yansheng Tian, Tong Hao, Bin Cao, Wei Zhang, Yan Ma, Qiang Lin, and Xiaomin Li Copyright © 2015 Yansheng Tian et al. All rights reserved. Molecular Identification and Susceptibility of Clinically Relevant Scedosporium spp. in China Wed, 07 Oct 2015 09:28:34 +0000 As various new sibling species within the Scedosporium spp. have been described recently, this study was conducted to investigate distribution and antifungal susceptibility profiles of the different species of Scedosporium spp. in China. Twenty-one clinical strains of Scedosporium from China and two strains from Japan were reidentified by MLSA. The analysis included BT2, CAL, RPB, SOD, and ACT and the combination of the five loci. Pseudallescheria boydii complex (17 strains) and S. apiospermum (6 strains) were identified. P. boydii complex included four closely related subgroups: P. boydii (9 strains), P. ellipsoidea (6 strains), P. fusoidea (1 strain), and P. angusta (1 strain). There were no significant differences in MICs for neither VOR, POS, nor AMB over all the five species in study. For itraconazole, intraspecific diversity was evident. Hong Wang, Zhe Wan, Ruoyu Li, Qiaoyun Lu, and Jin Yu Copyright © 2015 Hong Wang et al. All rights reserved. Genetic and Cultural Reconstruction of the Migration of an Ancient Lineage Wed, 30 Sep 2015 09:31:15 +0000 A rare R1a1 Y-haplogroup (Y-HG) L657 clade subtype designated as LPKSTR is found in most male members of a clan of “founder” families within the Goud Saraswat Brahmin community in Lotli town in Western India. TMRCA calculations using pairwise comparisons to control cohorts suggested a probable migration history distinct from the canonical narrative for medieval migration of orthodox Brahmin families to South India. Using Y-HG centroid analysis, chi-square analysis of TMRCA distributions and archeological find-spots, and discriminant function analysis we show that the parental Z93 L342.2 subclade in which LPKSTR occurs originated in West Asia and that LPKSTR individuals migrated toward the southeast by a Bolan Pass route distinct from the traditionally presumed route of Brahmin ingress into the Indian subcontinent. The proposed migration route is supported by archeological, toponymic, numismatic, linguistic, iconographic, and literary data. Lastly, we present cultural metrics demonstrating that these LPKSTR lineages retained distinct family practices with respect to literacy, religious practice, and emigration not shared with orthodox Brahmins of canonical geographic origin within the same community, despite centuries of intermarriage. Long-term transmission of differentiated family practices within a patrilineal endogamous community has rarely been documented. Desmond D. Mascarenhas, Anupuma Raina, Christopher E. Aston, and Dharambir K. Sanghera Copyright © 2015 Desmond D. Mascarenhas et al. All rights reserved. De Novo Assembly and Characterization of Oryza officinalis Leaf Transcriptome by Using RNA-Seq Mon, 02 Feb 2015 08:06:59 +0000 Although endeavors have been made to identify useful wild rice genes that can be used to improve cultivated rice, the virtual reservoir of genetic variation hidden within the wild relatives of cultivated rice is largely untapped. Here, using next-generation sequencing technology, we investigated the leaf transcriptome of a wild rice O. officinalis with CC genome. Approximately 23 million reads were produced in the species leaf transcriptome analysis and de novo assembly methods constructed 68,132 unigenes. Functional annotations for the unigenes were conducted using sequence similarity comparisons against the following databases: the nonredundant nucleotide database, the nonredundant protein database, the SWISS-PROT database, the Clusters of Orthologous Groups of proteins database, the Kyoto Encyclopedia of Genes and Genomes database, the Gene Ontology Consortium database, and the InterPro domains database. In addition, a total of 476 unigenes related to disease resistance were identified in O. officinalis, and these unigenes can serve as important genetic resources for cultivated rice breeding and quality improvement. The present study broadens our understanding of the genetic background of non-AA genomic wild rice species and it also provides a bridge to extend studies to other Oryza species with CC genomes. Ying Bao, Si Xu, Xiang Jing, Lu Meng, and Zongyan Qin Copyright © 2015 Ying Bao et al. All rights reserved. DBC1/CCAR2 and CCAR1 Are Largely Disordered Proteins that Have Evolved from One Common Ancestor Thu, 11 Dec 2014 00:10:50 +0000 Deleted in breast cancer 1 (DBC1, CCAR2, KIAA1967) is a large, predominantly nuclear, multidomain protein that modulates gene expression by inhibiting several epigenetic modifiers, including the deacetylases SIRT1 and HDAC3, and the methyltransferase SUV39H1. DBC1 shares many highly conserved protein domains with its paralog cell cycle and apoptosis regulator 1 (CCAR1, CARP-1). In this study, we examined the full-length sequential and structural properties of DBC1 and CCAR1 from multiple species and correlated these properties with evolution. Our data shows that the conserved domains shared between DBC1 and CCAR1 have similar domain structures, as well as similar patterns of predicted disorder in less-conserved intrinsically disordered regions. Our analysis indicates similarities between DBC1, CCAR1, and the nematode protein lateral signaling target 3 (LST-3), suggesting that DBC1 and CCAR1 may have evolved from LST-3. Our data also suggests that DBC1 emerged later in evolution than CCAR1. DBC1 contains regions that show less conservation across species as compared to the same regions in CCAR1, suggesting a continuously evolving scenario for DBC1. Overall, this study provides insight into the structure and evolution of DBC1 and CCAR1, which may impact future studies on the biological functions of these proteins. Jessica Brunquell, Jia Yuan, Aqeela Erwin, Sandy D. Westerheide, and Bin Xue Copyright © 2014 Jessica Brunquell et al. All rights reserved. Continental Monophyly and Molecular Divergence of Peninsular Malaysia’s Macaca fascicularis fascicularis Thu, 17 Jul 2014 06:33:21 +0000 The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysia’s M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnam and Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (, Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysia’s population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities). The results demonstrate that Peninsular Malaysia’s M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized Peninsular Malaysia ~0.47 million years ago (MYA) directly from Indochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations. Muhammad Abu Bakar Abdul-Latiff, Farhani Ruslin, Hamdan Faiq, Mohd Salleh Hairul, Jeffrine Japning Rovie-Ryan, Pazil Abdul-Patah, Salmah Yaakop, and Badrul Munir Md-Zain Copyright © 2014 Muhammad Abu Bakar Abdul-Latiff et al. All rights reserved. Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level Wed, 09 Jul 2014 14:09:19 +0000 Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant of site-specific rates of evolution is the Relative Solvent Accessibility (RSA). However, a recent study found that amino acid substitution rates correlate better with two Local Packing Density (LPD) measures, the Weighted Contact Number (WCN) and the Contact Number (CN), than with RSA. This work aims at a more thorough assessment. To this end, in addition to substitution rates, we considered four other sequence variability scores, four measures of solvent accessibility (SA), and other CN measures. We compared all properties for each protein of a structurally and functionally diverse representative dataset of monomeric enzymes. We show that the best sequence variability measures take into account phylogenetic tree topology. More importantly, we show that both LPD measures (WCN and CN) correlate better than all of the SA measures, regardless of the sequence variability score used. Moreover, the independent contribution of the best LPD measure is approximately four times larger than that of the best SA measure. This study strongly supports the conclusion that a site’s packing density rather than its solvent accessibility is the main structural determinant of its rate of evolution. So-Wei Yeh, Tsun-Tsao Huang, Jen-Wei Liu, Sung-Huan Yu, Chien-Hua Shih, Jenn-Kang Hwang, and Julian Echave Copyright © 2014 So-Wei Yeh et al. All rights reserved. Molecular Chaperones, Cochaperones, and Ubiquitination/Deubiquitination System: Involvement in the Production of High Quality Spermatozoa Thu, 19 Jun 2014 11:04:43 +0000 Spermatogenesis is a complex process in which mitosis, meiosis, and cell differentiation events coexist. The need to guarantee the production of qualitatively functional spermatozoa has evolved into several control systems that check spermatogenesis progression/sperm maturation and tag aberrant gametes for degradation. In this review, we will focus on the importance of the evolutionarily conserved molecular pathways involving molecular chaperones belonging to the superfamily of heat shock proteins (HSPs), their cochaperones, and ubiquitination/deubiquitination system all over the spermatogenetic process. In this respect, we will discuss the conserved role played by the DNAJ protein Msj-1 (mouse sperm cell-specific DNAJ first homologue) and the deubiquitinating enzyme Ubpy (ubiquitin-specific processing protease-y) during the spermiogenesis in both mammals and nonmammalian vertebrates. Rosaria Meccariello, Rosanna Chianese, Vincenza Ciaramella, Silvia Fasano, and Riccardo Pierantoni Copyright © 2014 Rosaria Meccariello et al. All rights reserved. Molecular Phylogeny of the Bamboo Sharks (Chiloscyllium spp.) Wed, 11 Jun 2014 08:59:49 +0000 Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences’ lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species. Noor Haslina Masstor, Abdullah Samat, Shukor Md Nor, and Badrul Munir Md-Zain Copyright © 2014 Noor Haslina Masstor et al. All rights reserved. Host-Range Dynamics of Cochliobolus lunatus: From a Biocontrol Agent to a Severe Environmental Threat Mon, 02 Jun 2014 09:10:55 +0000 We undertook an investigation to advance understanding of the host-range dynamics and biocontrol implications of Cochliobolus lunatus in the past decade. Potato (Solanum tuberosum L) farms were routinely surveyed for brown-to-black leaf spot disease caused by C. lunatus. A biphasic gene data set was assembled and databases were mined for reported hosts of C. lunatus in the last decade. The placement of five virulent strains of C. lunatus causing foliar necrosis of potato was studied with microscopic and phylogenetic tools. Analysis of morphology showed intraspecific variations in stromatic tissues among the virulent strains causing foliar necrosis of potato. A maximum likelihood inference based on GPDH locus separated C. lunatus strains into subclusters and revealed the emergence of unclustered strains. The evolving nutritional requirement of C. lunatus in the last decade is exhibited by the invasion of vertebrates, invertebrates, dicots, and monocots. Our results contribute towards a better understanding of the host-range dynamics of C. lunatus and provide useful implications on the threat posed to the environment when C. lunatus is used as a mycoherbicide. Bengyella Louis, Sayanika Devi Waikhom, Pranab Roy, Pardeep Kumar Bhardwaj, Chandradev K. Sharma, Mohendro Wakambam Singh, and Narayan Chandra Talukdar Copyright © 2014 Bengyella Louis et al. All rights reserved. Evolutionary Dynamics of rDNA Clusters in Chromosomes of Five Clam Species Belonging to the Family Veneridae (Mollusca, Bivalvia) Thu, 22 May 2014 11:25:42 +0000 The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescent in situ hybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata, Ruditapes philippinarum, Ruditapes decussatus, Dosinia exoleta, and Venus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but in R. decussatus one of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae. Concepción Pérez-García, Ninoska S. Hurtado, Paloma Morán, and Juan J. Pasantes Copyright © 2014 Concepción Pérez-García et al. All rights reserved. Resistant Traits in Digital Organisms Do Not Revert Preselection Status despite Extended Deselection: Implications to Microbial Antibiotics Resistance Tue, 20 May 2014 12:06:55 +0000 Antibiotics resistance is a serious biomedical issue as formally susceptible organisms gain resistance under its selective pressure. There have been contradictory results regarding the prevalence of resistance following withdrawal and disuse of the specific antibiotics. Here, we use experimental evolution in “digital organisms” to examine the rate of gain and loss of resistance under the assumption that there is no fitness cost for maintaining resistance. Our results show that selective pressure is likely to result in maximum resistance with respect to the selective pressure. During deselection as a result of disuse of the specific antibiotics, a large initial loss and prolonged stabilization of resistance are observed, but resistance is not lost to the stage of preselection. This suggests that a pool of partial persists organisms persist long after withdrawal of selective pressure at a relatively constant proportion. Hence, contradictory results regarding the prevalence of resistance following withdrawal and disuse of the specific antibiotics may be a statistical variation about constant proportion. Our results also show that subsequent reintroduction of the same selective pressure results in rapid regain of maximal resistance. Thus, our simulation results suggest that complete elimination of specific antibiotics resistance is unlikely after the disuse of antibiotics once a resistant pool of microorganisms has been established. Clarence F. G. Castillo and Maurice H. T. Ling Copyright © 2014 Clarence F. G. Castillo and Maurice H. T. Ling. All rights reserved. Identification and Characterization of the Grape WRKY Family Sun, 27 Apr 2014 12:47:08 +0000 WRKY transcription factors have functions in plant growth and development and in response to biotic and abiotic stresses. Many studies have focused on functional identification of WRKY transcription factors, but little is known about the molecular phylogeny or global expression patterns of the complete WRKY family. In this study, we identified 80 WRKY proteins encoded in the grape genome. Based on the structural features of these proteins, the grape WRKY genes were classified into three groups (groups 1–3). Analysis of WRKY genes expression profiles indicated that 28 WRKY genes were differentially expressed in response to biotic stress caused by grape whiterot and/or salicylic acid (SA). In that 16 WRKY genes upregulated both by whiterot pathogenic bacteria and SA. The results indicated that 16 WRKY proteins participated in SA-dependent defense signal pathway. This study provides a basis for cloning genes with specific functions from grape. Ying Zhang and Jian can Feng Copyright © 2014 Ying Zhang and Jian can Feng. All rights reserved. Genetic Diversity and Distribution of Human Norovirus in China (1999–2011) Tue, 21 Jan 2014 12:34:18 +0000 Noroviruses (NoVs) are a leading cause of epidemic and sporadic acute gastroenteritis worldwide. However, the genetic diversity and geographical distribution of NoV isolates from China have not been well described thus far. In this study, all NoV sequences obtained in China from 1999 to 2011 (), both partial and complete genomes, were downloaded from GenBank. Genotyping and phylogenetic and recombination analyses were performed in order to gain a better understanding of the distribution and genetic diversity of NoVs in China. The results indicated that approximately 90% of NoV sequences were obtained from the coastal regions of China, and most of the NoV sequences from distinct geographical regions appeared to be closely related. GII.4 was the most prevalent genotype, accounting for 64.4% of all genotypes, followed by GII.12 (13.9%) and GII.3 (7.0%). Over the last decade, the GII.4 variants were dominated by successive circulation of GII.4/2002, GII.4/2004, GII.4/2006b, and GII.4/2008, with GII.4/2006b continuing to date. A relatively high frequency of NoV intergenotype recombinants was identified. The most common ORF1/ORF2 intergenotype recombinant was GII.12/GII.4 (), and the relative frequency was up to 30% among all the recombinant strains (). These findings may aid in the evaluation and implementation of appropriate measures for monitoring NoV infectious diseases in China. Yongxin Yu, Shuling Yan, Bailin Li, Yingjie Pan, and Yongjie Wang Copyright © 2014 Yongxin Yu et al. All rights reserved. Genetic Structure and Preliminary Findings of Cryptic Diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae) Inferred from Mitochondrial DNA and Microsatellite Analyses Thu, 26 Dec 2013 14:27:42 +0000 This study examines the population genetic structure of Tor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8*), possibly representing a cryptic lineage of T. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8* in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed “genetic species” of mahseer. Yuzine Esa and Khairul Adha Abdul Rahim Copyright © 2013 Yuzine Esa and Khairul Adha Abdul Rahim. All rights reserved. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands Wed, 25 Sep 2013 13:19:42 +0000 Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associate with genes involved in neurological/psychological disorders and cancers. Therefore, the evolutionary comparative analyses of CGIs can provide insights on the functional role of these epigenome markers in both health and disease. Given the lack of specific tools, we developed CpGislandEVO. Briefly, we first compile a database of statistically significant CGIs for the best assembled mammalian genome sequences available to date. Second, by means of a coupled browser front-end, we focus on the CGIs overlapping orthologous genes extracted from OrthoDB, thus ensuring the comparison between CGIs located on truly homologous genome segments. This allows comparing the main compositional features between homologous CGIs. Finally, to facilitate nucleotide comparisons, we lifted genome coordinates between assemblies from different species, which enables the analysis of sequence divergence by direct count of nucleotide substitutions and indels occurring between homologous CGIs. The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website. Guillermo Barturen, Stefanie Geisen, Francisco Dios, E. J. Maarten Hamberg, Michael Hackenberg, and José L. Oliver Copyright © 2013 Guillermo Barturen et al. All rights reserved. Gradient Evolution of Body Colouration in Surface- and Cave-Dwelling Poecilia mexicana and the Role of Phenotype-Assortative Female Mate Choice Tue, 24 Sep 2013 15:41:42 +0000 Ecological speciation assumes reproductive isolation to be the product of ecologically based divergent selection. Beside natural selection, sexual selection via phenotype-assortative mating is thought to promote reproductive isolation. Using the neotropical fish Poecilia mexicana from a system that has been described to undergo incipient ecological speciation in adjacent, but ecologically divergent habitats characterized by the presence or absence of toxic H2S and darkness in cave habitats, we demonstrate a gradual change in male body colouration along the gradient of light/darkness, including a reduction of ornaments that are under both inter- and intrasexual selection in surface populations. In dichotomous choice tests using video-animated stimuli, we found surface females to prefer males from their own population over the cave phenotype. However, female cave fish, observed on site via infrared techniques, preferred to associate with surface males rather than size-matched cave males, likely reflecting the female preference for better-nourished (in this case: surface) males. Hence, divergent selection on body colouration indeed translates into phenotype-assortative mating in the surface ecotype, by selecting against potential migrant males. Female cave fish, by contrast, do not have a preference for the resident male phenotype, identifying natural selection against migrants imposed by the cave environment as the major driver of the observed reproductive isolation. David Bierbach, Marina Penshorn, Sybille Hamfler, Denise B. Herbert, Jessica Appel, Philipp Meyer, Patrick Slattery, Sarah Charaf, Raoul Wolf, Johannes Völker, Elisabeth A. M. Berger, Janis Dröge, Konstantin Wolf, Rüdiger Riesch, Lenin Arias-Rodriguez, Jeanne R. Indy, and Martin Plath Copyright © 2013 David Bierbach et al. All rights reserved. Genome Diversification Mechanism of Rodent and Lagomorpha Chemokine Genes Wed, 07 Aug 2013 16:01:00 +0000 Chemokines are a large family of small cytokines that are involved in host defence and body homeostasis through recruitment of cells expressing their receptors. Their genes are known to undergo rapid evolution. Therefore, the number and content of chemokine genes can be quite diverse among the different species, making the orthologous relationships often ambiguous even between closely related species. Given that rodents and rabbit are useful experimental models in medicine and drug development, we have deduced the chemokine genes from the genome sequences of several rodent species and rabbit and compared them with those of human and mouse to determine the orthologous relationships. The interspecies differences should be taken into consideration when experimental results from animal models are extrapolated into humans. The chemokine gene lists and their orthologous relationships presented here will be useful for studies using these animal models. Our analysis also enables us to reconstruct possible gene duplication processes that generated the different sets of chemokine genes in these species. Kanako Shibata, Hisayuki Nomiyama, Osamu Yoshie, and Sumio Tanase Copyright © 2013 Kanako Shibata et al. All rights reserved. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets Wed, 26 Jun 2013 18:00:44 +0000 Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed. Francesc López-Giráldez, Andrew H. Moeller, and Jeffrey P. Townsend Copyright © 2013 Francesc López-Giráldez et al. All rights reserved. In Situ Gene Mapping of Two Genes Supports Independent Evolution of Sex Chromosomes in Cold-Adapted Antarctic Fish Tue, 12 Feb 2013 10:11:23 +0000 Two genes, that is, 5S ribosomal sequences and antifreeze glycoprotein (AFGP) genes, were mapped onto chromosomes of eight Antarctic notothenioid fish possessing a X1X1X2X2/X1X2Y sex chromosome system, namely, Chionodraco hamatus and Pagetopsis macropterus (family Channichthyidae), Trematomus hansoni, T. newnesi, T. nicolai, T. lepidorhinus, and Pagothenia borchgrevinki (family Nototheniidae), and Artedidraco skottsbergi (family Artedidraconidae). Through fluorescence in situ hybridization (FISH), we uncovered distinct differences in the gene content of the Y chromosomes in the eight species, with C. hamatus and P. macropterus standing out among others in bearing 5S rDNA and AFGP sequences on their Y chromosomes, respectively. Both genes were absent from the Y chromosomes of any analyzed species. The distinct patterns of Y and non-Y chromosome association of the 5S rDNA and AFGP genes in species representing different Antarctic fish families support an independent origin of the sex heterochromosomes in notothenioids with interesting implications for the evolutionary/adaptational history of these fishes living in a cold-stable environment. Laura Ghigliotti, C.-H. Christina Cheng, Céline Bonillo, Jean-Pierre Coutanceau, and Eva Pisano Copyright © 2013 Laura Ghigliotti et al. All rights reserved.