PREFACE

First of all, I would like to introduce the predecessor of "Virologica Sinica (to be published in English) and its history of development. I was honored to participate in it. " Acta Virologica Sinica" (in Chinese with English abstract), which was first published in 1980, was the first virological journal issued in China. The editor in chief was Prof. Dr. Shangyin Gao (1909-1989), who was a famous virologist. He was the director of     

Stepping Stones：A New Future for Zoological Research

正This past year has been an auspicious one for Chinese science.With the recent lunar landing and the advances and the Chinese Academy of Sciences’growing reputation as the leader of scientific publishing in Asia,the media is now constantly reporting the"great leaps"that Chinese researchers have made.But we would do well to remember an old Chinese proverb:"It is better to take many small steps in the right direction than to make a great leap forward only to stumble backward."None of the recent advances of this year are great leaps in the sense that they occurred from     

Ray Wu and the CUSBEA Program

I first met Dr Ray Wu in the late seventies of the last century, when China was beginning to re-engage with the western world. Deng Xiaoping laid out a bold, ambitious plan for the country to rapidly modernize. To realize this plan, China would need a new kind of work force. The responsi-bility fell upon the Ministry of Education to find the brightest young minds in China and to dispatch them to "scientifically advanced western countries" for post-graduate studies.     

Asymmetric or diffusive co-evolution generates meta-populations in fig-fig wasp mutualisms

Co-evolutionary theory assumes co-adapted characteristics are a positive response to counter those of another species,whereby co-evolved species reach an evolutionarily stable interaction through bilateral adaptation.However,evidence from the fig-fig wasp mutualistic system implies very different co-evolutionary selection mechanisms,due to the inherent conflict among interacted partners.Fig plants appear to have discriminatively enforced fig wasps to evolve"adaptation characteristics"that provide greater benefit to the fig,and fig wasps appear to have diversified their evolutionary strategies in response to discriminative enforcement by figs and competition among different fig wasp species.In what appears to be an asymmetric interaction,the prosperity of cooperative pollinating wasps should inevitably lead to population increases of parasitic individuals,thus resulting in localized extinctions of pollinating wasps.In response,the sanctioning of parasitic wasps by the fig should lead to a reduction in the parasitic wasp population.The meta-populations created by such asymmetric interactions may result in each population of coevolved species chaotically oscillated,temporally or evolutionarily.     

Full-Color Publication in JIPB from January 1~(st),2017

正In order to increase the readability of papers published in JIPB,with the support from the Project for Enhancing International Impact of China STM Journals,JIPB has started to publish all contents in JIPB with full color,both in print andonline versions.The page charge will be 100 US$per printed page.If authors decide to choose OpenAccess,a one-time charge of 2,500 US$will be applied(no page charge is needed).All authors are advised to read the"Instructions for Authors"     

“Three Kingdoms”to Romance

For some historic reasons, our new journal is named "Genomics, Proteomics & Bioinformatics", or as we have nicknamed it in short the Journal of GPB. A growing number of "-ome" and "-omics" have appeared in many diverse fields of biology, especially in the recent years under profound influences of the Human Genome Project and many other genome projects completed or in progress. We had almost attempted to re-name this journal "Ever-more-omics" to in-     

Plant DNA barcoding in China

Identification is the keystone of biology (Bell, 1986).However, to biologists and students of biology, the total numbers of species that must be identified far outnumber the names commonly used in English, Chinese, or other living languages.In addition, the identification cues vary greatly between different taxonomical groups.Even for the taxonomists with long training and experience, it is difficult to remember all specific terms for a given group, e.g., Orchidaceae or Poaceae, without help of floristic books or monographs.It takes much time and effort to train a taxonomist, at a time when fewer and fewer young students are interested in this "classical" and "out-of-style", but extremely important, discipline.Many students elect to learn the more "advanced' and "modem" biological disciples like molecular biology and biochemistry.Thus, in China and therest of the world, taxonomists are themselves becoming "endangered".The rise of the DNA barcoding is expected to mitigate, at least in part, this dilemma.     

Effect of chitosan on tobacco mosaic virus(TMV) accumulation,hydrolase activity,and morphological abnormalities of the viral particles in leaves of N. tabacum L. cv. Samsun

The effect of chitosan on the development of infection caused by Tobacco mosaic virus(TMV) in leaves of Nicotiana tabacum L. cv. Samsun has been studied. It was shown that the infectivity and viral coat protein content in leaves inoculated with a mixture of TMV(2 μg/mL) and chitosan(1 mg/mL) were lower in the early period of infection(3 days after inoculation), by 63% and 66% respectively, than in leaves inoculated with TMV only. Treatment of leaves with chitosan 24 h before inoculation with TMV also caused the antiviral effects, but these were less apparent than when the virus and polysaccharide were applied simultaneously. The inhibitory effects of the agent decreased as the infection progressed. Inoculation of leaves with TMV together with chitosan considerably enhanced the activity of hydrolases(proteases, RNases) in the leaves, in comparison with leaves inoculated with TMV alone. Electron microscope assays of phosphotungstic acid(PTA)-stained suspensions from infected tobacco leaves showed that, in addition to the normal TMV particles(18 nm in diameter, 300 nm long), these suspensions contained abnormal(swollen, "thin" and "short") virions. The highest number of abnormal virions was found in suspensions from leaves inoculated with a mixture of TMV and chitosan. Immuno-electron microscopy showed that "thin" virus particles, in contrast to the particles of normal diameter, lost the ability to bind to specific antiserum. It seems that the chitosan-induced activation of hydrolases stimulates the intracellular degradation of TMV particles and hence hydrolase activation may be considered to be one of the polysaccharide-mediated cellular defense mechanisms that limit virus accumulation in cells.     

Special Issue on “Microbiome and Health”

正The journal Genomics,ProteomicsBioinformatics(GPB)is now inviting submissions to a special issue(to be published in the fall of 2018)on the topic of"Microbiome and Health".In the era of precision medicine,the human"2ndgenome",namely the human microbiome,is of increasing interest worldwide.Firstly,the human microbiome has been linked to various diseases including metabolic diseases,cancers,heart diseases,or brain disorders,and autoimmune diseases.Secondly,changes in the microbiome are known or hypothesized to be proxies for     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the fall of 2018,on "Plant Genomics"in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The     

Genetics of Nonalcoholic Fatty Liver Disease:An Overview

Nonalcoholic fatty liver disease(NAFLD) is the most common liver disease in the world today.Its incidence in adults and children is rising rapidly due to the ongoing epidemics of obesity and type 2 diabetes.Hence,it has become a global public health issue.Environmental factors have been found to play a major role in the etiology of NAFLD,especially for genetically susceptible populations. Among these,one of the most important factors is junk food,especially the typical "Western-style" diet rich in simple carbohydrates, saturated fat,and highly processed food materials.Genetic predisposition to NAFLD does occur;however,a precise definition of genetic factors responsible for NAFLD is still lacking.Specific variants of different genes have been shown to present a risk for NAFLD.Genetic studies might be helpful in the management of the disease by developing novel treatment strategies based on individual’s genotype.     

Theoretical investigation on peripheral ligands of oxygen-evolving center in photosystem II

The interaction between the Mn-cluster and its peripheral ligands in oxygen-evolving center is still unclear. Theoretical investigation on the coordination of histidine, H2O, and Cl to Mn2O2 units in OEC is conducted. The following conclusions are obtained: (i) both histidine and H2O molecule, bound to the two Mn ions, respectively, are vertical to the Mn2O2 plane, and maintain a large distance; (ii) the two H2O molecules cannot bind to the same Mn2O2 unit. Based on Mn-cluster structure in OEC, we theoretically predict that two H2O molecules bind to the two Mn ions at the "C"-shaped open end in S0 state, while two His residues at the closed end. Cl ion can only terminally ligate at the open end. Individual valence for the four Mn ions in S0 state is assigned.     

Tumor-specific gene expression patterns with gene expression profiles

Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, "RFE_Relief algorithm" was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.     

Three-dimensional morphology of the Sinocyclocheilus hyalinus(Cypriniformes: Cyprinidae) horn based on synchrotron X-ray microtomography

Sinocyclocheilus is a cave-dwelling cyprinid genus endemic to southwest China. Several species possess a conspicuous horn on their head, which has been suggested as a constructive troglomorphic trait but lacks substantial evidence. We used noninvasive, high spatial resolution synchrotron X-ray microtomography to investigate the three-dimensional(3D) morphology of the horn of Sinocyclocheilus hyalinus, one of eight such troglobiotic species. 3D renderings demonstrated the osteological components,which were comprised of a rear wall comprised of the supraoccipital bone, a remaining frontal wall with numerous fenestrae, and the bottom continuous with the parietal and epiotic. A horn cavity occurred within the horn. The fenestrae in the frontal wall were continuous in the horn cavity and showed elaborate channeling, and were, connected to the cranial cavity by soft tissue. We tentatively called this configuration the "otocornual connection" due to its anatomic and putative functional similarity to the otolateralic connection in clupeids and loricariids, which provide an indirect pathway to enhance perception of underwater sound signals. This study provides a functional morphology context for further histological and physiological investigations of such horn structures in Sinocyclocheilus cavefish, and we suggest that the horn might enhance acoustic perception to compensate for visual loss in subterranean life, which warrants future physiological examination as lab-reared S. hyalinus become available.     

Special Issue on “Single-cell Omics Analysis”

正We are very pleased to announce a special issue, to be published in the spring of 2020, on "Single-cell Omics Analysis" in the journal Genomics, Proteomics Bioinformatics(GPB). The cell has been primarily studied as a part of its bulk population for decades until recent     

Special Issue on “Big Data in Brain Science”

正The journal Genomics,ProteomicsBioinformatics(GPB)is now inviting submissions for a special issue(to be published in the Winter of 2017)on the topic of "Big data in brain science".It took 15 years,3 billion USD,and thousands of top scientists from all over the world to complete the Human Genome Project(HGP).Our next grand challenge in biological sciences,the     

JIPB is Introducing a New Category Breakthrough Reports

正JIPB will discontinue the category"Letter to the Editor",and launch a new publication category,"Breakthrough Reports"from January 1,2019.These Breakthrough Reports will present especially exciting and original research findings with a high degree of novelty,representing breakthroughs in understanding important biological processes,with the potential to open new areas of investigation in the field of plant biology.