“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-     

Introducing "Frontiers in Zoology"

As a biological discipline, zoology has one of the longest histories. Today it occasionally appears as though, due to the rapid expansion of life sciences, zoology has been replaced by more or less independent sub-disciplines amongst which exchange is often sparse. However, the recent advance of molecular methodology into "classical" fields of biology, and the development of theories that can explain phenomena on different levels of organisation, has led to a re-integration of zoological disciplines promoting a broader than usual approach to zoological questions. Zoology has re-emerged as an integrative discipline encompassing the most diverse aspects of animal life, from the level of the gene to the level of the ecosystem.The new journal Frontiers in Zoology is the first Open Access journal focussing on zoology as a whole. It aims to represent and re-unite the various disciplines that look at animal life from different perspectives and at providing the basis for a comprehensive understanding of zoological phenomena on all levels of analysis. Frontiers in Zoology provides a unique opportunity to publish high quality research and reviews on zoological issues that will be internationally accessible to any reader at no cost.     

The success of the RNase scaffold in the advance of biosciences and in evolution

In 1938 the new word "ribonuclease" was coined to name an enzyme capable of degrading RNA, before the name "ribonucleic acid" was accepted, as at that time RNA was still labeled YNA, for Yeast Nucleic Acid. Later, four Nobel prizes were awarded to investigators working with the "ribonuclease", RNase A from bovine pancreas. Their work greatly advanced our knowledge of protein chemistry and biology, by producing the first complete amino acid composition and the first covalent structure of a protein, the first complete synthesis of an enzyme, and the discovery that the three-dimensional structure of a protein is dictated by its amino acid sequence. Today, well over 100 homologs of RNase A have been identified in all tetrapods, and recently in fishes. Based on the latter findings, a vertebrate RNase superfamily has been appropriately defined, with RNase A as its prototype. Thus, the success of the RNase structure and function not only in promoting the advance of biosciences, but also in evolution, has become clear. Several RNases from the superfamily are endowed with non-catalytic "special" bioactions. Among these are angiogenins, characterized by their ability to stimulate the formation of blood vessels. Recently, four RNases have been identified in Danio rerio, or zebrafish, produced as recombinant proteins, and characterized. As two of them have angiogenic activity, the hypothesis is made that the whole superfamily of vertebrate RNases evolved from early angiogenic RNases. Given the microbicidal activity of some mammalian angiogenins, and of the reported fish angiogenins, the alternative hypothesis is also discussed, that the ancestral RNases were host-defense RNases.     

A new name for parasitology today

Parasitology Today is officially the Number One ranked journal in parasitology (impact factor 4.940). Since its launch in 1985, Parasitology Today has been part of the Trends Journal series - the most highly cited group of monthly review journals in the world, that includes Trends in Biochemical Sciences, Trends in Microbiology, Trends in Genetics, Immunology Today and Trends in Cell Biology.     

RELEVANCE IN MEDICAL EDUCATION—Some Thoughts from a Forum

For the past several months the editors of California Medicine have conducted a forum in this journal on “Relevance for Today and Tomorrow in Medical Education.” The participants were from widely different backgrounds and represented many points of view. This statement is a distillate from published and unpublished material contributed to the forum. If it proves useful to any who may be concerned with new developments in medical education it will have served its purpose.     

Progress in antiretroviral drugs

HIV-1, causative agent of acquired immunodeficiency syndrome, was identified in the early 1980s . The plague quickly spread throughout the world and today 40 million people are living with HIV/AIDS. The first anti-HIV drug "zidovudine", was discovered in 1985, and many other inhibitory compounds have been developed successfully in the last decade. Today, three classes 17 antiretroviral drugs are available in Japan. This article overviews the history of anti-HIV drug discovery, present HIV-1 treatment, and on-going drug discovery.     

Content Factor: A Measure of a Journal's Contribution to Knowledge

Impact Factor, the pre-eminent performance metric for medical journals, has been criticized for failing to capture the true impact of articles; for favoring methodology papers; for being unduly influenced by statistical outliers; and for examining a period of time too short to capture an article's long-term importance. Also, in the era of search engines, where readers need not skim through journals to find information, Impact Factor's emphasis on citation efficiency may be misplaced. A better metric would consider the total number of citations to all papers published by the journal (not just the recent ones), and would not be decremented by the total number of papers published. We propose a metric embodying these principles, "Content Factor", and examine its performance among leading medical and orthopaedic surgery journals. To remedy Impact Factor's emphasis on recent citations, Content Factor considers the total number of citations, regardless of the year in which the cited paper was published. To correct for Impact Factor's emphasis on efficiency, no denominator is employed. Content Factor is thus the total number of citations in a given year to all of the papers previously published in the journal. We found that Content Factor and Impact Factor are poorly correlated. We further surveyed 75 experienced orthopaedic authors and measured their perceptions of the "importance" of various orthopaedic surgery journals. The correlation between the importance score and the Impact Factor was only 0.08; the correlation between the importance score and Content Factor was 0.56. Accordingly, Content Factor better reflects a journal's "importance". In sum, while Content Factor cannot be defended as the lone metric of merit, to the extent that performance data informs journal evaluations, Content Factor- an easily obtained and intuitively appealing metric of the journal's knowledge contribution, not subject to gaming- can be a useful adjunct.     

Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7

This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the European Bioinformatics Institute, Cambridge, United Kingdom and included a two-day workshop focused on the refinement of the Genomic Contextual Data Markup Language (GCDML). GSC 7 was held as the opening day of the International Congress on Metagenomics 2008 in San Diego California. Major achievements of these combined meetings included an agreement from the International Nucleotide Sequence Database Consortium (INSDC) to create a "MIGS" keyword for capturing "Minimum Information about a Genome Sequence" compliant information within INSDC (DDBJ/EMBL /Genbank) records, launch of GCDML 1.0, MIGS compliance of the first set of "Genomic Encyclopedia of Bacteria and Archaea" project genomes, approval of a proposal to extend MIGS to 16S rRNA sequences within a "Minimum Information about an Environmental Sequence", finalization of plans for the GSC eJournal, "Standards in Genomic Sciences" (SIGS), and the formation of a GSC Board. Subsequently, the GSC has been awarded a Research Co-ordination Network (RCN4GSC) grant from the National Science Foundation, held the first SIGS workshop and launched the journal. The GSC will also be hosting outreach workshops at both ISMB 2009 and PSB 2010 focused on "Metagenomics, Metadata and MetaAnalysis" (M(3)). Further information about the GSC and its range of activities can be found at http://gensc.org, including videos of all the presentations at GSC 7.     

Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode

Angiostrongylus costaricensis is a nematode helminth that causes an intestinal acute inflammatory process known as abdominal angiostrongyliasis, which is a poorly understood human disease occurring in Latin America. Our aim was to study the proteomic profiles of adult parasites focusing on immunogenic proteins. Total cellular extracts from both genders showed similar 2-DE profiles, with 60% of all protein spots focused between pH 5-7 and presenting molecular masses from 20.1 to 66 kDa. A total of 53 different dominant proteins were identified in our dataset and were mainly associated with the following over-represented Gene Ontology Biological Process terms: "macromolecule metabolic process", "developmental process", "response to stress", and "biological regulation". Female and male immunoblots showed similar patterns of reactive proteins. Immunoreactive spots identified by MALDI-PSD were found to represent heat shock proteins, a putative abnormal DAuer Formation family member, and galectins. To date, very few biochemical analyses have focused on the nematode Angiostrongylus costaricensis. As such, our results contribute to a better understanding of its biology and the mechanisms underlying the host-parasite relationship associated with this species. Moreover, our findings represent a first step in the search for candidate proteins for diagnostic assays and the treatment of this parasitic infection.     

The malariology centenary (1898-1998). 1898

This editorial note presents the journal initiative to celebrate the Malariology Centenary. It includes the reprint of the first annual report of the Society for Malaria Studies (founded in 1898), presented by Angelo Celli on December 3rd, 1898, to the first meeting of the Society and published in the Journal of the Royal Italian Society of Hygiene (volume 20, issue 12, 31st December 1898). The text is followed by explanatory footnotes and relevant references. An exhaustive historical essai, including the english version of the Celli's report, is scheduled to appear as supplement to volume 41, and the same volume will host the contributions issued from the international conference. "The malaria challenge after one hundred years of malariology", held in Roma at the Accademia Nazionale dei Lincei on November 16-19, 1998.     

Defining the structure of irregular nucleic acids: conventions and principles

The algorithm "Curves", that we have recently presented in this journal (J. Biolmol. Str. Dynam. 6, 63-91 (1988], is updated to take into account the conventions developed at the Cambridge meeting on DNA curvature (September 1988) and extended to the calculation of local parameters. In addition, the principles which govern the choices made in establishing the Curves algorithm are compared with the approaches adopted by other authors.     

Editorial Note: Change of Publisher and New Policies

The first volume of DNA Research was published in 1994, andsince then, it has been published as a leading journal in thefield. The online version of the journal was launched in 2000.From its launch, the online journal has been freely accessibleto all readers without charge. Though thorough analysis hasnot been performed to     

Moscow University Biological Sciences Bulletin—a new era of evolution (2007–2013)

The paper considers the history of how the scientific journal Moscow University Biological Sciences Bulletin (MUBSB) evolved during the last 7 years. It is the English edition of the Russian scientific peer-reviewed journal of the School of Biology of Lomonosov Moscow State University MSU Vestnik (Herald). Series 16. Biology. MUBSB is published by Allerton Press, a member of the Nauka/Interperiodica International Academic Publishing Company since 2007. The rapid progress of MUBSB in recent years is apparently due to the journal having been distributed since 2007 by the internationally renowned Springer publishing consortium that places electronic versions of all articles on its website, which has, to all appearances, led to a manifold increase in the number of journal subscribers. As a result, the number of downloads of MUBSB papers from the publishing company website also raised by an order of magnitude from 2007 to 2013. The growing popularity of the journal is noted to have lead to its inclusion in a number of international databases, and this, in turn, has increased its attractiveness for a large number of authors, including Russian nonmembers of Moscow State University, as well as scientists from research institutes and universities of other countries. The main features of the spectrum of the papers published in MUBSB are briefly considered.     

The scientific names in the German edition of Parkinson's plants of use for food, medicine etc., in Otaheite

Sydney Parkinson, aged 18, was Sir Joseph Banks' private assistant and artist on Captain Cook's first voyage around the world. Parkinson died on the voyage. Among his effects delivered to his brother Stanfield were drawings and notes which the latter published as a journal. Included in it is a chapter on the economic plants of Tahiti, and most of them are given scientific names, some of which were new. In 1941 Fosberg adopted two of them to form names which were new combinations under Artocarpus , and Inocarpus . The writer now indicates that Parkinson's names of 1773 were mononomials, hence invalid, but that in the German edition of 1774, edited by Herr "Z", the names are valid binomials. For the two plants mentioned, the authorship of the combinations is revised.     

中国履行生物多样性公约的成就和展望

2004年是生物多样性公约实施10周年。中国于1993年1月7日作为第7个国家正式加入“公约”。接着就由国家环境保护总局牵头组建国家履约协调组和许多联络点,下设办公室负责日常工作。可见,国家对生物多样性工作的重视和认真的态度。10年来,中国在履约方面做了大量工作,成绩显著。例如,完成了“中国生物多样性国情研究报告”和“中国生物多样性保护行动计划”等一大批重要文件,建立了“生物多样性委员会”、“生物多样性保护基金会”和相应的科学与教育部门,开展了许多科研项目和讲授相关的课程,出版了系列丛书和“中国生物多样性”学术刊物,重视开展学术交流,建立了生物多样性数据库和相关的管理政策,生物多样性保护实体和产业日益增加和发展等就是明显的事例。履约10年的经验在于下列三个方面(1)保护和发展必须密切结合;(2)“统一协调、分散管理”的方针需要进一步完善;(3)基础性和综合性研究需要加强。展望未来,只有在加强基础和综合研究以及提高管理水平方面下一番功夫,履约工作才能取得更大的成绩。     

Impact analysis of a regional scientific journal (1980-2000): supporting promising local researchers pays the greatest dividends

During the past 28 years, the journal "Collegium Antropologicum" has continuously served as one of the main disseminators of anthropological scientific production in Central and Eastern Europe. The journal was committed to its role of a multidisciplinary platform for presenting wide range of research topics relevant to anthropology, from investigations within social and cultural anthropology and archaeology to those covering contemporary population genetics, human evolution and biomedical issues. Two key strategies aimed at sustaining and increasing the impact of this journal were oriented towards: (i) identification of promising local groups of researchers who were at disadvantage by many aspects (e.g. educational curricula, financial supports, language barriers etc.) when trying to publish their research internationally, and (ii) invitation and encouragement of already established international scientists to make contributions for "Collegium Antropologicum". From 1980-2000, 89 articles (or 6.3% of all published papers during that period) were cited 6 or more times, contributing disproportionately to journal's impact (nearly a third of all citations received). In an attempt to identify such papers more readily among the submissions to the journal in the future, we analyzed research topics and affiliations of the authors among the 89 papers receiving most citations in comparison to all papers published. Among the papers most frequently cited, we found greater-than-expected prevalence of Croatian researchers (especially when publishing in collaboration with international scientists) and studies of special populations. Several papers received more than 25 citations or had overall citation intensity greater than 2 per year. This implies that an interesting article from a local group of researchers can still resonate with international audience although published in a regional journal. Present analysis supports current editorial strategy that with a help of the international consulting editorial board continuously improves international recognition of this journal. The results imply that a balanced encouragement to promising local groups of researchers and to contributions of already established international scientists is a strategy superior to others in maintaining and increasing the impact of this regional journal.     

Biophysical reviews: call for nominations for the 2023 Michèle Auger Award

This Editorial for Issue 3 (Vol. 14 2022) of Biophysical Reviews first describes the Issue’s contents (five commentaries/editorials within the front matter and seven review/letter articles appearing within the main body) before going on to discuss a number of matters of potential importance to the journal and its readers. Amongst this second tranche of content is the opening of the call for nominations for the 2023 Michèle Auger Award for Young Scientists’ Independent Research.

Created in 2009, Biophysical Reviews is the flagship journal of IUPAB, the International Union for Pure and Applied Biophysics (IUPAB 2022). Each of the journal’s six issues per year are divided into a front section, dealing with journal process and points of interest to biophysicists and IUPAB society members, and a main section, that presents scientific Letters and Reviews that are written by recognized experts in the field and are selected with an eye to providing an as wide as possible level of international participation. The first duty of each Issue’s editorial is to provide a precis of both the non-scientific and scientific articles appearing within, and we carry this out forthwith.     

Immunome Research

Immunology research has been transformed in the post-genomics era, with high throughput molecular biology and information technologies taking an increasingly central role. This has led to the development of a new area of science termed "Immunomics", that encompasses genomic, high throughput and bioinformatic approaches to immunology. In recognition of the increasing importance of this field, Immunome Research is a new Open Access, online journal, that will publish cutting edge research across the field of Immunomics. Immunome Research will publish a wide range of article types including specialty immunology databases, immunology database tools, immunome epitope research, epitope analysis tools, high-throughput technologies (gene sequencing, microarrays, proteomics), white papers, mathematical and theoretical models, and prediction tools. Immunome Research is the official journal of the International Immunomics Society (IIMMS).