Author's letter 1

正I am writing to apologize for our negligence and in our paper [Hong JIN, Bin LU and Jinzhong FU. 2018. Massive molecular parallel evolution of the HSP90AA1 gene between high-elevation anurans. Asian Herpetological Research9(3):195-200], in which we failed to include the second cultivation unit of the first author Hong JIN. Here we provide the missing information by Supplement and Correction below.Apologize again for my negligence!     

Trichosanthin inhibits T cell activation by interfering with the recruitment of ZAP—70 to CD3 chain

Plant protein Trichosanthin(Tk) has been shown in our previous experiments to suppress antigenic response of T cells.Here we explored its inhibitory mechanisms on the proliferation of human Jurkat leukemia T cell triggered by anti-CD3 McAb,By examination of tyrosine phosphorylation of cell lysate,we were able to show that Tk could interfere with the PTK-related activity in the TCR/CD3-initiated signal transduction in addition to blocking the phosphorylation of PKC.As shown in our experiment the expression intensity of ZAP-70,a kind of protein tyrosine kinase,was not changed but its phosphorylation could be inhibited.When physical link between CD3 ζ chain and ZAP-70 was further examined by using coimmunoprecipitation after pluse-treatment of the cell line with Tk,the anti-CD3 McAb-induced recruitment of ZAP-70 to CD3 ζ chain was observed to be blocked in some extent.This may account for,at least in part,how Trichosanthin was able to inhibit the TCR-triggered T cell proliferation.     

Supplement and Correction

正A new species,Protobothrops dabieshanensis,was described in our paper[Xin HUANG,Tao PAN,Demin HAN,Liang ZHANG,Yinxu HOU,Lei YU,Heming ZHENG,Baowei ZHANG.2012.A New Species of the Genus Protobothrops(Squamata:Viperidae:Crotalinae)from the Dabie Mountains,Anhui,China.Asian Herpetol Res,3(3):213-218].However,some important information,including holotype number,deposited site     

Advanced glycation end products of bovine serum albumin affect the cell growth of human umbilical vein endothelial cells via modulation of MEG3/miR-93/p21 pathway

Advanced glycation end products of BSA (AGE-BSA) contribute to the pathogenesis of diabetic vascular diseases.However,the roles and underlying mechanisms of AGE-BSA in diabetic vascular diseases remain largely unclear.Long non-coding RNAs (lncRNAs) are widely identified and known as gene regulators.However,the roles of lncRNAs in diabetic vascular disease are still vague.In this study,we sought to investigate the contributions of lncRNAs in human umbilical vein endothelial cells (HUVECs) treated with AGE-BSA.We first demonstrated that AGE-BSA reduced the cell viability and inhibited the cell proliferation of HUVECs.Then,we found that lncRNA MEG3 was up-regulated in HUVECs treated with AGE-BSA.Furthermore,inhibition of MEG3 restored the AGE-BSA-induced repression of cell viability and proliferation.In addition,our results revealed that MEG3 played its role via modulation of miR-93 expression in HUVECs treated with AGE-BSA.Furthermore,we illustrated that miR-93 played its role via regulation of p21 in HUVECs treated with AGE-BSA.Ultimately,our study displayed that AGE-BSA exerted its function via modulation of MEG3/miR-93/p21 pathway in HUVECs.Thus,for the first time,we identified the MEG3/miR-93/p21 axis in HUVECs treated with AGE-BSA,which might be a novel regulatory network in diabetic vascular cells,and possess the potential therapeutic value for diabetes mellitus.     

2018 New Year Address of Zoological Research

正At the beginning of a wonderful new year,we look back at Zoological Research(ZR)in 2017.We are very grateful to all our readers and authors for your dedication and continued support of ZR.Your ideas,input,and enthusiasm have been of immense value in helping us to improve the journal.Here,we would like to share a few memorable events and people of the past year.     

A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts

The large amount of repeats, especially high copy repeats, in the genomes of higher animals and plants makes whole genome assembly (WGA) quite difficult. In order to solve this problem, we tried to identify repeats and mask them prior to assembly even at the stage of genome survey. It is known that repeats of different copy number have different probabilities of appearance in shotgun data, so based on this principle, we constructed a statistical model and inferred criteria for mathematically defined repeats (MDRs) at different shotgun coverages. According to these criteria, we developed software MDRmasker to identify and mask MDRs in shotgun data. With repeats masked prior to assembly, the speed of assembly was increased with lower error probability. In addition, clone-insert size affects the accuracy of repeat assembly and scaffold construction. We also designed length distribution of clone-inserts using our model. In our simulated genomes of human and rice, the length distribution of repeats is differ     

国际寒武纪友谊（英文）

正Professor Chang was a long-time friend and colleague.We began exchanging reprints in the 1950’s and finally,in 1976Iwas able to visit Nanjing and we met for the first time.Subsequently he came to the U.S.and I was able to show him some of our spectacular desert Cambrian exposures in the west.Later,he was a most gracious host as we toured much of eastern China,following an International Cambrian Symposium in Novosibirsk,dividing our time between Cambrian exposures and famous tourist sites.Our     

Opposite effects of Drosophila C3PO on gene silencing mediated by esi-2.1 and miRNA-bantam

Translin/TRAX complex,also named as C3PO,is evolutionarily conserved and participates in diverse cellular processes in different organisms from yeast to human.C3PO plays a critical role in the activation of RNA-induced silencing complexes by promoting the unwinding and degradation of passenger strand of exogenous siRNAs(exo-siRNAs)in Drosophila and human.Moreover,human C3PO(hC3PO)has been found to broadly repress miRNAs by degrading miRNA precursors.However,the effect of Drosophila melanogaster C3PO(dmC3PO)on endogenous siRNA(endo-siRNA)and miRNA pathways remains unknown.Here,we found that the loss of dmC3PO promoted the accumulation of the passenger strand of esi-2.1(hp-CG4068B),and resulted in the de-repression of the DNA-damage-response gene mutagensensitive 308(mus308),which is an endogenous slicer target of esi-2.1 in Drosophila.Moreover,we also found that depletion of dmC3PO increased the accumulation of miR-bantam.Taken together,our findings indicated that dmC3PO not only involves in siRNA pathway triggered by dsRNA,but also regulates the abundance of certain endogenous small RNAs in Drosophila.     

The Origin of Patterning Systems in Bilateria——Insights from the Hox and ParaHox Genes in Acoelomorpha

Hox and ParaHox genes constitute two families of developmental regulators that pattern the Anterior-Posterior body axis in all bilaterians.The members of these two groups of genes are usually arranged in genomic clusters and work in a coordinated fashion,both in space and in time. While the mechanistic aspects of their action are relatively well known,it is still unclear how these systems evolved. For instance,we still need a proper model of how the Hox and ParaHox clusters were assembled over time.This problem is due to the shortage of information on gene complements for many taxa (mainly basal metazoans) and the lack of a consensus phylogenetic model of animal relationships to which we can relate our new findings.Recently, several studies have shown that the Acoelomorpha most probably represent the first offshoot of the Bilateria. This finding has prompted us,and others, to study the Hox and ParaHox complements in these animals,as well as their activity during development.In this review,we analyze how the current knowledge of Hox and ParaHox genes in the Acoelomorpha is shaping our view of bilaterian evolution.     

A novel algorithm for finding interspersed repeat regions

The analysis of repeats in the DNA sequences is an important subject in bioinformatics. In this paper, we propose a novel projection-assemble algorithm to find unknown interspersed repeats in DNA sequences. The algorithm employs random projection algorithm to obtain a candidate fragment set, and exhaustive search algorithm to search each pair of fragments from the candidate fragment set to find potential linkage, and then assemble them together. The complexity of our projection-assemble algorithm is nearly linear to the length of the genome sequence, and its memory usage is limited by the hardware. We tested our algorithm with both simulated data and real biology data, and the results show that our projection-assemble algorithm is efficient. By means of this algorithm, we found an un-labeled repeat region that occurs five times in Escherichia coil genome, with its length more than 5,000 bp, and a mismatch probability less than 4%.     

2019 New Year Address of Zoological Research

正At the beginning of this new year full of exciting prospects and potential, we would first like to share our exciting news that Zoological Research (ZR) is now covered by Science Citation Index Expanded (SCI-E), with full coverage to be backdated to issue 1 in 2016. This encouraging progress demonstrates that ZR has taken a critical step on the journey to becoming one of the top journals in the field.We would like to sincerely thank every author, reader, and     

Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interac-tion data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automati-cally selects the most appropriate functional classes as specific as possible during the learning proc-ess, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to “biology process” by three measures particularly designed for functional classes organ-ized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.     

B-cell ligand processing pathways detected by large-scale comparative analysis

The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies.We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses.We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands.First,we compared the degree distributions of the generated networks.Second,we utilized a pairwise network alignment algorithm,BiNA,to align the networks based on the hubs in the networks.Third,we aligned the networks based on a set of K_EGG pathways.We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition.The resulting pathways were further validated through literature for their common physiological responses.Collectively,the results based on our comparative analyses of degree distributions,alignment of hubs,and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches(e.g.,gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells.     

Using MutPred derived mtDNA load scores to evaluate mtDNA variation in hypertension and diabetes in a two-population cohort:The SABPA study

Mitochondrial DNA(mt DNA) variation has been implicated in many common complex diseases, but inconsistent and contradicting results are common. Here we introduce a novel mutational load hypothesis, which also considers the collective effect of mainly rare variants, utilising the Mut Pred Program.We apply this new methodology to investigate the possible role of mt DNA in two cardiovascular disease(CVD) phenotypes(hypertension and hyperglycaemia), within a two-population cohort(n = 363; mean age 45 ± 9 yrs). Very few studies have looked at African mt DNA variation in the context of complex disease, and none using complete sequence data in a well-phenotyped cohort. As such, our study will also extend our knowledge of African mt DNA variation, with complete sequences of Southern Africans being especially under-represented. The cohort showed prevalence rates for hypertension(58.6%) and prediabetes(44.8%). We could not identify a statistically significant role for mt DNA variation in association with hypertension or hyperglycaemia in our cohort. However, we are of the opinion that the method described will find wide application in the field, being especially useful for cohorts from multiple locations or with a variety of mt DNA lineages, where the traditional haplogroup association method has been particularly likely to generate spurious results in the context of association with common complex disease.     

Canada and China working together in the Nature Reserves of Inner Mongolia Autonomous Region

The environment and its natural resources are one of the richest treasures in the world. The lands, forests, lakes and rivers are not only beautiful spaces in the world, but these ecosystems are the basis of life for all the people and creatures who inhabit the earth. As inhabitants of the earth, we all have a responsibility to take care of these important resources-to protect our biological diversity-for ourselves, for future generations and for the many other creatures that we share the world with. Indeed, as stewards of the environment we must ensure that our actions, and those of the people around us, are not harmful or damaging to the earth.     

Identification of a ubiquitin-binding structure in the S-locus F-box protein controlling S-RNase-based self-incompatibility

In flowering plants,self-incompatibility(SI) serves as an important intraspecific reproductive barrier to promote outbreeding.In species from the Solanaceae,Plantaginaceae and Rosaceae,S-RNase and SLF(S-locus F-box) proteins have been shown to control the female and male specificity of SI,respectively.However,little is known about structure features of the SLF protein apart from its conserved F-box domain.Here we show that the SLF C-terminal region possesses a novel ubiquitin-binding domain(UBD) structure conserved among the SLF protein family.By using an ex vivo system of Nicotiana benthamiana,we found that the UBD mediates the SLF protein turnover by the ubiquitin—proteasome pathway.Furthermore,we detected that the SLF protein was directly involved in S-RNase degradation.Taken together,our results provide a novel insight into the SLF structure and highlight a potential role of SLF protein stability and degradation in S-RNase-based self-incompatibility.     

Extracellular calmodulin: A polypeptide signal in plants?

Traditionally, calmodulin (CaM) was thought to be a multi-functional receptor for intra-cellular Ca2+ signals. But in the last ten years, it was found that CaM also exists and acts extracel-lularly in animal and plant cells to regulate many important physiological functions. Laboratory studies by the authors showed that extracellular CaM in plant cells can stimulate the proliferation of suspension cultured cell and protoplast; regulate pollen germination and pollen tube elongation, and stimulate the light-independent gene expression of Rubisco small subunit (rbcS). Furthermore, we defined the trans-membrane and intracellular signal transduction pathways for extracellular CaM by using a pollen system. The components in this pathway include heterotrimeric G-protein, phospholipase C, IP3, calcium signal and protein phosphorylation etc. Based on our findings, we suggest that extracellular CaM is a polypeptide signal in plants. This idea strongly argues against the traditional concept that there is no interce