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.     

Gene expression profiling of human epidermal keratinocytes in simulated microgravity and recovery cultures

Simulated microgravity （SMG） bioreactors and DNA microarray technology are powerful tools to identify ＂space genes＂ that play key roles in cellular response to microgravity. We applied these biotechnology tools to investigate SMG and post-SMG recovery effects on human epidermal keratinocytes by exposing cells to SMG for 3, 4, 9, and 10 d using the high aspect ratio vessel bioreactor followed by recovery culturing for 15, 50, and 60 d in normal gravity. As a result, we identified 162 differentially expressed genes, 32 of which were ＂center genes＂ that were most consistently affected in the time course experiments. Eleven of the center genes were from the integrated stress response pathways and were coordinately downregulated. Another seven of the center genes, which are all metallothionein MT-Ⅰ and MT-Ⅱ isoforms, were coordinately up-regulated. In addition, HLA-G, a key gene in cellular immune response suppression, was found to be significantly upregulated during the recovery phase. Overall, more than 80% of the differentially expressed genes from the shorter exposures （≤4 d） recovered in 15 d; for longer （≥9 d） exposures, more than 50 d were needed to recover to the impact level of shorter exposures. The data indicated that shorter SMG exposure duration would lead to quicker and more complete recovery from the microgravity effect.     

Ecological Niche Divergence between Trapelus ruderatus(Olivier,1807) and T.persicus(Blanford,1881)(Sauria:Agamidae) in the Middle East

Modeling the potential distribution areas for a given species is important in understanding the relationship between the actual distribution and the most suitable habitat for a species. In this study, we obtained all available records of Trapelus ruderatus and Trapelus persicus from museums, literature and fieldwork and used them with environmental layers in the Maximum Entropy algorithm to predict highly suitable habitat areas. The distribution model of T. ruderatus and T. persicus showed excellent performance for both models(T.ruderatus AUC =0.964 ± 0.001 and T.persicus AUC = 0.996 ± 0.003), and predicted suitable regions in Iran, Turkey, Iraq and Syria. Niche overlap was measured between the two groups by ENMtools and 13% overlapped. We used a niche identity test to determine differences between the niches of the two species. Finally, by comparing our null hypothesis to the true niche overlap of the two species, we were able to reject our null hypothesis of no difference between the niches. Due to the sympatric distribution pattern of these species, we do not need a background test for niche divergence.     

Cell Research Announces the Appointment of New Deputy Editor-in-chief

Cell Research is pleased to announce that Dr Dangsheng Li has been appointed as the new Deputy Editor-in-chief for our journal, starting March 2006. Dangsheng received his BS degree （in Cell Biology） from the University of Science and Technology of China, and obtained his PhD （in Molecular Biology） from Cornell University Graduate School of Medical Sciences. After extensive postdoctoral training at New York University Medical Center, he joined Cell Press in 2004 to serve as an Associate Editor for the premium biology journal Cell. Dangsheng will be in charge of the scientific editing operations of Cell Research, working closely with our academic Editors, members of our Editorial Board, as well as our expert reviewers. Dangsheng shares our goals of developing and growing Cell Research, and we are extremely pleased to be able to appoint him to this position.     

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.     

Carbon cycle of larch plantation based on CO2FIX model北大核心CSCD

Aims Plantations play important roles in modifying regional carbon budget and maintaining regional carbon balance. In this study, we assessed larch plantation (Larix gmelinii var. principis-rupprechtii) carbon dynamics in Weichang County from a perspective of the forest biomass-soil-wood-products chain. Our objectives were to elucidate the carbon sink capacity of larch plantation and the influences of biomass, soil and wood product pools on carbon balance. Methods CO2FIX model was used to evaluate the carbon storage and flow of larch plantation over a time span of 120 years. Input data for model were derived from practical investigations and published papers. We validated the simulated results and found that this model was suitable in the region and the simulated results were reliable. Important findings (1) Soil was the largest carbon pool for larch plantation and the wood product pool had the smallest carbon storage. Meanwhile, carbon storage in wood products gradually increased with time. (2) In a rotation of 50 years from secondary poplar-birch forest to larch plantation, 250 t C•hm2 was sequestrated by the larch plantation. 70% of the carbon was transferred into soil in the form of litter and logging slash and the other 30% was transferred into wood products. (3) Larch plantation was a carbon sink during most of its growing period and turned to temporary carbon source when it was harvested. Larch plantation could sequestrate about 0.3 t C•hm2•a1 in the long term. Our results indicated the importance of wood product carbon pool in carbon dynamics of plantation, which facilitated our understanding in the carbon dynamics and capacity of plantation.     

Dewlap size in male water anoles associates with consistent inter-individual variation in boldness

Male sexually selected signals can indicate competitive ability by honestly signaling fitnessrelevant traits such as condition or performance. However, behavior can also influence contest outcomes;in particular, boldness often predicts dominance rank and mating success. Here, we sought to determi ne whether male ornament size is associated with consiste nt in dividual differences in boldness in water anoles Anol is aquaticus. We measured the relative size of the dewlap, a flap of skin under the chin that is a sexually selected ornament in Anolis lizards, and tested for associations with responses to a novel and potentially risky environment: time to emerge from a refuge into an arena and number of head sea ns post-emergence. We found that in dividuals con siste ntly differed in both time to emerge and head sea nning (i.e., in dividual resp on ses were repeatable), and that dewlap size was negatively related to nu mber of head sea ns. This suggests that orname nt size could indicate male boldness if seanning represents antipredator vigilance. We found that males that had larger relative dewlaps were also in better body condition, but boldness (i.e., head scann ing) was not related to condition. Lastly, we found con siste nt d iff ere nces in behavior betwee n trials, showing that anoles were becoming habituated or sensitized to the testing arena. Overall, our study shows that in additi on to indicating con dition and perform a nee, dewlap size could also honestly indicate male boldness in Anolis lizards.     

Message from the Editor-in-Chief

The current issue of Acta Biochimica et Biophysica Sinica (ABBS) has turned a new page of this journal since its publication forty five years ago. It is perhaps an appropriate time to share with our readers about the evolution of this journal, the changes that have taken place, and the future that we are looking forward to. ABBS was first established in 1958 with Professor Ying-Lai WANG as the founding Editor-in-Chief and has been ever since an     

Sodium channel gene expression in mosquitoes, Aeries albopictus （S.）

A mosquito strain of Aedes albopictus, HAmAal^G0, from Huntsville, Alabama, USA, showed a normal susceptibility and low tolerance to permethrin and resmethrin （pyrethroid insecticides） compared to a susceptible Ikaken strain, even though these pyrethroid insecticides have been used in the field for a long period of time in Alabama. Recently, we treated HAmAal^G0 in the laboratory with permethrin for five generations and detected no significant change in the level of resistance to permethrin in the selected mosquitoes, HAmAal^G0, compared with the parental strain HAmAal^G0. We then examined the allelic expression at the L-to-F kdr site of the sodium channel gene in the Aedes mosquitoes to address our hypothesis that the L-to-F kdr mutation was not present in HAmAal^G0 and HAmAal^G5 mosquitoes. We found that every tested individual in Ikaken, HAmAal^G5, and HAmAal^G5 populations expressed a codon of CTA at the L-to-F kdr site encoding Leu, strongly corresponding to their susceptibility to insecticides.     

Comparative study on the performance of textural image features for active contour segmentation

We present a computerized method for the semi-automatic detection of contours in ultrasound images.The novelty of our study is the introduction of a fast and efficient image function relating to parametric active contour models.This new function is a combination of the gray-level information and first-order statistical features,called standard deviation parameters.In a comprehensive study,the developed algorithm and the efficiency of segmentation were first tested for synthetic images.Tests were also performed on breast and liver ultrasound images.The proposed method was compared with the watershed approach to show its efficiency.The performance of the segmentation was estimated using the area error rate.Using the standard deviation textural feature and a 5×5 kernel,our curve evolution was able to produce results close to the minimal area error rate(namely 8.88% for breast images and 10.82% for liver images).The image resolution was evaluated using the contrast-to-gradient method.The experiments showed promising segmentation results.     

Assessment of candidate plant DNA barcodes using the Rutaceae family

DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention.Here,seven regions (psbA-trnH,matK,ycf5,rpoC1,rbcL,ITS2,and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae.To evaluate each barcode’s utility for species authentication,PCR amplification efficiency,genetic divergence,and barcoding gaps were assessed.We found that the ITS2 region exhibited the highest inter-specific divergence,and that this was significantly higher than the intra-specific variation in the "DNA barcoding gap" assessment and Wilcoxon two-sample tests.The ITS2 locus had the highest identification efficiency among all tested regions.In a previous study,we found that ITS2 was able to discriminate a wide range of plant taxa,and here we confirmed that ITS2 was also able to discriminate a number of closely related species.Therefore,we propose that ITS2 is a promising candidate barcode for plant species identification.     

Persistence of VRC01-resistant HIV-1 during antiretroviral therapy

VRC01,a broadly neutralizing monoclonal antibody(bnmAb),can neutralize a diverse array of HIV-1 isolates by mimicking CD4 binding to the envelope glycoprotein gp120.We have previously demonstrated the presence of VRC01-resistant strains in an HIV-1 infected patient during antiretroviral therapy.Here,we report follow-up studies of two subsequent samples from the same patient.With genetic and phenotypic analysis of over 70 full-length molecular clones of the HIV-1 envelope,we show that VRC01-resistant HIV-1 continued to exist and change in its proportion of the infecting virus during treatment with a highly active antiretroviral therapy.Consistent with our previous observation,the resistant phenotype was associated with a single asparagine residue at position 460(N460),a potential N-linked glycosylation site in the V5 region.The persistence and continuing evolution of VRC01-resistant HIV-1 in vivo presents a great challenge to our future preventative and therapeutic interventions based on VRC01.     

GPB at 10

The arrival of 2013 marked the 10th anniversary of Genomics, Proteomics & Bioinformatics - GPB. According to our outline [1], we have been improving GPB with visible benchmarks and events. First, the numbers of submissions and published articles have both reached the highest in the history of GPB. Second, a special issue on microRNAs was successfully edited by our board members Tongbin Li and William Cho     

OsHT, a Rice Gene Encoding for a Plasma-Membrane Localized Histidine Transporter

Using a degenerative probe designed according to the most conservative region of a known Lys- and His-specific amino acid transporter (LHT 1) from Arabidopsis, we isolated a full-length cDNA named OsHT (histidine transporter of Oryza sativa L.) by screening the rice cDNA library. The cDNA is 1.3 kb in length and the open reading frame encodes for a 441 amino acid protein with a calculated molecular mass of 49 kDa. Multiple sequence alignments showed that OsHT shares a high degree of sequence conservation at the deduced amino acid level with the Arabidopsis LHT1 and six putative lysine and histidine transporters. Computational analysis indicated that OsHT is an integral membrane protein with 11 putative transmembrane helices. This was confirmed by the transient expression assay because the OsHT-GFP fusion protein was, indeed, localized mainly in the plasma membrane of onion epidermal cells. Functional complementation experiments demonstrated that OsHT was able to work as a histidine transporter in Saccharomyces cerevisiae, suggesting that OsHT is a gene that encodes for a histidine transporter from rice.This is the first time that an LHT-type amino acid transporter gene has been cloned from higher plants other than Arabidopsis.     

Proteogenomic review of the changes in primate apoC-I during evolution

Apolipoprotein C-I has evolved more rapidly than any of the other soluble apolipoproteins. During the course of primate evolution, the gene for this apolipoprotein was duplicated. Prompted by our observation that the two resulting genes encode two distinct forms of apoC-I in great apes, we have reviewed both the genomic and proteomic data to examine what changes have occurred during the course of primate evolution. We have found data showing that one of the duplicated genes, known to be a pseudogene in humans, was also a pseudogene in Denisovans and Neandertals. Using genomic and proteomic data for primates, we will provide in this review evidence that the duplication took place after the divergence of New World monkeys from the human lineage and that the formation of the pseudogene took place after the divergence of the bonobos and chimpanzees from the human lineage.     

Vocal individuality and rhythm in male and female duet contributions of a nonhuman primate

Duetting,or the stereotypical,repeated and often coordinated vocalizations between 2 individuals arose independently multiple times in the Order Primates.Across primate species,there exists substantial variation in terms of timing,degree of overlap,and sex-specificity of duet contributions.There is increasing evidence that primates can modify the timing of their duet contributions relative to their partner,and this vocal flexibility may have been an important precursor to the evolution of human language.Here,we present the results of a fine-scale analysis of Gursky’s spectral tarsier Tarsius spectrumgurskyae duet phrases recorded in North Sulawesi,Indonesia.Specifically,we aimed to investigate individual-level variation in the female and male contributions to the duet,quantify individual-and pair-level differences in duet timing,and measure temporal precision of duetting individuals relative to their partner.We were able to classify female duet phrases to the correct individual with an 80%accuracy using support vector machines,whereas our classification accuracy for males was lower at 64%.Females were more variable than males in terms of timing between notes.All tarsier phrases exhibited some degree of overlap between callers,and tarsiers exhibited high temporal precision in their note output relative to their partners.We provide evidence that duetting tarsier individuals can modify their note output relative to their duetting partner,and these results support the idea that flexibility in vocal exchanges—a precursor to human language—evolved early in the primate lineage and long before the emergence of modern humans.     

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     

Visualizing the microtubule-associated protein tau in the nucleus

Although tau is mainly known as an axonal microtubule-associated protein,many studies indicate that it is not restricted to this subcellular compartment.Assessing tau’s subcellular distribution,however,is not trivial as is evident from transgenic mouse studies.When human tau is over-expressed,it can be immunohistochemically localized to axons and the somatodendritic domain,modeling what is found in neurodegenerative diseases such as Alzheimer’s disease.Yet,in wild-type mice,despite its abundance,tau is difficult to visualize even in the axon.It is even more challenging to detect this protein in the nucleus,where tau has been proposed to protect DNA from damage.To establish a framework for future studies into tau’s nuclear functions,we compared several methods to visualize endogenous nuclear tau in cell lines and mouse brain.While depending on the fixation and permeabilization protocol,we were able to detect nuclear tau in SH-SY5Y human neuroblastoma cells,we failed to do so in N2a murine neuroblastoma cells.As a second method we used subcellular fractionation of mouse tissue and found that in the nucleus tau is mainly present in a hypophosphorylated form.When either full-length or truncated human tau was expressed,both accumulated in the cytoplasm,but were also found in the nuclear fraction.Because subcellular fractionation methods have their limitations,we finally isolated nuclei to probe for nuclear tau and found that the nuclei were free of cytoplasmic contamination.Together our analysis identifies several protocols for detecting tau in the nucleus where it is found in a less phosphorylated form.