Information-based methods for predicting gene function from systematic gene knock-downs

Background  

The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA interference phenotypes have been recorded for the nematode Caenorhabditis elegans. Although previous studies have demonstrated the merit of using knock-down phenotypes to predict gene function, it is unclear how the data can be used most effectively. An open question is how to optimally make use of phenotypic observations, possibly in combination with other functional genomics datasets, to identify genes that share a common role.     

Tomato transcriptional changes in response to Clavibacter michiganensis subsp. michiganensis reveal a role for ethylene in disease development

Clavibacter michiganensis subsp. michiganensis (Cmm) is a gram-positive actinomycete, causing bacterial wilt and canker disease in tomato (Solanum lycopersicum). Host responses to gram-positive bacteria and molecular mechanisms associated with the development of disease symptoms caused by Cmm in tomato are largely unexplored. To investigate plant responses activated during this compatible interaction, we used microarray analysis to monitor changes in host gene expression during disease development. This analysis was performed at 4 d postinoculation, when bacteria were actively multiplying and no wilt symptoms were yet visible; and at 8 d postinoculation, when bacterial growth approached saturation and typical wilt symptoms were observed. Of the 9,254 tomato genes represented on the array, 122 were differentially expressed in Cmm-infected plants, compared with mock-inoculated plants. Functional classification of Cmm-responsive genes revealed that Cmm activated typical basal defense responses in the host, including induction of defense-related genes, production and scavenging of free oxygen radicals, enhanced protein turnover, and hormone synthesis. Cmm infection also induced a subset of host genes involved in ethylene biosynthesis and response. After inoculation with Cmm, Never ripe (Nr) mutant plants, impaired in ethylene perception, and transgenic plants with reduced ethylene synthesis showed significant delay in the appearance of wilt symptoms, compared with wild-type plants. The retarded wilting in Nr plants was a specific effect of ethylene insensitivity, and was not due to altered expression of defense-related genes, reduced bacterial populations, or decreased ethylene synthesis. Taken together, our results indicate that host-derived ethylene plays an important role in regulation of the tomato susceptible response to Cmm.     

Abortion-seeking behaviour among Nigerian women

This study used data from a community-based survey to examine women's experiences of abortion in Nigeria. Fourteen percent of respondents reported that they had ever tried to terminate a pregnancy, and 10% had obtained an abortion. The majority of women who sought an abortion did so early in the pregnancy. Forty-two percent of women who obtained an abortion used the services of a non-professional provider, a quarter experienced complications and 9% sought treatment for complications from their abortions. Roughly half of the women who obtained an abortion used a method other than D&C or MVA. The abortion prevalence and conditions under which women sought abortions varied by women's socio-demographic characteristics. Because abortion is illegal in Nigeria except to save the woman's life, many women take significant risks to terminate unwanted pregnancies. Reducing the incidence of unwanted pregnancy and unsafe abortion can significantly impact the reproductive health of women in Nigeria.     

Plasmodium infection and endotoxic shock induce the expansion of regulatory dendritic cells

During an acute Plasmodium infection, uncontrolled proinflammatory responses can cause morbidity and mortality. Regulation of this response is required to prevent immunopathology. We therefore decided to investigate a recently characterized subset of regulatory dendritic cells (DCs) that expresses low levels of CD11c and high levels of CD45RB. During a Plasmodium yoelii infection, these regulatory CD11clowCD45RBhigh DCs become the prevalent CD11c-expressing cells in the spleen, overtaking the conventional CD11chigh DCs. Furthermore, the regulatory CD11clowCD45RBhigh DCs induce IL-10-expressing CD4 T cells. A similar change in splenic DC subsets is seen when mice are injected with sublethal doses of LPS, suggesting that shifting the splenic DC subsets in favor of regulatory CD11clowCD45RBhigh DCs can be triggered solely by a high inflammatory stimulus. This is the first time regulatory DCs have been observed in a natural immune response to an infectious disease or endotoxic shock.     

治疗用单抗制剂的研究进展

杂交瘤技术建立 2 0多年来 ,单抗走过了漫长而又曲折的历程 ,从最初的完全鼠源单抗 ,经含不同程度鼠源成份的人鼠嵌合单抗、人源化单抗 ,现已发展为完全人源单抗。抗体的人源化技术和噬菌体展示技术等技术的发展 ,使单抗从诊断工具变为有效的治疗药物 ,被人们誉为“生物魔弹”。鉴于单克隆抗体 (单抗 )对相应的抗原决定簇具有高度特异性以及抗体的均一性等特性 ,近2 0多年来单抗作为疾病诊断剂以及生物学研究试剂已得到广泛的应用 ,但作为治疗剂的应用进程则十分缓慢。近两年来 ,单抗作为治疗制品 ,获得了迅速的进展。     

The structural features of Trask that mediate its anti-adhesive functions

Trask/CDCP1 is a transmembrane protein with a large extracellular and small intracellular domains. The intracellular domain (ICD) undergoes tyrosine phosphorylation by Src kinases during anchorage loss and, when phosphorylated, Trask functions to inhibit cell adhesion. The extracellular domain (ECD) undergoes proteolytic cleavage by serine proteases, although the functional significance of this remains unknown. There is conflicting evidence regarding whether it functions to signal the phosphorylation of the ICD. To better define the structural determinants that mediate the anti-adhesive functions of Trask, we generated a series of deletion mutants of Trask and expressed them in tet-inducible cell models to define the structural elements involved in cell adhesion signaling. We find that the ECD is dispensable for the phosphorylation of the ICD or for the inhibition of cell adhesion. The anti-adhesive functions of Trask are entirely embodied within its ICD and are specifically due to tyrosine phosphorylation of the ICD as this function is completely lost in a phosphorylation-defective tyrosine-phenylalanine mutant. Both full length and cleaved ECDs are fully capable of phosphorylation and undergo phosphorylation during anchorage loss and cleavage is not an upstream signal for ICD phosphorylation. These data establish that the anti-adhesive functions of Trask are mediated entirely through its tyrosine phosphorylation. It remains to be defined what role, if any, the Trask ECD plays in its adhesion functions.     

Human disease classification in the postgenomic era: A complex systems approach to human pathobiology

Contemporary classification of human disease derives from observational correlation between pathological analysis and clinical syndromes. Characterizing disease in this way established a nosology that has served clinicians well to the current time, and depends on observational skills and simple laboratory tools to define the syndromic phenotype. Yet, this time-honored diagnostic strategy has significant shortcomings that reflect both a lack of sensitivity in identifying preclinical disease, and a lack of specificity in defining disease unequivocally. In this paper, we focus on the latter limitation, viewing it as a reflection both of the different clinical presentations of many diseases (variable phenotypic expression), and of the excessive reliance on Cartesian reductionism in establishing diagnoses. The purpose of this perspective is to provide a logical basis for a new approach to classifying human disease that uses conventional reductionism and incorporates the non-reductionist approach of systems biomedicine.