Yes-associated protein (YAP) functions as a tumor suppressor in breast

Yes-associated protein (YAP) has been shown to positively regulate p53 family members and to be negatively regulated by the AKT proto-oncogene product in promoting apoptosis. On the basis of this function and its location at 11q22.2, a site of frequent loss of heterozygosity (LOH) in breast cancer, we investigated whether YAP is a tumor suppressor in breast. Examination of tumors by immunohistochemistry demonstrated significant loss of YAP protein. LOH analysis revealed that protein loss correlates with specific deletion of the YAP gene locus. Functionally, short hairpin RNA knockdown of YAP in breast cell lines suppressed anoikis, increased migration and invasiveness, inhibited the response to taxol and enhanced tumor growth in nude mice. This is the first report indicating YAP as a tumor suppressor, revealing its decreased expression in breast cancer as well as demonstrating the functional implications of YAP loss in several aspects of cancer signaling.     

Novel mutations in TARDBP (TDP-43) in patients with familial amyotrophic lateral sclerosis

The TAR DNA-binding protein 43 (TDP-43) has been identified as the major disease protein in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin inclusions (FTLD-U), defining a novel class of neurodegenerative conditions: the TDP-43 proteinopathies. The first pathogenic mutations in the gene encoding TDP-43 (TARDBP) were recently reported in familial and sporadic ALS patients, supporting a direct role for TDP-43 in neurodegeneration. In this study, we report the identification and functional analyses of two novel and one known mutation in TARDBP that we identified as a result of extensive mutation analyses in a cohort of 296 patients with variable neurodegenerative diseases associated with TDP-43 histopathology. Three different heterozygous missense mutations in exon 6 of TARDBP (p.M337V, p.N345K, and p.I383V) were identified in the analysis of 92 familial ALS patients (3.3%), while no mutations were detected in 24 patients with sporadic ALS or 180 patients with other TDP-43-positive neurodegenerative diseases. The presence of p.M337V, p.N345K, and p.I383V was excluded in 825 controls and 652 additional sporadic ALS patients. All three mutations affect highly conserved amino acid residues in the C-terminal part of TDP-43 known to be involved in protein-protein interactions. Biochemical analysis of TDP-43 in ALS patient cell lines revealed a substantial increase in caspase cleaved fragments, including the approximately 25 kDa fragment, compared to control cell lines. Our findings support TARDBP mutations as a cause of ALS. Based on the specific C-terminal location of the mutations and the accumulation of a smaller C-terminal fragment, we speculate that TARDBP mutations may cause a toxic gain of function through novel protein interactions or intracellular accumulation of TDP-43 fragments leading to apoptosis.     

Human stem cells for modeling neurological disorders: accelerating the drug discovery pipeline

The availability of human stem cells heralds a new era for modeling normal and pathologic tissues and developing therapeutics. For example, the in vitro recapitulation of normal and aberrant neurogenesis holds significant promise as a tool for de novo modeling of neurodevelopmental and neurodegenerative diseases. Translational applications include deciphering brain development, function, pathologies, traditional medications, and drug discovery for novel pharmacotherapeutics. For the latter, human stem cell-based assays represent a physiologically relevant and high-throughput means to assess toxicity and other undesirable effects early in the drug development pipeline, avoiding late-stage attrition whilst expediting proof-of-concept of genuine drug candidates. Here we consider the potential of human embryonic, adult, and induced pluripotent stem cells for studying neurological disorders and preclinical drug development.     

Seasonal and interannual variations in carbon dioxide exchange over a cropland in the North China Plain

In China, croplands account for a relatively large form of vegetation cover. Quantifying carbon dioxide exchange and understanding the environmental controls on carbon fluxes over croplands are critical in understanding regional carbon budgets and ecosystem behaviors. In this study, the net ecosystem exchange (NEE) at a winter wheat/summer maize rotation cropping site, representative of the main cropping system in the North China Plain, was continuously measured using the eddy covariance technique from 2005 to 2009. In order to interpret the abiotic factors regulating NEE, NEE was partitioned into gross primary production (GPP) and ecosystem respiration (R_eco). Daytime R_eco was extrapolated from the relationship between nighttime NEE and soil temperature under high turbulent conditions. GPP was then estimated by subtracting daytime NEE from the daytime estimates of R_eco. Results show that the seasonal patterns of the temperature responses of R_eco and light‐response parameters are closely related to the crop phenology. Daily R_eco was highly dependent on both daily GPP and air temperature. Interannual variability showed that GPP and R_eco were mainly controlled by temperature. Water availability also exerted a limit on R_eco. The annual NEE was ?585 and ?533 g C m^?2 for two seasons of 2006–2007 and 2007–2008, respectively, and the wheat field absorbed more carbon than the maize field. Thus, we concluded that this cropland was a strong carbon sink. However, when the grain harvest was taken into account, the wheat field was diminished into a weak carbon sink, whereas the maize field was converted into a weak carbon source. The observations showed that severe drought occurring during winter did not reduce wheat yield (or integrated NEE) when sufficient irrigation was carried out during spring.     

用RACE技术扩增并克隆牛BMP4基因3′端序列

RACE技术是一项扩增基因末端序列的新技术。该研究从牛BMP4基因出发,以牛软骨的RNA为模板,按照不同物种BMP4基因的相似性设计特异引物,运用PCR和RACE技术扩增并获得了特异片段,该片段经PCR、酶切和测序验证,证实所克隆序列为牛BMP4的3′端序列,包含有1170bp组成的开放读码框(ORF),编码389个氨基酸,3′非编码区121bp个核苷酸和poly(A)15。同源性分析结果表明,牛BMP4 cDNA最大开放读码框所推测的氨基酸序列与已知人、小鼠、大鼠、狗、羊和鸡等真核生物BMP4氨基酸序列进行比较,分别有94.5%、93.1%、91.9%、87.4%、94.2%、79%的同源性。这为克隆其他物种的BMP4基因提供了依据,同时牛骨形态发生蛋白的测序为我们更好的理解牛的生骨机理提供帮助。     

小鼠淋巴细胞抗原CTLA-4的胞外肽段表达及纯化

目的: 真核细胞表达小鼠淋巴细胞抗原CTLA-4胞外段肽,研究表达肽段与抗原呈递细胞B7分子结合后减轻小鼠淋巴细胞刺激后的增殖抑制,从而启动T淋巴细胞进一步增殖。方法:从小鼠脾脏淋巴细胞获得总RNA,通过逆转录PCR扩增出CTLA-4全长基因,克隆并测序。依据胞外段序列和真核表达载体pcDNA3.1序列,合成引物扩增胞外片段,两者经内切核酸酶处理、连接构建重组表达pcDNA3.1载体,重组质粒经测序验证后,采用lipofectamine 2000转染入小鼠肝癌细胞Hepa1-6,经G418筛选获得稳定表达细胞株。结果:获得小鼠CTLA-4胞外段真核表达载体和小鼠肝癌细胞Hepa1-6稳定表达转染细胞株,制备了CTLA-4胞外肽段,经His标签抗体和小鼠CTLA-4抗体Western blot检测表达蛋白带均呈阳性。结论:获得CTLA-4胞外段肽,为进一步研究该肽的作用打下基础。     

Genomic network analysis of environmental and livestock F-type plasmid populations

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.Subject terms: Environmental microbiology, Genomics     

Environmental cues and extended estuarine residence in seaward migrating eels (Anguilla australis)

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