Membrane-bound peptides mimicking transmembrane Vph1p helix 7 of yeast V-ATPase: A spectroscopic and polarity mismatch study

The V-ATPases are a family of ATP-dependent proton pumps, involved in a variety of cellular processes, including bone breakdown. V-ATPase enzymes that are too active in the latter process can result in osteoporosis, and inhibitors of the enzyme could be used to treat this disease. As a first step in studying the structure and function of the membrane-embedded interface at which proton translocation takes place, and its role in V-ATPase inhibition, synthetic peptides P1 and P2 consisting of 25 amino acid residues are presented here that mimic Vph1p helix 7 of yeast V-ATPase. A single mutation R10A between peptide P1 and P2 makes it possible to focus on the role of the essential arginine residue R735 in proton translocation. In the present work, we use a novel combination of spectroscopic techniques, such as CD spectroscopy, tryptophan emission spectra, acrylamide quenching and parallax analysis, and polarity mismatch modeling to characterize the peptides P1 and P2 in lipid bilayer systems. Based on both the spectroscopic experiments and the polarity mismatch modeling, P1 and P2 adopt a similar transmembrane conformation, with a mainly α-helical structure in the central part, placing the tryptophan residue at position 12 at a location 4 ± 2 Å from the centre of the lipid bilayer. Furthermore, the arginine at position 10 in P1 does not have an effect on the bilayer topology of the peptide, showing that the long, flexible side chain of this residue is able to snorkel towards the lipid headgroup region. This large flexibility of R735 might be important for its function in proton translocation in the V-ATPase enzyme.     

Rearrangements of large-insert T-DNAs in transgenic rice

Introduction of large-DNA fragments into cereals by Agrobacterium-mediated transformation is a useful technique for map-based cloning and molecular breeding. However, little is known about the organization and stability of large fragments of foreign DNA introduced into plant genomes. In this study, we produced transgenic rice plants by Agrobacterium-mediated transformation with a large-insert T-DNA containing a 92-kb region of the wheat genome. The structures of the T-DNA in four independent transgenic lines were visualized by fluorescence in situ hybridization on extended DNA fibers (fiber FISH). By using this cytogenetic technique, we showed that rearrangements of the large-insert T-DNA, involving duplication, deletion and insertion, had occurred in all four lines. Deletion of long stretches of the large-insert DNA was also observed in Agrobacterium.     

Responses in organic matter accumulation and processing to an experimental wood addition in three headwater streams

1. Additions of large wood are being used to restore streams that have been subjected to channelization, wood removal or riparian timber harvest. This added wood potentially increases channel stability, habitat complexity and organic matter retention and improves habitat and productivity of higher trophic levels. However, few stream restorations monitor restoration effectiveness after project completion. 2. We added 25 aspen logs (each 2.5 m length × 0.5 m diameter) to 100‐m reaches of each of three forested headwater streams in the Upper Peninsula of Michigan, U.S.A. These wood‐poor streams drain forests that were completely harvested of timber over a century ago and have been selectively logged for the past 50–60 years. An upstream unmanipulateds 100‐m reach in each stream served as the control. 3. We evaluated responses in organic matter processing by measuring red maple leaf decomposition 1 year before and 2 years after wood addition. We also quantified coarse organic matter standing stocks in the main channel and in debris accumulations associated with large wood. In response to wood addition, we predicted both organic matter standing stocks and leaf decomposition rates would increase, thereby enhancing resource availability to higher trophic levels. 4. Leaf decomposition rates did not change following wood addition. Temporal variation in rates among streams was mostly explained by differences in degree days, water velocity, scour/burial and water column inorganic nitrogen concentrations, but not large wood. Variation within streams across years was explained by differences in degree days, water velocity and shredder biomass. 5. Contrary to our prediction, organic matter standing stocks did not increase significantly at the reach scale. However, the experimentally added wood retained c. 4% of total annual coarse benthic organic matter (CBOM) in the first year and an additional c. 15% in the second year, suggesting accumulation over time in the manipulated reaches. The CBOM held by the new logs may be more biologically available because it is less susceptible to burial and transport than material in the streambed. 6. Some shredding macroinvertebrates responded to changes caused by the wood additions. In particular, the common caddisfly shredder, Lepidostoma sp., increased in abundance in leaf bags following wood addition, whereas the biomass of the winter stoneflies, Capniidae, declined in the first year. 7. Considerable funds are spent to restore in‐stream habitat, but few restorations are monitored, particularly over long periods (>5 years). Our results show that longer‐term monitoring is needed to determine the efficacy of these restorations on ecosystem function; organic matter decomposition in our low‐gradient streams did not respond to a substantial increase in large wood after 2 years.     

Phosphorylation of NHERF1 S279 and S301 differentially regulates breast cancer cell phenotype and metastatic organotropism

Metastatic cancer cells are highly plastic for the expression of different tumor phenotype hallmarks and organotropism. This plasticity is highly regulated but the dynamics of the signaling processes orchestrating the shift from one cell phenotype and metastatic organ pattern to another are still largely unknown. The scaffolding protein NHERF1 has been shown to regulate the expression of different neoplastic phenotypes through its PDZ domains, which forms the mechanistic basis for metastatic organotropism. This reprogramming activity was postulated to be dependent on its differential phosphorylation patterns. Here, we show that NHERF1 phosphorylation on S279/S301 dictates several tumor phenotypes such as in vivo invasion, NHE1-mediated matrix digestion, growth and vasculogenic mimicry. Remarkably, injecting mice with cells having differential NHERF1 expression and phosphorylation drove a shift from the predominantly lung colonization (WT NHERF1) to predominately bone colonization (double S279A/S301A mutant), indicating that NHERF1 phosphorylation also acts as a signaling switch in metastatic organotropism.     

Genetic structure and domestication footprints of the tusk,coat color,and ear morphology in East Chinese pigs

The domestication and artificial selection of wild boars have led to dramatic morphological and behavioral changes, especially in East Chinese (ECN) pigs. Here, we provide insights into the population structure and current genetic diversity of representative ECN pig breeds. We identify a 500-kb region containing six tooth development-relevant genes with almost completely different haplotypes between ECN pigs and Chinese wild boars or European domestic pigs. Notably, the c.195A>G missense mutation in exon 2 of AMBN may cause alterations in its protein structure associated with tusk degradation in ECN pigs. In addition, ESR1 may play an important role in the reproductive performance of ECN pigs. A major haplotype of the large lop ear-related MSRB3 gene and eight alleles in the deafness-related GRM7 gene may affect ear morphology and hearing in ECN pigs. Interestingly, we find that the two-end black (TEB) coat color in Jinhua pigs is most likely caused by EDNRB with genetic mechanisms different from other Chinese TEB pigs. This study identifies key loci that may be artificially selected in Chinese native pigs related to the tusk, coat color, and ear morphology, thus providing new insights into the genetic mechanisms of domesticated pigs.     

驱除侵袭大质粒pINV对福氏2a志贺氏杆菌2457T影响的比较蛋白质组学研究

将福氏志贺氏杆菌2a 2457T及其驱除侵袭大质粒pINV的菌株培养至对数生长中期,制备了全细胞蛋白质。用双向电泳分离两种细胞蛋白质混合物并进行比较,找出差异点,这些点经过胶内酶切后进行MALDI_TOF质谱鉴定。每个蛋白质点的肽指纹图谱都在福氏志贺氏杆菌2a 2457T株的蛋白质数据库用Mascot进行检索,共发现了10个差异表达的蛋白质。结果显示驱除大质粒后几个参与核酸代谢途径的酶表达量有所上升。其中胞啶/脱氧胞啶脱氨酶、嘌呤核苷磷酸化酶和尿嘧啶核苷磷酸化酶表达量的上升可能造成尿嘧啶和尿（嘧啶核）苷合成的增加。     

Biomechanical models of hyphal growth in actinomycetes

The tip growth of filamentary actinomycetes is investigated within the framework of large deformation membrane theory in which the cell wall is represented as a growing elastic membrane with geometry-dependent elastic properties. The model exhibits realistic hyphal shapes and indicates a self-similar tip growth mechanism consistent with that observed in experiments. It also demonstrates a simple mechanism for hyphal swelling and beading that is observed in the presence of a lysing agent.     

HSP90 mRNA在胃癌和大肠癌中表达的研究

目的为探讨胃癌和大肠癌细胞HSP90 mRNA表达的特点.方法利用核酸原位杂交技术,对79例胃肠癌组织进行检测.结果表明HSP90 mRNA在胃癌和大肠癌中的阳性率分别为55.56%(15/27)和69.23%(36/52).mRNA表达与病理类型、分化程度和有否淋巴结转移有相关性.结论 HSP90 mRNA在胃肠癌中有较高表达,检测HSP90 mRNA可以作为提示预后的重要临床指标.     

对应分析和去趋势分析在有蹄类取食模式研究中的应用

本研究将2009年1月和2010年1月小兴安岭大沾河湿地自然保护区二可河林场内驼鹿冬季食性作为原始数据,分别以对应分析（CA）、去趋势分析（DCA）,并将数据以样本为单位进行标准化后,再进行去趋势分析（DCA_std）3种排序方法,对驼鹿冬季取食模式进行了研究,后通过普鲁克分析,比较了不同排序方法对大型有蹄类取食模式研究的效果。结果表明,3种排序法的1轴和2轴均能涵盖绝大多数信息量,CA涵盖79.27%,DCA涵盖66.65%,DCA_std涵盖68.22%;3种方法均能够在1轴上区分针叶树和落叶乔木类食物,在2轴上,3种方法主要能够达到针叶树种与除落叶乔木外的其他植物类别的区分。虽三者均能够展现有蹄类取食模式,但在图形可视化后,仅DCA_std无明显的弓形效应。普鲁克分析结果表明,DCA_std样本位移平方和与CA和DCA均有很大差异,即将数据先进行标准化再进行DCA分析能够有效去除弓形效应。因此,在由多度组成的食性数据在进行标准DCA分析前,应对数据进行前期处理会得到更好的效果。同时,以样本为单位的标准化将使排序分析结果生态学意义更明确。     

Models as tools for understanding past,recent and future changes in large lakes

Large lakes currently exhibit ecosystem responses to environmental changes such as climate and land use changes, nutrient loading, toxic contaminants, hydrological modifications and invasive species. These sources have impacted lake ecosystems over a number of years in various combinations and often in a spatially heterogeneous pattern. At the same time, many different kinds of mathematical models have been developed to help to understand ecosystem processes and improve cost-effective management. Here, the advantages and limitations of models and sources of uncertainty will be discussed. From these considerations and in view of the multiple environmental pressures, the following emerging issues still have to be met in order to improve the understanding of ecosystem function and management of large lakes: (1) the inclusion of thresholds and points-of-no-return; (2) construction of general models to simulate biogeochemical processes for a large number of lakes rather than for individual systems; (3) improvement of the understanding of spatio-temporal variability to quantify biogeochemical fluxes accurately; and (4) inclusion of biogeochemical linkages between terrestrial and aquatic ecosystems in model approaches to assess the effects of external environmental pressures such as land-use changes. The inclusion of the above-mentioned issues would substantially improve models as tools for the scientific understanding and cost-effective management of large lakes that are subject to multiple environmental pressures in a changing future.