Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya,North East India reveals novel genes

Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.     

Linking light attenuation and suspended sediment loading to benthic productivity within an Arctic kelp‐bed community1

Annual growth and productivity of kelp in the Stefansson Sound Boulder Patch, located along the Arctic coast of Alaska, is regulated almost entirely by PAR received during the summer open‐water period. Increased water turbidity during summer, often in response to storm activity, has been linked to low levels of ambient PAR and measurable decreases in kelp elongation. However, the relationship between PAR and water transparency has not been quantified, which compromises efforts to assess the effects of changing climate and weather conditions on kelp production. During the 2001–2002 summer periods, the inherent optical properties (IOPs) of Stefansson Sound waters were measured in conjunction with total suspended sediments (TSS) concentrations, which differed significantly between the 2 years, for input into a radiative transfer equation (RTE). In both years, the highest TSS levels (24.2 and 18.5 mg · L^?1 in 2001 and 2002, respectively) occurred in nearshore areas and were coincident with increased beam attenuations (13.8 and 8.3 m^?1). Lower TSS concentrations and attenuations were measured offshore. Data input to the RTE provided a TSS‐concentration‐specific attenuation coefficient that was used in a productivity model to estimate annual kelp productivities throughout the Boulder Patch based on modeled irradiance and averaged site‐specific TSS concentrations. Production estimates varied across the Boulder Patch but were lower in 2001 (0.12–0.34 g C · g dwt^?1 · year^?1, where dwt stands for dry weight) compared to 2002 (0.24–0.80 g C · g dwt^?1 · year^?1). Production in both years was greater in offshore locations with lower TSS loads. Results suggest that PAR availability during the summer is heavily influenced by TSS concentrations, and that changes in storm intensity and frequency, associated with current warming trends, may have significant effects on the primary production of these unique benthic algal communities.     

Multiple spatial-scale resource selection function models in relation to human disturbance for moose in northeastern China

The moose (Alces alces cameloides) population in northeastern China is on the southernmost edge of its distribution in Asia. A survey was conducted to determine moose resource selection and the effects of human disturbance on moose in a study area of 20,661 ha located on the northwestern slope of the Lesser Khingan Mountains, located in northeastern China. Predictive models of resource selection were developed using logistic and autologistic regression. All models considered resource variable selection at two spatial scales, patch and landscape. At the patch scale, moose preferred larger birch (Betula platyphylla) patches, but avoided larger tamarack (Larix gmelinii) patches. At the landscape scale, moose preferred higher densities of tamarack patches, i.e., heterogeneity of tamarack stands, selected areas with more abundant annual shoots, terrain conducive to better concealment, higher altitudes and areas saturated with soil moisture. Roads and forest harvest intervals were identified as important human disturbance factors. This is the first time that moose have been reported to avoid roads, and the avoidance distance was nearly 3 km. We believe that in this region moose under the influence of roads are behaviorally plastic, compared with the indifference of moose to the presence of roads in other regions. Moose avoided forest areas logged more than 3 years previously and preferred areas logged 1–2 years previously. In addition, it may be necessary to monitor the effect of the dynamic of density of roe deer on the spatial distribution of the moose population.     

基于滑动窗口的原核转录起始位点计算定位方法

转录起始位点的计算定位是基因转录调控研究的重要内容,但现有方法的识别性能较低。文章作者在已有原核启动子识别算法的基础上,提出了一种基于滑动窗口的原核转录起始位点计算定位方法,通过在合理限定的定位范围内对序列进行滑动扫描,来预测转录起始位点的位置。首先根据窗口序列的交迭组分特征和启动子其它特征分别建立二次判别分类器,用其计算对应位置的似然得分,再利用转录起始位点与翻译起始位点的间隔经验分布信息对似然得分进行修正,最后依照似然得分的分布情况由阈值定位算法确定预测位置。对大肠杆菌真实序列数据的测试结果表明,该定位算法可实现对真实转录起始位点位置的有效预测,与已有算法相比,当敏感性指标同为0.85左右时,特异性指标可从0.20提高至0.65,从而使得定位准确率提高了约20个百分点。