Putative osmosensor – OsHK3b – a histidine kinase protein from rice shows high structural conservation with its ortholog AtHK1 from Arabidopsis

Prokaryotes and eukaryotes respond to various environmental stimuli using the two-component system (TCS). Essentially, it consists of membrane-bound histidine kinase (HK) which senses the stimuli and further transfers the signal to the response regulator, which in turn, regulates expression of various target genes. Recently, sequence-based genome wide analysis has been carried out in Arabidopsis and rice to identify all the putative members of TCS family. One of the members of this family i.e. AtHK1, (a putative osmosensor, hybrid-type sensory histidine kinase) is known to interact with AtHPt1 (phosphotransfer proteins) in Arabidopsis. Based on predicted rice interactome network (PRIN), the ortholog of AtHK1 in rice, OsHK3b, was found to be interacting with OsHPt2. The analysis of amino acid sequence of AtHK1 showed the presence of transmitter domain (TD) and receiver domain (RD), while OsHK3b showed presence of three conserved domains namely CHASE (signaling domain), TD, and RD. In order to elaborate on structural details of functional domains of hybrid-type HK and phosphotransfer proteins in both these genera, we have modeled them using homology modeling approach. The structural motifs present in various functional domains of the orthologous proteins were found to be highly conserved. Binding analysis of the RD domain of these sensory proteins in Arabidopsis and rice revealed the role of various residues such as histidine in HPt protein which are essential for their interaction.     

Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM

The accurate identification of protein structure class solely using extracted information from protein sequence is a complicated task in the current computational biology. Prediction of protein structural class for low-similarity sequences remains a challenging problem. In this study, the new computational method has been developed to predict protein structural class by fusing the sequence information and evolution information to represent a protein sample. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark data-sets, 1189 and 25PDB with sequence similarity lower than 40 and 25%, respectively. Comparison of our results with other methods shows that the proposed method by us is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity data-sets.     

基于水声学方法的天目湖鱼类资源捕捞与放流的生态监测

本文在天目湖捕捞赶鱼前（2011年12月）、赶鱼后（2012年1月）、捕捞与放流后（2012年3月）3个渔业阶段,结合渔业捕捞统计,采用水声学方法对天目湖鱼类资源（赶鱼后为不包括集鱼网箱的湖区鱼类资源）的捕捞与放流进行了生态监测,并构建GIS模型,得到鱼类种群结构、大小组成、鱼类密度、鱼类集群、鱼类资源量及其分布,为天目湖保水渔业的实施和渔业生产提供科学依据。天目湖鱼类种群以鲤科鱼类为主,鲢鳙2011年捕捞统计重量占比为98.07%,单网簖采样尾数占比为68.72%,鱼类资源受放流种类和规格影响较大;赶鱼前后和捕捞与放流后3个渔业阶段的鱼类平均目标强度（TS）分别为（-47.84?4.79）dB、（-48.58?4.98）dB、（-47.24?5.10）dB,且差异性显著（P<0.05）,捕捞与放流后TS在-45—-40 dB的鱼类明显升高到24.40%;3个渔业阶段的鱼类密度（FPCM）分别为（0.0124?0.0292）ind/m3、（0.0062?0.0227）ind/m3、（0.0098?0.0185）ind/m3,捕捞赶鱼作业显著（P<0.05）降低了鱼类密度,而捕捞与放流后鱼类密度显著（P<0.05）低于赶鱼前则是由于水深上升所致;在冬季的中下层水体出现典型的鱼类聚群,且随温度降低团聚程度提高;通过构建GIS模型评估鱼类资源量,赶鱼前约61万尾、赶鱼后约38万尾、捕捞与放流后约67万尾,资源量在中下游分布较高。     

内蒙古达赉湖西岸地区大鵟巢穴特征和巢址选择

2010年和2011年3月-6月,对内蒙古达赉湖国家级保护区达赉湖西岸地区大鵟(Buteo hemilasius)的巢穴结构和巢址选择因子进行了调查研究.采用野外观察和样方法定位了13个大鵟巢址,并对巢址样方的20个生态因子进行测量,运用主成分分析法对影响大鵟巢址选择的主要因子进行了分析.测量显示,大鵟巢穴的基本结构特征为:外径(94.7+4.2) cm;巢高度(46.1±2.7) cm;内径(24.8±1.5)cm;巢深(14.0±+0.9)cm.生境因子分析结果表明,达赉湖西岸地区大鵟的巢集中分布在湖岸或水塘附近的悬崖,营巢点坡度为15°-45°之间的阳坡或半阳坡;隐蔽度高于20％;草本密度大于5株/m2;植被均高大于30cm;巢距悬崖上部距离2-5m;距水源l00m以内;距居民点距离大于lkm;距草原道路的距离大于0.5km;而对于物种丰富度没有特殊要求.主成分分析显示,影响大鵟巢址选择的主要因子有3个,依次为:隐蔽性因子(主要包括巢址区域的植物特征和地形特征)、干扰因子和食物因子.各主成分中,相对系数绝对值最高的变量依次是:植被盖度、距居民点距离、巢的高度和距草原道路距离.     

长期施肥对紫色土农田土壤动物群落的影响

土壤动物在陆地生态系统物质循环和能量流动中起着重要作用,直接或间接的参与土壤有机质的分解与矿化;长期施肥对土壤理化性质产生影响的同时,改变了土壤动物群落组成.为查明紫色土长期施肥对土壤动物群落的影响及其响应关系,于2008年的5、7、9和11月分别对紫色土农田无肥对照(CK)、单施氮肥(N)、常规化肥氮磷钾(NPK)、有机肥(OM)、有机肥与化肥氮磷钾混施(OMNPK)、秸秆还田(RSD)和秸秆还田与化肥氮磷钾混施(RSDNPK)等7种长期施肥定位试验地的土壤动物群落进行调查,采用改良的干漏斗和湿漏斗两种方法,共获得土壤动物9454只,隶属7门17纲24目.分析表明,OM和RSDNPK两种施肥方式下土壤动物群落的多样性显著高于CK、N和NPK等3种施肥方式,说明有机物料的长期投入有利于提高土壤动物群落丰富度和多样性.方差分析表明施肥方式对土壤动物主要类群密度的影响差异性极显著(F=42.412,P=0.0001),对土壤动物群落类群影响存在不均衡性.施肥方式主要影响农田土壤动物类群的种群个体数量、线虫动物门个体数量、大蚓类个体数量、甲螨亚目个体数量、密度-类群指数DG及土壤动物群落类群数等六个指标,初步认为这些主要类群因素能够预测长期施肥引起的土壤肥力变化,可能对指示土壤质量的变化具有一定潜力.     

Objective classification of scapular kinematics in participants with movement faults of the scapula on clinical assessment

The aim of this study was to assess the potential of employing a classification tool to objectively classify participants with clinically assessed movement faults (MFs) of the scapula. Six participants with a history of shoulder pain with MFs of the scapula and 12 healthy participants with no movement faults (NMFs) performed a flexion movement control test of the scapula, while scapular kinematic data were collected. Principal component scores and discrete kinematic variables were used as input into a classifier. Five out of the six participants with a history of pain were successfully classified as having scapular MFs with an accuracy of 72%. Variables related to the upward rotation of the scapula had the most influence on the classification. The results of the study demonstrate the potential of adopting a multivariate approach in objective classification of participants with altered scapular kinematics in pathological groups.     

Cytokinin‐dependent specification of the functional megaspore in the Arabidopsis female gametophyte

The life cycle of higher plants alternates between the diploid sporophytic and the haploid gametophytic phases. In angiosperms, male and female gametophytes develop within the sporophyte. During female gametophyte (FG) development, a single archesporial cell enlarges and differentiates into a megaspore mother cell, which then undergoes meiosis to give rise to four megaspores. In most species of higher plants, including Arabidopsis thaliana, the megaspore closest to the chalaza develops into the functional megaspore (FM), and the remaining three megaspores degenerate. Here, we examined the role of cytokinin signaling in FG development. We characterized the FG phenotype in three triple mutants harboring non‐overlapping T–DNA insertions in cytokinin AHK receptors. We demonstrate that even the strongest mutant is not a complete null for the cytokinin receptors. Only the strongest mutant displayed a near fully penetrant disruption of FG development, and the weakest triple ahk mutant had only a modest FG phenotype. This suggests that cytokinin signaling is essential for FG development, but that only a low threshold of signaling activity is required for this function. Furthermore, we demonstrate that there is elevated cytokinin signaling localized in the chalaza of the ovule, which is enhanced by the asymmetric localization of cytokinin biosynthetic machinery and receptors. We show that an FM‐specific marker is absent in the multiple ahk ovules, suggesting that disruption of cytokinin signaling elements in Arabidopsis blocks the FM specification. Together, this study reveals a chalazal‐localized sporophytic cytokinin signal that plays an important role in FM specification in FG development.     

LOV‐domain photoreceptor,encoded in a genomic island,attenuates the virulence of Pseudomonas syringae in light‐exposed Arabidopsis leaves

In Arabidopsis thaliana, light signals modulate the defences against bacteria. Here we show that light perceived by the LOV domain‐regulated two‐component system (Pst–Lov) of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) modulates virulence against A. thaliana. Bioinformatic analysis and the existence of an episomal circular intermediate indicate that the locus encoding Pst–Lov is present in an active genomic island acquired by horizontal transfer. Strains mutated at Pst–Lov showed enhanced growth on minimal medium and in leaves of A. thaliana exposed to light, but not in leaves incubated in darkness or buried in the soil. Pst–Lov repressed the expression of principal and alternative sigma factor genes and their downstream targets linked to bacterial growth, virulence and quorum sensing, in a strictly light‐dependent manner. We propose that the function of Pst–Lov is to distinguish between soil (dark) and leaf (light) environments, attenuating the damage caused to host tissues while releasing growth out of the host. Therefore, in addition to its direct actions via photosynthesis and plant sensory receptors, light may affect plants indirectly via the sensory receptors of bacterial pathogens.     

Application of higher order statistics for atrial arrhythmia classification

Atrial fibrillation (AF) and atrial flutter (AFL) are the two common atrial arrhythmia encountered in the clinical practice. In order to diagnose these abnormalities the electrocardiogram (ECG) is widely used. The conventional linear time and frequency domain methods cannot decipher the hidden complexity present in these signals. The ECG is inherently a non-linear, non-stationary and non-Gaussian signal. The non-linear models can provide improved results and capture minute variations present in the time series. Higher order spectra (HOS) is a non-linear dynamical method which is highly rugged to noise. In the present study, the performances of two methods are compared: (i) 3rd order HOS cumulants and (ii) HOS bispectrum. The 3rd order cumulant and bispectrum coefficients are subjected to dimensionality reduction using independent component analysis (ICA) and classified using classification and regression tree (CART), random forest (RF), artificial neural network (ANN) and k-nearest neighbor (KNN) classifiers to select the best classifier. The ICA components of cumulant coefficients have provided the average accuracy, sensitivity, specificity and positive predictive value of 99.50%, 100%, 99.22% and 99.72% respectively using KNN classifier. Similarly, the ICA components of HOS bispectrum coefficients have yielded the average accuracy, sensitivity, specificity and PPV of 97.65%, 98.16%, 98.75% and 99.53% respectively using KNN. So, the ICA performed on the 3rd order HOS cumulants coupled with KNN classifier performed better than the HOS bispectrum method. The proposed methodology is robust and can be used in mass screening of cardiac patients.