Prediction of subcellular protein localization based on functional domain composition

Assigning subcellular localization (SL) to proteins is one of the major tasks of functional proteomics. Despite the impressive technical advances of the past decades, it is still time-consuming and laborious to experimentally determine SL on a high throughput scale. Thus, computational predictions are the preferred method for large-scale assignment of protein SL, and if appropriate, followed up by experimental studies. In this report, using a machine learning approach, the Nearest Neighbor Algorithm (NNA), we developed a prediction system for protein SL in which we incorporated a protein functional domain profile. The overall accuracy achieved by this system is 93.96%. Furthermore, comparisons with other methods have been conducted to demonstrate the validity and efficiency of our prediction system. We also provide an implementation of our Subcellular Location Prediction System (SLPS), which is available at http://pcal.biosino.org.     

Energy efficient scheduling for parallel applications on mobile clusters

During the past decade, cluster computing and mobile communication technologies have been extensively deployed and widely applied because of their giant commercial value. The rapid technological advancement makes it feasible to integrate these two technologies and a revolutionary application called mobile cluster computing is arising on the horizon. Mobile cluster computing technology can further enhance the power of our laptops and mobile devices by running parallel applications. However, scheduling parallel applications on mobile clusters is technically challenging due to the significant communication latency and limited battery life of mobile devices. Therefore, shortening schedule length and conserving energy consumption have become two major concerns in designing efficient and energy-aware scheduling algorithms for mobile clusters. In this paper, we propose two novel scheduling strategies aimed at leveraging performance and power consumption for parallel applications running on mobile clusters. Our research focuses on scheduling precedence constrained parallel tasks and thus duplication heuristics are applied to schedule parallel tasks to minimize communication overheads. However, existing duplication algorithms are developed with consideration of schedule lengths, completely ignoring energy consumption of clusters. In this regard, we design two energy-aware duplication scheduling algorithms, called EADUS and TEBUS, to schedule precedence constrained parallel tasks with a complexity of O(n ²), where n is the number of tasks in a parallel task set. Unlike the existing duplication-based scheduling algorithms that replicate all the possible predecessors of each task, the proposed algorithms judiciously replicate predecessors of a task if the duplication can help in conserving energy. Our energy-aware scheduling strategies are conducive to balancing scheduling lengths and energy savings of a set of precedence constrained parallel tasks. We conducted extensive experiments using both synthetic benchmarks and real-world applications to compare our algorithms with two existing approaches. Experimental results based on simulated mobile clusters demonstrate the effectiveness and practicality of the proposed duplication-based scheduling strategies. For example, EADUS and TABUS can reduce energy consumption for the Gaussian Elimination application by averages of 16.08% and 8.1% with merely 5.7% and 2.2% increase in schedule length respectively.

秦岭南坡松栎林群落演替过程中物种组成及多样性动态分析

为揭示秦岭南坡植物群落演替与物种多样性之间的复杂关系,采用空间代替时间的方法在秦岭南坡油松林、松栎混交林和锐齿栎林群落典型分布区域设置45个样地进行了群落学调查,统计分析了油松林→松栎混交林→锐齿栎林这一演替序列过程中草、灌、乔3层的物种组成和α物种多样性动态。结果表明:(1)秦岭南坡油松林、松栎混交林和锐齿栎林3种群落共有维管植物312种,隶属于73科183属,其中草本植物136种,灌木(含木质藤本)98种,乔木78种;油松林群落包含52科117属190种,松栎混交林群落含有60科95属129种,锐齿栎林群落则为50科109属178种。(2)沿油松林→松栎混交林→锐齿栎林群落演替序列,草本层物种均匀度和物种多样性显著降低,物种丰富度呈"V"形变化趋势;灌木层物种丰富度、均匀度以及物种多样性均无显著差异;乔木层物种多样性呈明显的单峰型变化,其中松栎混交林群落物种多样性指数最高。研究表明,秦岭南坡松栎林群落物种多样性随演替进展总体上呈现单峰型变化,与中期物种多样性假说一致;物种多样性可能仅仅是群落稳定的一个基础或前提条件。     

中国地貌区划系统——以自然保护区体系建设为目标

地貌类型是重要的自然地理特征,是影响区域生物多样性空间格局变化的重要因子。地貌研究能使人们深入认识地理环境特点,有利于完善对区域自然环境和地域分异规律的认识,同时对生物地理区划和区域自然保护研究也具有很好的参考价值。采用"自上而下"的区域分割和"自下而上"的区域合并的区划方式,以中国地形DEM作为基础,使用GIS10.0对其进行高程重分类、坡度分析等量化分析,并结合现有气候区划、自然地理区划和地貌类型等资料,对中国地貌格局进行了分析。在考虑生物多样性保护过程中以地貌为主体的地理单元差异性基础上,根据分析结果,提出了以区域自然保护区体系构建为目标的中国地貌区划系统,该地貌区划系统包括了东部季风淋蚀地貌大区、西北干燥风蚀地貌大区、青藏高原高寒冻蚀地貌大区、南海诸岛地貌大区等4个地貌大区,大兴安岭、小兴安岭和内蒙古高原等40个地貌地区,完达山、老爷岭和张广才岭等127个地貌亚地区,以及473个地貌区。其地貌区划方案科学构建了区划等级系统,体现了中国地貌类型的基本特征和分布格局,其中地貌大区基本反映了中国大的地貌格局,地貌地区基本反映了高原、山地、平原等地貌特征的水平分异,地貌亚地区和地貌区基本反映了区域地貌特征。中国地貌区划系统为自然保护区体系构建提供了参考和依据,而且区划界线准确,便于使用。     

中国自然保护综合地理区划

综合自然地理区划可以为生物多样性保护和自然保护区体系建设等提供基础资料,为区域生物多样性政策的制定提供科学依据。随着我国自然保护区事业的不断发展,自然保护综合地理区划成为自然地理区划的重要研究内容之一。虽然我国自然保护区体系已经初步建立,但仍然没有一个同时依据生物因素和非生物因素分布规律,确定的自然保护综合地理区划方案,为生物多样性保护和自然保护区建设服务。利用GIS技术和PC-ORD4.0软件中的双向指示种分析(TWINSPAN)方法,将中国版图划分出3489个基本地理单元,并对这些地理单元进行了数量化分类。然后,根据这个分类结果,参考植被区划和地貌区划等,提出了中国自然保护综合地理区划方案。中国自然保护综合地理区划方案包括了8个自然保护地理大区、37个自然保护地理地区和117个自然保护地理亚地区。该区划具有以下特点:(1)利用TWINSPAN的数量分类方法进行地理区划的探索是区划方法上的创新,为自然地理区划的研究提供了新的研究途径。(2)选取的数量化指标是在结合已有专项区划资料提出的,有助于避免动植物分布指标的人为选择偏差,可以综合反映区域自然地理特征,对生物多样性就地保护和自然保护区体系建设具有较好的指导作用。(3)量化分析保证了地理区划的客观性,同时定性分析避免了量化分析过程中的误差,使区划结果更准确。     

A 10-miRNA risk score-based prediction model for pathological complete response to neoadjuvant chemotherapy in hormone receptor-positive breast cancer

Patients with hormone receptor(HR)-positive tumors breast cancer usually experience a relatively low pathological complete response(p CR) to neoadjuvant chemotherapy(NAC). Here, we derived a 10-micro RNA risk score(10-mi RNA RS)-based model with better performance in the prediction of p CR and validated its relation with the disease-free survival(DFS) in 755 HRpositive breast cancer patients(273, 265, and 217 in the training, internal, and external validation sets, respectively). This model,pres...     

小麦TaCO9基因的克隆及功能分析

为了明确TaCO9-1A基因在小麦生长发育中的具体调控机理,该研究以同源克隆的方法成功获得了大麦(Hordeum vulgare)光周期基因HvCO9在小麦(Triticum aestivum)中的直系同源基因TaCO9,并对其进行生物信息学分析、亚细胞定位、转录激活以及表达模式分析;利用农杆菌侵染法转化拟南芥,并对过表达株系进行表型分析。结果表明:(1)TaCO9包含2个外显子和1个内含子,CDS区全长876 bp,编码291个氨基酸,蛋白序列含有特有的CCT结构域,且在不同物种间高度保守。(2)生物信息学分析表明,TaCO9基因编码的蛋白质分子量约为30.7 kD,等电点为6.24;TaCO9的启动子区含有光响应、激素应答和胁迫应答等多种顺式作用元件。(3)亚细胞定位和转录活性分析表明,TaCO9主要定位于细胞核中,且具有转录激活活性。(4)qRT-PCR结果表明,TaCO9基因在各个组织中均有表达,叶片中的表达量最高;在光照14 h条件下TaCO9的表达量显著高于光照10 h和12 h条件下的表达量,且TaCO9在大粒小麦‘西农817’子房与籽粒中的表达量显著高于‘中国春’。(5)经潮霉素筛选成功获得3个转基因拟南芥株系;进一步功能鉴定结果表明,过表达转TaCO9基因拟南芥植株的开花期迟于野生型(对照)3~4 d,但角果和籽粒较野生型大。     

迁地麋鹿对野鸭湖植被的保护性生物控制

利用食草动物来管理自然保护地的植被平衡具有很大的应用潜力,一方面可提升动物的生态价值,另一方面通过控制取食规模,改变植被的生物多样性,达到对自然保护地生态平衡管理的目的。基于此于2021年6月5日引入4头麋鹿(2雄2雌),对野鸭湖自然保护区的“芦苇优势群落”采取保护性的生物控制研究,从项目的实施来看：1)单纯收割不能控制芦苇的生长扩张;对芦苇区系植物多样性的影响有限,未改变芦苇区系结构;2)麋鹿引入该区域后,通过取食、游泳、躺卧和踩踏等活动有效控制了芦苇和香蒲的过度扩张;1年后芦苇和香蒲面积下降了21.96%,为三棱水葱、水蓼等提供了生长空间,逐渐形成了仍以芦苇和香蒲为主且更多样的湿地环境;3)增加滩涂和开阔水面等景观,使多样性指数进一步提升,未改变周边区系湿地生态结构;4)麋鹿迁入可降低野鸭湖“脆弱物种”芦苇区系的丰富度,由引入前的(r=3.67)下降到引入后的(r=1.97);麋鹿迁入提升了野鸭湖植被区系物种多样性,芦苇区系的多样性指数由引进前的(r=0.90)上升到引进后的(r=2.11);麋鹿引入的第一年结果显示,整个引入区域的植被多样性指数由r=0.51上升到r=0.91。麋...     

Electroless Plating of Highly Efficient Bifunctional Boride‐Based Electrodes toward Practical Overall Water Splitting

Exploring highly‐efficient and low‐cost electrodes for both hydrogen and oxygen evolution reaction (HER and OER) is of primary importance to economical water splitting. Herein, a series of novel and robust bifunctional boride‐based electrodes are successfully fabricated using a versatile Et₂NHBH₃‐involved electroless plating (EP) approach via deposition of nonprecious boride‐based catalysts on various substrates. Owing to the unique binder‐free porous nodule structure induced by the hydrogen release EP reaction, most of the nonprecious boride‐based electrodes are highly efficient for overall water splitting. As a distinctive example, the Co‐B/Ni electrode can afford 10 mA cm^?2 at overpotentials of only 70 mV for HER and 140 mV for OER, and can also survive at large current density of 1000 mA cm^?2 for over 20 h without performance degradation in 1.0 m KOH. Several boride‐based two‐electrode electrolyzers can achieve 10 mA cm^?2 at low voltages of around 1.4 V. Moreover, the facile EP approach is economically viable for flexible and large size electrode production.