An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.     

生境片段化对千岛湖地表甲虫物种多样性的影响

在千岛湖片段化景观中选取20个陆桥岛屿和8个大陆样点,从2012年7月到2014年4月,按季度(春、夏、秋季)6次采用巴氏陷阱法收集地表甲虫,分析其物种多度、组成、多样性和季节动态,以及不同岛屿上的地表甲虫的物种多样性与岛屿面积和隔离度等岛屿空间特征的关系.结果表明: 共收集记录到地表甲虫26科101种3370头.大陆和大岛地表甲虫的物种丰富度有显著差异,且小岛地表甲虫密度显著高于大陆;大陆地表甲虫的物种组成变化较大,而岛屿上分布的地表甲虫的物种组成则变化较小.地表甲虫的物种丰富度与岛屿面积呈显著正相关,密度与隔离度呈显著正相关.夏季岛屿上地表甲虫物种丰富度高于春秋两季,岛屿与大陆样地的Shannon指数、Simpson指数和Pielou均匀度指数均在夏季最高、秋季最低.     

食物源距离对中华姬鼠贮藏策略的影响

在围栏条件下, 检验食物源距离对中华姬鼠贮藏策略的影响,并检验根据快速隔离假说和最优贮藏空间分布模型做出的两个预测：（1）3个释放点无论距离远近,种子均先被大量分散贮藏在各个释放点周围;（2）随着释放点远离巢穴,种子被集中贮藏的比例下降。结果发现: 分散贮藏是中华姬鼠的主要贮藏方式,3个释放点种子被分散贮藏的数量无显著差异,这个结果支持预测（1）;3个种子释放点（1m,5m,13m）被集中贮藏的比例分别为(1m: 6.25%; 5m: 1.88%; 13m: 1.25%),说明被集中贮藏的种子数量随种子释放点与巢穴距离的增大而逐渐减少,这个结果支持预测（2）。本研究表明中华姬鼠应对捕食风险升高的策略是降低取食量和贮藏量。     

贵州清水苑大洞遗址发掘简报

清水苑大洞位于贵州省惠水县摆金镇,遗址发现于1998年9月,因发现丰富石制品、骨制品、灰烬层和哺乳动物化石等遗物而为学术界所关注。2013年9至11月,中国科学院古脊椎动物与古人类研究所和贵州省文物考古研究所联合对清水苑大洞进行考古发掘,发掘区分A、B两区,揭露面积分别为4 m~2和6 m~2。A区揭露地层厚度约90cm,堆积物为灰白-灰黄色-灰黑色砂质黏土,共出土石制品2398件、动物化石及碎骨2000余件。石制品组合以小型石片工业为体,类型包括石核、石器、各类废片、石锤、磨石等,此外还有5件砸击品。石制品原料大多取自围岩内的燧石,剥片以硬锤锤击法为主,石制品以小型居多;刮削器为石器的主要类型,另有少量凹缺器;石器修理多以锤击法向片状毛坯的背面修理为主。~(14)C测年显示遗址形成于距今约11-14 ka BP,为旧-新石器时代过渡期。该遗址的发掘和研究对于探讨更新世末期古人类在贵州中部低海拔地区的适应生存方式具有重要意义。     

许家窑遗址马科动物的死亡年龄

普氏野马(Equus przewalskii)和野驴(Equus hemionus)是许家窑遗址动物群中的优势属种。本文基于对这两种动物牙齿材料的测量与分析,确定了遗址中马科动物的死亡年龄,并对上、下文化层的死亡年龄分布进行了研究,以期探知古人类获取肉食资源的方式与特点。通过与马科动物在自然生存状态下以及死于不同原因(如疾病或营养衰竭、食肉动物猎杀、现代人类狩猎等)的年龄结构对比,结果表明:古人类在许家窑文化早期(下文化层)可能通过捡拾自然死亡的动物尸体、与食肉类动物抢夺猎物、主动狩猎等多种方式获取马科动物,而在许家窑文化晚期(上文化层)可能以主动狩猎作为获取马科动物的主要方式。此外,古人类在遗址的早期就可能已经具有捕获整个马科动物居群中任意年龄个体的能力,并能做出最优化判断,有选择地去捕猎脂肪和肉量较高的壮年动物群体。     

黑龙江省桃山遗址2014年度发掘报告

桃山遗址发现于2011年,2013年进行试掘,并于次年展开系统的考古发掘工作。遗址2014年度发掘总面积36m~2,揭露出3个史前文化层,出土了丰富的遗物,包括石制品1943件,陶片12件,装饰品备料2件,植物果壳1件。石制品类型包括石核、石片、细石叶、鸡冠状石叶、削片、刮削器、锯齿刃器、端刮器、凹缺器、斧形器、锛形器和石镞等。此次发掘出土遗物从数量和类型两个方面均突破了2013年试掘工作对遗址认识的局限,更全面地展现出桃山遗址的文化面貌。遗址各阶段石制品原料及技术类型虽存在一定相似性,但也表现出较为明显的差异。光释光和AMS~(14)C年代测定表明古人类在该遗址活动的时间从旧石器晚期后段一直延续到新石器时代。     

赤峰兴隆沟遗址人类椎骨疾病的生物考古学研究

对赤峰兴隆沟遗址第一地点出土的人类椎骨上椎体的退行性关节病(DJD)和黄韧带骨化(OLF)进行了生物考古学研究,制订了这两种病症患病程度的分级记录标准,并对患病率和患病程度均值进行了统计分析。对两性的对比发现DJD的差异主要体现在男性颈椎患病较多而女性腰椎患病较多,OLF的主要差异则是男性胸椎患病率显著高于女性。通过与对比组的比较,发现兴隆沟组腰椎、颈椎DJD患病率相对较高,并再次验证了两性患病情况存在的明显差异;兴隆沟组OLF患病率与对比组也有显著差异。兴隆沟组的椎骨患病情况不一定与生业模式有关,只反映了脊柱承受负荷的情况,其差异暗示行为模式上的差异。建议开展其他方面研究以详细了解其行为模式,同时要重视建立统一的古病理研究标准的重要性。     

Nesting Success in Crimson Finches: Chance or Choice?

In avian systems, nest predation is one of the most significant influences on reproductive success. Selection for mechanisms and behaviours to minimise predation rates should be favoured. To avoid predation, breeding birds can often deter predators through active nest defence or by modifying behaviours around the nest (e.g. reducing feeding rates and vocalisations). Birds might also benefit from concealing nests or placing them in inaccessible locations. The relative importance of these strategies (behaviour vs. site selection) can be difficult to disentangle and may differ according to life history. Tropical birds are thought to experience higher rates of predation than temperate birds and invest less energy in nest defence. We monitored a population of crimson finches (Neochmia phaeton), in the Australian tropics, over two breeding seasons. We found no relationship between adult nest defence behaviour (towards a model reptile predator) and the likelihood of nest success. However, nest success was strongly related to the visibility of the nest and the structure of the vegetation. We found no evidence that adult nest building decisions were influenced by predation risk; individuals that re‐nested after a predation event did not build their nest in a more concealed location. Therefore, predator avoidance, and hence nest success, appears to be largely due to chance rather than due to the behaviour of the birds or their choice of nesting sites. To escape high predation pressures, multiple nesting attempts both within and between seasons may be necessary to increase reproductive success. Alternatively, birds may be limited in their nest‐site options; that is, high‐quality individuals dominate quality nest sites.