A Brief Review on the Human Encyclopedia of DNA Elements (ENCODE) Project

The ENCyclopedia Of DNA Elements (ENCODE) project is an international research consortium that aims to identify all functional elements in the human genome sequence. The second phase of the project comprised 1640 datasets from 147 different cell types, yielding a set of 30 publications across several journals. These data revealed that 80.4% of the human genome displays some functionality in at least one cell type. Many of these regulatory elements are physically associated with one another and further form a network or three-dimensional conformation to affect gene expression. These elements are also related to sequence variants associated with diseases or traits. All these findings provide us new insights into the organization and regulation of genes and genome, and serve as an expansive resource for understanding human health and disease.     

Creating a human brain proteome atlas--13th HUPO BPP Workshop March 30-31, 2010, Ochang, Korea

The HUPO Brain Proteome Project (HUPO BPP) held its 13th workshop in Ochang from March 30th to 31st, 2010 prior to the Korean HUPO 10th Annual International Proteomics Conference. The principal aim of this project is to obtain a better understanding of neurodiseases and aging with the ultimate objective of discovering prognostic and diagnostic biomarkers, in addition to the development of novel diagnostic techniques and new medications. The attendees came together to discuss progress in the clinical neuroproteomics of human and to define the needs and guidelines required for more advanced proteomics approaches.     

Interaction between hypertension and HSP70 variants increase the risk of cerebral ischemia in Chinese Han population: An association study

Cerebral infarction has become one of the leading diseases and a major mortality factor around the world. Atherosclerosis is recognized as one of the important causes of ischemic stroke. Recently, accumulating evidences have indicated that the anti-inflammatory and anti-apoptotic functions of the HSP70 family play an important role in cerebral ischemia. However, the association between HSP70 SNPs and ischemic stroke was also not well established. We chose 101 cases of cerebral ischemia and 100 healthy people from the Chinese Han population as our study subjects, and PCR-RFLP was employed to analyze HSP70 polymorphisms: HSP70-1+190G/C, HSP70-2+1267A/G and HSP70-hom+2437T/C. There were no significant differences in + 1267A/G allele or genotype frequencies between patients with stroke and healthy controls. However, genotypes of + 190CG and + 2437TT were differentially distributed between the patients and controls. A significant difference of T allele distribution in the HSP70-hom+2437T/C site was observed. Logistic regression analysis indicated that genotypes of + 190CG, + 2437TT and T allele in HSP70-hom were risk factors of ischemic stroke. Moreover, the study has formulated that the interactions between hypertension and + 190CG or + 2437TT may increase the risks of ischemic stroke. The results from this study have suggested a clinical indicator for assessing the possibilities of cerebral stroke, and supply basis to clinicians to give precaution to people who are at risk of stroke.     

Evidence of colorectal cancer risk associated variant Lys25Ser in the proximity of human bone morphogenetic protein 2

Colorectal cancer (CRC) is the third most prevalent cancer and fourth leading cause of cancer-related deaths globally. It has been shown that the nsSNP variants play an important role in diseases, however it remained unclear how these variants are associated with the disease. Recently, several CRC risk associated SNPs have been discovered, however rs961253 (Lys25Arg at 20p12.3) located in the proximity of bone morphogenetic protein 2 (Bmp2) and fermitin family homolog 1 Fermt1 genes have been reported to be highly associated with the CRC risk. Here we provide evidence for the first time in silico biological functional and structural implications of non-synonymous (nsSNPs) CRC disease-associated variant Lys25Arg via molecular dynamic (MD) simulation. Protein structural analysis was performed with a particular variant allele (A/C, Lys25Arg) and compared with the predicted native protein structure. Our results showed that this nsSNP will cause changes in the protein structure and as a result is associated with the disease. In addition to the native and mutant 3D structures of CRC associated risk allele protein domain (CRAPD), they were also analyzed using solvent accessibility models for further protein stability confirmation. Taken together, this study confirmed that this variant has functional effect and structural impact on the CRAPD and may play an important role in CRC disease progression; hence it could be a reasonable approach for studying the effect of other deleterious variants in future studies.     

浅谈网络分析法及其在古生物学中的应用

网络分析作为一种新的数据可视化途径和定量方法, 能简化复杂系统而发现元素间的关系模式。它在定量社会科学、计算机科学与机器学习等领域均有众多应用实例。近年来, 在古生物学, 特别是古生物地理学相关研究中逐渐受到关注。本文介绍了网络的基本构成、常见网络类型及其数据储存方式、以及网络分析中的重要参数及其定义, 同时给出了两种实现网络分析的方法及相关工具, 即Gephi软件与R语言平台。通过分析比较两种方法的步骤及结果, 发现Gephi虽成图简洁美观, 但算法功能有限, 且无法完成成图前的数据处理以及成图后的多元分析, 因而最终推荐使用R语言编程进行网络分析。本文以奥陶纪末大灭绝后复苏期全球腕足动物数据为例, 详细展现了利用R语言及其应用包“igraph”编程进行网络分析的过程, 并实现了古生物地理学数据资料的处理以及网络分析图件的绘制。希望对即将接触此类工具的古生物学科研人员在进行网络分析时提供借鉴与参考。     

Concordance between ecotypes and macroinvertebrate assemblages in Mediterranean streams

1. According to the guidelines of the European Water Framework Directive, assessment of the ecological quality of streams and rivers should be based on ecotype-specific reference conditions. Here, we assess two approaches for establishing a typology for Mediterranean streams: a top-down approach using environmental variables and bottom-up approach using macroinvertebrate assemblages.
2. Classification of 162 sites using environmental variables resulted in five ecotypes: (i) temporary streams; (ii) evaporite calcareous streams at medium altitude; (iii) siliceous headwater streams at high altitude; (iv) calcareous headwater streams at medium to high altitude and (v) large watercourses.
3. Macroinvertebrate communities of minimally disturbed sites ( n  = 105), grouped using UPGMA (unweighted pair-group method using arithmetic averages) on Bray–Curtis similarities, were used to validate four of the five ecotypes obtained using environmental variables; ecotype 5, large watercourses, was not included as this group had no reference sites.
4. Analysis of similarities ( anosim ) showed that macroinvertebrate assemblage composition differed among three of the four ecotypes, resulting in differences between the bottom-up and top-down classification approaches. Siliceous streams were clearly different from the other three ecotypes, evaporite and calcareous ecotypes did not show large differences in macroinvertebrate assemblages and temporary streams formed a very heterogeneous group because of large variability in salinity and hydrology.
5. This study showed that stream classification schemes based on environmental variables need to be validated using biological variables. Furthermore, our findings indicate that special attention should be given to the classification of temporary streams.     

模拟放牧干扰对黄土丘陵区生物结皮坡面土壤水分入渗的影响

水分是黄土高原地区植被恢复的关键影响因子,该区广泛分布的生物结皮显著影响土壤水分入渗。干扰影响生物结皮土壤水分入渗,但目前不同强度的干扰对生物结皮土壤水分入渗的影响仍不明确。本研究以黄土丘陵区吴起县合沟小流域的生物结皮坡面为对象,模拟羊蹄踩踏干扰,研究10%、20%、30%和40%干扰强度(以生物结皮破损度表征)对生物结皮坡面地表覆被的影响,采用线源入流入渗法观测了不同强度干扰后土壤水分入渗特征,通过结构方程模型和相关性分析,探索了干扰对生物结皮坡面土壤水分入渗的影响机制。结果表明:与对照(不干扰)相比,10%干扰强度下藻结皮盖度显著增加33.6%,20%干扰强度对藻结皮盖度无显著影响,30%和40%干扰强度下藻结皮盖度分别显著降低了36.1%和75.0%;40%干扰强度显著增加了枯落物盖度(34.3%),其他处理无显著影响;10%、20%和30%干扰强度下地表粗糙度分别显著降低了22.3%、11.1%和5.6%,40%干扰强度下增加了8.2%;40%干扰强度下初始入渗率显著增加了77.1%,其他干扰强度无显著影响;不同干扰对土壤稳定入渗率和平均入渗率无显著影响。可见,干扰主要通过降低藻结皮盖度,增加枯落物盖度和改变地表粗糙度,进而促进了土壤水分初始入渗。本研究可为黄土高原退耕地生物结皮管理提供科学依据。     

阿根廷文化景观研究、项目和表现

旨在促进应用“文化景观”概念作为分析和开发阿根廷地域项目的工具。第1部分,力图总结有关文化景观的概念,术语名词的起源、传播以及其所暗含的可能性和矛盾性。第2部分,讨论这个概念成为项目工具的方式。第3部分中,强调了绘图在分析和项目中的核心作用。第4部分,以2个案例研究表明在前3个部分中阐述的问题。结论提出了这种开展项目的方式的潜能、挑战和矛盾。而只有针对地域特性的详细研究才能使找到一种回馈当地发展的管理方式成为可能。     

Oral health of the Paleoamericans of Lagoa Santa,central Brazil

The peopling, origins, and early prehistory of the Americas are topics of intense debate. However, few studies have used human remains to document and interpret patterns of health and lifestyle of Paleoamericans. This study provides the first investigation to characterize oral health in a series of early Holocene skeletal remains from Lagoa Santa, Brazil, a locality containing the remains of some of the earliest inhabitants of South America (10,000–7,000 BP). The sample is composed of 949 teeth and 1925 alveoli from an estimated 113 individuals excavated from 17 archaeological sites located in the State of Minas Gerais. We compare dental caries and abscess prevalence at Lagoa Santa to a large sample of human skeletons from the Western Hemisphere Project (WHP) database using both individual and tooth/alveolus count methods. In addition, antemortem tooth loss and tooth wear were analyzed in Lagoa Santa by sex and age. The results show that Lagoa Santa dental caries and abscess prevalence are significantly higher than observed among other hunter–gatherers included in the WHP database, except when abscess prevalence is considered by individual count. Adult females have less tooth wear coupled with higher prevalence of dental caries and antemortem tooth loss than adult males. These results point to an unexpected record of poor oral health at Lagoa Santa, especially among females. A diet based on a highly cariogenic combination of wild tubers and fruits is suggested as an explanation for the elevated rate, characterizing an early adaptation to a tropical environment in South America. Am J Phys Anthropol 154:11–26, 2014. © 2014 Wiley Periodicals, Inc.