Induction of oxidative DNA damage in the peri-infarct region after permanent focal cerebral ischemia

To address the role of oxidative DNA damage in focal cerebral ischemia lacking reperfusion, we investigated DNA base and strand damage in a rat model of permanent middle cerebral artery occlusion (MCAO). Contents of 8-hydroxyl-2'-deoxyguanosine (8-OHdG) and apurinic/apyrimidinic abasic sites (AP sites), hallmarks of oxidative DNA damage, were quantitatively measured in nuclear DNA extracts from brains obtained 4-72 h after MCAO. DNA single- and double-strand breaks were detected on coronal brain sections using in situ DNA polymerase I-mediated biotin-dATP nick-translation (PANT) and terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL), respectively. Levels of 8-OHdG and AP sites were markedly elevated 16-72 h following MCAO in the frontal cortex, representing the peri-infarct region, but levels did not significantly change within the ischemic core regions of the caudateputamen and parietal cortex. PANT- and TUNEL-positive cells began to be detectable 4-8 h following MCAO in the caudate-putamen and parietal cortex and reached maximal levels at 72 h. PANT- and TUNEL-positive cells were also detected 16-72 h after MCAO in the lateral frontal cortex within the infarct border, where many cells also showed colocalization of DNA single-strand breaks and DNA fragmentation. In contrast, levels of PANT-positive cells alone were transiently increased (16 h after MCAO) in the medial frontal cortex, an area distant from the infarct zone. These data suggest that within peri-infarct brain regions, oxidative injury to nuclear DNA in the form of base and strand damage may be a significant and contributory cause of secondary expansion of brain damage following permanent focal ischemia.     

西藏米拉卡黑白仰鼻猴的栖息地变化

黑白仰鼻猴(Rhinopithecus bieti)分布在我国金沙江和澜沧江之间的横断山脉的一个狭小区域内(26°14′N-29°20′N,99°15′E-99°37′E),海拔分布范围2600(南部)-4200m(北部);目前大约有15群,约1700只。本文所研究的西藏米拉卡猴群分布在我国西藏藏族自治区芒康县的南部,数量约50只。基于野外调查和过去的报道,此地的暗针叶林和针阔叶混交林是猴群的适宜栖息地,而由于人口数量增加所导致的夏季牧场和农田面积不断扩增正在逐渐侵蚀着这里的暗针叶林。为了评估该猴群的栖息地现状、变化趋势和变化原因,我们通过野外调查工作,利用GIS和RS技术,分别解译了当地过去5年(1986-2006年)冬季的Landsat TM卫星影像,并对解译结果进行了分析和计算,得到了该猴群栖息地的主要结果有:1)2006年暗针叶林面积是13600hmP2P,夏季牧场面积是4900hmP2P,农田面积是3300hmP2P;2)在过去20年(1986-2006年),暗针叶林面积减少了15.5%(2500hmP2P),牧场面积增加了58.1%(1800hmP2P),农田面积增加了17.8%(500hmP2P);3)暗针叶林的斑块数量增加了75.6%,平均斑块面积下降了51.8%(从1986年的15.3hmP2P到2006年的7.4hmP2P),最大斑块指数下降了54.7%;景观丰富度并没有变化,但Shannon多样性指数和Shannon均匀度指数分别增加了4.0%;4)暗针叶林面积变化与当地的人口数量呈显著负相关(r=?1.000),而夏季牧场和农田面积分别和当地人口呈显著正相关(r=1.000)。表明黑白仰鼻猴米拉卡猴群栖息地的丧失和破碎化程度较为严重;栖息地丧失和破碎化是当地传统生产方式和人口增长共同作用的结果。     

Standard quantitative assays for apoptosis

The term apoptosis refers to a peculiar morphology of cell death. It is of special interest because it can be triggered physiologically (and pathologically), and it is regulated by the actions of specific gene products. Therefore, it can in principle be activated and suppressed by medical intervention. It thus is often important to determine whether cells are dying by apoptosis (or its less regulated counterpart, necrosis) and also to quantity the effect in a population of cells. Here the classic methods of apoptosis quantitation are described; they will be of particular use to those whose laboratories are set up for standard microscopical and biochemical techniques, who do apoptosis assays infrequently but wish them to be widely accepted and reproducible. A simple microscopic observation, using blue light illumination and a pair of fluorescent dyes, is recommended for most applications.     

Testing hypotheses driving genetic structure in the cooperatively breeding Brown‐headed Nuthatch Sitta pusilla

Habitat fragmentation has often been implicated in the decline of many species. For habitat specialists and/or sedentary species, loss of habitat can result in population isolation and lead to negative genetic effects. However, factors other than fragmentation can often be important and also need to be considered when assessing the genetic structure of a species. We genotyped individuals from 13 populations of the cooperatively breeding Brown‐headed Nuthatch Sitta pusilla in Florida to test three alternative hypotheses regarding the effects that habitat fragmentation might have on genetic structure. A map of potential habitat developed from recent satellite imagery suggested that Brown‐headed Nuthatch populations in southern Florida occupied smaller and more isolated habitat patches (i.e. were more fragmented) than populations in northern Florida. We also genotyped individuals from a small, isolated Brown‐headed Nuthatch population on Grand Bahama Island. We found that populations associated with more fragmented habitat in southern Florida had lower allelic richness than populations in northern Florida (P = 0.02), although there were no differences in heterozygosity. Although pairwise estimates of F_ST were low overall, values among southern populations were generally higher than northern populations. Population assignment tests identified K = 3 clusters corresponding to a northern cluster, a southern cluster and a unique population in southeast Florida; using sampling localities as prior information revealed K = 7 clusters, with greater structure only among southern Florida populations. The Bahamas population showed moderate to high differentiation compared with Florida populations. Overall, our results suggest that fragmentation could affect gene flow in Brown‐headed Nuthatch populations and is likely to become more pronounced over time.     

闽江口芦苇沼泽湿地土壤产甲烷菌群落结构的垂直分布

应用PCR-RFLP技术及测序分析对闽江口芦苇湿地土壤产甲烷菌群落结构的垂直分布特征进行了研究。在构建的6个克隆文库中,每个克隆文库随机挑选100个克隆进行菌落PCR验证,共得到591个阳性克隆。PCR产物经限制性内切酶MspⅠ进行RFLP分析后得到37个不同的分类操作单元(OTUs)。对37个克隆子进行了序列测定,与GenBank数据库中的序列进行比对,最近相似性在91%—99%之间。RFLP分析和系统发育分析表明,闽江口芦苇湿地土壤中产甲烷菌群落包括3大类群:甲烷杆菌目(Methanobacteriales)、甲烷微菌目(Methanomirobiales)和甲烷八叠球菌目(Methanosarcinales)。不同土壤深度中产甲烷菌群落的分布呈现出不同的特征。土壤表层(0—10 cm)优势产甲烷菌类群为Methanoregula,约占76%;10—20 cm土层主要的产甲烷菌类群为Methanolinea和Methanoregula,分别约占23%和29%;20—30cm土层优势的产甲烷菌类群为Methanolinea,约占66%。Shannon指数(H’)和Simpson多样性指教(D)表明,10—20cm土层产甲烷菌多样性高于土壤表层(0—10 cm)和20—30 cm土层。37个测序OTUs中有26个OTUs属于不可培养的产甲烷菌序列,表明闽江口芦苇湿地土壤中存在大量不可培养的产甲烷菌。     

人工管理和自然驱动下盐城海滨湿地互花米草沼泽演变及空间差异

将盐城国家级自然保护区核心区划分为人工管理区和自然湿地区两种模式,根据2000年、2006年、2011年3个时相的ETM+影像,运用RS、GIS技术和景观生态学方法,分析不同驱动力下互花米草沼泽景观变化的差异.结果表明:(1)人工管理区,2000-2011年,互花米草沼泽面积由272hm2增加到781hm2;平均分维数呈下降的趋势,聚合度指数呈上升的趋势,表明互花米草沼泽在空间上趋于聚集,在形状上趋于规则;从互花米草沼泽增长速率看,2000-2011年,呈现先快后慢的特征.在景观空间演变上,互花米草沼泽的平均宽度从598.679m增加到1719.002m,表现出向海陆两个方向扩张的特征.(2)自然湿地区,2000-2011年互花米草沼泽面积由2023hm2增加到3974hm2;平均分维数和聚合度指数呈先上升后下降的趋势;米草沼泽增长稳定,年增长约160-180 hm2/a,单位长度岸线年增长面积约为15 hm2· km-1·a-1左右;比较发现,自然湿地区互花米草沼泽的增长速度高于人工管理区的增长速度.在景观空间演变上,互花米草沼泽平均宽度从1625.586m增加到3193.317m,2000-2006年表现出向海洋单方向扩张的特征,2006-2011年表现出向海陆两个方向扩张的性质.(3)在自然条件下互花米草沼泽扩张受到气候、地貌过程、水文过程、植被类型及种间竞争的影响,表现出明显的带状特征.在人工管理下,通过建设拦水堤坝等,阻止了潮汐作用下海水的扩散能力,生态过程发生改变,致使生态系统类型向淡水湿地方向演变,抑制了互花米草沼泽的扩张,表现出一定的镶嵌格局.     

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.     

Quality of Seeds Produced by Psychotria tenuinervis (Rubiaceae): Distance from Anthropogenic and Natural Edges of Atlantic Forest Fragment

The aim of this study was to investigate whether there were differences in the genetic variability and rate and velocity of the seed germination produced by Psychotria tenuinervis located at anthropogenic edges, natural edges, and in the forest interior. The populations of P. tenuinervis showed no differences in genetic variability or structure among the three habitats. There was, however, an indication of inbreeding, which was significantly higher in natural edges than in anthropogenic edges and the forest interior. Within-habitat variation was considerable, but there were no differences in seed mass or rate and velocity of germination among the three habitats. These results suggest that seed characteristics were not influenced by the genetic pattern of P. tenuinervis and that other characteristics of the forest fragment, such as gaps, edge age, and type of matrix exert more influence on seed mass and germination than the distance from the edges.     

Vegetation:environment relationships and water management in Shark Slough,Everglades National Park

The hydrologic regime of Shark Slough, the most extensive long hydroperiod marsh in Everglades National Park, is largely controlled by the location, volume, and timing of water delivered to it through several control structures from Water Conservation Areas north of the Park. Where natural or anthropogenic barriers to water flow are present, water management practices in this highly regulated system may result in an uneven distribution of water in the marsh, which may impact regional vegetation patterns. In this paper, we use data from 569 sampling locations along five cross-Slough transects to examine regional vegetation distribution, and to test and describe the association of marsh vegetation with several hydrologic and edaphic parameters. Analysis of vegetation:environment relationships yielded estimates of both mean and variance in soil depth, as well as annual hydroperiod, mean water depth, and 30-day maximum water depth within each cover type during the 1990's. We found that rank abundances of the three major marsh cover types (Tall Sawgrass, Sparse Sawgrass, and Spikerush Marsh) were identical in all portions of Shark Slough, but regional trends in the relative abundance of individual communities were present. Analysis also indicated clear and consistent differences in the hydrologic regime of three marsh cover types, with hydroperiod and water depths increasing in the order Tall Sawgrass < Sparse Sawgrass < Spikerush Marsh. In contrast, soil depth decreased in the same order. Locally, these differences were quite subtle; within a management unit of Shark Slough, mean annual values for the two water depth parameters varied less than 15 cm among types, and hydroperiods varied by 65 days or less. More significantly, regional variation in hydrology equaled or exceeded the variation attributable to cover type within a small area. For instance, estimated hydroperiods for Tall Sawgrass in Northern Shark Slough were longer than for Spikerush Marsh in any of the other regions. Although some of this regional variation may reflect a natural gradient within the Slough, a large proportion is the result of compartmentalization due to current water management practices within the marsh. We conclude that hydroperiod or water depth are the most important influences on vegetation within management units, and attribute larger scale differences in vegetation pattern to the interactions among soil development, hydrology and fire regime in this pivotal portion of Everglades.