Genetic diversity of X-chromosome in populations of aboriginal Siberian ethnic groups: linkage disequilibrium structure and haplotype philogeography of ZFX locus

The structure of gene pool of the Siberian aboriginal population has been described based on the data on polymorphism of ZFX gene located on X-chromosome. In ten populations under study 49 haplotypes have been determined, three of which are presented with high frequency. Comparing the obtained results with the available data from HapMap project unique "African" haplotypes were revealed, which occurred in Yoruba population with the frequency of 3-7% and were not found in other populations. A coefficient of genetic differentiation of the Siberian ethnic groups under study amounted to 0.0486. Correlation analysis involving Mantel test did not reveal any significant correlations between a matrix of genetic distances and the matrices of geographic, linguistic and anthropological differences, where a maximum coefficient was obtained at the comparison with the anthropological matrix. Phylogenetic analysis proved strong isolation of African population from the other investigated ethnic groups. The Siberian populations were subdivided into two separate clusters: the first one included Yakuts, Buryats and Kets, while the second cluster included Altaians, Tuvinians and Khanty. A principal component analysis enabled to combine the investigated populations in three groups, which clearly differed by a degree of manifestation of Caucasoid and Mongoloid components. The first group included Europe inhabitants and one of Khanty populations, the second one--populations of South Siberia and China inhabitants. Mongoloid populations of East Siberia, the Japanese and Kets were combined in the third group. The results of barrier analysis revealed similar structure of genetic differentiation in the Siberian population. Linkage disequilibrium structure was obtained for six ethnic groups of Siberia. A unified linkage block by ten SNP of ZFX gene was found in five of the presented ethnic groups (excluding Ket population).     

近17年新疆干旱时空分布特征及影响因素

新疆是我国西北区重要的粮食和商品棉生产基地,受地理环境的影响,干旱频发,给社会经济及农业生产造成了巨大的损失。基于MODIS遥感数据和气象数据,估算温度植被干旱指数(Temperature Vegetation Dryness Index, TVDI),分析新疆2000—2016年干旱的年际、年内时空变化特征及其与气象因子的关系,结果表明:1)TVDI可以有效地描述新疆的干旱状况,适用于对该地区进行干旱监测;2)2000—2016年间新疆TVDI空间分布具有较强的地域分异性,呈现为天山山脉以北及昆仑山脉地区较湿润,塔里木盆地地区较干旱,新疆TVDI多年均值为0.751,整体上处于中旱状态。年内TVDI季节空间分布差异显著,不同季节的干旱程度大小为:夏季>春季>秋季>冬季;3)新疆各地州TVDI年内月变化整体上呈现为先增加后降低的趋势,最小值在1月(0.267),最大值在6月(0.930),在14个地州中,伊犁哈萨克、阿勒泰和博尔塔拉多年间基本处于无旱状态;4)17年间不同土地利用类型干旱程度表现为林地<草地<建筑用地<耕地,干旱类型转移的主要特点为无...     

Spatial and temporal distribution of atrial natriuretic factor in the rat testis.

The atrial natriuretic factor (ANF) is a cardiac hormone whose gene and receptor are widely expressed in extracardiac tissues and organs. ANF induces its biological effects by binding to its specific guanylyl-cyclase-A receptor, which synthesizes the intracellular second messenger cGMP. Increasing evidences indicate that the testis shows the highest reactivity of stimulation of guanylate cyclase by ANF. The well-established functionally active ANF receptors in seminiferous tubules raise the question of the origin and function of ANF in the testis. Therefore, the current study was carried out to investigate the spatial and temporal distribution of ANF in the rat testis by use of immunocytochemistry. Our immunocytochemical results showed that at different pre- and postnatal ages of testicular development ANF was constantly expressed in Leydig cell cytoplasm. However, the intensity of immunoreaction varied between the different Leydig cell populations (fetal, progenitor and immature) and apparently depends on the acquisition of testosterone producing ability. In seminiferous tubules ANF staining was established in the cytoplasm of the developing spermatocytes, in degenerating germ cells (23-day of age) in the cytoplasm of Sertoli cells, cap phase of acrosomal development and in the spermatids (55-day of age). The observed staining patterns suggest a broader spectrum of ANF activities and a possible participation in the whole process of regulation of germ cell development. Our data provide additional support for the hypothesis that ANF plays a major role in autocrine/paracrine regulation of the rat male gonad.     

The structure of the Polar Eskimo genealogy.

The structure of the genealogy of the Polar Eskimos from the Thule District of North Greenland is studied by a variety of computational and graphical means, some of them novel. It is shown that although the level of inbreeding in the population is low, the genealogy is intricately connected, as if conforming to the requirement that spouses are as unrelated as is possible in a small population.     

Spatial and temporal distribution of Caulobacter spp. in two mesotrophic lakes

The seasonal distribution of Caulobacter spp. has been determined in the water column of two mesotrophic lakes using most probable number (MPN) viable counting techniques from April, 1972 to March, 1973. Concentrations in Lake Washington, a monomictic lake, peaked at 1000–3300 per ml in the epilimnion during the late spring and summer and reached lows in October of less than 2 per ml prior to fall turnover. The reason for the decrease in viable numbers is not known. Caulobacter spp. began to increase gradually in December, during the winter mixing period well before the spring bloom. Concentrations in Hall Lake, a small kettle lake, were somewhat higher than in Lake Washington, ranging from 0.27 per ml in October to over 5000 per ml during May. In contrast to Lake Washington, the highest populations were found in the metalimnion and upper hypolimnion of Hall Lake. Caulobacter spp. were also found in the anaerobic depths of the hypolimnion. However, these did not grow anaerobically, suggesting that they had settled into the hypolimnion and survived in the cold anaerobic zone. The populations of Caulobacter spp. reached maximum numbers at the approximate times and depths at which algal biomass would be expected to be greatest.     

Light distribution in mesic grasslands: Spatial patterns and temporal dynamics

Abstract. Spatial patterns and temporal dynamics of light distribution were investigated using lacunarity analysis, a multi‐scale measure of spatial heterogeneity, in three mesic grasslands with different disturbance regimes. Frequency distributions of relative light intensity (RLI) were similar for the two non‐disturbed grasslands, despite different composition (forbs vs. caespitose grass) resulting from different historical disturbance regimes prior to 1985, and different from the annually disturbed grassland. Spatial heterogeneity of light distribution was greater at all scales in the native, annually disturbed grassland than in the two non‐disturbed grasslands. The disturbance regime affected temporal dynamics of the spatial patterns of light distribution in each grassland. The annually disturbed grassland exhibited a dramatic decrease in lacunarity (heterogeneity) from early to late April, likely the result of considerable growth of a cool‐season grass. A general decrease in lacunarity occurred in the native, non‐disturbed grassland, although the magnitude was much less than in the annually disturbed grassland. The reverted, non‐disturbed grassland did not exhibit an appreciable change in lacunarity until later in the growing season, and then only at smaller scales. Combining the frequency distribution of RLI and the lacunarity curves provided an effective approach to assess relationships between the dynamics of spatial pattern of light distribution and ecological processes as influenced by different disturbance regimes. Integrating lacunarity analysis with more traditional measurements of grassland ecosystems (plant spatial distribution and arrangement and plant species composition and architecture) may be an effective way to assess functional consequences of structural changes in grassland ecosystems.     

中国青褶伞时空分布研究

近年来在中国,蘑菇中毒已成为食物中毒事件中威胁人民生命健康的重要因素,其中青褶伞Chlorophyllum molybdites是最常见的毒蘑菇种类。为切实预防该种中毒,揭示其在我国的时空分布特征及规律就显得尤为重要和紧迫。本研究通过系统收集、整理、分析青褶伞在中国的时空分布信息,发现该种在1978-2020年中的20个年份中共出现于我国包含台湾省在内的17个省份,主要集中在热带和亚热带地区,东北地区（黑龙江和内蒙古东部）偶有分布,华北和西北没有记载。青褶伞在我国不同地区一年四季均有分布,具体时间为3-12月份,集中出现在6-10月份。该种最早于仲春出现在华南地区（广东）,随即向热带、亚热带的华南其他地区、华东、华中和西南地区扩散并持续至中秋,从晚秋至初冬,该种分布范围不断南移萎缩至西南热带地区（云南勐腊县）;在温带至寒温带,该种仅在夏末秋初出现在东北地区。     

Spatial and temporal distribution of Patched-related protein in the Drosophila embryo

Patched-related (Ptr) encodes a protein with 12 potential transmembrane domains and a sterol-sensing domain that is closely related in predicted topology and domain organization to Patched, the canonical receptor of the Hedgehog pathway. Here we describe the production of an antibody specific for Drosophila Ptr and analyse its spatial and temporal distribution in the embryo. We find that at early developmental stages Ptr is predominantly localized at cell periphery but later on it becomes strongly and almost exclusively expressed in hemocytes. Interestingly Ptr null mutant embryos died without hatching. Our findings suggest that Ptr plays an essential function in Drosophila development, perhaps as a new receptor of embryonic hemocytes.     

Spatial and temporal distribution of copepod communities in the Adriatic Sea

The distribution of planktonic copepods in the Adriatic Seahas been analyzed on the basis of 132 samples collected at 35fixed stations during 4 seasonal cruises. A total of 127 specieshave been determined and 3 characteristic copepod communitieshave been identified. The distribution of copepod species hasbeen found to reflect the dual physiognomy of the Adriatic.The shallow northern section is characterized by high densityvalues, low species diversity, and the dominance of speciesbelonging to the estuarine and coastal communities. The relativelydeep waters of the southern section are characterized by lowdensity values, high species diversity, and the presence ofmany species belonging to the upper, middle, and lower zonesof the oceanic community. Temporal variations in the horizontalspread of these 3 communities are discussed in relation to seasonalcycles in abundance, vertical migration patterns, and the currentregime in the Adriatic.     

Spatial and temporal distribution patterns of Cladocera in the Argentine Sea

In the marine sciences, continuous monitoring systems have been regarded as very useful tools to provide continuous high frequency measurements of many parameters. We analyse here a high frequency time series of temperature measurements recorded every 10 min between 1997 and 2004 in the macro tidal Seine estuary (France) by a Marel buoy, an automatic monitoring network for littoral environment. We have adapted multi-scale data analysis methods to deal with the many missing values present in the time series. A power spectral density analysis is performed over time scales spanning 5 decades, from 20 min to more than 7 years. A scale invariant behaviour of the form with β = 2.2 is revealed for scales below 5 h. Over this scaling range, we have performed structure functions analysis, and shown that the Seine river temperature data exhibit turbulent-like intermittent properties, with multifractal statistics. The multifractal exponents obtained possess some similarities with passive scalar turbulence results. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Spatial and temporal predictions of moose winter distribution

Herbivores are usually distributed unevenly across the landscape often because of variation in resource availability. We used zero-inflated generalised additive models (to account for data with a high number of zeros) that include georeferences to predict winter distribution of a large herbivore (moose Alces alces). Moose distribution was analysed in relation to forage availability and distance to neighbouring sites. Our results showed that the ability to explain moose distribution indexed by pellet count data at a local scale increased when spatial information (longitude and latitude) was added to the model compared to the model only including food availability. By using the relationship between moose and forage distribution, and the spatial information, we predicted patch choice by moose reasonably well in 2 out of 4?years. However, the distribution of moose was also influenced by weather conditions, as it was most clumped in the year with most snow. In conclusion, our study lends support for a non-linear approach using georeferences for a comprehensive understanding of herbivore distribution at a small scale. This result also indicates that the use of a certain patch by moose not only depends on the selected patch itself but is also influenced by the neighbouring patch and factors at a larger spatial scale, such as moose management influencing the density above moose home range level. The relatively high proportion of unexplained variation suggests that the use of a certain patch is also influenced by other factors such as topography, predation, competition, weather conditions, and wildlife management strategies.     

Spatial and temporal distribution patterns of flying Diptera

The temporal and spatial distributions of flying Diptera have been studied using suction traps hung at three levels and two distances from an emergent hedgerow tree. Most families were far more abundant in 1987 than in 1986, but patterns of spatial and temporal abundance were basically the same. Most families showed a marked concentration close to the tree. Scatopsidae accumulated away from the tree in large numbers. Most families concentrated at the mid-level, except the Anisopodidae and Mycetophilidae (top and bottom levels, respectively). Vertical distributions showed discontinuities for almost all families. It is suggested that the emergent hedgerow tree plays a very important part in the life of flying insects.     

Single-nucleotide polymorphisms and haplotype analysis in beta-defensin genes in different ethnic populations

Beta-defensins are cationic antimicrobial peptides expressed by epithelial cells and exhibit antibacterial, antifungal, and antiviral properties. The defensins are part of the innate host defense network and may have a significant protective role in the oral cavity and other mucosa. Defects or alteration in expression of the beta-defensins may be associated with susceptibility to infection and mucosal disorders. We examined the occurrence of single-nucleotide polymorphisms (SNPs) in the human beta-defensin genes DEFB1 and DEFB2 encoding human beta-defensin-1 and -2 (hBD-1, hBD-2), respectively, in five ethnic populations and defined haplotypes in these populations. Fifteen SNPs were identified in both DEFB1 and DEFB2. Coding region SNPs were found in very low frequency in both genes. One nonsynonymous DEFB1 SNP, G1654A (Val --> Ile), and one nonsynonymous DEFB2 SNP, T2312A (Leu --> His), were identified. Seven sites in each gene exhibited statistically significant differences in frequency between ethnic groups, with the greatest variation in the promoter and in the 5'-untranslated region of DEFB1. DEFB1 displayed 10 common haplotypes, including one cosmopolitan haplotype. Eight common haplotypes were found in DEFB2, including one cosmopolitan haplotype shared among all five ethnic groups. Our results show that genotypic variability among ethnic groups will need to be addressed when performing associative genetic studies of innate defense mechanisms and susceptibility to disease.     

iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

Background  

The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations.     

Spatial and temporal variability in the structure of a tropical forest

This study examines spatial and temporal variation in the forest structure of the Kibale National Park, Uganda by contrasting tree density, tree size, and forest composition among four areas each separated by less than 15 km, and by quantifying changes in the composition of one of these forests over a 20‐year period. Densities of some tree species differed markedly between sites, and some species common at one location were absent at others. Monthly phenological monitoring demonstrated that it was not uncommon for phenological patterns to differ between the forests. To examine temporal variation in the tree composition over a 20‐year period, a sampling regime that was carried out in the early 1970s was replicated on the floristic composition of one of these sites, using identical methods in the same sampling areas. While no form of human intervention occurred in this area between the early 1970s and 1992, there were marked changes in the densities of some tree species. Twenty‐seven percent of the identified species increased in abundance, 33% decreased, and 40% remained relatively unchanged. The observed spatial and temporal variation in forest composition could be the result of abiotic factors, such as altitude or rainfall, or biotic factors such as elephant and/or human influences on ecosystem dynamics; the implications of this variation for frugivores are discussed.     

PCR-based genotyping and haplotype analysis of human TCRBV gene segment polymorphisms

There are at least 63 tandemly arranged human T-cell receptor (Tcr) -chain variable region (BV) gene segments, which have presumably arisen by repeated gene duplication events. The 5-most half of the TCRBV gene loci is particularly complex in organization due to the presence of multiple interspersed members of the largest BV subfamilies, BV5, BV6, and BV13. Polymorphism and linkage relationships among these genes has been poorly characterized in part due to the high similarity of these duplicands. Germline DNA polymorphisms were specifically examined in the exons and introns of these and other BV gene segments distributed across 240 kilobases (kb) in this 5-most region. Polymerase chain reaction restriction enzyme-based assays were used to genotype ten point mutations in seven of the BV gene segments. Eight of these polymorphisms altered an amino acid of the BV gene segment. In addition, length polymorphisms due to simple sequence repeats were noted in the introns of six BV6 subfamily members. Approximately 250 unrelated haplotypes were constructed by segregation analyses of fifteen of these TCRBV polymorphisms. Linkage disequilibrium analyses indicated that haplotypic relationships are not detectable over a distance of more than 55 kb in this genomic region. These TCRBV polymorphisms, and the haplotypic analysis, provide important resources and guidance for future attempts to associate Tcr germline DNA differences in the human population with immune response differences, such as might occur in some autoimmune diseases.     

Spatial and temporal population structure of Brevicoryne brassicae

Allozymes from individual aphids were used as markers to examine the structure of Brevicoryne brassicae colonies collected from field experiments at Horticulture Research International, Wellesbourne, during the summers of 1991, 1992 and 1993. Eighteen enzyme systems were examined using cellulose acetate electrophoresis, but only 6-phosphogluconate dehydrogenase (6-PGDH) showed polymorphism (three alleles) in the samples. There were significant differences in gene frequencies between populations at some sites within 1 kilometre and between times of sampling, with an increase in the proportion of the most common genotype AA later in the season, possibly due to selection during the summer of the best adapted clones. These changes in gene frequency might produce biased results in trials screening brassica crops against aphids.     

Spatial and temporal distribution of nanoflagellates in the northern South China Sea

Seasonal variation, horizontal and vertical distribution, and cell size of nanoflagellates, together with physico-chemical and biological factors, were studied in the northern South China Sea (SCS). It was found that nanoflagellate abundance ranged from 0.157 × 10³ to 9.193 × 10³ cells/ml (with a mean of 0.891 × 10³) in winter (February, 2004), while it ranged from 0.107 × 10³ to 5.417 × 10³ cells/ml (with a mean of 0.599 × 10³) in summer (July, 2004). Nanoflagellates were more abundant in winter than summer in offshore regions, showing an unique seasonal pattern in this subtropical marginal sea. The abundance of nanoflagellates decreased from the estuary to the offshore region. Vertical distribution of nanoflagellates coupled well with that of bacteria and Chl a. The small size fraction of less than 5 μm dominated the nanoflagellate populations. Wind-driven mixing, eddies, availability of nutrients as well as Chl a and abundance of picoplankton seemed to be the major controlling factors for the spatial distribution and seasonal variation of nanoflagellates in the study area. Handling editor: P. Tasman     

Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay

The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a transect from the head to the mouth of the Chesapeake Bay during cruises in April and October 2001 and 2002. Standard curves for the quantitative PCR assays demonstrated that the relationship between gene copies and cycle threshold was linear and highly reproducible from 1 to 10(7) gene copies. The maximum number of 907h22 gene copies detected was approximately 140 ml(-1) and the maximum number of 912h4 gene copies detected was approximately 340 ml(-1). Sequence 912h4 was most abundant at the mouth of the Chesapeake Bay, and in general, its abundance increased with increasing salinity, with the highest abundances observed in April 2002. Overall, the 907h22 phylotype was most abundant at the mid-bay station. Additionally, 907h22 was most abundant in the April samples from the mid-bay and mouth of the Chesapeake Bay. Despite the fact that the Chesapeake Bay is rarely nitrogen limited, our results show that individual nitrogen-fixing bacteria have distinct nonrandom spatial and seasonal distributions in the Chesapeake Bay and are either distributed by specific physical processes or adapted to different environmental niches.