单细胞RNA测序技术在病毒研究中的应用

单细胞RNA测序(single-cell RNA sequencing, scRNA-seq)技术已经成为不同领域中研究细胞异质性的有效工具。在病毒研究领域中,利用该技术分析病毒和细胞的转录组,可以在单细胞水平上检测病毒感染的动态变化,了解病毒与细胞间复杂的相互作用。本文简述了scRNA-seq技术,着重介绍病毒感染宿主细胞后scRNA-seq研究的最新进展,同时也描述了细胞周期、基因表达、细胞状态等细胞异质性对病毒感染过程的影响,以及病毒变异对其本身感染过程的影响。此外,本文还分析了scRNA-seq在研究病毒–宿主互作动态变化方面具有的独特优势,及其在病毒研究领域中广阔的应用前景,为揭示病毒的感染与致病机制、抗病毒靶标的开发等提供参考。     

Spatial covariation of fish population vital rates in a stream network

Animal populations are spatially structured in heterogeneous landscapes, in which local patches with differing vital rates are connected by dispersal of individuals to varying degrees. Although there is evidence that vital rates differ among local populations, much less is understood about how vital rates covary among local patches in spatially heterogeneous landscapes. In this study, we conducted a nine-year annual mark–recapture survey to characterize spatial covariation of survival and growth for two Japanese native salmonids, white-spotted charr Salvelinus leucomaenis japonicus and red-spotted masu salmon Oncorhynchus masou ishikawae, in a headwater stream network composed of distinctly different tributary and mainstem habitats. Spatial structure of survival and growth differed by species and age class, but results provided support for negative covariation between vital rates, where survival was higher in the tributary habitat but growth was higher in the mainstem habitat. Thus, neither habitat was apparently more important than the other, and local habitats with complementary vital rates may make this spatially structured population less vulnerable to environmental change (i.e. portfolio effect). Despite the spatial structure of vital rates and possibilities that fish can exploit spatially distributed resources, movement of fish was limited due partly to a series of low-head dams that prevented upstream movement of fish in the study area. This study shows that spatial structure of vital rates can be complex and depend on species and age class, and this knowledge is likely paramount to elucidating dynamics of spatially structured populations.     

Joint analysis of single-cell and bulk tissue sequencing data to infer intratumor heterogeneity

Many computational methods have been developed to discern intratumor heterogeneity (ITH) using DNA sequence data from bulk tumor samples. These methods share an assumption that two mutations arise from the same subclone if they have similar mutant allele-frequencies (MAFs), and thus it is difficult or impossible to distinguish two subclones with similar MAFs. Single-cell DNA sequencing (scDNA-seq) data can be very informative for ITH inference. However, due to the difficulty of DNA amplification, scDNA-seq data are often very noisy. A promising new study design is to collect both bulk and single-cell DNA-seq data and jointly analyze them to mitigate the limitations of each data type. To address the analytic challenges of this new study design, we propose a computational method named BaSiC (B ulk tumor a nd Si ngle C ell), to discern ITH by jointly analyzing DNA-seq data from bulk tumor and single cells. We demonstrate that BaSiC has comparable or better performance than the methods using either data type. We further evaluate BaSiC using bulk tumor and single-cell DNA-seq data from a breast cancer patient and several leukemia patients.     

Heterogeneous diffusion in aerobic granular sludge

Aerobic granular sludge (AGS) technology allows simultaneous nitrogen, phosphorus, and carbon removal in compact wastewater treatment processes. To operate, design, and model AGS reactors, it is essential to properly understand the diffusive transport within the granules. In this study, diffusive mass transfer within full-scale and lab-scale AGS was characterized with nuclear magnetic resonance (NMR) methods. Self-diffusion coefficients of water inside the granules were determined with pulsed-field gradient NMR, while the granule structure was visualized with NMR imaging. A reaction-diffusion granule-scale model was set up to evaluate the impact of heterogeneous diffusion on granule performance. The self-diffusion coefficient of water in AGS was ∼70% of the self-diffusion coefficient of free water. There was no significant difference between self-diffusion in AGS from full-scale treatment plants and from lab-scale reactors. The results of the model showed that diffusional heterogeneity did not lead to a major change of flux into the granule (<1%). This study shows that differences between granular sludges and heterogeneity within granules have little impact on the kinetic properties of AGS. Thus, a relatively simple approach is sufficient to describe mass transport by diffusion into the granules.     

锡林河流域不同植被带土壤绿菌门微生物群落的空间分布特征

[目的] 为了探究锡林河流域中游不同植被带土壤绿菌门（Chlorobi）成员的空间分布特征及驱动因子。[方法] 本文选择典型河滨带环境为研究对象,沿河流中心至河流阶地（陆向）方向,在无植被带（BC）、水莎草沼泽（BS）、灯芯草沼泽化草甸（LF）、鹅绒委陵菜草甸（HF）、河流阶地羊草草原（LT）、丘陵坡地大针茅典型草原（HT）中分别采集0-10 cm土壤样品。基于16S rRNA基因高通量测序分析土壤绿菌门微生物群落的组成、丰度及空间分布特征;结合土壤理化因子分析绿菌门微生物群落空间异质性的驱动因子。[结果] 在属水平上共检测到来自绿菌目（Chlorobiales）和Ignavibacteriales目的9个类群。Chlorobiales1、2、6及Ignavibacteriales7、9类群的最高相对丰度低于0.40%;Ignavibacteriales3、4、5、8类群的最高相对丰度介于0.54%-1.06%。Chlorobiales1、2类群在HF、LT和HT的相对丰度显著高于BS（P<0.05）,Chlorobiales1类群的相对丰度与pH和总有机碳含量呈极显著正相关（P<0.01）;Chlorobiales2类群的相对丰度与粉黏粒含量呈极显著正相关（P<0.01）;Ignavibacteriales3、5、7、9和Ignavibacterium4类群在LF的相对丰度显著高于BC（P<0.05）,与含水量呈极显著正相关（P<0.01）;Chlorobiales6和Ignavibacteriales8类群在BS的相对丰度显著高于其他植被带（P<0.05）,与氨态氮含量呈极显著正相关（P<0.01）。变异权重分析表明,土壤含水量解释了绿菌门微生物群落空间变异的65.7%。[结论] 锡林河流域不同植被带土壤绿菌门微生物群落存在明显的空间异质性;土壤含水量是不同植被带绿菌门微生物群落空间异质性的主要驱动因子。     

The hMLH1 promoter polymorphisms and cancer susceptibility in Asian populations: A meta-analysis

Background

A variety of studies have evaluated the associations between polymorphisms in the promoter regions of the hMLH1 and cancer risk. However, the results remain inconclusive. To better understand the roles of the hMLH1 polymorphisms and cancer risk, we conducted a comprehensive meta-analysis to investigate the association between the hMLH1 − 93G/A and 1151T/A (Val384Asp) polymorphisms and cancer risk in Asian population.

Methods

We performed a meta-analysis by conducting searches of the published studies in Pub Med, CNKI, CBM, ISI web of knowledge and Google scholar search databases. Finally, 12 studies were included into our meta-analysis. Overall and subgroup analyses were performed. Odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the associations between hMLH1 polymorphisms and cancer risk. Statistical analysis was performed with Review Manager 5.0.

Results

Twelve studies addressing two hMLH1 polymorphisms were analyzed among a total of 4128 cancer cases and 4678 controls. For hMLH1 − 93G/A, there was no evidence that the hMLH1 − 93G/A polymorphism was significantly associated with an increased cancer risk (P > 0.05) in Asian populations (heterozygote comparison: OR = 0.89 [95% CI (0.75, 1.060)] P = 0.20; dominant model comparison: OR = 0.98 [95% CI (0.83, 1.15)] P = 0.79). In subgroup analysis based on cancer types and the sources of control, no associations were found in colorectal cancer, gastric cancer and “other cancers” under the any gene model except for lung cancer (recessive model comparison: OR = 1.69 [95% CI (1.30, 2.19)] P < 0.0001). For hMLH1 1151T/A, the polymorphism significantly associated with an increased cancer risk in Asians: OR = 1.88 [95% CI (1.49, 2.25)], P < 0.0001, and OR = 1.87 [95% CI (1.49, 2.25)], P < 0.0001.

Conclusions

Our investigations demonstrated that the hMLH1 − 93G/A polymorphism is not a candidate for susceptibility to overall cancers, and that the hMLH1 1151T/A polymorphism is significantly associated with higher cancer risk in Asian populations. Further studies with large sample size for hMLH1 should be conducted.     

TAXONOMIC STATUS OF

Association of Cattle Egrets Bubulcus ibis with large herbivores is well documented, but there are few records of their association with large birds. Here we describe the first-known records of foraging interactions between Shoebill Balaeniceps rex and Cattle Egrets. The observations were made at the Malagarasi-Muyovozi Ramsar Site in western Tanzania. Small flocks of egrets approached and foraged within 5 m of a Shoebill, which was sometimes forced to move from its hunting pool and by doing so it likely flushed more prey for egrets. Interactions occurred almost exclusively in the driest months, which suggested that prey were more difficult to locate by egrets during this period. The Shoebill inhabits inaccessible swamps and is a rare species with low density throughout its range. It is therefore possible that egret–Shoebill associations, in addition to being infrequent and highly seasonal, may have gone unnoticed.     

SHORT NOTES

Hockey, P.A.R., Plagényi, É.E., Turpie, J.K. &; Phillips, T.E. 1996. Foraging behaviour of Crab Plovers Dromas ardeola at Mida Creek, Kenya. Ostrich 67:33-44.

The foraging behaviour of Crab Plovers is directly analogous to the ‘walk-stop-search-walk’ hunting behaviour of true plovers, and changes slightly depending whether the birds are foraging on sand or in water: they are nonterritorial when foraging. Crabs dominate the diet, but other invertebrates and fish are also eaten. Foraging efficiency increases with age and adults and subadults are able to satisfy their daily energy requirements in a single tidal cycle. The population of Crab Plovers at Mida Creek was much larger in 1994 than in 1992, but in 1994 adults achieved much higher intake rates than in 1992, suggesting considerable year-to-year variation in the carrying capacity of Mida Creek for Crab Plovers. The world population of 43–50 000 birds breeds at very few colonies and the species is thus a potential conservation concern. Because of the relative accessibility of large concentrations of Crab Plovers away from the breeding grounds, we suggest that a programme to monitor numbers and population demography should be targeted at nonbreeding aggregations.     

Beaver dams maintain fish biodiversity by increasing habitat heterogeneity throughout a low‐gradient stream network

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High assemblage persistence in heterogeneous habitats: an experimental test with stream benthic algae

1. The persistence of biological assemblages is positively affected by spatial heterogeneity. This influence may be indirect, through increased species richness. Another possibility is the increased availability of refuges from disturbances, which would prevent local loss. 2. We conducted a field experiment to test the hypothesis that greater roughness (a form of spatial heterogeneity) on the surface of substrata allows higher persistence of assemblages of stream benthic algae and that this relationship does not depend on species richness. Samples were taken on six occasions from smooth and rough artificial substrata used for algal colonisation. We calculated the persistence of assemblages using two analytical approaches: the mean distance to group centroid and the sum of the Euclidean distances between consecutive sampling occasions, both in a multivariate space. We also subsampled the data to take into account differences in species richness between treatments and thus to evaluate the effect of species richness on persistence. 3. Assemblages on rough substrata were more persistent than assemblages on smooth substrata. The effects detected were not due to the greater species richness on rough substrata, since a higher persistence of the assemblages on rough substrata remained after the subsampling procedures. 4. Our results indicate a strong positive relationship between substratum roughness and the persistence of stream benthic algal assemblages. We suggest that this is due to the presence of physical refuges in heterogeneous habitats.