Genome size of termites (Insecta, Dictyoptera, Isoptera) and wood roaches (Insecta, Dictyoptera, Cryptocercidae)

The evolution of genome size has been discussed in relation to the evolution of various biological traits. In the present study, the genome sizes of 22 dictyopteran species were estimated by Feulgen image analysis densitometry and 6-diamidino-2-phenylindole (DAPI)-based flow cytometry. The haploid genome sizes (C-values) of termites (Isoptera) ranged from 0.58 to 1.90 pg, and those of Cryptocercus wood roaches (Cryptocercidae) were 1.16 to 1.32 pg. Compared to known values of other cockroaches (Blattaria) and mantids (Mantodea), these values are low. A relatively small genome size appears to be a (syn)apomorphy of Isoptera + Cryptocercus, together with their sociality. In some phylogenetic groups, genome size evolution is thought to be influenced by selective pressure on a particular trait, such as cell size or rate of development. The present results raise the possibility that genome size is influenced by selective pressures on traits associated with the evolution of sociality.     

The Impact of Winter Relocation and Depuration on Norovirus Concentrations in Pacific Oysters Harvested from a Commercial Production Site

Oysters contaminated with norovirus present a significant public health risk when consumed raw. In this study, norovirus genome copy concentrations were determined in Pacific oysters (Magallana gigas) harvested from a sewage-impacted production site and then subjected to site-specific management procedures. These procedures consisted of relocation of oysters to an alternative production area during the norovirus high-risk winter periods (November to March) followed by an extended depuration (self-purification) under controlled temperature conditions. Significant differences in norovirus RNA concentrations were demonstrated at each point in the management process. Thirty-one percent of oyster samples from the main harvest area (Site 1) contained norovirus concentrations >?500 genome copies/g and 29% contained norovirus concentrations <?100 genome copies/g. By contrast, no oyster sample from the alternative harvest area (Site 2) or following depuration contained norovirus concentrations >?500 genome copies/g. In addition, 60 and 88% of oysters samples contained norovirus concentrations <?100 genome copies/g in oysters sampled from Site 2 and following depuration, respectively. These data demonstrate that site-specific management processes, supported by norovirus monitoring, can be an effective strategy to reduce, but not eliminate, consumer exposure to norovirus genome copies.     

生物陶粒与生物活性炭上微生物群落结构的PCR-SSCP技术解析

采用PCR-SSCP(单链构象多态性)技术,以16S rRNA基因的V4-V5区为靶对象,分析用于饮用水处理的生物陶粒和生物活性炭上的微生物群落结构.对生物陶粒和生物活性炭上的微生物分别进行超声波洗脱、R2A和LB平板培养后提取基因组DNA.结果表明,除生物活性炭超声波洗脱不能提取到DNA外,其他处理均能提取到大小在10 kb以上的基因组DNA,但所提取的量有较大差异.以提取的DNA为模板分别进行PCR,均能扩增到408 bp的基因片段.这些片段经λ核酸外切酶消化处理后进行SSCP电泳.结果显示,超声波洗脱、R2A和LB培养对试验结果影响不明显.生物陶粒的微生物基因扩增片段SSCP图谱相同,且只出现1条带.测序后与基因组数据库对比,结果显示其与uncultured Pseudomonas sp. clone FTL201 16S rDNA （GenBank登录号AF509293.1）片段同源性为92%.生物活性炭的微生物基因扩增片段SSCP图谱也相同,但有2条带.测序对比的结果表明, 这2个基因片段与Bacillus sp. JH19 16S rDNA （GenBank 登录号DQ232748.1）片段和Bacterium VA-S-11 16S rDNA （GenBank登录号AY395279.1）片段的同源性分别为100%和99%.     

斑马鱼基因组随机扩增DNA多态性研究

采用随机扩增DNA多态性（RAPD）技术，对毒性试验的模式生物斑马鱼（Danio rerio）基因组进行了分析。结果显示，在Amersham Pharmacia公司随机扩增引物系列中，分别在01号引物的829bp、534bp，02号引物的572bp，及06号引物的495pb，各出现1条稳定条带，而环磷酰胺作用后的斑马鱼基因组DAN随机扩增产物中，缺少了部分稳定条带。这可以明确判定受试斑马鱼的基因发生了改变，为水环境遗传毒性效尖的研究提供了初步的数据基础。     

Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress

Polycyclic aromatic hydrocarbons(PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome’s functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size w...     

Antimony transformation and mobilization from stibnite by an antimonite oxidizing bacterium Bosea sp. AS-1

Soils and waters are heavily contaminated by antimony in Xikuangshan（XKS） mine area.It is widely accepted that oxidative dissolution of sulfide minerals and aqueous dissolution are the most prevalent geochemical mechanisms for the release of Sb to the environment.Bosea sp. AS-1 is an antimonite-oxidizer isolated from the mine slag in Xikuangshan Sb mine. Whole genome sequencing revealed the presence of multiple sulfur-oxidizing genes,antimony（Sb） metabolism genes and carbon fixation genes in AS-...     

The Presence of Norovirus and Adenovirus on Environmental Surfaces in Relation to the Hygienic Level in Food Service Operations Associated with a Suspected Gastroenteritis Outbreak

Norovirus (NoV) gastroenteritis outbreaks appear frequently in food service operations (FSOs), such as in restaurants and canteens. In this study the presence of NoV and adenovirus (AdV) genomes was investigated on the surfaces of premises, especially in kitchens, of 30 FSOs where foodborne gastroenteritis outbreaks were suspected. The objective was to establish a possible association between the presence of virus genomes on surfaces and a visual hygienic status of the FSOs. NoV genome was found in 11 and AdV genome in 8 out of 30 FSOs. In total, 291 swabs were taken, of which 8.9% contained NoV and 5.8% AdV genome. The presence of NoV genomes on the surfaces was not found to associate with lower hygiene level of the premises when based on visual inspection; most (7/9) of the FSOs with NoV contamination on surfaces and a completed evaluation form had a good hygiene level (the best category). Restaurants had a significantly lower proportion of NoV-positive swabs compared to other FSOs (canteens, cafeteria, schools etc.) taken together (p = 0.00014). The presence of a designated break room for the workers was found to be significantly more common in AdV-negative kitchens (p = 0.046). Our findings suggest that swabbing is necessary for revealing viral contamination of surfaces and emphasis of hygiene inspections should be on the food handling procedures, and the education of food workers on virus transmission.     

Molecular Characterization of a Complete Genome and 12 Nsp2 Genes of PRRSV of Southwestern China

One genome and 12 Nsp2 genes of porcine reproductive and respiratory syndrome virus (PRRSV), isolated from southwestern China during 2009?C2010, were sequenced and analyzed. The whole genome comparison analysis revealed that SCwhn09CD is a North American-type PRRSV with separate 30aa deletion in Nsp2 gene, and its sequence highly identical to highly pathogenic PRRSV (HP-PRRSV) outbreak in 2006 in almost half area of China. However, an extra 7aa deletion was detected in its Nsp2 coding region. Based on the phylogenetic analysis of Nsp2 gene, all the 12 viruses were grouped into North American-type PRRSV, but two in classical-PRRSV (C-PRRSV) subcluster without typical 30aa deletion and ten in HP-PRRSV subcluster with the signature deletion. In addition, many nucleotide substitutions were found in all 12 Nsp2 genes and extra three novel deletions were identified in three out of ten HP-PRRSV. Combining the above data, it may be concluded that: (1) HP-PRRSV and C-PRRSV co-existed in the local pig farms and the majority of the viruses is HR-PRRSV, and (2) the HR-PRRSV continues to undergo its genomic divergence although it does not outbreak in large-scale in recent years. Therefore, continuous surveillance on PRRSV is necessary for the controlling of the virus in this region.     

Miniaturization,genome size and the origin of functional constraints in the visual system of salamanders

During their evolution, many species of lungless salamanders (fam. Plethodontidae) have experienced a great increase in genome size and consequently in the size of their cells, including sensory receptors and neurons. In addition, some have become extremely miniaturized. The consequences of these events and the morphological compensatory processes are studied in the visual system of juvenile and adult salamanders.     

Virus Genome Quantification Does not Predict Norovirus Infectivity After Application of Food Inactivation Processing Technologies

When determining the effect of food processing on the infectivity of any contaminating virus, it is necessary to distinguish unambiguously between infectious and non-infectious viruses present. However, this can be difficult in the particular case of noroviruses (NoVs) because no reliable cell culture model is available. The aim of this study was to assess the use of molecular methods—RT real-time PCR (RT-qPCR) and enzymatic treatment (ET) coupled to RT-qPCR—to quantify the infectivity of NoV after application of various inactivating food-processing technologies. RT-qPCR and ET-RT-qPCR gave significantly different (P < 0.01) results concerning the reduction in viral genome counts by all inactivation procedures and conditions used, except for HHP treatment at 600 MPa for 5 min. These findings indicate that the ET prior to RT-qPCR has an effect on the estimation of the reduction of virus genome counts, and may eliminate genomes of affected virus particles. However, no correlation was found between the results obtained by ET-RT-qPCR and those obtained by cell culture. Therefore, the effect is presumably only partial, and not adequate to allow accurate estimation of virus inactivation. Consequently, our results indicate that the quantification of virus genomes by PCR, regardless of prior ET, is not adequate for establishing virus inactivation and/or infectivity. In addition, our results also illustrate that the general effect of virus inactivation is not directly correlated to effects on the integrity of virus genome and protein capsid. Presumably, inactivation by food processing is the consequence of effects on proteins involved in adhesion and invasion stages.     

Promises,pitfalls and practicalities of prenatal whole exome sequencing

Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd.     

紫外线消毒中的光复活作用

近年来,紫外线消毒技术在水处理中得到了越来越广泛的应用,它主要是利用短波紫外对微生物的伤害作用,通过在DNA中形成环丁烷嘧啶二聚体,阻碍基因的正常复制,从而导致细菌失活.但是细菌体内的光裂解酶在远紫外光和可见光作用下能够使失活的细菌重新获得活性,这就是光复活作用.低压消毒设备处理后大肠杆菌表现出了一定的光复活能力,但中压消毒设备能够有效的抑制其光复活作用;而噬肺军团菌在低压和中压设备处理后都表现出了很强的光复活能力.在应用紫外线消毒技术时光复活作用的影响不容忽视.     

Drake’s rule as a consequence of approaching channel capacity

How mutations accumulate in genomes is the central question of molecular evolution theories. However, our understanding of this process is far from complete. Drake’s rule is a notoriously universal property of genomes from microbes to mammals—the number of (functional) mutations per-genome per-generation is approximately constant within a phylum, despite the orders of magnitude differences in genome sizes and diverse populations’ properties. So far, there is no concise explanation for this phenomenon. A formal model for the storage of genetic information suggests that a genome of any species operates near its maximum informational storage capacity, and the mutation rate per-genome per-generation is near its upper limit, providing a simple explanation for the rule with minimal assumptions.     

Phylogenetically clustering of rhizobia by genome structure: application to unclassified Rhizobium

Introduction The rhizobia can change nitrogen in the air into ammonia and provide nitrogenous nutrition to the plant. This will make us independent from the use of nitrogenous fertilizers so as to minimize pollution of water tables, lakes and rivers and r…     

Qualitative and Quantitative Assessment of Hepatitis A Virus in Wastewaters in Tunisia

Hepatitis A causes substantial morbidity in both industrialized and non-industrialized countries and represents an important health problem in several southern Mediterranean countries. The objectives of the study were as follows: (a) to assess the occurrence of hepatitis A virus (HAV) in Tunisia through the monitoring of urban wastewaters collected at wastewater treatment plants (WTPs); (b) to characterize environmental strains; and (c) to estimate the viral load in raw and treated sewages, in order to evaluate the potential impact on superficial waters receiving discharges. A total of 150 raw and treated wastewaters were collected from three WTPs and analyzed by both qualitative (RT-PCR/nested) and quantitative (qRT-PCR) methods. Of these, 100 (66 %) were found to be positive for HAV by the qualitative assay: 68.3 % in influents and 64.7 % in effluents. The vast majority of HAV sequences belonged to sub-genotype IA, with 11 different strains detected found to be identical to clinical strains isolated from Tunisian patients with acute hepatitis. Five unique variants were also detected, not previously reported in clinical cases. Only two IB strains were found, confirming the rarity of this sub-genotype in this country. The results of the present study indicate a wide circulation of the pathogen in the population, most probably in the form of asymptomatic infections, a finding consistent with the classification of the country as having intermediate/high endemicity. Quantitative data showed high viral loads in influents (3.5E+05 genome copies/liter, mean value) as well as effluents (2.5E+05 genome copies/liter, mean value), suggesting that contaminated water could be a critical element in transmission.     

Coxsackievirus B4 as a Causative Agent of Diabetes Mellitus Type 1: Is There a Role of Inefficiently Treated Drinking Water and Sewage in Virus Spreading?

This study proposed to detect the enterovirus (EV) infection in children with type 1 diabetes mellitus (T1D) and to assess the role of insufficiently treated water and sewage as sources of viral spreading. Three hundred and eighty-two serum specimens of children with T1D, one hundred serum specimens of children who did not suffer from T1D as control, and forty-eight water and sewage samples were screened for EV RNA using nested RT-PCR. The number of genome copies and infectious units of EVs in raw and treated sewage and water samples were investigated using real-time (RT)-PCR and plaque assay, respectively. T1D markers [Fasting blood glucose (FBG), HbA1c, and C-peptide], in addition to anti-Coxsackie A & B viruses (CVs A & B) IgG, were measured in control, T1D-negative EV (T1D–EV^?), and T1D-positive EV (T1D–EV⁺) children specimens. The prevalence of EV genome was significantly higher in diabetic children (26.2%, 100 out of 382) than the control children (0%, 0 out of 100). FBG and HbA1c in T1D–EV^? and T1D–EV⁺ children specimens were significantly higher than those in the control group, while c-peptide in T1D–EV^? and T1D–EV⁺ children specimens was significantly lower than that in the control (n = 100; p < 0.001). Positivity of anti-CVs A & B IgG was 70.7, 6.7, and 22.9% in T1D–EV⁺, T1D–EV^?, and control children specimens, respectively. The prevalence of EV genome in drinking water and treated sewage samples was 25 and 33.3%, respectively. The prevalence of EV infectious units in drinking water and treated sewage samples was 8.5 and 25%, respectively. Quantification assays were performed to assess the capabilities of both wastewater treatment plants (WWTPs) and water treatment plants (WTPs) to remove EV. The reduction of EV genome in Zenin WWTP ranged from 2 to 4 log₁₀, while the reduction of EV infectious units ranged from 1 to 4 log₁₀. The reduction of EV genome in El-Giza WTP ranged from 1 to 3 log₁₀, while the reduction of EV infectious units ranged from 1 to 2 log₁₀. This capability of reduction did not prevent the appearance of infectious EV in treated sewage and drinking water. Plaque purification was performed for isolation of separate EV isolates from treated and untreated water and sewage samples. Characterization of the EV amplicons by RT-PCR followed by sequencing of these isolates revealed high homology (97%) with human coxsackievirus B4 (CV B4) in 60% of the isolates, while the rest of the isolates belonged to poliovirus type 1 and type 2 vaccine strains. On the other hand, characterization of the EV amplicons by RT-PCR followed by sequencing for T1D–EV⁺ children specimens indicated that all samples contained CV B4 with the same sequence characterized in the environmental samples. CV B4-contaminated drinking water or treated sewage may play a role as a causative agent of T1D in children.     

暴露组及其研究方法进展

过去20年中,基因组学的研究成果未能对疾病发生原因提供本质的认识,人们较早意识到环境因素对于人体健康的重要性.早期对于人体暴露的研究主要集中在内外暴露的研究,未综合考虑人体总的环境暴露.自暴露组(exposome)概念提出以来,得到了广泛关注,也使暴露科学的内涵和外延得到了延伸.暴露组是指一个人从出生至生命结束全过程各种暴露的总和,真正意义上探讨污染暴露、人体健康和疾病发生的实在本质,包括了外暴露、内暴露和社会暴露.研究方法上结合了基于生物监测的"自上向下"法和基于监测空气、水和食物等"自下向上"法,而在研究手段上涉及了环境科学的外暴露和基因组学的分子生物学等中广泛应用的研究技术.然而当前准确测量暴露组仍然是一个巨大的挑战,只有多学科技术手段和研究方法发展和融合才能更好地促进暴露组研究的进步.我国暴露科学研究起步较晚,目前学者对于暴露组的研究仍然薄弱,本文主要从暴露组的概念、研究方法以及测量技术手段入手,介绍这一新兴的研究科学.