基于生物信息学的致病菌特有基因预测及分析

目的:利用生物信息学方法对致病菌特有基因进行大规模预测,同时探讨致病菌特有基因与致病菌毒力之间的关系。方法:构建致病性细菌蛋白质序列数据库和非致病性细菌蛋白质序列数据库,利用同源性比对的方法(BlastP工具)对致病菌特有基因进行预测;同时从文献中提取与致病菌毒力紧密相关的毒力因子,构建具有代表性的毒力因子分析库,对预测的致病菌特有基因进行比较分析。结果:在致病菌780310个基因中,预测了致病菌特有基因79166个,约占致病菌总基因的10.15%;预测的致病菌特有基因包含了构建的毒力因子分析库中的大部分毒力基因。结论:预测的致病菌特有基因与致病菌毒力紧密相关,大大减少了进一步在致病菌基因组中鉴定毒力基因时整个基因组的数据量。     

具有空间自相关残差的回归模型及其应用

提出了具有空间自相关残差的多变量回归问题,这种残差包括单点、局部和区域化三种尺度.文中提出了两种处理空间自相关的方法:把自相关加入残差协方差作参数的改进估计──相邻相关方法和把残差作区域化最优自相关估计──一般空间自相关方法.用森林对舞毒蛾危害敏感性概率的大范围估计为例,比较了传统回归方法和本文方法间的差异,交叉检验结果表明本文的方法明显优于直接回归方法,这说明加入空间自相关对空间回归问题是必要的.     

Severity of Bovine Tuberculosis Is Associated with Co-Infection with Common Pathogens in Wild Boar

Co-infections with parasites or viruses drive tuberculosis dynamics in humans, but little is known about their effects in other non-human hosts. This work aims to investigate the relationship between Mycobacterium bovis infection and other pathogens in wild boar (Sus scrofa), a recognized reservoir of bovine tuberculosis (bTB) in Mediterranean ecosystems. For this purpose, it has been assessed whether contacts with common concomitant pathogens are associated with the development of severe bTB lesions in 165 wild boar from mid-western Spain. The presence of bTB lesions affecting only one anatomic location (cervical lymph nodes), or more severe patterns affecting more than one location (mainly cervical lymph nodes and lungs), was assessed in infected animals. In addition, the existence of contacts with other pathogens such as porcine circovirus type 2 (PCV2), Aujeszky''s disease virus (ADV), swine influenza virus, porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Haemophilus parasuis and Metastrongylus spp, was evaluated by means of serological, microbiological and parasitological techniques. The existence of contacts with a structured community of pathogens in wild boar infected by M. bovis was statistically investigated by null models. Association between this community of pathogens and bTB severity was examined using a Partial Least Squares regression approach. Results showed that adult wild boar infected by M. bovis had contacted with some specific, non-random pathogen combinations. Contact with PCV2, ADV and infection by Metastrongylus spp, was positively correlated to tuberculosis severity. Therefore, measures against these concomitant pathogens such as vaccination or deworming, might be useful in tuberculosis control programmes in the wild boar. However, given the unexpected consequences of altering any community of organisms, further research should evaluate the impact of such measures under controlled conditions. Furthermore, more research including other important pathogens, such as gastro-intestinal nematodes, will be necessary to complete this picture.     

圈养林麝脓肿病病原菌分离鉴定及药敏分析

目的 确定林麝化脓性疾病的主要病原菌,寻找有效的治疗措施(药物).方法 采用3种培养基对28个人工饲养的发病林麝脓灶进行病原菌的分离培养、细菌革兰氏染色、镜检,然后对分离病原菌进行16S rRNA 基因PCR扩增及测序分析鉴定,再进一步用BIOLOG自动微生物鉴定系统对3种可疑菌进行生理生化鉴定,用昆明小鼠分组进行系列病理实验,最后用纸片扩散法测定病原菌对22种抗生素的敏感性.结果 脓灶中共分离到12种细菌,其中化脓隐秘杆菌Arcanobacterium pyogenes、绿脓杆菌Pseudomonas aeruginosa、蜡状芽孢杆菌Bacillus cereus的检出率分别为100.0%、21.4%、14.3%,其他菌的检出率较低.用BIOLOG自动微生物鉴定系统鉴定结果与16S rRNA鉴定结果完全一致;小鼠致病性实验中进行了脓液培养后注射,分离到单菌鉴定后进一步分别注射,剖检后进行接种划线鉴定并得到与注射前相同的病菌,确定了这几种菌均具有较强的致病性;药敏实验最终确定针对化脓隐秘杆菌的有效药物为环丙沙星,对这3种病菌的有效药物为克林霉素、环丙沙星.结论 初步确定林麝脓肿病主要是由于化脓隐秘杆菌原发感染,进而引起其他病菌的继发感染和混合感染,最终导致病重死亡;环丙沙星等为敏感药物.     

Methylation Levels of SLC23A2 and NCOR2 Genes Correlate with Spinal Muscular Atrophy Severity

Spinal muscular atrophy (SMA) is a monogenic neurodegenerative disorder subdivided into four different types. Whole genome methylation analysis revealed 40 CpG sites associated with genes that are significantly differentially methylated between SMA patients and healthy individuals of the same age. To investigate the contribution of methylation changes to SMA severity, we compared the methylation level of found CpG sites, designed as “targets”, as well as the nearest CpG sites in regulatory regions of ARHGAP22, CDK2AP1, CHML, NCOR2, SLC23A2 and RPL9 in three groups of SMA patients. Of notable interest, compared to type I SMA male patients, the methylation level of a target CpG site and one nearby CpG site belonging to the 5’UTR of SLC23A2 were significantly hypomethylated 19–22% in type III-IV patients. In contrast to type I SMA male patients, type III-IV patients demonstrated a 16% decrease in the methylation levels of a target CpG site, belonging to the 5’UTR of NCOR2. To conclude, this study validates the data of our previous study and confirms significant methylation changes in the SLC23A2 and NCOR2 regulatory regions correlates with SMA severity.     

Expression of Lignin Biosynthetic Genes in Wheat during Development and upon Infection by Fungal Pathogens

As a major component of the cell wall, lignin plays an important role in plant development and defense response to pathogens, but negatively impacts biomass processability for biofuels. Silencing the target lignin genes for greater biomass processability should not significantly affect plant development and biomass yield but also must not compromise disease resistance. Here, we report experiments to identify a set of lignin genes that may be silenced without compromising disease resistance. We profiled the expression of 32 lignin biosynthetic candidate genes by qRT-PCR in 17 wheat tissues collected at three developmental stages. Twenty-one genes were expressed at a much higher level in stems compared to sheaths and leaf blades. Expression of seven these genes significantly correlated with lignin content. The co-expression patterns indicated that these 21 genes are under strong developmental regulation and may play a role in lignin biosynthesis. Profiling gene expression of same tissues challenged by two fungal pathogens, Fusarium graminearum and Puccina triticina indicated that expression of 17 genes was induced by F. graminearum. Only PAL1, a non-developmental-regulated gene, was induced by P. triticina. Thus, lignin biosynthetic pathway overlaps defense response to F. graminearum. Based on these criteria, 17 genes, F5H1, F5H2, 4CL2, CCR2, COMT1, and COMT2 in particular that do not overlap with disease resistance pathway, may be the targets for downregulation.     

Factors Associated with Shooting Accuracy and Wounding Rate of Four Managed Wild Deer Species in the UK,Based on Anonymous Field Records from Deer Stalkers

The amount of wounding during routine culling is an important factor in the welfare of wild deer. Little information exists on factors determining shooting accuracy and wounding rates under field conditions in the UK. In this study, 102 anonymous stalkers collected data on the outcomes and circumstances of 2281 shots. Using hot-deck imputation and generalised linear mixed modelling, we related the probability that a shot hit its target, and the probability that the shot killed the deer if it was hit, to 28 variables describing the circumstances of the shot. Overall, 96% of deer were hit, of which 93% were killed outright. A reduced probability of hitting the target was associated with an uncomfortable firing position, too little time available, shooting off elbows or freehand, taking the head or upper neck as point of aim, a heavily obscured target, a distant target, shooting at females, lack of shooting practice and a basic (or no) stalker qualification. An increase in the likelihood of wounding was associated with an uncomfortable firing position, shooting with insufficient time, a distant target (only when time was not sufficient), a bullet weight below 75 grains, a target concealed in thicket or on the move and an area rarely stalked. To maximise stalking success and deer welfare, we recommend that stalkers ensure a comfortable firing position, use a gun rest, aim at the chest, use bullets heavier than 75 grains, avoid taking a rushed shot, shoot a distant animal only if there is plenty of time, fire only when the target is stationary, avoid shooting at an obscured animal, take care when the ground is unfamiliar, and do shooting practice at least once a month. The high miss rate of basic-level stalkers suggests that training should include additional firing practice under realistic shooting conditions.     

一株病原拮抗野生菌株的筛选、鉴定及其发酵工艺优化

为获得广谱抗菌功能野生菌株并提高其发酵产物中抗菌物质的含量。采用管碟法和菌丝生长速率法筛选功能菌株,ITS序列分析鉴定功能菌株,通过响应面法和正交设计优化发酵生产抗菌物质的工艺。筛选到一株强效、广谱抗菌功能菌株,鉴定为Cerrena sp.,其发酵产物对金黄色葡萄球菌、大肠杆菌、白色念珠菌、枯草芽孢杆菌和水稻纹枯病菌有显著拮抗作用。该菌株的摇甁发酵配方及培养条件为：马铃薯13.99 g/L,蔗糖 41.58 g/L,VB1 0.027 g/L,麸皮7 g/L,KH₂PO₄ 2 g/L,MgSO₄·7H₂O 2 g/L;摇床温度28 ℃、发酵周期10 d、种龄4 d、接种量8%、初始pH为5.0、装液量110 ml/250 ml。该菌株有明显抑菌活性,发酵工艺优化后抗菌活性提高了30.37%,为该菌株今后的应用、抗菌剂的分离提纯和产业化提供了实验依据。     

Retransformation of Marker-Free Potato for Enhanced Resistance Against Fungal Pathogens by Pyramiding Chitinase and Wasabi Defensin Genes

Multi-auto-transformation vector system has been one of the strategies to produce marker-free transgenic plants without using selective chemicals and plant growth regulators and thus facilitating transgene stacking. In the study reported here, retransformation was carried out in marker-free transgenic potato CV. May Queen containing ChiC gene (isolated from Streptomyces griseus strain HUT 6037) with wasabi defensin (WD) gene (isolated from Wasabia japonica) to pyramid the two disease resistant genes. Molecular analyses of the developed shoots confirmed the existence of both the genes of interest (ChiC and WD) in transgenic plants. Co-expression of the genes was confirmed by RT-PCR, northern blot, and western blot analyses. Disease resistance assay of in vitro plants showed that the transgenic lines co-expressing both the ChiC and WD genes had higher resistance against the fungal pathogens, Fusarium oxysporum (Fusarium wilt) and Alternaria solani (early blight) compared to the non-transformed control and the transgenic lines expressing either of the ChiC or WD genes. The disease resistance potential of the transgenic plants could be increased by transgene stacking or multiple transformations.     

水稻野生种质优异基因分子标记定位和利用的研究进展

野生稻由于长期处于野生状态,经受了各种灾害和不良环境的自然选择,抗逆性较强,是天然的基因库,保存着栽培稻不具有或已经消失了的特异基因。挖掘野生稻特异基因的研究日益受到重视。本文总结了近3年来在野生稻特异性状基因定位、克隆和育种利用方面的研究进展。 Abstract:Wild rice has adapted to weather and unfavorable environments under natural selection.It has been well recognized as a natural gene bank that conserves a lot of specific genes presently not available for extinct in the cultivated rice.There is an urgent need to explore these specific genes.The present paper summarized current researches in molecular mapping and cloning of useful genes from wild rice,and their potential application in breeding.     

不同年龄麇鹿角的脱落时间与形态特征比较

鹿角是大部分鹿科动物的第二性征.麋鹿仅雄性具角,且角枝向后分杈,呈多回分支状,形态特征与其他鹿科动物不同.针对麋鹿的脱落时间、角型特征、外部形态与年龄关系等问题,2008年12月～2009年3月在北京麋鹿苑对麋鹿角进行了标记、收集与测量.结果 表明:解角期持续时间长短与种群年龄结构有关;麋鹿角的重量、角基周长、主干长度、后枝长和角宽5个变量与年龄显著线性相关,其中重量和角基周长与年龄的相关性最显著.麋鹿角并不完全是每增加1岁就增加1个分枝,依据鹿角分枝数只能对年龄进行大致判断.     

Correlation of TBE Incidence with Red Deer and Roe Deer Abundance in Slovenia

Tick-borne encephalitis (TBE) is a virus infection which sometimes causes human disease. The TBE virus is found in ticks and certain vertebrate tick hosts in restricted endemic localities termed TBE foci. The formation of natural foci is a combination of several factors: the vectors, a suitable and numerous enough number of hosts and in a habitat with suitable vegetation and climate. The present study investigated the influence of deer on the incidence of tick-borne encephalitis. We were able to obtain data from deer culls. Using this data, the abundance of deer was estimated and temporal and spatial analysis was performed. The abundance of deer has increased in the past decades, as well as the incidence of tick-borne encephalitis. Temporal analysis confirmed a correlation between red deer abundance and tick-borne encephalitis occurrence. Additionally, spatial analysis established, that in areas with high incidence of tick-borne encephalitis red deer density is higher, compared to areas with no or few human cases of tick-borne encephalitis. However, such correlation could not be confirmed between roe deer density and the incidence of tick-borne encephalitis. This is presumably due to roe deer density being above a certain threshold so that availability of tick reproduction hosts has no apparent effect on ticks'' host finding and consequently may not be possible to correlate with incidence of human TBE.     

Ascidian and Amphioxus Adh Genes Correlate Functional and Molecular Features of the ADH Family Expansion During Vertebrate Evolution

The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolutionary analysis of the family was performed gathering data from protein and gene structures, exon–intron distribution, and functional features through chordate lines. Our data strongly support that the ADH family expansion occurred 500 million years ago, after the cephalochordate/vertebrate split, probably in the gnathostome subphylum line of the vertebrates. Evolutionary rates differ between the ancestral, ADH3 (glutathione-dependent formaldehyde dehydrogenase), and the emerging forms, including the classical alcohol dehydrogenase, ADH1, which has an evolutionary rate 3.6-fold that of the ADH3 form. Phylogenetic analysis and chromosomal mapping of the vertebrate Adh gene cluster suggest that family expansion took place by tandem duplications, probably concurrent with the extensive isoform burst observed before the fish/tetrapode split, rather than through the large-scale genome duplications also postulated in early vertebrate evolution. The absence of multifunctionality in lower chordate ADHs and the structures compared argue in favor of the acquisition of new functions in vertebrate ADH classes. Finally, comparison between B. floridae and B. lanceolatum Adhs provides the first estimate for a cephalochordate speciation, 190 million years ago, probably concomitant with the beginning of the drifting of major land masses from the Pangea. Received: 10 April 2001 / Accepted: 23 May 2001     

天津八仙山国家级自然保护区野生狍集群模式和时空活动规律

2017年6月—2019年3月,以天津八仙山国家级自然保护区为研究地点,首次应用红外相机技术综合关注野生狍Capreolus pygargus的集群模式和时空活动规律.结果发现,狍表现出5种集群模式,以单雄和单雌模式为主;各种集群模式的出现频次呈显著的季节差异(χ2=10.867,df=3,P=0.012)、温度区段差...     

Fecal Shedding of Zoonotic Food-Borne Pathogens by Wild Rodents in a Major Agricultural Region of the Central California Coast

Recent outbreaks of food-borne illness associated with the consumption of produce have increased concern over wildlife reservoirs of food-borne pathogens. Wild rodents are ubiquitous, and those living close to agricultural farms may pose a food safety risk should they shed zoonotic microorganisms in their feces near or on agricultural commodities. Fecal samples from wild rodents trapped on 13 agricultural farms (9 produce, 3 cow-calf operations, and 1 beef cattle feedlot) in Monterey and San Benito Counties, CA, were screened to determine the prevalence and risk factors for shedding of several food-borne pathogens. Deer mice (Peromyscus maniculatus) were the most abundant rodent species trapped (72.5%). Cryptosporidium species (26.0%) and Giardia species (24.2%) were the predominant isolates from rodent feces, followed by Salmonella enterica serovars (2.9%) and Escherichia coli O157:H7 (0.2%). Rodent trap success was significantly associated with detection of Salmonella in rodent feces, while farm type was associated with fecal shedding of Cryptosporidium and Giardia. Seasonal shedding patterns were evident, with rodents trapped during the spring and summer months being significantly less likely to be shedding Cryptosporidium oocysts than those trapped during autumn. Higher rodent species diversity tended to correlate with lower fecal microbial prevalence, and most spatiotemporal pathogen clusters involved deer mice. Rodents in the study area posed a minimal risk as environmental reservoirs of E. coli O157:H7, but they may play a role in environmental dissemination of Salmonella and protozoa. Rodent control efforts that potentially reduce biodiversity may increase pathogen shedding, possibly through promotion of intraspecific microbial transmission.     

Distribution of Indigenous Bacterial Pathogens and Potential Pathogens Associated with Roof-Harvested Rainwater

The harvesting of rainwater is gaining acceptance among many governmental authorities in countries such as Australia, Germany, and South Africa, among others. However, conflicting reports on the microbial quality of harvested rainwater have been published. To monitor the presence of potential pathogenic bacteria during high-rainfall periods, rainwater from 29 rainwater tanks was sampled on four occasions (during June and August 2012) in a sustainable housing project in Kleinmond, South Africa. This resulted in the collection of 116 harvested rainwater samples in total throughout the sampling period. The identities of the dominant, indigenous, presumptive pathogenic isolates obtained from the rainwater samples throughout the sampling period were confirmed through universal 16S rRNA PCR, and the results revealed that Pseudomonas (19% of samples) was the dominant genus isolated, followed by Aeromonas (16%), Klebsiella (11%), and Enterobacter (9%). PCR assays employing genus-specific primers also confirmed the presence of Aeromonas spp. (16%), Klebsiella spp. (47%), Legionella spp. (73%), Pseudomonas spp. (13%), Salmonella spp. (6%), Shigella spp. (27%), and Yersinia spp. (28%) in the harvested rainwater samples. In addition, on one sampling occasion, Giardia spp. were detected in 25% of the eight tank water samples analyzed. This study highlights the diverse array of pathogenic bacteria that persist in harvested rainwater during high-rainfall periods. The consumption of untreated harvested rainwater could thus pose a potential significant health threat to consumers, especially children and immunocompromised individuals, and it is recommended that harvested rainwater be treated for safe usage as an alternative water source.