Nesting of the Chinese Bush Warbler (Tribura tacsanowskia,Sylviidae, Passeriforms) in the Amur Region

Biology Bulletin - A nest of the Chinese bush warbler (Tribura tacsanowskia) has been found and monitored in the Amur region for the first time. This is a poorly studied species distributed in...     

三参数增长模型拟合:以季风常绿阔叶林中两个优势乔木种群为例

Logistic、Mitscherlich、Gompertz方程是一类三参数饱和增长曲线模型,广泛地应用于许多学科领域．本文基于logistic方程饱和值K估计的三点法、四点法,推导出Mitscherlich、Gompertz方程K值的三点法、四点法估计公式,并以南亚热带季风常绿阔叶林中两种优势乔木厚壳桂、黄果厚壳桂种群为例,先用三点法或四点法估计出K值,再通过线性回归与非线性回归相结合的方法,可获得三个增长模型中三个参数的最优无偏估计．实例研究表明,两个优势种群增长数据均符合三个增长模型,但更符合增长曲线呈S形的logistic、Gompertz方程,且以logistic方程最适合于观察;黄果厚壳桂种群增长快于厚壳桂种群．     

AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals

Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program, AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space. Individuals are depicted as length-fixed bars partitioned into colored segments representing different ancestries, and the population of interest can be highlighted as a pie chart in the center of the circle plot. In addition, AncestryPainter can also be applied to display personal ancestry in a way similar to that for displaying population ancestry. AncestryPainter is publicly available at http://www.picb.ac.cn/PGG/resource.php.     

广西鸟类一新纪录——白眶鹟莺

2006年12月,在广西西南部靖西县底定自然保护区考察时,采到一号雀形目鸟类标本,经鉴定为白眶鹟莺(Seicercus affinis),是广西鸟类新纪录。从2005年1月-2007年5月,在多次鸟类考察过程中都观察到野外活动的白眶鹟莺。在底定,白眶鹟莺通常多在常绿阔叶林的林下灌丛和山间农耕地周边的灌丛中活动,其栖息地海拔高度大致在500-700m。全世界记录有2亚种,我国现已知仅有白眶鹟莺的一个亚种分布。该标本经鉴定为Seicercus affinis intermedius。文中还就白眶鹟莺在中国的分布情况作了讨论。标本现保存于广西大学动物科学技术学院动物标本室。     

Alcohol Induces Sensitization to Gluten in Genetically Susceptible Individuals: A Case Control Study

Background

The mechanisms of cerebellar degeneration attributed to prolonged and excessive alcohol intake remain unclear. Additional or even alternative causes of cerebellar degeneration are often overlooked in suspected cases of alcohol-related ataxia. The objectives of this study were two fold: (1) to investigate the prevalence of gluten-related serological markers in patients with alcohol-related ataxia and; (2) to compare the pattern of brain involvement on magnetic resonance imaging between patients with alcohol and gluten ataxias.

Materials & Methods

Patients diagnosed with alcohol and gluten ataxias were identified from a retrospective review of patients attending a tertiary clinic. HLA genotype and serological markers of gluten-related disorders were recorded. Cerebellar volumetry, MR spectroscopy and voxel-based morphometric analyses were performed on patients and compared with matched control data.

Results

Of 904 registered patients, 104 had alcohol ataxia and 159 had gluten ataxia. 61% of the alcohol ataxia group and 70% of the gluten ataxia group had HLA DQ2/DQ8 genotype compared to 30% in healthy local blood donors. 44% of patients with alcohol ataxia had antigliadin antibodies compared to 12% in the healthy local population and 10% in patients with genetically confirmed ataxias. None of the patients with alcohol ataxia and antigliadin antibodies had celiac disease compared to 40% in patients with gluten ataxia. The pattern of structural brain abnormality in patients with alcohol ataxia who had antigliadin antibodies differed from gluten ataxia and was identical to that of alcohol ataxia.

Conclusions

Alcohol related cerebellar degeneration may, in genetically susceptible individuals, induce sensitization to gluten. Such sensitization may result from a primary cerebellar insult, but a more systemic effect is also possible. The duration and amount of exposure to alcohol may not be the only factors responsible for the cerebellar insult.     

Dawn Singing Intensity of the Male Brownish‐Flanked Bush Warbler: Effects of Territorial Insertions and Number of Neighbors

The dawn chorus is a period of peak singing activity of many songbirds. Numerous studies have sought to understand this widespread phenomenon, and many hypotheses have been proposed to explain the dawn chorus. The social dynamics hypothesis proposes that dawn singing plays an important role in the announcement of territorial occupancy and the regulation of social relationships between males; it predicts that the dawn chorus vocal behavior varies with changes in social relationships. In this study, we tested the influence of territorial insertions and the number of neighbors, on the intensity of the brownish‐flanked bush warbler (Cettia fortipes)'s dawn singing. We found that simulated territorial insertions (playback) caused the males to increase their dawn singing significantly the next day, and males that had many neighbors exhibited more intense dawn singing than did males with few neighbors. Our study provides evidence that dawn singing plays an important role in the announcement of territorial occupancy and the regulation of the social relationships between the males.     

Identification of Unusual E6 and E7 Proteins within Avian Papillomaviruses: Cellular Localization,Biophysical Characterization,and Phylogenetic Analysis

Papillomaviruses (PVs) are a large family of small DNA viruses infecting mammals, reptiles, and birds. PV infection induces cell proliferation that may lead to the formation of orogenital or skin tumors. PV-induced cell proliferation has been related mainly to the expression of two small oncoproteins, E6 and E7. In mammalian PVs, E6 contains two 70-residue zinc-binding repeats, whereas E7 consists of a natively unfolded N-terminal region followed by a zinc-binding domain which folds as an obligate homodimer. Here, we show that both the novel francolin bird PV Francolinus leucoscepus PV type 1 (FlPV-1) and the chaffinch bird PV Fringilla coelebs PV contain unusual E6 and E7 proteins. The avian E7 proteins contain an extended unfolded N terminus and a zinc-binding domain of reduced size, whereas the avian E6 proteins consist of a single zinc-binding domain. A comparable single-domain E6 protein may have existed in a common ancestor of mammalian and avian PVs. Mammalian E6 C-terminal domains are phylogenetically related to those of single-domain avian E6, whereas mammalian E6 N-terminal domains seem to have emerged by duplication and subsequently diverged from the original ancestral domain. In avian and mammalian cells, both FlPV-1 E6 and FlPV-1 E7 were evenly expressed in the cytoplasm and the nucleus. Finally, samples of full-length FlPV-1 E6 and the FlPV-1 E7 C-terminal zinc-binding domain were prepared for biophysical analysis. Both constructs were highly soluble and well folded, according to nuclear magnetic resonance spectroscopy measurements.Papillomaviruses (PVs) are nonenveloped, epitheliotropic, double-stranded DNA viruses that cause a variety of diseases in a multitude of hosts. Based on available whole-genome sequences and subgenomic amplicons, more than 200 human and over 55 nonhuman mammalian PV types have been described (7, 34, 35, 37, 38). To date, two avian PV types have been characterized (37, 38).The genomic organizations of the PVs are remarkably similar. The genome is ca. 8 kb in length and comprises an upstream regulatory region (URR), the early genes (E1, E2, E4, E6, and E7), and the late genes that encode the capsid proteins (L1 and L2). Although most PVs code for these seven open reading frames (ORFs), only the URR, the replicative proteins E1 and E2 (and possibly the E4 gene), and the capsid proteins L1 and L2 are strictly conserved in all PVs (11).Upon infection of the stratified squamous epithelia, PV gene expression is linked to the differentiation state of the infected epithelium cells. The expression of early PV proteins, in particular E6 and E7, primes the proliferation of the infected epithelium. This proliferation, which is absolutely required for viral replication, may become malignant depending on the PV strain considered. Several “high-risk” mucosal human PV (HPV) strains (predominantly HPV type 16 [HPV-16], HPV-18, and HPV-45) have been shown to be responsible for cervical cancer (19).The ability of PVs to induce proliferation of the infected cells has been attributed mainly to two small “oncoproteins,” E6 and E7. In genital high-risk HPVs, these proteins play a prominent role in cell immortalization and transformation (31). In most mammalian PVs, E6 is a small protein of about 150 amino acids, with two conserved N- and C-terminal zinc-binding domains, E6N and E6C, respectively (12). The solution structure of the HPV-16 E6C domain was recently determined (23). The sequence alignments pointed to a structural similarity between the E6C and E6N domains, suggesting that a single-domain protein possessing the same fold might have once existed. Earlier phylogenetic studies had suggested that gene duplication may have given rise to the current double-domain E6 proteins (5). Interestingly, although the E6 ORF has been found in most mammalian PVs (with the exception of bovine papillomavirus type 3 [BPV-3], BPV-4, BPV-6, HPV-101, and HPV-103 [3, 7]), it was not detected in the two avian PVs previously sequenced (37, 38).In this study, we present the full sequence of the genome of a novel PV from a francolin bird (Francolinus leucoscepus PV type 1 [FlPV-1]) and compare it to the two other avian PV genomes known to date (Psittacus erithacus PV [PePV] and Fringilla coelebs PV [FPV]). In light of recent structural data, we compare the unusual avian E6 and E7 ORFs to their mammalian orthologs. We describe the expression and purification of recombinant avian PV E6 and E7 proteins, their biophysical characterization, and cellular localization. Finally, we use phylogenetic techniques to investigate the evolutionary history of the E6 protein family.     

Identification of a Core Bacterial Community within the Large Intestine of the Horse

The horse has a rich and complex microbial community within its gastrointestinal tract that plays a central role in both health and disease. The horse receives much of its dietary energy through microbial hydrolysis and fermentation of fiber predominantly in the large intestine/hindgut. The presence of a possible core bacterial community in the equine large intestine was investigated in this study. Samples were taken from the terminal ileum and 7 regions of the large intestine from ten animals, DNA extracted and the V1-V2 regions of 16SrDNA 454-pyrosequenced. A specific group of OTUs clustered in all ileal samples and a distinct and different signature existed for the proximal regions of the large intestine and the distal regions. A core group of bacterial families were identified in all gut regions with clear differences shown between the ileum and the various large intestine regions. The core in the ileum accounted for 32% of all sequences and comprised of only seven OTUs of varying abundance; the core in the large intestine was much smaller (5-15% of all sequences) with a much larger number of OTUs present but in low abundance. The most abundant member of the core community in the ileum was Lactobacillaceae, in the proximal large intestine the Lachnospiraceae and in the distal large intestine the Prevotellaceae. In conclusion, the presence of a core bacterial community in the large intestine of the horse that is made up of many low abundance OTUs may explain in part the susceptibility of horses to digestive upset.     

Industrial Symbiosis in China: A Case Study of the Guitang Group

The Guitang Group (GG), which operates one of China's largest sugar refineries, has been developing and implementing an internal and external industrial symbiosis strategy for more than four decades. The GG first invested in developing its own collection of downstream companies to utilize nearly all byproducts of sugar production. This strategy has generated new revenues and reduced environmental emissions and disposal costs, while simultaneously improving the quality of sugar. Internally, the GG's complex consists of interlinked production of sugar, alcohol, cement, compound fertilizer, and paper and includes recycling and reuse. Externally, the GG has established a strong customer base as a result of its product quality, has worked to maintain and expand its supply base through technological and economic incentives to farmers (and even to competitors), and has had to react to a strong government presence that fundamentally affects its operations. Operations to date support some of the fundamental concepts of industrial symbiosis. Significant challenges exist, though, if the company is to continue to prosper in the volatile globalized sugar market.     

Shifts in the Spatiotemporal Dynamics of Schistosomiasis: A Case Study in Anhui Province,China

Background

The Chinese national surveillance system showed that the risk of Schistosoma japonicum infection fluctuated temporally. This dynamical change might indicate periodicity of the disease, and its understanding could significantly improve targeted interventions to reduce the burden of schistosomiasis. The goal of this study was to investigate how the schistosomiasis risk varied temporally and spatially in recent years.

Methodology/Principal Findings

Parasitological data were obtained through repeated cross-sectional surveys that were carried out during 1997-2010 in Anhui Province, East China. A multivariate autoregressive model, combined with principal oscillation pattern (POP) analysis, was used to evaluate the spatio-temporal variation of schistosomiasis risk. Results showed that the temporal changes of schistosomiasis risk in the study area could be decomposed into two sustained damped oscillatory modes with estimated period of approximately 2.5 years. The POPs associated with these oscillatory components showed that the pattern near the Yangtze River varied markedly and that the disease risk appeared to evolve in a Southwest/Northeast orientation. The POP coefficients showed decreasing tendency until 2001, then increasing during 2002-2005 and decaying afterwards.

Conclusion

The POP analysis characterized the variations of schistosomiasis risk over space and time and demonstrated that the disease mainly varied temporally along the Yangtze River. The schistosomiasis risk declined periodically with a temporal fluctuation. Whether it resulted from previous national control strategies on schistosomiasis needs further investigations.     

ITS鉴定真菌病原:一例司法鉴定研究实例

本研究选择一例疑似空气污染物伤害松树的司法鉴定案作为研究实例,在现场勘察和初步形态鉴定的基础上,应用ITS序列分析鉴定了对疑似空气污染物伤害松树的病原做了分子鉴定。我们对委托鉴定的疑似空气污染物伤害松树的地及周边地区进行了勘查,现场勘查结果并不支持空气污染物伤害松树的看法。为明确松树枯死的原因,对取样病枝上的疑似病原物进行了显微镜观察和培养性状观察,根据显微镜下孢子的形态和病原菌的培养性状,初步判断导致马尾松枯死的病原可能为拟盘多毛孢属(Pestalotipsis)真菌。为进一步确定病原种类,我们应用分子生物学技术对危害马尾松的病原物进行了ITS分子鉴定。测定了疑似真菌的ITS序列,并进行了比对和系统发育分析。研究结果表明,导致松树枯死的病原菌系韦司梅拟盘多毛孢(Pestalotipsis vismiae)。在本研究案例中,利用真菌ITS序列的系统发育分析,快速、准确地鉴定了真正导致松树枯死的病原,为今后类似司法鉴定案件审理提供了证据鉴定的新手段。     

Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients β_ij exerted by variant j on variant i are equal to their fitness ratio, r_j/r_i. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F_ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts.     

一个可用于复杂大群体的可视化系谱绘制和分析软件

对于在遗传研究和家系研究中大的系谱结构图还很难分析。系谱的绘制通常是遗传性状的分析研究的第一步。系图可以反映整个群体的结构、每个个体之间的相互关系以及基因流的走向,便于理解遗传性状的本质。因为所用家系数目的增大和复杂性的增加,绘制1个清晰的系谱有时变得十分困难。因此开发了1种名为Pedigraph软件,可以解决这个问题。Pedigraph能够完成对于大的复杂的群体的系谱绘制工作,并能进行相应的系谱分析。初步的测试表明这个软件在研究动植物的遗传育种中是1个有用的工具,同时它也可以用于人类的群体和历史等方面的研究。     

Impact of Nesting Mortality on Avian Breeding Phenology: A Case Study on the Red-Backed Shrike (Lanius collurio)

The seasonal timing of avian reproduction is supposed primarily to coincide with favourable feeding conditions. Long-term changes in avian breeding phenology are thus mostly scrutinized in relation to climatic factors and matching of the food supplies, while the role of nesting mortality is largely unexplored. Here we show that higher seasonal mean daily mortality rate leads to a shift in the distribution of breeding times of the successful nests to later dates in an an open-nesting passerine bird, the red-backed shrike Lanius collurio. The effect appeared to be strong enough to enhance or counteract the influence of climatic factors and breeding density on the inter-annual variation in mean hatching dates. Moreover, the seasonal distribution of reproductive output was shifted to larger, or smaller, broods early in the season when the nesting mortality increased, or decreased, respectively, during the season. We suggest that population level changes in timing of breeding caused by a general advancement of spring and of the food supplies might be altered by the seasonality in nesting mortality. Hence, we argue that consideration of nesting mortality is of major importance for understanding long-term trends in avian phenology, particularly in species capable of renesting.     

Reanalysis of Wupus agilis (Early Cretaceous) of Chongqing,China as a Large Avian Trace: Differentiating between Large Bird and Small Non-Avian Theropod Tracks

Trace fossils provide the only records of Early Cretaceous birds from many parts of the world. The identification of traces from large avian track-makers is made difficult given their overall similarity in size and tridactyly in comparison with traces of small non-avian theropods. Reanalysis of Wupus agilis from the Early Cretaceous (Aptian-Albian) Jiaguan Formation, one of a small but growing number of known avian-pterosaur track assemblages, of southeast China determines that these are the traces of a large avian track-maker, analogous to extant herons. Wupus, originally identified as the trace of a small non-avian theropod track-maker, is therefore similar in both footprint and trackway characteristics to the Early Cretaceous (Albian) large avian trace Limiavipes curriei from western Canada, and Wupus is reassigned to the ichnofamily Limiavipedidae. The reanalysis of Wupus reveals that it and Limiavipes are distinct from similar traces of small to medium-sized non-avian theropods (Irenichnites, Columbosauripus, Magnoavipes) based on their relatively large footprint length to pace length ratio and higher mean footprint splay, and that Wupus shares enough characters with Limiavipes to be reassigned to the ichnofamily Limiavipedidae. The ability to discern traces of large avians from those of small non-avian theropods provides more data on the diversity of Early Cretaceous birds. This analysis reveals that, despite the current lack of body fossils, large wading birds were globally distributed in both Laurasia and Gondwana during the Early Cretaceous.