Estimating number of families for an urban fox population by using two public data sets

The number of families in the urban fox population of Sapporo, Japan, was estimated from two sets of data reported by the public to government: records of road-killed foxes (information-A) and records of complaints about foxes (information-B). We assumed that fox populations consist of families that have exclusive home ranges, i.e., territories, during the period between gestation and dispersal. The urban area was then divided into hexagons that correspond to the territories. The locations from the two sets of records during the territorial period were plotted on the map. The number of fox families for which information-A and/or B was reported was estimated by counting the number of hexagons that include the record. The total number of families was estimated by using a double-observation method. We adopted Chapman’s unbiased estimator which is based on the hypergeometric distribution that corresponds to the conditional likelihood. We demonstrated the possibility of estimating the abundance of animals from government data such as road kill and complaints if the animals have territories. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

应用数学统计法优化副干酪乳杆菌HD1.7固定化细胞制备和产细菌素发酵

摘要：【目的】应用数学统计法对副干酪乳杆菌HD1.7的固定细胞制备和发酵条件进行优化,以提高细菌素产量。【方法】用26?2部分因子分析法筛选对细菌素产量影响显著的因子,发现海藻酸钠浓度、接种量和发酵时间对细菌素的产生影响显著。利用最陡爬坡法逼近最大响应区域。用Box-Behnken设计确定最佳海藻酸钠浓度、接种量和发酵时间,并进行分批重复发酵。【结果】固定化生产细菌素的最佳条件是海藻酸钠浓度2.8%、CaCl2浓度5%、固定化时间4 h、菌体包埋量1/20、发酵时间63 h和固定化细胞的接种量8.2%,在此基础上用固定化细胞进行分批重复发酵,每批细菌素的发酵周期为24 h,产量为游离发酵的70%,比游离细胞发酵周期缩短1/2。【结论】通过对固定化细胞制备和发酵条件的优化,固定化细胞在327 h的分批重复发酵中细菌素的总体产量比游离细胞提高了19%,发酵液中无明显细胞渗漏现象且实现了细胞的重复利用,为细菌素的进一步研究和最终提取奠定了基础。     

Development of effective isolation method of ES cells for analysis of differentiation

Neuroectoderm development is a milestone of vertebrate neurogenesis. However, the molecular mechanism underlying the differentiation of neuroectoderm is still unclear, especially in mammals. ES cells co-cultured with PA6 cells can differentiate to neuroectoderm by the stromal cell-derived inducing activity method (SDIA method), but contamination of PA6 cells is an obstacle to the analysis of molecular mechanisms of differentiation. Here we describe a novel method by which differentiated ES cells are easily isolated from PA6 cells. We attempted to induce the differentiation of ES cells using paraformaldehyde-fixed PA6 cells. RT-PCR and DNA microarray analysis revealed that the background noise derived from contaminated PA6 cells disappeared when fixed PA6 cells were used. Furthermore, genes up-regulated during the differentiation of ES cells were expressed in a developing mouse embryo. Thus, our newly developed method will be very useful for identifying novel genes associated with mouse neuroectoderm development in vitro and in vivo.     

Structure of the breeding bird assemblage of a primeval alder swamp in the ?úr National Nature Reserve

The structure of a breeding bird assemblage of a primeval alder swamp in the Šúr National Nature Reserve (the Danube Basin) was studied in the period 1992–1995. A 16 ha forest interior study plot was established for bird censusing. Population abundances were estimated by a combined version of the mapping method from the end of March to the beginning of July. Altogether, 42 breeders were recorded and the mean total density of species total across years was 125.15 ± 12.73 pairs/10 ha (CV = 10.17%). Two species were eudominant (≥ 10%): Sturnus vulgaris and Anas platyrhynchos, and six species were dominant (5% ≤ 10% <): Ficedula albicollis, Fringilla coelebs, Phylloscopus collybita, Parus major, Sylvia atricapilla, Erithacus rubecula. The Shannon diversity index (H′) varied between 3.98–4.10 bites. The evenness index (J′) reached values between 0.79–0.81. Expected species diversity in a random sample of 100 pairs calculated by rarefaction [E (S _{100 pairs})] was 21.35 ± 0.92 species derived as a mean value from the years 1992–1995. The mean rarefaction estimate on the area [E (S _{10 ha})] was 22.75 ± 1.58 species. Bird species richness and diversity were significantly higher in the study plot in comparison to the mean value of European wet alder forests. These results are comparable with the values of structural assemblage parameters of the primeval stands dominated by alder within the Białowieża National Park, Poland.     

Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics with a Grain of Salt

In recent years, a growing number of protein folding studies have focused on the unfolded state, which is now recognized as playing a major role in the folding process. Some of these studies show that interactions occurring in the unfolded state can significantly affect the stability and kinetics of the protein folding reaction. In this study, we modeled the effect of electrostatic interactions, both native and nonnative, on the folding of three protein systems that underwent selective charge neutralization or reversal or complete charge suppression. In the case of the N-terminal L9 protein domain, our results directly attribute the increase in thermodynamic stability to destabilization of the unfolded ensemble, reaffirming the experimental observations. These results provide a deeper structural insight into the ensemble of the unfolded state and predict a new mutation site for increased protein stability. In the second case, charge reversal mutations of RNase Sa affected protein stability, with the destabilizing mutations being less destabilizing at higher salt concentrations, indicating the formation of charge-charge interactions in the unfolded state. In the N-terminal L9 and RNase Sa systems, changes in electrostatic interactions in the unfolded state that cause an increase in free energy had an overall compaction effect that suggests a decrease in entropy. In the third case, in which we compared the β-lactalbumin and hen egg-white lysozyme protein homologues, we successfully eliminated differences between the folding kinetics of the two systems by suppressing electrostatic interactions, supporting previously reported findings. Our coarse-grained molecular dynamics study not only reproduces experimentally reported findings but also provides a detailed molecular understanding of the elusive unfolded-state ensemble and how charge-charge interactions can modulate the biophysical characteristics of folding.     

OPUS-Dom: Applying the Folding-Based Method VECFOLD to Determine Protein Domain Boundaries

In this article, we present a de novo method for predicting protein domain boundaries, called OPUS-Dom. The core of the method is a novel coarse-grained folding method, VECFOLD, which constructs low-resolution structural models from a target sequence by folding a chain of vectors representing the predicted secondary-structure elements. OPUS-Dom generates a large ensemble of folded structure decoys by VECFOLD and labels the domain boundaries of each decoy by a domain parsing algorithm. Consensus domain boundaries are then derived from the statistical distribution of the putative boundaries and three empirical sequence-based domain profiles. OPUS-Dom generally outperformed several state-of-the-art domain prediction algorithms over various benchmark protein sets. Even though each VECFOLD-generated structure contains large errors, collectively these structures provide a more robust delineation of domain boundaries. The success of OPUS-Dom suggests that the arrangement of protein domains is more a consequence of limited coordination patterns per domain arising from tertiary packing of secondary-structure segments, rather than sequence-specific constraints.     

Malaria Diagnosis: A Brief Review

Malaria is a major cause of death in tropical and sub-tropical countries, killing each year over 1 million people globally; 90% of fatalities occur in African children. Although effective ways to manage malaria now exist, the number of malaria cases is still increasing, due to several factors. In this emergency situation, prompt and effective diagnostic methods are essential for the management and control of malaria. Traditional methods for diagnosing malaria remain problematic; therefore, new technologies have been developed and introduced to overcome the limitations. This review details the currently available diagnostic methods for malaria.     

Prediction of Interacting Protein Pairs from Sequence Using a Bayesian Method

With the development of bioinformatics, more and more protein sequence information has become available. Meanwhile, the number of known protein–protein interactions (PPIs) is still very limited. In this article, we propose a new method for predicting interacting protein pairs using a Bayesian method based on a new feature representation. We trained our model using data on 6,459 PPI pairs from the yeast Saccharomyces cerevisiae core subset. Using six species of DIP database, our model demonstrates an average prediction accuracy of 93.67%. The result showed that our method is superior to other methods in both computing time and prediction accuracy.     

DETs缓冲液对肠道微生物DNA的保存效果

方便高效的保存方法是开展动物肠道微生物研究的重要前提,用T-RFLP（末端限制性片段长度多态性）结合16S rDNA分析评估了野外采样常用的DETs（20%DMSO,0.25 M sodium-EDTA,100 mM Tris,pH 7.5,and NaCl to saturation）缓冲液对不同保存时间（24h,7天,30天,90天）粪便样品肠道微生物DNA的保存效果。结果表明,DETs保存在30天保存时间内微生物群落结构无显著变化,95.6%的T-RFs仍然存在,能效好的保护肠道微生物DNA。     

一种检测新型生物高分子材料聚γ-谷氨酸的新方法

通过聚γ-谷氨酸（γ-PGA）与氯化十六烷基吡啶（CPC）的乙酸钠水溶液反应形成混悬液,采用分光光度计于波长680nm处比浊,研究γ-PGA浓度与吸收度之间的线性关系,并研究本方法测定γ-PGA的稳定性、重现性和回收率。在一定pH值和离子强度下,γ-PGA在12.5~50μg/ml范围内与CPC的乙酸钠水溶液生成的混悬液在波长680nm处的吸收度与其浓度呈线性关系,R2=0.9939.本方法在2h内吸收度保持稳定(RSD=0.154%,n=10 ),CPC法测定浓度为5,10和 40μg/ml时的平均回收率分别为86%,77%和99.75%,RSD分别为0.14%,0.23%和0.025%应用比浊法测定γ-PGA的含量方便、简洁、重现性好,可用于γ-PGA浓度的检测。