牛白细胞粘附缺陷病(BLAD)的调查

牛白细胞粘附缺陷病(BLAD)是一种常染色体单基因隐性遗传疾病, 病因为白细胞表面整合素CD18亚单位基因突变所致。为了解我国奶牛群中BLAD的携带和发生情况, 本研究采用RT-PCR扩增CD18基因片段后, 用TaqⅠ内切酶对扩增产物进行酶切的方法检测了1 000头1~6岁的奶牛, 结果有19头奶牛为BLAD携带牛, 即BLAD携带率为1.9%; 1头为BLAD病牛。     

Bovine Leukocyte Adhesion Deficiency in Danish Holstein-Friesian Cattle

A screening program for bovine leukocyte adhesion deficiency (BLAD) in Danish Holstein-Friesian cattle has been initiated. During the first months 1611 animals were tested by a PCR based assay. Of these animals 1256, 346, and 8 were assigned normal, BLAD carriers, and BLAD affected animals, respectively One bull, born as a co-twin, showed weak reaction for the BLAD allele on DNA isolated from leukocytes, but a normal genotype on DNA isolated from semen. Chromosome analysis showed that this bull was a blood chimaera. Estimation of the BLAD allele frequency upon the PCR test results showed that around 450 Danish calves born in 1991 might have been affected with the recessive disorder.     

Enhanced Expression of Fc Receptors on Neutrophils from Calves with Leukocyte Adhesion Deficiency

The expression of Fc receptors for immunoglobulin G(IgG) and concanavalin A (con A)-binding receptors, luminol-dependent chemiluminescent (LDCL) responses, and the effect of anti-bovine IgG on LDCL responses were evaluated in neutrophils from Holstein calves with leukocyte adhesion deficiency (BLAD). Neutrophils from affected calves showed a 2.1- to 2.5-fold increase in Fc receptor expression compared with those of control calves by flow cytometric analysis. Con A-binding activities of neutrophils from affected calves were similar to those of control calves. Neutrophils from a calf with BLAD, when stimulated with zymosan opsonized with bovine serum (OPZ), heat-aggregated bovine IgG (Agg-bovine IgG), sheep red blood cells (SRBC) sensitized with anti-SRBC antibody (SRBC-anti-SRBC Ab), or con A had LDCL responses of 36 (P<0.05), 77, 126 and 119% of peak LDCL values of controls, respectively. The NBT-reducing value of neutrophils from a calf with BLAD when stimulated with Agg-bovine IgG after pretreatment with anti-bovine IgG was 116.5% of the values of neutrophils from control calves, but the difference was not significant. The LDCL responses of neutrophils from a control calf and a calf with BLAD stimulated with OPZ were inhibited markedly by pre-incubation with anti-bovine IgG antiserum at concentrations ranging from 1.25 to 20 or 40 μg/ml. Although an increase in Fc receptor expression on neutrophils from calves with BLAD was observed, the LDCL responses stimulated with SRBC-anti-SRBC Ab and NBT-reducing activity stimulated with Agg-bovine IgG after pretreatment with anti-bovine IgG did not correlate significantly with the increased Fc receptor expression. These results support that neutrophil functions mediated by the Fc receptors are associated synergistically with the presence of the complement receptor type 3 (CR3)(CD11b/CD18).     

Spin-Trapping and Chemiluminescence Studies of Neutrophils from a Holstein-Friesian Calf with Bovine Leukocyte Adhesion Deficiency

The ability of neutrophils from a Holstein-Friesian calf with bovine leukocyte adhesion deficiency (the proband with a genetic deficiency of the Mac-1 (CD11b/CD18) glycoprotein corresponding to the receptor of complement iC3b) to generate oxygen radicals was examined using electron spin resonance spectrometry (ESR) combined with a spin-trapping technique and luminol-dependent chemiluminescence spectrometry. When the neutrophils were stimulated with phorbol 12-myristate 13-acetate (PMA), an ESR spectrum confirming the generation of superoxide anions (O₂^-) was clearly observed in both healthy and diseased calves. However, when the neutrophils were stimulated by opsonized zymosan, appearance of the ESR spectrum was recognized in the healthy calves but not in the diseased calf. Similar results were obtained from chemiluminescence experiments.     

Spin-Trapping and Chemiluminescence Studies of Neutrophils from a Holstein-Friesian Calf with Bovine Leukocyte Adhesion Deficiency

The ability of neutrophils from a Holstein-Friesian calf with bovine leukocyte adhesion deficiency (the proband with a genetic deficiency of the Mac-1 (CD11b/CD18) glycoprotein corresponding to the receptor of complement iC3b) to generate oxygen radicals was examined using electron spin resonance spectrometry (ESR) combined with a spin-trapping technique and luminol-dependent chemiluminescence spectrometry. When the neutrophils were stimulated with phorbol 12-myristate 13-acetate (PMA), an ESR spectrum confirming the generation of superoxide anions (O₂^?) was clearly observed in both healthy and diseased calves. However, when the neutrophils were stimulated by opsonized zymosan, appearance of the ESR spectrum was recognized in the healthy calves but not in the diseased calf. Similar results were obtained from chemiluminescence experiments.     

Microbial Communities in Acid Mine Drainage and Their Interaction with Pyrite Surface

Microbes such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans have been investigated a lot, because of their important role in acid mine drainage (AMD) generation. In this article, the composition of microbial communities in two AMD samples was studied. A culture-independent 16S rDNA-based cloning approach, restriction fragment length polymorphism has been used. The interaction between microbes and natural pyrite specimen surface was researched by scanning electrode microscopy (SEM) and fluorescence in situ hybridization (FISH). The phylogenetic analysis revealed bacteria in these two samples fell into three major groups: Proteobacteria, Nitrospira, and Firmicutes. Archaea was also detected in these two samples. Thermoplasma and Ferroplasma lineages were abundant. From SEM and FISH, a number of A. ferrooxidans, a few cells of Archaea and Acidiphilium were detected adsorbed on the pyrite specimen surface. Leptospirillum sp. (hybridize with the probe LF655) has not been detected to be present on the pyrite specimen surface.     

甲状腺癌组织中ALCAM 的表达及其与临床病理参数及预后的关系

目的:探讨甲状腺癌组织中活化白细胞黏附分子(activated leukocyte cell adhesion molecule,ALCAM)的表达及其与临床病理参数及预后的关系。方法:选择2011年1月到2013年1月在我院确诊为甲状腺癌的患者60例作为研究对象。收集所有患者甲状腺癌组织及其癌旁正常组织标本,采用免疫组织化学法检测不同组织中ALCAM蛋白表达,分析其与甲状腺癌患者临床病理参数的相关性,并对所有患者随访3年以上,并记录3年生存率。结果:ALCAM蛋白在甲状腺癌组织中的总阳性率为71.67%,明显高于癌旁正常组织的31.67%(P0.05)。ALCAM蛋白在高分化型甲状腺癌组织中的表达率明显高于低分化及无分化型癌组织(P0.05)。ALCAM蛋白高表达的甲状腺癌患者的3年生存率为81.45%,明显高于ALCAM蛋白低表达者的51.32%(P0.05)。结论:组织中ALCAM蛋白表达与甲状腺癌的发生、发展及患者预后密切相关。     

Microbial Communities in Pre-Columbian Coprolites

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures.     

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences (“markers”) and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred     

Effect of Concentration of Organic Chemicals on Their Biodegradation by Natural Microbial Communities

The effect of concentration on the biodegradation of synthetic organic chemicals by natural microbial communities was investigated by adding individual ¹⁴C-labeled organic compounds to stream water at various initial concentrations and measuring the formation of ¹⁴CO₂. The rate of degradation of p-chlorobenzoate and chloroacetate at initial concentrations of 47 pg/ml to 47 μg/ml fell markedly with lower initial concentrations, although half or more of the compound was converted to CO₂ in 8 days or less. On the other hand, little mineralization of 2,4-dichlorophenoxyacetate and 1-naphthyl-N-methylcarbamate, or the naphthol formed from the latter, occurred when these compounds were present at initial concentrations of 2 to 3 ng/ml or less, although 60% or more of the chemical initially present at higher concentrations was converted to CO₂ in 6 days. It is concluded that laboratory tests of biodegradation involving chemical concentrations greater than those in nature may not correctly assess the rate of biodegradation in natural ecosystems and that low substrate concentration may be important in limiting biodegradation in natural waters.     

Disordered Microbial Communities in Asthmatic Airways

Background

A rich microbial environment in infancy protects against asthma [1], [2] and infections precipitate asthma exacerbations [3]. We compared the airway microbiota at three levels in adult patients with asthma, the related condition of COPD, and controls. We also studied bronchial lavage from asthmatic children and controls.

Principal Findings

We identified 5,054 16S rRNA bacterial sequences from 43 subjects, detecting >70% of species present. The bronchial tree was not sterile, and contained a mean of 2,000 bacterial genomes per cm² surface sampled. Pathogenic Proteobacteria, particularly Haemophilus spp., were much more frequent in bronchi of adult asthmatics or patients with COPD than controls. We found similar highly significant increases in Proteobacteria in asthmatic children. Conversely, Bacteroidetes, particularly Prevotella spp., were more frequent in controls than adult or child asthmatics or COPD patients.

Significance

The results show the bronchial tree to contain a characteristic microbiota, and suggest that this microbiota is disturbed in asthmatic airways.     

Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions

High-throughput technologies are urgently needed for monitoring the formidable biodiversity and functional capabilities of microorganisms in the environment. Ten years ago, DNA microarrays, miniaturized platforms for highly parallel hybridization reactions, found their way into environmental microbiology and raised great expectations among researchers in the field. In this article, we briefly summarize the state-of-the-art of microarray approaches in microbial ecology research and discuss in more detail crucial problems and promising solutions. Finally, we outline scenarios for an innovative combination of microarrays with other molecular tools for structure-function analysis of complex microbial communities.     

Stereoselectivity of Isoflurane in Adhesion Molecule Leukocyte Function-Associated Antigen-1

Background

Isoflurane in clinical use is a racemate of S- and R-isoflurane. Previous studies have demonstrated that the effects of S-isoflurane on relevant anesthetic targets might be modestly stronger (less than 2-fold) than R-isoflurane. The X-ray crystallographic structure of the immunological target, leukocyte function-associated antigen-1 (LFA-1) with racemic isoflurane suggested that only S-isoflurane bound specifically to this protein. If so, the use of specific isoflurane enantiomers may have advantage in the surgical settings where a wide range of inflammatory responses is expected to occur. Here, we have further tested the hypothesis that isoflurane enantioselectivity is apparent in solution binding and functional studies.

Methods

First, binding of isoflurane enantiomers to LFA-1 was studied using 1-aminoanthracene (1-AMA) displacement assays. The binding site of each enantiomer on LFA-1 was studied using the docking program GLIDE. Functional studies employed the flow-cytometry based ICAM binding assay.

Results

Both enantiomers decreased 1-AMA fluorescence signal (at 520 nm), indicating that both competed with 1-AMA and bound to the αL I domain. The docking simulation demonstrated that both enantiomers bound to the LFA-1 “lovastatin site.” ICAM binding assays showed that S-isoflurane inhibited more potently than R-isoflurane, consistent with the result of 1-AMA competition assay.

Conclusions

In contrast with the x-ray crystallography, both enantiomers bound to and inhibited LFA-1. S-isoflurane showed slight preference over R-isoflurane.     

Strain Identification and Quantitative Analysis in Microbial Communities

Microbiology has long studied the ways in which subtle genetic differences between closely related microbial strains can have profound impacts on their phenotypes and those of their surrounding environments and communities. Despite the growth in high-throughput microbial community profiling, however, such strain-level differences remain challenging to detect. Once detected, few quantitative approaches have been well-validated for associating strain variants from microbial communities with phenotypes of interest, such as medication usage, treatment efficacy, host environment, or health. First, the term “strain” itself is not used consistently when defining a highly-resolved taxonomic or genomic unit from within a microbial community. Second, computational methods for identifying such strains directly from shotgun metagenomics are difficult, with several possible reference- and assembly-based approaches available, each with different sensitivity/specificity tradeoffs. Finally, statistical challenges exist in using any of the resulting strain profiles for downstream analyses, which can include strain tracking, phylogenetic analysis, or genetic association studies. We provide an in depth discussion of recently available computational tools that can be applied for this task, as well as statistical models and gaps in performing and interpreting any of these three main types of studies using strain-resolved shotgun metagenomic profiling of microbial communities.     

石油污染海域的微生物群落及烃的降解

目前世界海洋石油污染问题已经严重威胁到海洋生态环境的安全,生物修复是一种处理石油污染的新方法。综述了海洋环境中烃降解微生物生态学方面的一些研究进展,包括探测未培养细菌的新方法、新的分离方法及主要的烃降解菌株的特性,以便努力改进现有分离石油降解菌及石油乳化细菌的方法,同时发现对于石油降解有益的新菌种。     

P-选择素糖蛋白配体1与白细胞的起始黏附

P-选择素糖蛋白配体1（P—selectin glycoprotein ligand 1,PSGL-1）是20世纪90年代初期发现的一种具同源二聚体结构的跨膜糖蛋白,表达于几乎所有白细胞表面,是迄今为止阐述得最为详尽的选择素配体。PSGL-1是以P-选择素为亲和探针分离得到的,与P-选择素有高度的亲和性。近年来,越来越多的研究证明了PSGL-1同时也是L-选择素和E-选择素的生理配体。通过PSGL-1与选择素分子间的相互作用,白细胞在血管内皮细胞上产生滚动（即起始黏附）,进而使白细胞逐步活化并稳定黏附于血管内皮。现从PSGL-1的结构、分布、表达调控、信号转导、生理病理角色、临床应用等方面进行综述。     

Submarine Hydrothermal Vents of the Aeolian Islands: Relationship Between Microbial Communities and Thermal Fluids

The relationship between fluid geochemistry and microbial communities was investigated for shallow (&lt; 25 m) submarine hydrothermal vents in the Aeolian Islands (Southern Italy). Thermal waters, gases, and deposits of white filamentous material were collected from 11 sites. The geochemical analyses showed a magmatic component was present in all sampled fluids. The total microbial abundances, evaluated as direct counts of picoplanktonic cells (ranging from 0.2 to 2 mu m in diameter), were between 1.55 107 and 4.18 108 cells per liter. Picophytoplankton (total autofluorescent cells) ranged from 9.6 105 to 7.88 106 cells per liter. Yellow-orange autofluorescent prokaryotes belonging to the cyanobacteria were more abundant than red autofluorescent eukaryotic cells. Chemolithoautotrophic, sulfur-oxidizing, rod-shaped Bacteria were isolated from venting water samples and identified as Thiobacillus -like. Microscopic examination of the white mat deposits showed the presence of filamentous microorganisms.     

Defining Division of Labor in Microbial Communities

In order to survive and reproduce, organisms must perform a multitude of tasks. However, trade-offs limit their ability to allocate energy and resources to all of these different processes. One strategy to solve this problem is to specialize in some traits and team up with other organisms that can help by providing additional, complementary functions. By reciprocally exchanging metabolites and/or services in this way, both parties benefit from the interaction. This phenomenon, which has been termed functional specialization or division of labor, is very common in nature and exists on all levels of biological organization. Also, microorganisms have evolved different types of synergistic interactions. However, very often, it remains unclear whether or not a given example represents a true case of division of labor. Here we aim at filling this gap by providing a list of criteria that clearly define division of labor in microbial communities. Furthermore, we propose a set of diagnostic experiments to verify whether a given interaction fulfills these conditions. In contrast to the common use of the term, our analysis reveals that both intraspecific and interspecific interactions meet the criteria defining division of labor. Moreover, our analysis identified non-cooperators of intraspecific public goods interactions as growth specialists that divide labor with conspecific producers, rather than being social parasites. By providing a conceptual toolkit, our work will help to unambiguously identify cases of division of labor and stimulate more detailed investigations of this important and widespread type of inter-microbial interaction.     

Microbial Communities and Exopolysaccharides from Polynesian Mats

Microbial mats present in two shallow atolls of French Polynesia were characterized by high amounts of exopolysaccharides associated with cyanobacteria as the predominating species. Cyanobacteria were found in the first centimeters of the gelatinous mats, whereas deeper layers showing the occurrence of the sulfate reducers Desulfovibrio and Desulfobacter species as determined by the presence of specific biomarkers. Exopolysaccharides were extracted from these mats and partially characterized. All fractions contained both neutral sugars and uronic acids with a predominance of the former. The large diversity in monosaccharides can be interpreted as the result of exopolymer biosynthesis by either different or unidentified cyanobacterial species. Received July 25, 2000; accepted October 21, 2000