Probiotic bacteria maintain normal growth mechanisms of heat stressed broiler chickens

Probiotics have growth promoting effects even under periods of heat stress challenge. More information is needed to understand the mechanisms by which probiotics maintain the growth performance. The aim of this study was to evaluate the effect of a probiotic based on Bacillus subtilis bacteria on growth related mechanisms of broilers under heat stress conditions. Specifically, growth performance, skeletal bone characteristics, skeletal muscles size, intestinal villus-crypt structure, intestinal bacteria, growth hormone (GH), insulin-like growth factor-1 (IGF-1), cholesterol, and glucose. A total of 1200 one day old Ross 308 male broilers were randomly distributed into 4 treatments, with 12 replicates per treatment and 25 birds per replicate. A 2 × 2 factorial arrangement was used; the main factors were environmental temperature (thermoneutral or heat stress) and diet (control or control + B. subtilis; 3 × 10⁷ cfu/kg of feed). From d 22 to 35 of age, birds were either exposed to thermoneutral conditions (21 °C) or chronic heat stress (30 °C). During the same period, each group was divided into 2 subgroups and fed either the control diet or the B. subtilis supplemented diet. The results demonstrated that B. subtilis had positive effects (P < 0.05) on the body weight gain, feed conversion ratio, villus height, crypt depth, villus surface area, absorptive epithelial cell area and viable counts of intestinal beneficial bacteria. B. subtilis increased (P < 0.05) serum GH, IGF-1 and maintain normal levels of cholesterol and glucose under heat stress conditions. In addition, broilers fed B. subtilis under heat stress conditions exhibited higher (P < 0.05) skeletal muscles size and improved (P < 0.05) tibia traits and lower (P < 0.05) abdominal fat pads deposition compared with the controls. B. subtilis had no effect on rectal temperature under thermoneutral or heat stress conditions. It is concluded that B. subtilis can be used as growth promoters in broilers, particularly during the periods of heat stress conditions.     

Thymidine kinase diversity in bacteria

Thymidine kinases (TKs) appear to be almost ubiquitous and are found in nearly all prokaryotes, eukaryotes, and several viruses. They are the key enzymes in thymidine salvage and activation of several anti-cancer and antiviral drugs. We show that bacterial TKs can be subdivided into 2 groups. The TKs from Gram-positive bacteria are more closely related to the eukaryotic TK1 enzymes than are TKs from Gram-negative bacteria.     

Environmental diversity of bacteria and archaea

The microbial way of life spans at least 3.8 billion years of evolution. Microbial organisms are pervasive, ubiquitous, and essential components of all ecosystems. The geochemical composition of Earth's biosphere has been molded largely by microbial activities. Yet, despite the predominance of microbes during the course of life's history, general principles and theory of microbial evolution and ecology are not well developed. Until recently, investigators had no idea how accurately cultivated microorganisms represented overall microbial diversity. The development of molecular phylogenetics has recently enabled characterization of naturally occurring microbial biota without cultivation. Free from the biases of culture-based studies, molecular phylogenetic surveys have revealed a vast array of new microbial groups. Many of these new microbes are widespread and abundant among contemporary microbiota and fall within novel divisions that branch deep within the tree of life. The breadth and extent of extant microbial diversity has become much clearer. A remaining challenge for microbial biologists is to better characterize the biological properties of these newly described microbial taxa. This more comprehensive picture will provide much better perspective on the natural history, ecology, and evolution of extant microbial life.     

Evolution and diversity of Rickettsia bacteria

Background

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder associated with the partial deletion of integral numbers of 3.3 kb D4Z4 DNA repeats within the subtelomere of chromosome 4q. A number of candidate FSHD genes, adenine nucleotide translocator 1 gene (ANT1), FSHD-related gene 1 (FRG1), FRG2 and DUX4c, upstream of the D4Z4 array (FSHD locus), and double homeobox chromosome 4 (DUX4) within the repeat itself, are upregulated in some patients, thus suggesting an underlying perturbation of the chromatin structure. Furthermore, a mouse model overexpressing FRG1 has been generated, displaying skeletal muscle defects.

Results

In the context of myogenic differentiation, we compared the chromatin structure and tridimensional interaction of the D4Z4 array and FRG1 gene promoter, and FRG1 expression, in control and FSHD cells. The FRG1 gene was prematurely expressed during FSHD myoblast differentiation, thus suggesting that the number of D4Z4 repeats in the array may affect the correct timing of FRG1 expression. Using chromosome conformation capture (3C) technology, we revealed that the FRG1 promoter and D4Z4 array physically interacted. Furthermore, this chromatin structure underwent dynamic changes during myogenic differentiation that led to the loosening of the FRG1/4q-D4Z4 array loop in myotubes. The FRG1 promoter in both normal and FSHD myoblasts was characterized by H3K27 trimethylation and Polycomb repressor complex binding, but these repression signs were replaced by H3K4 trimethylation during differentiation. The D4Z4 sequences behaved similarly, with H3K27 trimethylation and Polycomb binding being lost upon myogenic differentiation.

Conclusion

We propose a model in which the D4Z4 array may play a critical chromatin function as an orchestrator of in cis chromatin loops, thus suggesting that this repeat may play a role in coordinating gene expression.     

Genetic diversity of phosphate-solubilizing peanut (Arachis hypogaea L.) associated bacteria and mechanisms involved in this ability

In this study, attempts were made to analyze mechanisms involved in the bacterial phosphate-solubilizing ability of peanut isolates. Bacteria were taxonomically identified by analysis of 16S rDNA sequence. Levels of soluble P released by the isolates in unbuffered or buffered with Tris–HCl or MES NBRIP-BPB medium as well as the production of D-gluconic acid were determined in their culture. Presence of two of the genes encoding the cofactor PQQ of GDH enzyme was analyzed in the genome of this bacterial collection. 16S rDNA sequence analysis indicated that isolates belong to genera Serratia, Enterobacter, Pantoea, Acinetobacter, Bacillus and Enterococcus. All bacteria showed ability to solubilize tricalcium phosphate either in unbuffered or buffered medium. Nevertheless, addition of buffer solutions reduced levels of Pi liberated by the isolates. Although almost all isolates produced detectable amounts of D-gluconic acid, no correlation with levels of P soluble released were observed. The presence of pqqE and pqqC genes was detected only in Gram negative bacteria. It was concluded from this study that the mechanism involved in phosphate solubilization is organic acids production and, presence of pqq genes in all Gram negative bacteria analyzed encourages to confirm their role in bacterial phosphate solubilizing ability as well to identify genes involved in this PGP trait in Gram positive bacteria.     

Complement-resistance mechanisms of bacteria

Despite more than a century of parallel research on bacteria and the complement system, relatively little is known of the mechanisms whereby pathogenic bacteria can escape complement-related opsonophagocytosis and direct killing. It is likely that pathogenicity in bacteria has arisen more accidentally than in viruses, and on the basis of selection from natural mutants rather than by outright stealing or copying of genetic codes from the host. In this review we will discuss complement resistance as one of the features that makes a bacterium a pathogen.     

Anion-exchange mechanisms in bacteria.

This article discusses the physiological, biochemical, and molecular properties of bacterial anion-exchange reactions, with a particular focus on a family of phosphate (Pi)-linked antiporters that accept as their primary substrates sugar phosphates such as glucose 6-phosphate (G6P), mannose 6-phosphate, or glycerol 3-phosphate. Pi-linked antiporters may be found in both gram-positive and gram-negative cells. As their name suggests, these exchange proteins accept both inorganic and organic phosphates, but the two classes of substrate interact very differently with the protein. Thus, Pi is always accepted with a relatively low affinity, and when it participates in exchange, it is always taken as the monovalent anion. By contrast, when the high-affinity organic phosphates are used, these same systems fail to discriminate between monovalent and divalent forms. Tests of heterologous exchange (e.g., Pi: G6P) indicate that these proteins have a bifunctional active site that accepts a pair of negative charges, whether as two monovalent anions or as a single divalent anion. For this reason, exchange stoichiometry moves between limits of 2:1 and 2:2, according to the ratio of mono- and divalent substrates at either membrane surface. Since G6P has a pK2 within the physiological range (pK of 6.1), this predicts a novel reaction sequence in vivo because internal pH is more alkaline than external pH. Accordingly, one expects an asymmetric exchange as two monovalent G6P anions from the relatively acidic exterior move against a single divalent G6P from the alkaline interior. In this way an otherwise futile self-exchange of G6P can be biased towards a net inward flux driven (indirectly) by the pH gradient. Despite the biochemical complexity exhibited by Pi-linked antiporters, they resemble all other secondary carriers at a molecular level and show a likely topology in which two sets of six transmembrane alpha-helices are connected by a central hydrophilic loop. Speculations on the derivation of this common form suggest a limited number of structural models to accommodate such proteins. Three such models are presented.     

Water-stressed maize, barley and rice seedlings show species diversity in mechanisms of leaf growth inhibition

The possible occurrence of species diversity in mechanisms underlying leaf-growth inhibition by water stress, was investigated in related cereal plants. Water stress was generated by additions of the osmoticum polyethylene glycol 6000 to the root medium. Effects of external water potentials ranging from 0 to -0.6MPa, on early growth parameters of emerging leaves were measured under controlled environment conditions, using pairs of maize, barley or rice genotypes with differing resistance to water stress under field conditions. Water potentials of -0.4 MPa for 24 h, similarly reduced leaf growth, comparative production rates of leaf epidermal cells and cell size in all genotypes. These reductions did not appear to be caused by reductions in the osmotic potential gradients between the expanding leaf cells and their external water source. However, growth inhibition in maize and barley, was accompanied by significant reductions in comparative leaf and cell wall extensibility. Moreover, regression plots revealed good linear correlations (r=0.83** for maize and r=0.77** for barley) between the reductions in leaf growth induced by a series of water potentials and associated reductions in leaf extensibility. In contrast, the reduction in growth of rice leaves, was not accompanied by any significant changes in leaf or cell wall extensibility. Similarly, regression plots revealed poor correlations between leaf growth and leaf extensibility in both paddy and upland rice (r=0.17 and r=0.07, respectively). Thus, despite numerous inter-species similarities, biophysical changes associated with stress-induced leaf growth inhibition in maize and barley, differed from those in rice.Key words: Cell walls, extensibility, water stress, cereal diversity, leaf growth.      

Copper resistance mechanisms in bacteria and fungi

Abstract: Copper is both an essential micronutrient and a toxic heavy metal for most living cells. The presence of high concentrations of cupric ions in the environment promotes the selection of microorganisms possessing genetic determinants for copper resistance. Several examples of chromosomal and plasmid copper-resistance systems in bacteria have been reported, and the mechanisms of resistance have started to be understood at the molecular level. Bacterial mechanisms of copper resistance are related to reduced copper transport, enhanced effiux of cupric ions, or copper complexation by cell components. Copper tolerance in fungi has also been ascribed to diverse mechanisms involving trapping of the metal by cell-wall components, altered uptake of copper, extracellular chelation or precipitation by secreted metabolites, and intracellular complexing by metallothioneins and phytochelatins; only the metallothionein chelation mechanism has been approached with molecular detail.     

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

The mammalian gut is an attractive model for exploring the general question of how habitat impacts the evolution of gene content. Therefore, we have characterized the relationship between 16 S rRNA gene sequence similarity and overall levels of gene conservation in four groups of species: gut specialists and cosmopolitans, each of which can be divided into pathogens and non-pathogens. At short phylogenetic distances, specialist or cosmopolitan bacteria found in the gut share fewer genes than is typical for genomes that come from non-gut environments, but at longer phylogenetic distances gut bacteria are more similar to each other than are genomes at equivalent evolutionary distances from non-gut environments, suggesting a pattern of short-term specialization but long-term convergence. Moreover, this pattern is observed in both pathogens and non-pathogens, and can even be seen in the plasmids carried by gut bacteria. This observation is consistent with the finding that, despite considerable interpersonal variation in species content, there is surprising functional convergence in the microbiome of different humans. Finally, we observe that even within bacterial species or genera 16S rRNA divergence provides useful information about average conservation of gene content. The results described here should be useful for guiding strain selection to maximize novel gene discovery in large-scale genome sequencing projects, while the approach could be applied in studies seeking to understand the effects of habitat adaptation on genome evolution across other body habitats or environment types.     

Functional diversity and mechanisms of action of the semaphorins

The second EMBO workshop on ;Semaphorin function and mechanisms of action', held in the gorgeous surroundings of the 12th Century Abbaye des Vaulx de Cernay near Paris, France this May, brought together a wide range of scientists working in diverse systems with a common interest: the semaphorins. Emerging new themes discussed at the meeting included the recognition of an increasingly complex way in which different cells regulate responsiveness, and the significance of considering semaphorins in the pathology of various diseases.     

番茄青枯病拮抗菌的定向筛选及其抗病促生机制研究

[目的] 从抑病型番茄根际土壤中筛选青枯病的高效拮抗促生菌,阐明其防病促生机制。[方法] 以番茄青枯雷尔氏菌（Ralstonia solanacearum）为靶病原菌,采用平板抑菌圈法,筛选拮抗菌;通过BOX-PCR指纹图谱鉴定菌株多样性,以平板透明圈法评价其产酶活性,并针对抑菌能力强、产酶种类多的拮抗菌开展16S rRNA基因系统发育分析;通过温室试验评价拮抗菌的防病促生能力,并在此基础上通过实时荧光定量PCR研究生防细菌对番茄青枯病的防病促生机制。[结果] 从番茄根际土壤分离获得29株细菌,其中15株对青枯菌具有拮抗功能,进一步通过BOX-PCR指纹图谱、酶活分析获得4株具有潜在防治番茄青枯病、促进生长的功能菌（B2、B5、B20、B23）,通过16S rRNA系统发育分析鉴定B2拮抗菌为解淀粉芽孢杆菌（Bacillus amyloliquefaciens）,B5和B20拮抗菌为枯草芽孢杆菌（Bacillus subtilis）,B23拮抗菌为贝莱斯芽孢杆菌（Bacillus velezensis）;温室试验表明,B2、B5、B20、B23拮抗菌的抑病效果分别为35.59%、8.47%、32.20%、96.61%,并且均能显著增加番茄生物量和生理性状,如地上部鲜重、总叶绿素含量、地下部根尖数等。B2、B5、B23拮抗菌显著促进番茄株高和根长,B2、B20、B23拮抗菌显著增加茎粗;而B23拮抗菌显著增加根系分叉数;实时荧光定量分析表明,B2、B20、B23拮抗菌株可促进抗病相关功能基因PR1α、POD1的表达量,B2、B5、B23拮抗菌促进吲哚乙酸（IAA）信号通路应答关键基因ctd1的表达量,B2、B5、B20、B23拮抗菌均降低乙烯（ETH）信号通路应答关键基因ERF2的表达量。[结论] 本研究分离筛选获得4株对番茄青枯病具有显著防治效果以及促进番茄生长的PGPR菌株,可为定向筛选植物促生防病菌提供理论依据。     

High diversity in DNA of soil bacteria

Soil bacterium DNA was isolated by minor modifications of previously described methods. After purification on hydroxyapatite and precipitation with cetylpyridinium bromide, the DNA was sheared in a French press to give fragments with an average molecular mass of 420,000 daltons. After repeated hydroxyapatite purification and precipitation with cetylpyridinium bromide, high-pressure liquid chromatography analysis showed the presence of 2.1% RNA or less, whereas 5-methylcytosine made up 2.9% of the total deoxycytidine content. No other unusual bases could be detected. The hyperchromicity was 31 to 36%, and the melting curve in 1 X SSC (0.15 M NaCl plus 0.015 M sodium citrate) corresponded to 58.3 mol% G+C. High-pressure liquid chromatography analysis of two DNA samples gave 58.6 and 60.8 mol% G+C. The heterogeneity of the DNA was determined by reassociation of single-stranded DNA, measured spectrophotometrically. Owing to the high complexity of the DNA, the reassociation had to be carried out in 6 X SSC with 30% dimethyl sulfoxide added. Cuvettes with a 1-mm light path were used, and the A275 was read. DNA concentrations as high as 950 micrograms ml-1 could be used, and the reassociation rate of Escherichia coli DNA was increased about 4.3-fold compared with standard conditions. C0t1/2 values were determined relative to that for E. coli DNA, whereas calf thymus DNA was reassociated for comparison. Our results show that the major part of DNA isolated from the bacterial fraction of soil is very heterogeneous, with a C0t1/2 about 4,600, corresponding to about 4,000 completely different genomes of standard soil bacteria.(ABSTRACT TRUNCATED AT 250 WORDS)     

Polarity and growth of caulonema tip cells of the moss Funaria hygrometrica

In the caulonema tip cells of Funaria hygrometrica, chloroplasts, mitochondria, and dictyosomes have differences in structure which are determined by cell polarity. In contrast to the slowly growing chloronema tip cells the apical cell of the caulonema contains a tip body. Colchicine stops tip growth; it causes the formation of subapical cell protrusions, redistribution of the plastids, and a loss of their polar differentiation. Cytochalasin B inhibits growth and affects the position of cell organelles. After treatment with ionophore A23 187, growth is slower and shorter and wider cells are formed. D₂O causes a transient reversion of organelle distribution but premitotic nuclei are not dislocated. In some tip cells the reversion of polarity persists; they continue to grow with a new tip at their base. During centrifugation, colchicine has only a slight influence on the stability of organelle anchorage. The former polar organization of most cells is restored within a few hours after centrifugation, and the cells resume normal growth. In premitotic cells the nucleus and other organelles cannot be retransported, they often continue to grow with reversed polarity. Colchicine retards the redistribution of organelles generally and increases the number of cells that form a basal outgrowth. The interrelationship between the peripheral cytoplasm and the nucleus and the role of microtubules in maintaining and reestablishing cell polarity are discussed.Abbreviations DMSO dimethylsulfoxide - CB cytochalasin B Dedicated to Prof. Dr. A. Pirson on the occasion of his 70. birthday     

Adaptive survival mechanisms and growth limitations of small-stature herb species across a plant diversity gradient

Several biodiversity experiments have shown positive effects of species richness on aboveground biomass production, but highly variable responses of individual species. The well-known fact that the competitive ability of plant species depends on size differences among species, raises the question of effects of community species richness on small-stature subordinate species. We used experimental grasslands differing in species richness (1-60 species) and functional group richness (one to four functional groups) to study biodiversity effects on biomass production and ecophysiological traits of five small-stature herbs (Bellis perennis, Plantago media, Glechoma hederacea, Ranunculus repens and Veronica chamaedrys). We found that ecophysiological adaptations, known as typical shade-tolerance strategies, played an important role with increasing species richness and in relation to a decrease in transmitted light. Specific leaf area and leaf area ratio increased, while area-based leaf nitrogen decreased with increasing community species richness. Community species richness did not affect daily leaf carbohydrate turnover of V. chamaedrys and P. media indicating that these species maintained efficiency of photosynthesis even in low-light environments. This suggests an important possible mechanism of complementarity in such grasslands, whereby smaller species contribute to a better overall efficiency of light use. Nevertheless, these species rarely contributed a large proportion to community biomass production or achieved higher yields in mixtures than expected from monocultures. It seems likely that the allocation to aboveground plant organs to optimise carbon assimilation limited the investment in belowground organs to acquire nutrients and thus hindered these species from increasing their performance in multi-species mixtures.     

溶藻细菌的功能多样性及其菌剂应用

溶藻细菌(algicidal bacteria)是一种以直接或间接方式杀灭藻细胞或抑制其生长的细菌.本文聚焦溶藻细菌的应用研究现状,从溶藻菌剂的类型、搭配策略、应用形式与场景等角度综述了 5个门78个属的溶藻细菌以及7个门56个属的目标藻类的研究进展.总结发现Bacillus spp.、Streptomyces spp...