PHYPred:a tool for identifying bacteriophage enzymes and hydrolases

Dear Editor,Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle.Many studies have reported that phages are more specific to bacteria than antibiotics are;thus,phage therapy has many potential applications in human medicine,with the advantage of having few side effects(Keen,2012).Investigating the mechanisms of bacteria-killing phages will therefore aid     

Morphological diversity of cultured cold-active lytic bacteriophages isolated from the Napahai plateau wetland in China

<正>Dear Editor,Viruses are the most abundant,diverse,and ubiquitous entities(approximately 1031)on Earth.They play major roles in horizontal gene transfer,the regulation of bacterial community structures,as well as nutrient and energy cycles of marine ecosystems(Danovaro et al.,2008).In particular,lytic bacteriophages(phages)can infect and kill bacteria without harming human or animal     

Application of phage-displayed single chain antibodies in western blot

A phage display single chain fragment variable library constructed on pⅢ protein of M13 filamentous phage was screened using B-lymphocyte stimulator and FP248 as selective molecules. After four rounds of panning, there was a remarkable enrichment in the titer of bound phages. Twenty phage clones were selected from the last round and screened by means of phage-ELISA. With the antibody phages as primary antibodies in Western blot, we developed a method for detecting the specific antigen. The dilutions of antibody phages depend on the affinity between antibody-displayed phage particles and antigens.     

CRISPR-Cas adaptive immune systems in Sulfolobales: genetic studies and molecular mechanisms

CRISPR-Cas systems provide the small RNA-based adaptive immunity to defend against invasive genetic elements in archaea and bacteria. Organisms of Sulfolobales, an order of thermophilic acidophiles belonging to the Crenarchaeotal Phylum, usually contain both type I and type Ⅲ CRISPR-Cas systems. Two species, Saccharolobus solfataricus and Sulfolobus islandicus, have been important models for CRISPR study in archaea, and knowledge obtained from these studies has greatly expanded our understanding of molecular mechanisms of antiviral defense in all three steps: adaptation, expression and crRNA processing, and interference. Four subtypes of CRISPR-Cas systems are common in these organisms, including I-A, I-D, Ⅲ-B, and Ⅲ-D. These cas genes form functional modules, e.g., all genes required for adaptation and for interference in the I-A immune system are clustered together to form aCas and i Cas modules. Genetic assays have been developed to study mechanisms of adaptation and interference by different CRISPR-Cas systems in these model archaea, and these methodologies are useful in demonstration of the protospacer-adjacent motif(PAM)-dependent DNA interference by I-A interference modules and multiple interference activities by Ⅲ-B Cmr systems. Ribonucleoprotein effector complexes have been isolated for Sulfolobales Ⅲ-B and Ⅲ-D systems, and their biochemical characterization has greatly enriched the knowledge of molecular mechanisms of these novel antiviral immune responses.     

Genetic diversity of Harpins from Xanthomonas oryzae and their activity to induce hypersensitive response and disease resistance in tobacco

The hrp (hypersensitive response and patho-genicity) gene clusters in Gram-negative phytopatho-genic bacteria determine hypersensitive response (HR) in non-host plants and pathogenicity in host plants of the bacteria[1—3]. An hrp gene cluster usually contains genes coding for the components of the type Ⅲ se-cretion pathway, effectors and the proteins that regu-late the productions and transportations of effectors[4]. Many effectors such as Harpins and Avr proteins are believed secreted by …     

Pollen Morphology of Eight Genera of the Subtribe Mutisiinae Less. sensu Bremer （Compositae） from Asia

The pollen morphology of 28 species and one variety representing eight genera of the subtribe Mutisiinae Less. sensu Bremer （Compositae） was investigated by scanning electron microscopy （SEM） and light microscopy. The pollen grains are usually radically symmetrical, isopolar, and tricolporate. The shape varies from spheroidal to subprolate in equatorial view and is three-lobed circular in polar view. Based on exine sculpturing observed under SEM, the pollen grains can be divided into three types： （i） type Ⅰ, with macrogranulate sculpture; （ii） type Ⅱ, with a finely granulate sculpture; and （iii） type Ⅲ with spiny sculpture. The palynological data showed that the Macroclinidium Maxim. was remarkably distinguished from those of the other seven genera. The variation of pollen characteristics within the Mutisiinae in Asia is little at species level, but it proves some useful information for studying the relationships among genera and it has an important significance in further understanding the evolutionary history of Mutisiinae.     

The host type I interferon response to viral and bacterial infections

Type I interferons (IFN) are well studied cytokines with anti-viral and immune-modulating functions. Type I IFNs are produced following viral infections, but until recently, the mechanisms of viral recognition leading to IFN production were largely unknown. Toll like receptors (TLRs) have emerged as key transducers of type I IFN during viral infections by recognizing various viral components. Furthermore, much progress has been made in defining the signaling pathways downstream of TLRs for type I IFN production. TLR7 and TLR9 have become apparent as universally important in inducing type I IFN during infection with most viruses, particularly by plasmacytoid dendritic cells. New intracellular viral pattern recognition receptors leading to type I IFN production have been identified. Many bacteria can also induce the up-regulation of these cytokines. Interestingly, recent studies have found a detrimental effect on host cells if type Ⅰ IFN is produced during infection with the intracellular gram-positive bacterial pathogen, Listeria monocytogenes. This review will discuss the recent advances made in defining the signaling pathways leading to type I IFN production.     

Effects of different molecular weight fractions of dissolved organic matter on the growth of bacteria,algae and protozoa from a highly humic lake

Effects of different molecular size fractions (< 1000 MW, < 10 000 MW, < 100 000 MW and <0.1 μm) of dissolved organic matter (DOM) on the growth of bacteria, algae and protozoa from a highly humic lake were investigated. DOM from catchment drainage water as well as from the lake consisted mostly (59–63%) of high molecular weight (HMW) compounds (> 10 000 MW). With excess inorganic nutrients, the growth rate and yield of bacteria were almost identical in all size fractions. However, in < 1000 MW fractions and with glucose added, a longer lag phase occurred. Without added nutrients both the growth rates and biomasses of bacteria decreased towards the smaller size fractions and the percentage of dissolved organic carbon (DOC) used during the experiment and the growth efficiency of bacteria were lower than with excess nutrients. The growth efficiency of bacteria was estimated to vary between 3–66% in different MW fractions, largely depending on the nutrient concentrations, but the highest growth efficiencies were observed in HMW fractions and with glucose. The growth of algae was clearly lowest in the < 1000 MW fraction. In dim light no net growth of algae could be found. In contrast, added nutrients substantially enhanced algal growth and in deionized water with glucose, algae achieved almost the same growth rate and biomass as in higher MW fractions of DOM. The results suggested that bacteria and some algae were favoured by DOM, but protozoans seemed to benefit only indirectly, through bacterial grazing. The utilization of DOM by bacteria and algae was strongly affected by the availability of phosphorus and nitrogen.     

Community composition and spatial variation of bacteria in the sediments of a eutrophic fresh water urban lake， East Lake， Wuhan， China北大核心CSCD

［Objective］ Sediment bacteria are the important biological factors for remediating of eutrophic environments. To enrich our understanding of the bacteria communities in eutrophic urban lake sediments for better environment protection and pollution control in urban lake eco-systems, we resolved the composition of bacteria communities and their spatial variation in the sediments of a middle-size eutrophic urban lake, East Lake. ［Methods］We used 16S rRNA gene RFLP and sequencing methods to generate the phylogeny information of the bacteria community, used principal coordinates analysis （PCoA） and canonical correspondence analysis （CCA） methods to resolve the relationship between East Lake and other lakes, and the relationship between environmental factors and the bacteria communities. ［Results］ Sediments inhabited 13 phyla and 2 unclassified clusters. PCoA further revealed that the bacteria communities in three sub-lakes of East Lake sediments were closely related to the communities in similar eutropic lake environments, and divergent from the hypereutrophic sub-lake Miao Lake, which was also found to inhabit a relative abundant amount of Thermogymnomonas-type archaea. CCA further revealed that the distribution of bacteria was closely correlated with the carbon, nitrogen and phosphate contents in the sediments. ［Conclusion］The environment factors regulated the bacteria community composition and distribution. The results of this study providereference to the research, protection and pollution control on urban lake eco-systems.     

Identification of one peptide which inhibited infectivity of avian infectious bronchitis virus in vitro

Purified avian infectious bronchitis virus (IBV) was used to screen a random phage display peptide library. After the fourth panning, 10 positive phages were sequenced and characterized. The phages specifically inhibited IBV infectivity in HeLa cells and blocked IBV haemagglutination. One linear peptide “GSH HRH VHS PFV” from the positive phages with the highest neutralization titer was synthesized and this peptide inhibited IBV infection in HeLa as well. The results may contribute to development of antiviral therapeutics for IBV and studying the determinants for viral and cell interac-tion.     

Defined medium for primary culture de novo of adult rat alveolar epithelial cells

Summary Isolated type II pneumocytes grown in serum on tissue culture-treated polycarbonate filters form monolayers with characteristic bioelectric properties, and change morphologically with time in culture to resemble type I cells. Concurrently, the cells express type I cell surface epitopes, making this a potentially useful in vitro model with which to study regulation of alveolar epithelial cell function and differentiation. To define specific soluble growth factors and matrix substances that may regulate these processes, it would be preferable to culture isolated pneumocytes de novo under completely defined, serum-free conditions. In this study, we developed a completely defined serum-free medium that is capable of supporting alveolar epithelial cells in primary culture, allowing the formation of monolayers with characteristic bioelectric and phenotypic properties. Freshly isolated rat type II cells were resuspended in completely defined serum-free medium and plated de novo on polycarbonate filters. Plating efficiency, bioelectric properties, morphology, and binding of a type I cell-specific monoclonal antibody were determined as functions of time. Plating efficiency plateaus at about 14% by Day 3 in culture. Transepithelial resistance rises to high levels, peaking at 1.76±0.14 KΩ-cm² by Day 5 in culture. Short-circuit current peaks on Day 3 in culture at 2.71±0.35 μA/cm². With time, the cells gradually become flattened with protuberant nuclei and long cytoplasmic extensions, more closely resembling type I cells, and begin to express a type I cell surface epitope. These observations indicate that it is feasible to culture alveolar epithelial cell monolayers under completely defined serum-free conditions de novo. This culture system should prove useful for identifying soluble growth factors and matrix substances that modulate alveolar epithelial cell biological properties.     

Isolation and characterization of a lytic bacteriophage φKp-lyy15 of Klebsiella pneumoniae

<正>Dear Editor,Bacteriophages(phages)are viruses that specifically infect and kill bacteria.They are ubiquitous throughout all environments that bacteria inhabit.Following their discovery by F.W.Twort in 1915 and F.d'Herele in 1917,bacteriophages were recognized as potential agents to treat bacterial diseases and phage therapy has been used     

The Xanthomonas type Ⅲ effector Xop AP prevents stomatal closure by interfering with vacuolar acidification

Plant stomata close rapidly in response to a rise in the plant hormone abscisic acid(ABA) or salicylic acid(SA) and after recognition of pathogenassociated molecular patterns(PAMPs). Stomatal closure is the result of vacuolar convolution, ion efflux, and changes in turgor pressure in guard cells. Phytopathogenic bacteria secrete type Ⅲ effectors(T3Es) that interfere with plant defense mechanisms, causing severe plant disease symptoms. Here, we show that the virulence and infection of Xanthomonas...     

Vertical distributions of bacteria and algae in a steeply stratified humic lake under high grazing pressure from Daphnia longispina

The vertical distributions of bacteria and algae in a steeply stratified, highly humic lake were studied during three 24 h periods in summer. The highest bacterial and algal densities and biomasses were recorded in the anoxic hypolimnion. The bacterial biomass in the hypolimnion was composed mainly of photosynthetic green sulphur bacteria (Chlorobium) which occurred at very low light intensity (< 1.5 μmol m⁻² s⁻¹). The numbers and biomasses of bacteria, both in the epilimnion and hypolimnion, were mostly higher at night than during the day, indicating possible asynchrony between the production and loss of bacteria. Because of vertical migration, the diurnal vertical distribution of algae was more variable than that of bacteria. Particularly in July and August, when cryptomonads were abundant, the biomass of algae was much higher in the epilimnion during the day than at night. The flagellated chlorophytes, Chlamydomonas spp. and Scourfieldia cordiformis, stayed mainly in the upper hypolimnion close to the oxic-anoxic boundary zone where only a small proportion of Daphnia longispina was continuously present. Unpalatable Mallomonas chrysophytes with silicified plates and bristles, and small, presumably heterotrophic, flagellates stayed in the oxic epilimnion together with a dense (up to 300 ind l⁻¹) population of D. longispina. The results indicated that, besides the physical and chemical properties of the water column, grazing pressure by Daphnia longispina strongly affected the vertical distribution of microorganisms in this polyhumic lake.     

A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604 (ATCC 27647)

<正>Dear Editor,Transposable phages,which are reproduced by transposition(Harshey,2012;Taylor,1963),have been widely applied in the field of biotechnology to manipulate operon/gene fusions,in vivo cloning,randomion mutagenesis,and integration of DNA into bacterial genomes(Abalakina et al.,2008;Akhverdyan et al.,2011).One of the best-studied transposable phages is     

MicroRNAs and type 2 diabetes/obesity

MicroRNAs belong to a newly identified class of small non-coding RNAs that have been widely implicated in the fine-tuning of many physiological processes such as the pathogenesis of type 2 diabetes(T2D) and obesity.Microarray studies have highlighted an altered profile of miRNA expression in insulin target tissues in diabetic and obese models.Emerging evidences suggest that miRNAs play significant roles in insulin production,secretion and actions,as well as in diverse aspects of glucose homeostasis and adipocyte differentiation. The identification of tissue-specific miRNAs implicated in T2D and obesity might be useful for the future development of effective strategies for early diagnosis and therapeutic intervention of obesity-related medical complications.     

Nitrogen transformations in stratified aquatic microbial ecosystems

New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a μm–mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.     

Two distinct conjugal transfer systems on Streptomyces plasmid pZL1

The mechanism of conjugal transfer of plasmids in Gram-negative and unicellular Gram-positive bacteria is commonly via a type IV secretion system （T4SS） [1]. The genes encoding the T4S proteins are usually arranged in a single operon or a few operons. In Gram-negative Agrobacterium tumefaciens, the T4SS is encoded by the virB and virD operons （11 and 5 genes, respectively） [2]. Streptomyces are multicellular mycelial Gram-positive bac- teria that form unicellular spores. There are fundamental dif- ferences in the mechanisms of conjugal transfer between Streptomyces plasmids and those of Gram-negative and uni- cellular Gram-positive bacteria. Conjugal transfer of Streptomyces plasmids requires a tra gene encoding an FtsK/SpolIIE-family DNA translocator and a few adjacent genes [3]. No bacterial T4SS has previously been found on Streptomyces conjugative plasmids. We reported here the co- existence of both a T4SS-like and an FtsK/SpolIIE-family DNA translocator on a 128-kb Streptomyces plasmid, pZL 1.     

不同悉生培养条件下食细菌线虫对细菌种群的影响

A gnotobiotic microcosm experiment was conducted to study the influence of bacterivorons nematodes (Protorhab-ditis sp. ) on bacteria (Pseudomonas fluorescens) population under different conditions including substrate concen-tration, oscillation pattern, and numbers of nematodes inoculated. When the bacteria were incubated under intermit-tent oscillation by hand (6 times at 0.5 h intervals, 22℃ ), their growth was stimulated in the presence of nema-todes, and the bacteria grew faster with the increase of nematode numbers and substrate (liquid potato-sucrose medi-um) concentration. However, when the incubation was under continuous oscillation (100 rpm, 22℃ ), bacteria pop-ulation was deflated with the addition of nematodes, and the inhibition was greater when a higher concentration of substrate was used. It was found that the stimulation or inhibition of bacteria population by nematodes occurred in the logarithmic stage of bacteria growth. The optimal and over-grazing of nematodes on regulating bacteria popula-tion was discussed.