Low Level Of Similarity Research Articles

Variabilities on DNA Level of Two Selected Potato Genotypes under Seawater Salinity

Random Amplified Polymorphic DNA (RAPD) banding patterns of selected potato (Cara) and (Lady Rosetta), under seawater salinity stress, on agarose gel showed (9 and 10) distinct RAPD profiles generated by five of different 10-mers oligonucleotides primers. The recorded RAPD data of both potato genotypes showed highly polymorphism and low levels of similarity between and inside the treated samples and the untreated control sample. The RAPD analysis of the treated plants of Lady Rosetta showed 363 amplified bands of the treated and control plants whereas the treated plants distributed as ~50.41% unique polymorphic bands, ~29.75% of repeated polymorphic bands and ~6.89% of monomorphic bands as compared with the control plants which showed ~8% unique polymorphic bands and ~4.95% monomorphic bands. However, with Cara, the RAPD analysis showed 227 amplified bands of the treated and control plants whereas the treated plants distributed as ~48.02% of unique polymorphic bands and ~31.28% of repeated polymorphic bands and ~4.4% of monomorphic bands as compared with the control plants which showed ~13.22% unique polymorphic bands and ~3.08% monomorphic bands as compared with the treated plants. There is no doubt that, the gain or the loss of parts of the DNA may consider as speculation the reason for salinity tolerance in the presented work. On the other hand, the exposure to the salinity stress leads to induce changes on the DNA level.

Genetic Diversity Analysis of Forty Pearl Millet (<i>Pennisetum glaucum</i> (L.) R. Br) Accessions from Sudan Using Agronomical Descriptors and DNA Molecular Markers

Morphological descriptors and Random Amplification of Polymorphic DNA (RAPD) technique were used to assess the genetic variation among and within forty Pennesitum glaucum accessions from Sudan. Accessions were collected from 30 villages representing Darfur, North Kordofan, South Kordofan, and Blue Nile states. 64 amplified fragments were distinguished using ten primers. 63 bands were polymorphic among the forty accessions with an average of 6.3 polymorphic bands per primer. Low level of genetic similarity was observed (4% - 43%). The PhiPT (analogue of FST fixation index) value for genetic variability obtained over the four regions was 0.169 with high significance (P = 0.01). AMOVA analysis showed higher variance components within regions (80%) than among regions (20%). The two dendrograms obtained by Random Amplification of Polymorphic DNA (RAPD) data; and morphological data based on 26 descriptors did not fit together. PCA (Principal coordinate’s analysis) showed geographic structuring of pearl millet according to its growing regions in Sudan.

High-resolution melting PCR assay, applicable for diagnostics and screening studies, allowing detection and differentiation of several Babesia spp. infecting humans and animals

The goal of the study was to design a single tube PCR test for detection and differentiation of Babesia species in DNA samples obtained from diverse biological materials. A multiplex, single tube PCR test was designed for amplification of approximately 400 bp region of the Babesia 18S rRNA gene. Universal primers were designed to match DNA of multiple Babesia spp. and to have low levels of similarity to DNA sequences of other intracellular protozoa and Babesia hosts. The PCR products amplified from Babesia DNA isolated from human, dog, rodent, deer, and tick samples were subjected to high-resolution melting analysis for Babesia species identification. The designed test allowed detection and differentiation of four Babesia species, three zoonotic (B. microti, B. divergens, B. venatorum) and one that is generally not considered zoonotic—Babesia canis. Both detection and identification of all four species were possible based on the HRM curves of the PCR products in samples obtained from the following: humans, dogs, rodents, and ticks. No cross-reactivity with DNA of Babesia hosts or Plasmodium falciparum and Toxoplasma gondii was observed. The lack of cross-reactivity with P. falciparum DNA might allow using the assay in endemic malaria areas. The designed assay is the first PCR-based test for detection and differentiation of several Babesia spp. of medical and veterinary importance, in a single tube reaction. The results of the study show that the designed assay for Babesia detection and identification could be a practical and inexpensive tool for diagnostics and screening studies of diverse biological materials.

Improving insect control protein activity for GM crops: A case study demonstrating that increased target insect potency can be achieved without impacting mammalian safety

Many insect-protected crops express insecticidal crystal (Cry) proteins derived from the soil bacterium Bacillus thuringiensis (Bt), including both naturally-occurring Cry proteins and chimeric Cry proteins created through biotechnology. The Cry51Aa2 protein is a naturally-occurring Cry protein that was modified to increase its potency and expand its insect activity spectrum through amino acid sequence changes. The improved Cry51Aa2 variant, Cry51Aa2.834_16, and other developmental variants belong to the ETX_MTX2 family of proteins but share a low level of sequence similarity to other members of this family. This similarity is largely localized to the pore-forming and oligomerization protein domains, while sequence divergence is observed within the head domain that confers receptor binding specificity. The intact Cry51Aa2.834_16 protein was heat labile at temperatures ≥55 °C, and was rapidly degraded after exposure to the gastrointestinal protease pepsin. No acute oral toxicity was observed in mice for three protein variants of Cry51Aa2, including Cry51Aa2.834_16, at doses exceeding 1000 mg/kg body weight. The weight-of-evidence therefore supports the conclusion of safety for Cry51Aa2.834_16 and demonstrates that amino acid sequence modifications can be used to substantially increase insecticidal activity of a protein without an increased hazard to mammals.

Multi-indicator Evaluation and Analysis of Coordinated Industrial Development of Urban Agglomerations

The level of coordinated industrial development in a region is considered as an important factor of measuring the construction of urban agglomerations. As the economic development patterns and stages vary in regions, a single-standard evaluation system is generally insufficient in evaluating and analyzing the coordinated industrial development of urban agglomerations. This paper, with multivariate values and diversified development demands considered, quantitatively describes the industrial development of urban agglomerations from four dimensions: economics, specialization, balance, and friendliness. On this basis, it synthesizes the indicator parameters effectively and proposes a multi-indicator evaluation model. Through the model, the paper comparatively analyzes the present status and development course of coordinated industrial development of typical urban agglomerations (Beijing–Tianjin–Hebei urban agglomeration, the Yangtze River Delta urban agglomeration, and the Pearl River Delta urban agglomeration) in China. The results show that Beijing–Tianjin–Hebei urban agglomeration has the clearest division of industries, but its industrial spillover effect is limited, the industrial structure of small and medium cities is too simple, and the economic gap among cities narrows at a very slow rate. The core cities in the Yangtze River Delta urban agglomeration exert certain driving effect upon the economy of their surrounding areas. However, they hardly give full play to their comparative advantages due to a low level of regional integration and high industrial similarity among cities. Compared with the above two urban agglomerations, the Pearl River Delta urban agglomeration enjoys more reasonable division of industries among cities, significant driving effect of core cities, and higher level of coordinated industrial development as driven by the market economy.

Perceptions of Vocational Interest

The current study investigated how self- and other-ratings of vocational interests converge among student–parent dyads. Using the Personal Globe Inventory–Short, we obtained data from a pooled sample of 271 (high school senior and university) student–parent dyads. Participants rated their own vocational interests and those of the other dyad member. First, profile correlations revealed high levels of self-other agreement, moderate levels of assumed similarity, and low levels of similarity and reciprocity in vocational interests. These correlations are highly similar to those found in personality research. Second, profile elevation showed a reversed pattern compared to interest perceptions, with high levels of self-other agreement and moderate levels of assumed similarity, indicating that profile elevation may mostly be an artifact/rater bias and not a substantive factor. Ipsatization of the vocational interest scales somewhat reduced profile elevation bias. Third, same-gender dyads overestimated their similarity in vocational interests more than different-gender dyads.

Exploitation and Exploration in International Joint Ventures: Moderating Effects of Partner Control Imbalance and Product Similarity

International joint ventures (IJVs) need to exploit their existing resources as well as explore new capabilities to capture the potential in emerging markets. This study develops a contingent view, arguing that the efficacy of exploitation and exploration depends on the levels of control imbalance and product similarity between an IJV's foreign and local partners. A sample of 198 IJVs in China reveals that partner control imbalance has a U-shaped moderating effect on the relationship between exploitation and IJV new product performance but has an inverted U-shaped moderating effect on the effectiveness of exploration. Exploitation relates more strongly to IJV new product performance when partner product similarity is high, whereas exploration has a stronger impact on IJV new product performance at low levels of partner product similarity. These findings provide novel insights for IJVs to better manage exploitation and exploration in their new product development.

Genetic Relationship and Similarity of Some Chicken Strains

Blood samples were collected from the four chicken strain (twenty males and twenty females) . (Ross, Indian River as meat type and, ISA Brown, Hy Line Brown as egg type chicken ) . Blood samples were collected in 3 ml tubes containing EDTA. Genomic DNA was extracted from 300 μl of blood. DNA purity and concentrations have been measured by Nano Drop® spectrophotometer. Random amplification of polymorphic DNA (RAPD-PCR) was done by using 35 primers from GenScript USA company. A total of 21 Primers gave results to find a complementary DNA Genomic sites. The PCR program included an initial denaturation step at 94 °C for 5 minutes followed by 40 cycles with 94 °C for 1 minutes for DNA denaturation, annealing as mentioned with each primer, extension at 72 °C for 1 minutes and final extension at 72 °C for 5 minute were carried out. The PCR products were tested with electrophoresis on 2 % agarose gels in 1x TBE buffer stained by Ethidium bromide. The amplified pattern was visualized on a UV trans and photographed .Statistical Analysis of RAPD bands were scored for their presence (1) or absence (0). The index of similarity between each two population’s genetic distances was calculated. Polymorphism of each primer was calculated. The highest number of bands was 134 bands among all groups used and which was created by the OPA-13 Primer, and the lowest number of bands was 5 bands, which was created by OPA-03 Primer. The total number of bands created by all the Primers was 1724 and the total number of polymorphic band created by all the Primers was 216. The Primer OPQ-O4 had the highest number of polymorphic bands being 18 bands. While the Primer OPA-15 possessed the lowest number of polymorphic band being 2 bands. The average number was 12.77 of polymorphic bands per primer. The highest percentage of the Polymorphisms observed in the primer OPA-19, was 29.09% when compared with other primers in this study, where the lowest percentage of Polymorphisms was of primer of OPA-15 being 4.55%. A high level of genetic similarity was also observed between the meat type chickens and it was 0.741 between Ross ♀ and Indian ♀. A low level of genetic similarity was also observed between the meat and eggs chickens being 0.587 between Ross ♀ and ISA ♀.

Similarity and diversity of the tumor microenvironment in multiple metastases: critical implications for overall and progression-free survival of high-grade serous ovarian cancer.

The tumor microenvironment is pivotal in influencing cancer progression and metastasis. Different cells co-exist with high spatial diversity within a patient, yet their combinatorial effects are poorly understood. We investigate the similarity of the tumor microenvironment of 192 local metastatic lesions in 61 ovarian cancer patients. An ecologically inspired measure of microenvironmental diversity derived from multiple metastasis sites is correlated with clinicopathological characteristics and prognostic outcome. We demonstrate a high accuracy of our automated analysis across multiple sites. A low level of similarity in microenvironmental composition is observed between ovary tumor and corresponding local metastases (stromal ratio r = 0.30, lymphocyte ratio r = 0.37). We identify a new measure of microenvironmental diversity derived from Shannon entropy that is highly predictive of poor overall (p = 0.002, HR = 3.18, 95% CI = 1.51-6.68) and progression-free survival (p = 0.0036, HR = 2.83, 95% CI = 1.41-5.7), independent of and stronger than clinical variables, subtype stratifications based on single cell types alone and number of sites. Although stromal influence in ovary tumors is known to have significant clinical implications, our findings reveal an even stronger impact orchestrated by diverse cell types. Quantitative histology-based measures can further enable objective selection of patients who are in urgent need of new therapeutic strategies such as combinatorial treatments targeting heterogeneous tumor microenvironment.

Rhizobium gei sp. nov., a bacterial endophyte of Geum aleppicum.

A bacterial strain, designated as ZFJT-2T, was isolated from the stem of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain ZFJT-2T were Gram-stain-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, 11-methyl C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), and the DNA G+C content was 58.3 mol% (HPLC). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFJT-2T was a member of the genus Rhizobium and was most closely related to Rhizobium giardinii KACC 10720T (98.6 % similarity) and Rhizobium herbae CCBAU 83011T (98.5 %). The low levels of sequence similarity found between the atpD, recA and glnII gene sequences of strain ZFJT-2T and those of recognized species of the genus Rhizobium (no more than 94.4, 87.2 and 89.5 %, respectively) indicated that it may represent a separate species of the genus Rhizobium. The DNA-DNA relatedness values for strain ZFJT-2T with respect to R. giardinii KACC 10720T and R. herbae CCBAU 83011T were 17.6 and 41.9 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, strain ZFJT-2T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium gei sp. nov. is proposed. The type strain is ZFJT-2T (=CCTCC AB 2013015T=KCTC 32301T=LMG 27603T).

Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system.

BackgroundBiofloc technology (BFT), a rearing method with little or no water exchange, is gaining popularity in aquaculture. In the water column, such systems develop conglomerates of microbes, algae and protozoa, together with detritus and dead organic particles. The intensive microbial community presents in these systems can be used as a pond water quality treatment system, and the microbial protein can serve as a feed additive. The current problem with BFT is the difficulty of controlling its bacterial community composition for both optimal water quality and optimal shrimp health. The main objective of the present study was to investigate microbial diversity of samples obtained from different culture environments (Biofloc technology and clear seawater) as well as from the intestines of shrimp reared in both environments through high-throughput sequencing technology.ResultsAnalyses of the bacterial community identified in water from BFT and “clear seawater” (CW) systems (control) containing the shrimp Litopenaeus stylirostris revealed large differences in the frequency distribution of operational taxonomic units (OTUs). Four out of the five most dominant bacterial communities were different in both culture methods. Bacteria found in great abundance in BFT have two principal characteristics: the need for an organic substrate or nitrogen sources to grow and the capacity to attach to surfaces and co-aggregate. A correlation was found between bacteria groups and physicochemical and biological parameters measured in rearing tanks. Moreover, rearing-water bacterial communities influenced the microbiota of shrimp. Indeed, the biofloc environment modified the shrimp intestine microbiota, as the low level (27 %) of similarity between intestinal bacterial communities from the two treatments.ConclusionThis study provides the first information describing the complex biofloc microbial community, which can help to understand the environment-microbiota-host relationship in this rearing system.

Study of bacterial community structure and diversity during the maturation process of a therapeutic peloid

The presence of bacteria in peloids is essential for the development of their therapeutic properties. Therefore, the study of bacterial community composition in peloids and its changes along the maturation process is of paramount importance. For this purpose, samples of thermal waters and peloids at different stages of maturation were collected and the MiSeq Illumina sequencing platform was employed to obtain information on bacterial diversity and community structure. Richness and diversity indices showed that a clear change during the first period of maturation occurred, while, after two months, the community seemed to stabilize. The same results were obtained based on the different OTU present. A phylogenetic analysis was performed and taxonomic affiliations for sequences with abundance higher than 1% and important to determine differences among samples were obtained. Relative abundance of bacterial community composition was also investigated. Analysis indicated a dominance of α- and β-Proteobacteria in water samples, while γ-Proteobacteria prevailed in peloids. Again, biodiversity profiles showed a low level of similarity between water and peloids, while in all peloid samples the populations were almost the same. Results demonstrate that the bacterial community in peloids changed mostly on the early stages of maturation and it reached stability after two months.

Transcriptome Analysis of the Sydney Rock Oyster, Saccostrea glomerata: Insights into Molluscan Immunity

BackgroundOysters have important ecological functions in their natural environment, acting as global carbon sinks and improving water quality by removing excess nutrients from the water column. During their life-time oysters are exposed to a variety of pathogens that can cause severe mortality in a range of oyster species. Environmental stressors encountered in their habitat can increase the susceptibility of oysters to these pathogens and in general have been shown to impact on oyster immunity, making immune parameters expressed in these marine animals an important research topic.ResultsPaired-end Illumina high throughput sequencing of six S. glomerata tissues exposed to different environmental stressors resulted in a total of 484,121,702 paired-end reads. When reads and assembled transcripts were compared to the C. gigas genome, an overall low level of similarity at the nucleotide level, but a relatively high similarity at the protein level was observed. Examination of the tissue expression pattern showed that some transcripts coding for cathepsins, heat shock proteins and antioxidant proteins were exclusively expressed in the haemolymph of S. glomerata, suggesting a role in innate immunity. Furthermore, analysis of the S. glomerata ORFs showed a wide range of genes potentially involved in innate immunity, from pattern recognition receptors, components of the Toll-like signalling and apoptosis pathways to a complex antioxidant defence mechanism.ConclusionsThis is the first large scale RNA-Seq study carried out in S. glomerata, showing the complex network of innate immune components that exist in this species. The results confirmed that many of the innate immune system components observed in mammals are also conserved in oysters; however, some, such as the TLR adaptors MAL, TRIF and TRAM are either missing or have been modified significantly. The components identified in this study could help explain the oysters’ natural resilience against pathogenic microorganisms encountered in their natural environment.

Demographic variability indicators of somatically healthy men from different administrative and territorial regions of Ukraine

Abstract Our work has revealed a rather low level of similarity in regard to the finger dermatoglyphics of somatically healthy men, 19-35 years old, between Ukraine’s north and west, north and south, center and west, center and south, as well as the palmar dermatoglyphics between central regions and the east, center and west, center and south. The obtained finger/palmar dermatoglyphics did not differentiate administrative-territorial local groups of men between the north and the center, south and west (quantitative characteristics); or palmar – between the north and west, north and east, south and west, south and east, north and center. The differences between the administrative and territorial division of dermatoglyphic signs are a reflection of the historical and cultural differences induced by migration, as well as the intensive process of mixing, in addition to the isolation of particular groups.

Rubiaceae in Brazilian Atlantic Forest remnants: floristic similarity and implications for conservation.

Brazil holds most of the Atlantic Forest Domain and is also one of the Rubiaceae diversity centers in the Neotropics. Despite the urban expansion in the state of Rio de Janeiro, large areas of continuous vegetation with high connectivity degree can still be found. Recently, new Rubiaceae species have been described in the Rio de Janeiro flora, which present small populations and very particular distribution. The current paper analyzed the similarity in the floristic composition of the Rubiaceae in eight Atlantic Forest remnants of Rio de Janeiro state protected by Conservation Units. We also surveyed and set guidelines for conservation of microendemic species. The similarity analysis were based on previously published studies in Área de Proteção Ambiental de Grumari, Área de Proteção Ambiental Palmares, Parque Estadual da Serra da Tiririca, Parque Nacional do Itatiaia, Parque Nacional de Jurubatiba, Reserva Biológica de Poço das Antas, Reserva Biológica do Tinguá and Reserva Ecológica de Macaé de Cima - using the PAST software (“Paleontological Statistics”) with Sørensen coefficient. The floristic similarity analysis revealed two groups with distinct physiographic characteristics and different vegetation types. Group A consisted in two Restinga areas, Área de Proteção Ambiental de Grumari and Parque Nacional de Jurubatiba, which showed strong bootstrap support (98 %). Group B included forest remnants with distinct phytophisiognomies or altitudes, but with moderate bootstrap support. Low similarity levels among the eight areas were found due to the habitats’ heterogeneity. The current study pointed out 19 microendemic species from the Atlantic Forest, they present a single-site distribution or a distribution restricted to Mountain and Metropolitan regions of Rio de Janeiro state. Concerning the conservation status of microendemic species, discrepancies between the Catalogue of Flora of Rio de Janeiro and the Red Book of Brazilian Flora (two of the main reference catalogs of Brazilian flora) have been identified. We have also highlighted the need for recollecting microendemic species from the Atlantic Forest, and for properly assessing the degree of threat faced by these taxons early.

The relationship between standing vegetation and the soil seed bank along the shores of Lake Taihu, China

Understanding the basic characteristics of wetland seed banks and the distribution of those seeds is fundamental to providing a theoretical basis for vegetation restoration and wetland management. This study explored the relationship between standing vegetation and the soil seed bank representing four vegetation cover types on the shoreline of Lake Taihu (China) using a seed germination method. The vegetation cover types consisted of the fleabane lakeshore zone (Zone A), bush and grass lakeshore zone (Zone B), crop lakeshore zone (Zone C), and natural reed lakeshore zone (Zone D). The viability of the seeds of all species found during a survey of standing vegetation in the summer of 2010 was assessed using greenhouse germination trials. The fleabane, bush and grass, crop, and natural reed lakeshore zones had 4, 16, 8, and 6 species from the seed bank, respectively. Sorensen similarity coefficients resulting from comparisons of the species found in the seed bank and in the standing vegetation of those same four habitats were 0.250, 0.333, 0.143, and 0.154, respectively. Low similarity levels between standing vegetation and the seed banks indicate that we should increase work on wetland protection and management because of its potentially low recovery ability. Seed density was significantly lower in Zone B (4933±1683 number/m2) than in the other zones (Zone A: 1160±502 number/m2; Zone C: 1360±587 number/m2; and Zone D: 1200±961 number/m2. The vertical distribution of seeds in the seed bank at the four zones showed a significant decreasing trend with increasing soil depth. The reserves of seeds in the topsoil seed bank accounted for 64.10%, 60.00%, 56.86%, and 68.89% of the entire seed bank in Zones A, B, C, and D, respectively. This research can promote to instruct and inform management practices in wetland protection, wetland management, and restoration and reconstruction in damaged wetlands.

Chania multitudinisentens gen. nov., sp. nov., an N-acyl-homoserine-lactone-producing bacterium in the family Enterobacteriaceae isolated from landfill site soil.

Phylogenetic and taxonomic characterization was performed for bacterium RB-25T, which was isolated from a soil sample collected in a former municipal landfill site in Puchong, Malaysia. Growth occurred at 20-37 °C at pH 5-8 but not in the presence of 9 % (w/v) NaCl or higher. The principal fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Ubiquinone-8 was the only isoprenoid quinone detected. Polar lipid analysis revealed the presence of phospholipid, phosphoaminolipid, phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. DNA G+C content was 50.9 mol% phylogenetic analysis based on 16S rRNA gene sequence showed that strain RB-25T formed a distinct lineage within the family Enterobacteriaceae of the class Gammaproteobacteria. It exhibited a low level of 16S rRNA gene sequence similarity with its phylogenetic neighbours Pantoea rwandensis LMG 26275T (96.6 %), Rahnella aquatilis CIP 78.65T (96.5 %), Pectobacterium betavasculorum ATCC 43762T (96.4 %), Pantoea rodasii LMG 26273T (96.3 %), Gibbsiella dentisursi NUM 1720T (96.3 %) and Serratia glossinae C1T (96.2 %). Multilocus sequence analyses based on fusA, pyrG, rplB, rpoB and sucA sequences showed a clear distinction of strain RB-25T from the most closely related genera. Isolate RB-25T could also be distinguished from members of these genera by a combination of the DNA G+C content, respiratory quinone system, fatty acid profile, polar lipid composition and other phenotypic features. Strain RB-25T represents a novel species of a new genus, for which the name Chaniamultitudinisentens gen. nov., sp. nov. is proposed. The type strain is RB-25T (=DSM 28811T=LMG 28304T).

Characteristics of a macrozoobenthic community in the sea adjacent to the Yangtze River estuary during the wet season

To explore the characteristics of a macrozoobenthic community in the sea adjacent to the Yangtze River estuary during the wet season, macrozoobenthic samples were collected during June, August, and October, 2012, and data were analyzed using statistical methods including Two-Way ANOVA, Cluster analysis, Non-metric Multidimensional Scaling (NMDS), and Abundance-Biomass Comparison Curves (ABC Curves). A total of 181 macrozoobenthic species were recorded, with 82 species of Polychaeta, 46 Crustacea, 31 Mollusca, 11 Echinodermata and 11 species belonging to other groups. The abundance, biomass, Margalef’s richness index (d), Shannon-Wiener index (H'), and Pielou index (J') did not show any significant temporal or spatial differences except that J' in the offshore area was significantly higher than that found in the inshore area. Three to four macrozoobenthic assemblages were identified using the 20% similarity level and a low similarity level among stations was also observed. ABC curves revealed that the macrozoobenthic community in the offshore area was less disturbed than that in the inshore area. As a result of the continuous impact of anthropogenic activities, the macrozoobenthic community was severely disturbed and unevenly distributed in the sea adjacent to the Yangtze River estuary.

Biogeography of globally distributed bacteria in temperate and boreal Québec lakes as revealed by tag pyrosequencing of 16S rRNA genes

Sequence data of 16S rRNA genes reveal that many bacterial taxa are found in all freshwater lakes. However, the global data set is highly weighted toward lakes in temperate regions of North America and northern Europe, and it is unclear whether bacterial communities in other northern latitude environments, such as boreal lakes in North America, differ from those in lower latitudes. This study used pyrosequences of the 16S rRNA gene to examine bacterial diver- sity in 37 temperate and boreal lakes in Quebec, Canada, over the course of a year. Nearly all taxa in the global data set were also found in the Quebec lakes, but relative abundances differed. Com- munity structure varied geographically and seasonally for 97% similar operational taxonomic units (OTUs) but not at lower levels of similarity. Seasonal shifts in community structure were larger in temperate lakes than in boreal lakes, and community structure differed between boreal and temperate lakes in summer but not in winter. The differences in taxonomic composition between temperate and boreal lakes appear to be driven mostly by environmental processes influ- encing community structure of temperate lakes in summer. Our results provide a baseline for interpreting impacts of climate change in boreal biomes where community structure is driven by environmental factors.

Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC).

Avian pathogenic Escherichia coli (APEC) is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. Here, bacteriophage KBNP1315, infecting APEC strain KBP1315, was genomically and functionally characterized. The evolutionary relationships of KBNP1315 were analyzed at the genomic level using gene (protein)-sharing networks, the Markov clustering (MCL) algorithm, and comparative genomics. Our network analysis showed that KBNP1315 was connected to 30 members of the Autographivirinae subfamily, which comprises the SP6-, T7-, P60-, phiKMV-, GAP227- and KP34-related groups. Network decomposition suggested that KBNP1315 belongs to the SP6-like phages, but our comparison of putative encoded proteins revealed that key proteins of KBNP1315, including the tail spike protein and endolysin, had relative low levels of amino acid sequence similarity with other members of the SP6-like phages. Thus KBNP1315 may only be distantly related to the SP6-like phages, and (based on the difference in endolysin) its lysis mechanism may differ from theirs. To characterize the lytic functions of the holin and endolysin proteins from KBNP1315, we expressed these proteins individually or simultaneously in E. coli BL21 (DE3) competent cell. Interestingly, the expressed endolysin was secreted into the periplasm and caused a high degree of host cell lysis that was dose-dependently delayed/blocked by NaN3-mediated inhibition of the SecA pathway. The expressed holin triggered only a moderate inhibition of cell growth, whereas coexpression of holin and endolysin enhanced the lytic effect of endolysin. Together, these results revealed that KBNP1315 appears to use a pin-holin/signal-arrest-release (SAR) endolysin pathway to trigger host cell lysis.