Partial Nucleotide Sequences Research Articles

Effect of dietary Sargassum wightii and its fucoidan-rich extract on growth, immunity, disease resistance and antimicrobial peptide gene expression in Labeo rohita

This work aimed to appraise growth performance, immune responsiveness, bacterial disease resistance and mRNA expression of two antimicrobial peptides in Labeo rohita fingerlings fed diets supplemented with seaweed Sargassum wightii and its fucoidan-rich extract. Two hundred and twenty-five fingerlings were divided into five experimental groups in triplicates, each replicate having 15 fish in a 90-L tank. Different groups were fed with isonitrogenous (35% crude protein) and isoenergetic (1408.16 kJ/100 g) diets containing either 0% fucoidan-rich seaweed extract (FRSE), 1% FRSE, 2% FRSE, 3% seaweed powder and 6% seaweed powder for 60 days. Partial nucleotide sequences of the antimicrobial peptides, hepcidin and defensin, were characterized in Labeo rohita fingerlings, and gene expression in the different tissues of experimental fish was studied. The fish-fed FRSE-supplemented diets showed significant increase (P < 0.05) in the mRNA expression of antimicrobial peptides in liver, skin and intestine tissues. Bacterial challenge study using Aeromonas hydrophila showed higher survival in the FRSE-fed groups. Fish-fed FRSE-supplemented diets also showed better non-specific immune response (NBT reduction, serum lysozyme activity, serum albumin: globulin ratio and phagocytic activity) in pre-challenge and post-challenge periods. No significant difference was observed in the growth performance in the different experimental groups. The study indicates that although dietary FRSE is a potential immunostimulant in Labeo rohita fingerlings, it does not improve growth performance.

Isolation, identification and in silico analysis of alpha-amylase gene of Aspergillus niger strain CSA35 obtained from cassava undergoing spoilage

In this investigation, a gene (CDF_Amyl) encoding extracellular α-amylase in Aspergillus niger strain CSA35 associated with cassava spoilage was amplified using specific primers and characterized in silico. The gene had a partial nucleotide sequence of 968 bp and encoded a protein of 222 aa residues with a molecular weight and isoelectric point of 25.13 kDa and 4.17, respectively. Its catalytic site was located in the active site domain. BLASTp analysis showed that the protein primary sequence of the α-amylase gene had 98% and 99% homologies with the α-amylase of A. niger and A. oryzae RIB40, respectively. The gene is more closely related to α-amylase genes from fungi than to bacterial, plant, or animal α-amylase genes. Restriction mapping of the gene showed it can be digested with restriction enzymes like NcoI, PstI, SmaI, and BcLI among others but not with EcoRI and EcoRV. Its protein product had a hydrophobicity score of − 0.43 but no transmembrane helix. The CDF_Amyl protein was subcellularly localized in the secretory pathway, an indication of its release into extracellular space after secretion. Also, the 3D structure of the CDF-Amyl protein was barrel-shaped with domains characteristic of α-amylases. The encoded α-amylase Vmax is 6.90 U/mg protein and Km is 6.70 mg/ml. It was concluded that the unique characteristics of the CDF_Amyl gene and its deduced protein could find applications in biotechnological, food and pharmaceutical industries where cloning and further modification of this gene would be required for product development and improvement.

Molecular epidemiology and temporal evolution of norovirus associated with acute gastroenteritis in Amazonas state, Brazil

BackgroundGlobally, Norovirus (NoV) is considered the most common cause of diarrheal episodes across all age groups. Despite its wide genetic diversity, the GII.4 strain is the most predominant and has been associated with epidemics worldwide. In this study, we characterized sporadic cases of diarrhea from NoV-positive children, during a five-year period (2010–2014).MethodsA total of 250 NoV-positive samples identified by an enzyme immunoassay (EIA) were subjected to RT-PCR and partial nucleotide sequencing for polymerase and capsid genes. Phylogenetic analysis was performed to identify NoV genotypes using the binary classification. In addition, sequences from the P2 subdomain (capsid) gene of GII-4 variants were characterized by evolutionary analyses, using the MCMC method implemented in the BEAST package. A 3D structure was built using protein modeling.ResultsPhylogenetic analysis demonstrated a predominance of genotype GII.4 (52.4% - 99/189), variants New Orleans_2009 and Sydney_2012 followed by GII.P7/GII.6 with 6.3% (12/189). Amino acid analyses of the GII.4 strains showed several important amino acid changes. A higher evolutionary rate was found, 7.7 × 10− 3 in the Sydney variant and 6.3 × 10− 3 in the New Orleans. Based in evolutionary analysis the time to the most recent common ancestor (TMRCA) has been calculated as estimates of the population divergence time. Thus, TMRCA for New Orleans and Sydney variant were 2008.7 and 2010.7, respectively. Also, we observed a lineage of transition between New Orleans and Sydney.ConclusionThis study describes the different strains of norovirus isolated from Amazonas state in Brazil during a five-year period. Considering that NoV are capable of changing their antigenic epitopes rapidly, a continuous surveillance is important to monitor the occurrence and changes of the NoV in the community through epidemiological studies. These results contribute to the understanding of NoV molecular epidemiology and its evolutionary dynamics in Amazonas state, Brazil.

Sequence typing of human adenoviruses isolated from Polish patients subjected to allogeneic hematopoietic stem cell transplantation – a single center experience

ABSTRACT Purpose: Human adenoviruses (HAdV) from species A, B and C are commonly recognized as pathogens causing severe morbidity and mortality in hematopoietic stem cell transplant (HSCT) recipients. The purpose of the present study was to determine HAdV types responsible for viremia in HSCT recipients at a large tertiary hospital in Poland. Methods: Analysis of partial nucleotide sequences of HAdV hexon gene was used to type 40 clinical isolates of HAdV obtained from 40 HSCT recipients. Results: We identified six different HAdV serotypes belonging to species B, C and E. We demonstrated high variability in sequences of detected HAdV types, and patients infected with the same HAdV types were not hospitalized at the same time, which suggests the low possibility of cross-infection. In almost all patients, anti-HAdV antibodies in IgG class were detected, which indicates a history of HAdV infection in the past. Clinical symptoms accompanying HAdV viremia were in 89%, and in 61.5% of individuals, HAdV was a sole pathogen detected. There were no cases with high-level HAdV viremia and severe systemic or organ infections. Graft-versus-host disease (GvHD) was present in patients infected with species B and C, but grade II of GvHD was observed only in patients infected with HAdV-B. Conclusions: The predominance of HAdV-C and common presence of anti-HAdV antibodies in IgG class may strongly suggest that most infections in the present study were reactivations of HAdV persisting into the patient’s mucosa-associated lymphoid tissues. Variability of HAdV sequences suggests that cross-infections between patients were very rare. ABBREVIATIONS: GvHD: graft-versus-host disease; HAdV: human adenoviruses; HSCT: hematopoietic stem cell transplantation

Geomorphology Influencing the Diversification of Fish in Small-Order Rivers of Neighboring Basins.

The current analysis investigates whether the uplift of the Serra da Esperança and the Ponta Grossa Arch in the Serra Geral resulted in ichthyofaunistic changes in adjacent basins. For this, we describe the phylogeographic structure among populations of Trichomycterus collected in hydrographic basins in southern Brazil by using partial nucleotide sequences of the mitochondrial gene Cytochrome C Oxidase subunit I. Analyses revealed that the nomenclature Trichomycterus davisi fails to contain the whole genetic diversity range found in the collected specimens and indicates at least six genetic lineages in Trichomycterus. Diagnostic morphological characteristics not associated to T. davisi could be identified in some specimens from the Iguaçu Piquiri haplogroup, indicating the occurrence of species Trichomycterus stawiarski. The lack of morphological differences among the other clades clearly suggests a cryptic species case. Molecular analyses revealed at least five new species besides T. davisi in the hydrographic basins and support the interpretation that genetic structure in T. davisi species complex is explained by tectonic events intrinsic to the areas of influence of Serra da Esperança and the Ponta Grossa Arch which occurred around 1.7 My.

Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo

This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals.

First report on characterization and pathogenicity study of emerging Lactococcus garvieae infection in farmed rainbow trout, Oncorhynchus mykiss (Walbaum), from India.

"Warm water lactococcosis" in farm-reared rainbow trout, Oncorhynchus mykiss (Walbaum) in the northern Himalayan region of India, caused by bacterium Lactococcus garvieae is described in this study. Nine bacterial isolates were recovered from the organs of haemorrhagic septicaemia rainbow trout and were subjected to biochemical and molecular identification. Cell surface characteristics and virulence of the bacterial isolates are also described. All the nine bacterial isolates had homogenous biochemical characteristics and were Gram-positive, short chains forming (two to eight cells long), α-haemolytic, non-motile ovoid cocci. Partial 16S rDNA nucleotide sequence (~1,400bp) of current isolates shared 99% identities with the 16S rDNA nucleotide sequence of L.garvieae R421, L.garvieae FMA395 and L.garvieae CAU:1730. The identity of the bacterial isolates was further confirmed by PCR amplification of L.garvieae-specific ~1,100bp fragment. Transmission electron microscopy (TEM) of one representative isolate, L.garvieae RTCLI04, indicates that the isolated strain lacks thick outer capsule and is of KG+ (non-capsulates) phenotype. An intraperitoneal and intramuscular injection (2.6×105 CFU ml-1 ) and also immersion in bacterial suspension @ of 2.6×105 CFU ml-1 to healthy rainbow trout juveniles (body weight: 27.5±3.7g) with L.garvieae RTCLI04 caused 80%, 60% and 10% cumulative mortality in challenged fish, respectively, within 15days post-infection. The haemorrhagic septicaemic disease was reproduced experimentally. Histopathological examination of organs of experimentally infected fish revealed extensive degenerative and inflammatory changes in eye, kidney, gill and liver. PCR amplification of several putative virulence genes such as haemolysins, adhesins, LPxTG-containing surface proteins and adhesins cluster confirms the virulence of our Indian L.garvieae isolates. To the best of our knowledge, we are reporting for the first time that L.garvieae is associated with fatal haemorrhagic septicaemia in farmed rainbow trout in India.

Detection and phylogenetic analysis of phlebovirus, including severe fever with thrombocytopenia syndrome virus, in ticks collected from Tokyo, Japan.

Severe fever with thrombocytopenia syndrome (SFTS) was detected for the first time in China in 2011. Since then, human cases have been reported in endemic regions, including Japan. To investigate the presence of tick-borne pathogens in Tokyo, 551 ticks (266 samples) were collected from October 2015 to October 2016. Although the SFTS virus was not detected by RT-PCR, a novel phlebovirus was detected in one sample. In a phylogenetic analysis based on the partial nucleotide sequences of the L and S segments of the virus, the virus clustered with Lesvos virus (Greece), Yongjia tick virus, and Dabieshan tick virus (China). Further studies involving virus isolation are required to characterize this novel phlebovirus and to expand the epidemiological knowledge of related pathogens.

Presence of Recombinant Strain of Cucurbit Aphid Borne Yellows Virus in Iran.

Background:Cucurbit aphid-borne yellows virus (CABYV) is among the most important yellowing viruses on cucurbits in Iran. The presence of CABYV has been previously reported from the major cucurbit growing areas in Iran, however, there are few studies concerning the detection of the different strains of this virus in the grower's fields, and especially, there is no report of the weed host plants near crop fields. Objectives: This study was done in order to detect the new strains of the CABYV polerovirus in cucurbits and the weed plants in the Lorestan province, Iran, as an introductory investigation for initiating a program of the breeding for resistance. Material and Methods: During a survey carried out in 2013-2014 in Lorestan province; Iran, 189 cucurbit and 261 weed samples were investigated for the presence of CABYV using RT-PCR. In addition, the phylogeny and nucleotide similarities were discussed on the basis of the partial nucleotide sequence of RNA dependent RNA polymerase (RdRP) gene. Results: The RT-PCR carried out on leaf samples revealed the infection with the CABYV in 43 cucumber and 12 weed samples. RT-PCR using strain specific primers detected the presence of the both common (C) and recombinant (R) strains of CABYV in the tested samples. On the basis of the phylogenetic analyses, the CABYV-C isolates from Iran were clustered into two distinct sub-populations (CI and CII), such that all the weed samples with two sequenced cucumber isolates were clustered in the CI sub-population. Meanwhile, a distinct sub-population of the isolates was clustered in the CABYV-R group showed a shared sequence identity of 97% to a Taiwanese isolate (JQ700306). Conclusions: This study has indicated the incidence of CABYV-R in the Southwest Asia; Iran for the first time. We were also able to show CABYV occurrence in Sysimbrium irio and Citrullus colocynthis from this area of the world. Identification of cucurbit infecting viruses and studying their distribution and potential reservoir hosts are important for developing successful control programs for virus disease management.

Diagnostic Approach and Genetic Diversity of JackFruit Bronzing Bacterium in Malaysia

A serious problem faced in the jack fruit industry in Malaysia caused by bronzing disease by pathogen Pantoea stewartii subspe. stewartii (P. stewartii subsp. stewartii ) as it reduces the quality of the fresh jack fruit, hence, affects the consumer preference towards the fruits. It is important to keep the fruit healthy as it provides revenue to the local and export markets in Malaysia. This review aimes to present an overview and diagnostic approach of jackfruit bronzing disease in Malaysia. Detection and identification methods following past and recent study of the causal pathogen via phenotypic identification, molecular identification, pathogenicity test, genetic relationship and genetic diversity. Successful detection and identification were obtained with appropriate phenotypic tests performed and molecular identification using CPSL1/CPSR2c primers and ES16/ESIG2c primers. Pantoea stewartii subsp. stewartii strains were also pathogenic to healthy detached and attached jack fruit and the high liability of the phylogenetic and clustering analyses in the causal pathogen via multilocus sequencing analysis (MLSA) of the partial nucleotide sequences of the genes gyrB, rpoB, atpD and infB, using a bootstrap analysis with 1000 replicates on the individual and concatenated peptide sequence trees. The presented review provides an overview on bronzing disease of jackfruit in Malaysia, the appropriate detection, identification, pathogenicity of its causal pathogen and the application of multilocus sequence analysis (MLSA) as the best tool to study the pathogen diversity and evolution. Up to now, little information and studies have been done on bronzing disease of jackfruit and its causal agent, P. stewartii subsp. stewartii in Malaysia.

First Report of Coriander (Coriandrum sativum) Seedling Damping-Off Caused by Pythium irregulare in Brazil

Coriander (Coriandrum sativum) is among the most important herbs cultivated in Northeastern Brazil. Root diseases are considered the main limiting factor for coriander production, drastically reducing the number of plants in affected areas and causing great economic losses (Noronha et al. 2015). In May 2015, soil samples from coriander-growing areas displaying seedling damping-off were collected in the county of Arapiraca, Alagoas State, Brazil. This disease affected between 90 and 100% of the plants in the field. Symptoms on coriander initially appeared as yellowing and wilt, and plants quickly declined owing to foot and root rot. To isolate the putative etiologic agent from soil samples, coriander seedlings were used as baits. A typical Pythium sp. isolate was obtained from symptomatic seedling tissues on potato dextrose agar (PDA), and the Pythium-derived culture was deposited at the Colecao de Culturas de Fungos Fitopatogenicos of the Universidade Federal de Alagoas (code COUFAL1986). The colony on PDA was cottony and white, with a growth rate of 22.8 mm/day at 25°C. Sporangia were globose and nonpapillate, 10.9 to 22.5 μm in diameter; spherical oogonia, 9.2 to 14.5 μm in diameter, being observed on one or two antheridia per oogonium (Van der Plaats-Niterink 1981). To confirm identification, partial nucleotide sequences of the internal transcribed spacer (ITS) and cytochrome c oxidase subunit 2 (Cox2) were obtained and deposited in GenBank (accession nos. KX869910 and KX869911). The ITS and Cox2 sequences showed 99% identity with sequences from Pythium irregulare culture collection CBS 250.28. Furthermore, the COUFAL1986 isolate grouped with other P. irregulare in a Bayesian phylogenetic tree inferred from nucleotide concatenated data (ITS and Cox2; S19898 deposited in TreeBASE). The pathogenicity of the COUFAL1986 isolate was confirmed on coriander plants (cultivated in a greenhouse) from the Verdao variety. Coriander seeds were sown (1-cm depth) in five 400 mL plastic pots (20 seeds/pot) containing soil (previously sterilized) infested with a mycelial suspension taken from a 7-day-old culture (grown on PDA at 25°C) and kept at 25 ± 2°C and a photoperiod of 12 h for 10 days. The control (three pots) consisted of sterilized distilled water. Seedlings showed wilt, yellowing, and foot and root rot 4 days after emergence. To fulfill Koch’s postulates, P. irregulare was successfully reisolated from symptomatic plants and molecularly identified. No disease symptoms were observed in the control treatment. Pythium spp. have been reported inducing coriander seedling damping-off in India (P. irregulare; Misra and Hall 1997), Italy (P. ultimum; Garibaldi et al. 2010), and Puerto Rico (P. dissotocum; Romero et al. 2012). To our knowledge, this is the first report of P. irregulare causing coriander seedling damping-off in Brazil.

Eimeria taggartiN. Sp., a Novel Coccidian (Apicomplexa: Eimeriorina) in the Prostate of anAntechinus flavipes

A novel coccidian species was discovered in the prostate of an Antechinus flavipes (yellow-footed antechinus) in South Australia during the period of postmating male antechinus immunosuppression and mortality. This novel coccidian is unusual because it develops extraintestinally and sporulates endogenously within the prostate gland of its mammalian host. Histological examination of prostatic tissue revealed dense aggregations of spherical and thin-walled tetrasporocystic, dizoic, sporulated coccidian oocysts within tubular lumina, with unsporulated oocysts and gamogonic stages within the cytoplasm of glandular epithelial cells. This coccidian was observed occurring concurrently with dasyurid gammaherpesvirus 1 infection of the antechinus' prostate. Eimeria-specific 18S small-subunit ribosomal (r)DNA polymerase chain reaction amplification was used to obtain a partial 18S rDNA nucleotide sequence from the antechinus coccidian. Bayesian phylogenetic analysis based on 18S rDNA gene sequences revealed that the novel coccidian clusters with reptile-host coccidians, forming an ancestral basal lineage of the eimeriid clade. The species has been named Eimeria taggarti n. sp. on the basis of both sporulated oocyst morphology and molecular characterization. It is suspected that E. taggarti is sexually transmitted via excretion of sporulated oocysts or free sporocysts with prostatic secretions in semen.

Isolation and screening of Lactobacillus species from dogs for probiotic action

The present study aimed at the detection of suitable Lactobacillus species from dogs for usage as probiotic. A total of 67 rectal swabs from healthy pups were analyzed and 49 (73.1%) Lactobacillus isolates were identified based on morphological, biochemical characteristics and confirmed by genus specific PCR targeting 16S rRNA gene. A total of 20 isolates that showed strong aggregation, high cell surface hydrophobicity, acid and bile tolerance were screened for in-vitro antibacterial activity by agar well diffusion assay, where prominent inhibitory zones were observed against majority of the test pathogens. Reduction in antibacterial activity was noticed after neutralization, proteinase K and heat treatment of supernatants. Partial 16S rRNA nucleotide sequence analysis of seven Lactobacillus isolates that showed prominent in-vitro antibacterial activity revealed maximum sequence homology with Lactobacillus fermentum (for six isolates) and Lactobacillus agilis (for one isolate). The in-vitro antibacterial activity results highlighted the need for in-vivo studies in India to establish probiotic potential of canine faecal Lactobacillus species in the near future.

HTLV-1 intrafamilial transmission among Japanese immigrants in Brazil.

Human T-lymphotropic virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia/lymphoma and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The aim of this study was to investigate the intrafamilial transmission of HTLV-1 among Japanese immigrants and their descendants living in a non-endemic area of central Brazil. Six families were investigated. Thirty-seven relatives of the six index cases were tested by ELISA for the presence of anti-HTLV antibodies, and the positive cases were confirmed by Western blot. HTLV-1 isolates were genotyped by partial nucleotide sequencing (5' LTR) of the proviral DNA. All individuals, including index cases and relatives, were asymptomatic. In five families, at least one relative was infected with HTLV-1. In all, eight (22%) relatives (one mother, four wives, one brother, and two brothers-in-law) were infected. However, none of the 22 individuals under 55 years of age was infected. In each family, the HTLV-1 sequences from the relatives were identical or almost identical to that of the index case, except in one case. Pedigrees of the families, together with socio-demographic data of the HTLV-1 infected individuals, strongly suggested the occurrence of both vertical and sexual transmission, with breastfeeding as an important risk factor. Whether and why the virus transmission is less effective among younger generations deserves to be further investigated.

In-Silico Construction of Phylogenetic Relationships Between Ampullariidae and Viviparidae Families (Gastropoda: Caenogastropoda) Using Partial Mitochondrial COI Sequences

Freshwater biota especially molluscs are more vulnerable because even the slightest change in the quality of their habitat possibly leads to their mortality. In addition, their importance is felt that particularly molluscs contribute toward carbon sequestering from the environment as atmospheric carbon gets deposited as carbonates in their shell which constitute 10% of their body mass. Hence, the molecular phylogenetic relationships of two families inhabiting freshwater streams viz., Ampullariidae and Viviparidae considering the genera dwelling in Indian subcontinent namely Pila globosa and Bellamya bengalensis using the partial nucleotide sequence of mitochondrial COI gene were of considerable importance in building conservational strategies. The phylogenetic analysis of ampullariid and viviparid species inferred that these two chosen families were paraphyletic and rooted on the genera of Cyclophoroidea and possibly with Saulea vitrea as the connecting link.

First evidence of dengue infection in domestic dogs living in different ecological settings in Thailand.

BackgroundDengue is a vector-borne disease transmitted by Aedes mosquitoes. It is considered an important public health problem in many countries worldwide. However, only a few studies have been conducted on primates and domestic animals that could potentially be a reservoir of dengue viruses. Since domestic dogs share both habitats and vectors with humans, this study aimed to investigate whether domestic dogs living in different ecological settings in dengue endemic areas in Thailand could be naturally infected with dengue viruses.Methodology/Principal findingsSerum samples were collected from domestic dogs in three different ecological settings of Thailand: urban dengue endemic areas of Nakhon Sawan Province; rubber plantation areas of Rayong Province; and Koh Chang, an island tourist spot of Trat Province. These samples were screened for dengue viral genome by using semi-nested RT-PCR. Positive samples were then inoculated in mosquito and dog cell lines for virus isolation. Supernatant collected from cell culture was tested for the presence of dengue viral genome by semi-nested RT-PCR, then double-strand DNA products were double-pass custom-sequenced. Partial nucleotide sequences were aligned with the sequences already recorded in GenBank, and a phylogenetic tree was constructed. In the urban setting, 632 domestic dog serum samples were screened for dengue virus genome by RT-PCR, and six samples (0.95%) tested positive for dengue virus. Four out of six dengue viruses from positive samples were successfully isolated. Dengue virus serotype 2 and serotype 3 were found to have circulated in domestic dog populations. One of 153 samples (0.65%) collected from the rubber plantation area showed a PCR-positive result, and dengue serotype 3 was successfully isolated. Partial gene phylogeny revealed that the isolated dengue viruses were closely related to those strains circulating in human populations. None of the 71 samples collected from the island tourist spot showed a positive result.Conclusions/SignificanceWe concluded that domestic dogs can be infected with dengue virus strains circulating in dengue endemic areas. The role of domestic dogs in dengue transmission needs to be further investigated, i.e., whether they are potential reservoirs or incidental hosts of dengue viruses.

Noroviruses and sapoviruses associated with acute gastroenteritis in pediatric patients in Thailand: increased detection of recombinant norovirus GII.P16/GII.13 strains.

Enteric caliciviruses, including noroviruses (NoVs) and sapoviruses (SaVs), are recognized as important etiologic agents of acute gastroenteritis (AGE) with considerable genetic diversity. In order to gain an overview of the molecular epidemiology of human NoVs and SaVs in children hospitalized with AGE in Chiang Mai, Thailand, a total of 889 fecal specimens were collected from 2012 to 2014 and screened for NoVs and SaVs. Out of 889 fecal specimens, 154 (17.3%) and 6 (0.7%) were positive for NoV GII isolates and SaV, respectively. Among the NoV GII, 10 different genotypes were identified with genotype GII.4 being predominant (103 strains), followed by GII.3 (17 strains), GII.13 (13 strains), GII.1 (7 strains), GII.6 (7 strains), GII.7 (2 strains), GII.17 (2 strains), and one each of GII.2, GII.15, and GII.21 genotypes. It was observed that four variants of NoV GII.4 (Den Haag 2006b, Apeldoorn 2007, New Orleans 2009, Sydney 2012) were detected from 2012 to 2014. Analysis of partial nucleotide sequences of RdRp and VP1 of the emerging NoV GII.13 strains (9 of 13 strains) revealed that they all were GII.P16/GII.13 recombinants. In addition, four different genotypes of SaV, GI.1 (2 strains), GII.1 (1 strain), GII.4 (2 strains), and GIV.1 (1 strain) were detected. The data revealed heterogeneity and a highly dynamic distribution of NoV and SaV genotypes circulating in children admitted to hospitals with AGE in Chiang Mai, Thailand, during the period of 2012 to 2014.

Novel mannose binding natterin-like protein in the skin mucus of Atlantic cod (Gadus morhua)

This study presents the first report of purification of natterin-like protein (Nlp) in a non-venomous fish. The peptide identities of purified cod Nlp were confirmed through LC-MSMS and matched to a cod expressed sequence tag (EST). A partial cod nlp nucleotide sequence was amplified and sequenced based on this EST. Multiple sequence alignment of cod Nlp showed considerable homology with other teleost Nlps and the presence of an N-terminal jacalin-like lectin domain coupled with a C-terminal toxin domain. nlp expression was higher in skin, head kidney, liver and spleen than in other tissues studied. Hemaggluttination of horse red blood cells by Nlp was calcium dependent and inhibited by mannose. A Vibrio anguillarum bath challenge however, did not alter the expression of cod nlp transcripts in the skin and gills. Further functional characterization is required to establish the significance of this unique protein in Atlantic cod and other teleosts.

Degradation of polyvinyl alcohol by a novel bacterial strain Stenotrophomonas sp. SA21

ABSTRACTIn this study, polyvinyl alcohol (PVA)-degrading bacteria were screened from oil sludge using PVA as a sole source of carbon in the culture medium. A novel strain, SA21, was obtained and identified as a member of the Stenotrophomonas genus based on the analysis of a partial 16S rDNA nucleotide sequence, morphological and biochemical characteristics, and phylogenetic analysis. This Stenotrophomonas isolate had not previously been reported as a PVA-degrading bacterium. Stenotrophomonas sp. strain SA21 degraded 90% of the PVA present in the culture medium after 4 days. The effect of nitrogen sources on the production of PVA-degrading enzyme involved in the biodegradation process was significant, and the enzymatic activity reached 82 U/ml when ammonium nitrate or urea was used in the optimized medium. The information obtained in this study will provide a foundation for improving industrial wastewater treatment.Abbreviations: DCW: dry cell weight; FTIR: Fourier Transform Infrared Spectroscopy; NCBI: National Center for Biotechnology Information; PCR: polymerase chain reaction; PVA: polyvinyl alcohol; SEM: scanning electron microscope

Molecular identification of the fish parasite Lernaea

Isolates of the fish parasitic copepod Lernaea from four different freshwater fishes viz., catla (Catla catla), guppy (Poecilia reticulata), platy (Xiphophorus naculatus) and gold fish (Carassius auratus) were selected for the study. The isolates had considerably differing anchor shapes and were likely to be grouped as different species. Partial nucleotide sequences of the 18S and 28S rDNA regions of the Lernaea isolates were determined. Phylogenetic trees generated by the neighbour joining method revealed that the Lernaea isolates examined in this study were of similar genotype and were identified to be Lernaea cyprinacea.