Phylogenetic Relationship Among Brackishwater Vibrio Species

Vibriosis is regarded as an important disease of penaeid shrimps affecting larvae in hatcheries. Among the Vibrio species, Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio furnissii, Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus, and Vibrio anguillarum are often associated with diseases in finfish and shellfish of brackishwater ecosystem. Accurate species differentiating methods for the organisms present in an ecosystem are required for precise classification of the species and to take steps for their management. Conventional methods like 16s rRNA phylogeny and multilocus sequence typing (MLST) have often failed to correctly identify Vibrio species. This has necessitated a comprehensive investigation on methodologies available to distinguish Vibrio species associated with brackishwater aquaculture system. To achieve this, 35 whole genomes belonging to 7 Vibrio species were subjected to phylogenetic analysis based on 16s rRNA gene, MLST genes, single-copy orthologous genes, and single-nucleotide polymorphisms. In addition, genome-based similarity indices like average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) were computed as confirmatory tests to verify the phylogenetic relations. There were some misclassifications occurred regarding phylogenetic relations based on 16s rRNA genes and MLST genes, while phylogeny with single-copy orthologous genes produced accurate species-level clustering. Study reveals that the species identification based on whole genome-based estimates or genome-wide variants are more precise than the ones done with single or subset of genes.

Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture

In recent years, the importance of viral and host microRNAs (miRNAs) in mediating viral replication and control of host cellular machinery, has been realised and increasing efforts have been taken in order to understand the interactions of miRNAs from host and pathogen during infection. However, all existing studies has thus far been conducted in controlled experimental conditions and the veracity of these data for field conditions are yet to be established. In this framework, small RNA sequencing was performed to identify the miRNAs involved in shrimp (Penaeus vannamei) immune responses under two different WSSV infection conditions of natural infection and experimentally challenged conditions. The expression profiles of miRNAs of shrimp infected with WSSV under two contrasting conditions were compared and as a result, 23365 known miRNAs and 481 novel miRNAs were identified. Amongst the most abundantly expressed miRNAs, the hypoxia related miR-210 and immune pathway related miR-29b were expressed only in infected shrimps of both conditions. miR-8-5p, having a functional role in modulation of chitin biosynthesis was exclusively represented in higher numbers in the WSSV -infected shrimps under natural conditions whilst four of the miRNAs (mja-miR-6493-5p, mja-miR-6492, mmu-miR-3968, tcf-miR-9b-5p) identified from shrimps collected from pond culture targeted chitinase, an important enzyme involved in growth and moulting in shrimps, indicating an interaction between WSSV infection and moult cycle under culture conditions. Some of the miRNAs (tca-miR-87b-3p, cte-miR-277a) and miRNAs belonging to class miR-9, miR-981 that were identified only in WSSV infected shrimps under experimental conditions, are known to respond against WSSV infection in shrimps. Moreover, the miRNA target prediction revealed several immune-related gene targets such as cathepsin, c-type lectin, haemocyanin and ubiquitin protein ligase were commonly identified under both the conditions. However, the miRNAs identified from challenge experiment had wide number of gene targets as compared to the miRNAs of natural infection. The shrimp miRNA mja-miR-6489-3p, was also found to target early virus gene wsv001 of WSSV. Our study, therefore, provides the comparative analysis of miRNA expression from shrimp during WSSV infection in two different conditions.

Genotypic characterization of Listeria monocytogenes isolated from humans in India

Listeria monocytogenes is a foodborne pathogen associated with severe diseases in humans and animals. The genotypic analysis of 17 L. monocytogenes isolates recovered from humans in India during 2006-2009 using multiplex serotyping PCR allowing serovar predictions, conventional serology and by pulsed field gel electrophoresis (PFGE) is presented. The isolates were recovered from patients exhibiting various clinical conditions. A multiplex-PCR based serotyping assay revealed 88·24% (15/17) of the strains belonging to the serovar group 4b, 4d, 4e and 11·76% (2/17) to the serovar group 1/2b, 3b. Conventional serology indicated that 13 (76·47%) L. monocytogenes isolates to be of serotype 4b, 2 (11·76%) serotype 4d, and 2 (11·76%) serotype 1/2b. Ten ApaI and nine AscI pulsotypes were recognized among the 17 human isolates. PFGE analysis allowed discrimination among isolates of the same serotype and among isolates from the same sampling areas or those isolated from different areas. Thus, PFGE together with multiplex-PCR serotyping allows rapid discrimination of L. monocytogenes strains. In addition, the predominance of L. monocytogenes serotype 4b is of concern, as this serotype has been most frequently associated with human listeriosis outbreaks.

Epidemiology and risk management of listeriosis in India

Listeria monocytogenes is a foodborne pathogen that can cause serious invasive illness, mainly in certain well-defined high-risk groups, including elderly and immunocompromised patients, pregnant women, newborns and infants. In India, this pathogen has been isolated from humans, animals and foods. The incidence of Listeria is generally comparable to those reported elsewhere in the world. In humans, maternal/neonatal listeriosis is the most common clinical form reported. Among animal populations, spontaneous abortions, subclinical mastitis, meningoencephalitis and endometritis were the commonest forms reported. The disease largely remains undiagnosed and under reported. From reported analyses of a variety of foods for Listeria, milk and milk products, meat and meat products, seafood and vegetables have been reported to be contaminated in India. The legal framework for microbiological safety of foods against microbes including L. monocytogenes is summarised. The epidemiological studies would help in understanding of the sources of infection and persistence and their risk assessment, routes of transmission, clinical forms and allow for better management of the infection.

Cytogenetic analysis of acute myeloid leukemia with t(8;21) from a tertiary care center in India with correlation between clinicopathologic characteristics and molecular analysis

The t(8;21)(q22;q22) is the most common translocation in acute myeloid leukemia (AML). We describe the clinicopathologic and cytogenetic profile of 117 patients with t(8;21) AML. There were 76 males and 88 adults. The median age was 26 years. Most patients (80%) had AML M2. Dysplasia was present in 68% of patients and eosinophilia in 18%. Eight patients had fewer than 20% blasts. Additional chromosomal aberrations were seen in 103 patients (88%) with loss of a sex chromosome (LSC) in 78 patients (66%) and deletion 9q in 21 (18%). The other recurrent abnormalities were trisomies 4, 8 and 15, monosomy 17 and deletion 7q (less than 5% each). Three- or four-way variant t(8;21) were seen in 6% of patients and 3% had tetraploidy. Aberrant expression of CD19 was seen in 54% of patients. FLT3 mutations were seen in 7.5% of patients (3/40) and c-KIT mutations in 6.6% (2/30). None had NPM1 or JAK2 V617F mutations. One patient had a granulocytic sarcoma. Complete remission was achieved in 96% of the 26 newly diagnosed patients after first induction. The median follow-up was 25 months (range 4-68). The overall survival was 69% at 31 months.

The t(6;9)(p22;q34) in myeloid neoplasms: a retrospective study of 16 cases

Among patients with acute myeloid leukemia (AML), the t(6;9) (p22;q34) is a rare but defined subset with a poor prognosis. We report 16 patients with the t(6;9), of whom 13 had AML, 2 had myelodysplastic syndrome (MDS), and 1 had chronic myeloid leukemia in myeloid blast crisis (CML-BC). All except for one were evaluated at diagnosis. The median age was 34.5 (range: 7-62 years), with 12 adults and 12 males. Trilineage dysplasia was present in 13 (81%). Marrow basophilia was seen in only two patients, one of whom had CML-BC. HLA-DR was positive in all 12 patients assessed, CD33 in 11, CD13 in 10, and CD34 in seven. Four patients had one other abnormality apart from the t(6;9). These were the t(9;22) in the patient with CML and deletion 9q, addition 13q, and an isochromosome 8q in the other three patients. There were no complex karyotypes. Fms-related tyrosine kinase 3--internal tandem duplication (FLT3-ITD) mutations were seen in seven of 13 patients. Follow-up details were available for six patients. Three received palliative care, and follow-up details were not available for the other seven. The response to chemotherapy was poor in the remaining patients. The only patients who survived were three out of the four who had allogeneic hematopoietic stem cell transplantation (HSCT).

Cytokine gene polymorphisms in irritable bowel syndrome in Indian population--a pilot case control study

AIM

This study aimed at evaluating the single nucleotide polymorphisms (SNPs) in five cytokine genes regulating inflammation at altogether 8 different loci and compared their frequencies in patients with Irritable bowel syndrome (IBS) versus healthy age and sex matched controls.

METHODS

Peripheral blood was collected for DNA cytokine analysis from 23 patients with lBS and 20 healthy controls. The cytokine SNPs studied include TNF-alpha (-308G/A), TGF-alpha1 (codon10T/C, codon25G/C), IL-6 promoter (-1082A/G; -819T/C; -592A/C), IL-6 promoter (-174G/C), and IFN-alpha (+874T/A).

RESULTS

There was a significant difference between a SNP in IL-b (-592A/C) among cases and controls. There was also a trend to significance as regards to IL-6 promoter (-174G/C). Frequencies of other SNPs were not significantly different between the two groups.

CONCLUSION

This pilot study shows that there are polymorphism differences in cytokine genes between patients with lBS and healthy controls from India.

alpha-Glucosidase inhibitory antihyperglycemic activity of substituted chromenone derivatives

Series of 3,4- and 3,6-disubstituted chromenones including new chromenone derivatives were synthesized applying various synthetic strategies including Pechmann condensation, Knoevenagel condensation, Reimer-Tiemann reaction and Suzuki coupling in very good yields. Synthesized compounds (4a-z) were screened for in vitro alpha-glucosidase inhibitory and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activities. Majority of compounds displayed varying degrees of alpha-glucosidase inhibitory and DPPH scavenging activity. Compound 4x emerged as the most potent alpha-glucosidase inhibitor in present series of compounds owing to the presence of 3-acetyl-6-(6-methoxy-3-pyridyl) group on chromenone; however, it could not display DPPH scavenging activity and was found to be mixed non-competitive type inhibitor of rat intestinal alpha-glucosidase. When tested in vivo for antihyperglycemic activity in starch loaded Wistar rats, it displayed significant antihyperglycemic property. This is the first report assigning rat intestinal alpha-glucosidase inhibitory property for this class of new chromenones and presents new family of compounds possessing alpha-glucosidase inhibitory activities and antihyperglycemic property. Compound 4x may serve as an interesting new compound for the development of therapeutics targeted against diet-induced hyperglycemia in diabetes.

A rapid decision sampling plan for implementing area-wide management of the red palm weevil, Rhynchophorus ferrugineus, in coconut plantations of India

The red palm weevil Rhynchophorus ferrugineus Olivier (Curculionidae/Rhynchophoridae/Dryophthoridae) is a lethal pest of young coconut palms, Cocos nucifera L. (Arecales: Arecaceae), with a highly aggregated population distribution pattern. R. ferrugineus is managed in several coconut growing countries using area-wide pheromone based programmes that need a substantial commitment of funds over a period of time. Often, decisions to implement area-wide management of R. ferrugineus are based on pheromone trap captures in surveillance traps and or infestation reports. Implementing area-wide management of this pest on the basis of such data can be inaccurate, as it may either under or over estimate the pest intensity in the field. This study presents sampling plans for rapid and accurate classification of R. ferrugineus infestation in coconut plantations of India by inspecting palms to detect infestation in a sequence until a decision to either implement or not to initiate area-wide management of R. ferrugineus can be made. The sampling plans are based on a common aggregation index of 3.45, assumed action threshold values of either 1.0 (plan A) or 0.5 (plan B) per cent infested palms and a risk factor of making the wrong decision set at 0.05. Using plans A and B, if the cumulative number of infested palms in a young 1 hectare coconut plantation is zero out of 150 palms for both plans, then area-wide management is not required, while on the other hand, if the cumulative number of infested palms for the same area is 6 (plan A), or 5 (plan B), then area-wide management of R. ferrugineus is essential. The proposed sampling plans are efficient tools in decision making, particularly at very low and high levels of infestation and can also be used to assess the performance of R. ferrugineus IPM programmes that are in progress. These plans not only save time and money as only a small area needs to be sampled to arrive at a correct decision, but are also efficient in rating the infestation level accurately.