Cucurbit aphid-borne yellows virus (CABYV) infecting melon and bitter gourd in Java, Indonesia

Recently, Cucurbit aphid-borne yellows polerovirus (CABYV) had been reported firstly to infect cucumber in Java. The typical symptoms of CABYV infection are leaf yellowing with green veins and the thickening of older leaves. This study aimed to detect and identify the occurrence of CABYV infection on other cucurbit hosts in Java. A total of 600 Polerovirus-like symptomatic leaves were taken from open-fields cultivated plants in West Java, Central Java, and East Java. The virus incidence was determined serologically, RT-PCR and DNA sequencing confirmed the identity of CABYV. Based on serological test revealed six virus species in single or multiple infections with varying incidence. Among tested plants, the CABYV DNA with size ± 489 bp was successfully amplified from melon in Kediri, Tulungagung, Nganjuk (East Java), Kulonprogo, and bitter gourd in Bogor. The sequencing result confirmed the identity of melon isolates from Nganjuk showed the highest similarity with the CABYV cucumber isolate from Nganjuk and Tulungagung. In contrast, bitter gourd isolates with melon isolates from France and squash isolates from Spain. These are the first reports of CABYV infection on melon and bitter gourd in Java, indicating its rapid host expansion on Cucurbitaceae.

Molecular Characterization of Hemagglutinin-Neuraminidase Protein Virus Newcastle disease (ND) in Surabaya during 2003 and 2016

This study aimed to determine the mutation of amino acid, nucleotide homology, phylogenetic tree, epitope prediction of Hemagglutinin-Neuraminidase protein Newcastle Disease (ND) Virus isolated from traditional market around Surabaya. Samples were from 37 chicken with cloacal swab and one positive samples for control (LaSota). Samples were inoculated on embyonate chicken eggs and identified with HA test confirmed with HI test. Positive samples processed by PCR using forward and reverse primer with 503 bp RNA target. The PCR result then analyzed with sequencing. Result of sequencing analysis showed that theres similiarity between samples amino acid and vaccine isolate its effect the percentage of nucleotide homology and phylogenetic relation between isolate. Epitope NGAANNSGWGAPIHDPDYIGG have high immunogenic value at all of isolate which good as vaccine candidate.

Comparative Analysis of Intestinal Bacterial Communities in Healthy and Diseased Nibea albiflora

Background: The gut microbiota is an integral part of the host and plays an important role in both growth and development of host. The research on intestinal microbiota of Nibea albiflora and its relationship to fish disease have not been reported before. This study aimed to investigate the composition and differences of gut bacteria between healthy and diseased Nibea albiflora. Methods: The intestines were collected from forty fish (twenty healthy fish and twenty diseased). Total DNA was extracted and then amplified by nested PCR. The PCR product was subjected to the DGGE test and performed at the IlluminaMiseq sequencing. Result: The obtained results of both utilized techniques (DGGE and Next generation sequencing) showed that dominant bacteria could be grouped into four populations and the composition of intestinal bacteria differed significantly between healthy (NH) and diseased (ND) Nibea albiflora. NH has higher levels of γ-Proteobacteria and Firmicutes and with 46.91% Photobacterium supplied the dominant genus in NH. Fusobacteria and Bacteroidetes were higher in ND and Cetobacterium occupied 62.31% and was the dominant genus in ND. More probiotics were detected in NH, such as Lactobacillus, Brevibacillus, Enterococcus and Lactococcus (occupying 1.77% -19.76%), while less than 0.2% were detected for both in ND. More genera that belonged to Vibrionaceae, such as Enterovibrio (9.27%) and Vibrio (2.17%), were detected in ND and their abundances in NH were 0.79% and 0.03%, respectively.

Wastewater-based epidemiology for tracking COVID-19 trend and variants of concern in Ohio, United States

The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 129 million confirm cases. Many health authorities around the world have implemented wastewater-based epidemiology as a rapid and complementary tool for the COVID-19 surveillance system and more recently for variants of concern emergence tracking. In this study, three SARS-CoV-2 target genes (N1, N2, and E) were quantified from wastewater influent samples (n = 250) obtained from the capital city and 7 other cities in various size in central Ohio from July 2020 to January 2021. To determine human-specific fecal strength in wastewater samples more accurately, two human fecal viruses (PMMoV and crAssphage) were quantified to normalize the SARS-CoV-2 gene concentrations in wastewater. To estimate the trend of new case numbers from SARS-CoV-2 gene levels, different statistical models were built and evaluated. From the longitudinal data, SARS-CoV-2 gene concentrations in wastewater strongly correlated with daily new confirmed COVID-19 cases (average Spearman r = 0.70, p < 0.05), with the N2 gene being the best predictor of the trend of confirmed cases. Moreover, average daily case numbers can help reduce the noise and variation from the clinical data. Among the models tested, the quadratic polynomial model performed best in correlating and predicting COVID-19 cases from the wastewater surveillance data, which can be used to track the effectiveness of vaccination in the later stage of the pandemic. Interestingly, neither of the normalization methods using PMMoV or crAssphage significantly enhanced the correlation with new case numbers, nor improved the estimation models. Whole-genome sequencing result showed that those detected SARS-CoV-2 variants of concern from the wastewater matched with the clinical isolates from the communities. The findings from this study suggest that wastewater surveillance is effective in COVID-19 trend tracking and variant emergence and transmission within a community.

Effects of Tea Polyphenol Treatments on the Quality and Microbiota of Crisp Grass Carp Fillets during Storage at 4 °C

We investigated the effects of tea polyphenol treatments on the quality and microbiota of crisp grass carp fillets during cold storage at 4 °C. Changes in the total viable count (TVC) and total volatile base nitrogen (TVB-N) of fillets were measured. The microbiota of the crisp grass carp was analyzed using high-throughput sequencing technique. The results indicated that tea polyphenol treatments inhibited bacterial growth and reduced TVB-N values of fish fillets, and subsequently extended their shelf life by 6 days. The high-throughput sequencing result showed that Pseudomonas was the most abundant bacteria in tea polyphenol-treated fish fillets at the end of shelf life, while Pseudomonas and Aeromonas were the most abundant bacteria in control samples. These findings suggested that tea polyphenol treatments could be used in future to extend the shelf life of crisp grass carp fillets and alter the bacterial communities responsible for spoiling fish.

Bias in RNA-seq Library Preparation: Current Challenges and Solutions

Although RNA sequencing (RNA-seq) has become the most advanced technology for transcriptome analysis, it also confronts various challenges. As we all know, the workflow of RNA-seq is extremely complicated and it is easy to produce bias. This may damage the quality of RNA-seq dataset and lead to an incorrect interpretation for sequencing result. Thus, our detailed understanding of the source and nature of these biases is essential for the interpretation of RNA-seq data, finding methods to improve the quality of RNA-seq experimental, or development bioinformatics tools to compensate for these biases. Here, we discuss the sources of experimental bias in RNA-seq. And for each type of bias, we discussed the method for improvement, in order to provide some useful suggestions for researcher in RNA-seq experimental.

Molecular identification and life cycle of Black Soldier fly (Hermetia illucens) in laboratory

Molecular identification and life cycle of the Black Soldier Fly (BSF), Hermetia illucens were carried out from the Bangladesh bio-geographical area. The sequencing result and phylogenetic analysis of BSF showed 99-100% similarity with H. illucens from GenBank. The average duration of life cycle of male and female were 45.08±4.46d and 46.15± 4.12d respectively. The adult female is 16.3±0.91mm long, whereas the adult male is 14.30±0.19 mm long and smaller than female. The number of eggs per clutch was 537.37±40.21 which hatched in 4.36±0.24 days. The mean duration of the developmental stages were 16.07±2.59, 15.4±2.50, 9.95±1.48 and 10.33±1.89 d for larva, pupa, male and female respectively, when cultured at 29.40±1.77° C, RH 68.25±2.32 %, 14:10 (L: D) photoperiod. The mature larval weight (0.20±0.03 g) was highest among other developmental stages. Bangladesh J. Zool. 48(2): 429-440, 2020

TRACING THE KINSHIP OF BRUCELLA SP. BY USINGA POLYMERASE CHAIN REACTION TECHNIQUE WITH A SHORT PRIMER

Brucellosis is a zoonotic disease that has spread throughout the world and has an important impacton both human and animal health. The four species of Brucella that cause disease in humans are Brucellaabortus, B. suis, B. melitensis and B. canis, and B. melitensis as the most pathogenic species. This Researchused 46 samples were collected from Government Small Ruminants Abattoir in Bogor Regency. Thirty twospleen samples were examined by previous research and showed a positive result when were tested withCFT and PCR techniques, but sequencing has not yet been done. Fourteen serum and spleen samples wereexamined by the similar techniques. The Research aimed to determined the genetic relationship of Brucellasp. using a PCR technique with a specific short primer to B. mellitensis. Cloning technique was appliedpreviously to five PCR positive samples before sequencing. Cloning and sequencing result of the Sample91 showed higher homology to B. melitensis and B. abortus for 127 nucleotide lengths, 97.6% -100% and99.2% -100% respectively. In the phylogenic tree, the Sample 91 was part of B melitensis sequences 1, 2,and 3 with accession numbers LT962930.1 and LT962936.1, B abortus sequences 1 and 2 with accessionnumbers CP033079.1 and B. abortus sequence 1 with accession number CP034695.1. Sample of 95, 97, 7,and 13 have lower homologies than Sample 91.

Caseinase Production and Media Optimization from Bacillus subtilis

Caseinase is involved in the breakdown of milk protein casein and converts casein into smaller simple sugars which can be easily utilized by the body for the production of ATP and Fat. Casein can be an instant energy source to the body and involves in muscle building. Caseinase enzyme can be extensively used at the industrial scale for Milk, Textile, Dairy, Paper industry and several other medical purposes. In view of the importance of caseinase, the current research deals with the isolation and identification of caseinase producing bacteria from soil. This is followed by the production of enzyme and its purification. The study also includes its kinetic characterization using the parameters Temperature, pH as well as Carbon and Nitrogen Sources. The organism which was isolated from soil and capable of producing the caseinase enzyme was identified to be Bacillus subtilis based on the Biochemical tests and 16S rRNA sequencing result. The optimal carbon and nitrogen sources were identified to be Glucose and casein respectively. Regarding the optimal conditions, the suitable temperature for maximum enzyme production was found to be 40 0C and pH was 9. When the organism was cultured under the optimal condition using casein as a nitrogen source and glucose as the carbon source, at 40 0C and pH 9, 1590 ng/mL of enzyme production was estimated.

Differentially Expressed miRNAs in Mouse Uterus during Embryo Implantation

Background: MicroRNAs (miRNAs) play key roles in posttranscriptional regulation during the window of implantation. However, which miRNA may play regulatory role during the window of implantation remains to be studied in depth. This paper aimed to explore the miRNAs that played regulatory roles during the process of implantation. Methods: RNA sequencing was performed to analyze mice uterus tissue in gestation day 1 (D1), gestation day 4 (D4) and gestation day5 (D5). The tissues in D5 were divided into embryo implantation sites (D5IMS) and inter-implantation sites (D5IIS). The differentially expressed miRNAs were screened and bioinformatics analyzed. Transfecting miR-183-5p mimics into HEC-1-A cells, genes regulated by miR-183-5p were analyzed by transcriptome sequencing. Result: Eleven differentially expressed miRNAs were identified during the window of implantation. KEGG enrichment analysis showed that the most differentially expressed miRNAs mainly related to binding and signaling transduction related pathways. Especially miR-183-5p, miR-182-5p, miR-199b-5p and miR-218-5p play a crucial role in regulating many important pathways. Transcriptome sequencing results showed that there were 19 up-regulated and 31 down-regulated genes in the miR-183-5p mimics group compared with the negative control (NC) group. This work laid a foundation for the study of miRNA in early pregnancy.