Sarita Mallik

Aquaculture is one of the fastest-growing food production sectors worldwide and plays a crucial role in ensuring food security, nutrition, and livelihoods. In India, this sector significantly contributes to employment and income generation, especially among smallholder farmers. This study assessed the status, practices, and key constraints of freshwater fish farming in the peri-urban areas of the National Capital Region (NCR) of India. Data were collected via a structured questionnaire survey conducted from September 2021 to April 2022 across four districts of NCR: Gautam Buddha Nagar, Ghaziabad, Bulandshahr (Uttar Pradesh), and Sonipat (Haryana), covering 100 fish farms. According to the findings of the survey, the most common species farmed (98%) were Indian major carps (Catla catla, Labeo rohita, and Cirrhinus mrigala), and the primary source of water was groundwater along with mixed sources such as canal and untreated sewage water. More than half of the farmers were not aware enough of important water quality parameters like ammonia, dissolved oxygen (DO), and pH. Moreover, 28% regularly monitored water quality, and merely 5% demonstrated comprehensive knowledge of water-quality parameters. Additionally, farmers lacked knowledge about the appropriate use of antimicrobials. The main obstacles included poaching, poor market connections, high input costs, limited or very low access to technical equipment, and insufficient professional assistance. Statistical analysis using the chi-square test revealed a significant correlation between farming practices and geographic location. A statistically significant association was observed between knowledge constraints and testing frequency and methods (p<0.001). Overall, a significant knowledge gap was observed among farmers, impacting water quality management. To improve the sustainability and productivity of smallholder aquaculture in the NCR region, the study emphasises the necessity of better technical trainings with extension services and water quality monitoring programmes. Thus, this initiative study would certainly lead to the nation's nutritional stability and development goals in aquaculture.

Escherichia coli 's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that the in vitro interaction between Rep and Pol IV reported previously also occurs in vivo . Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecA in vivo and is recruited to sites of DSBs to aid in the restoration of DNA replication. IMPORTANCE DNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstrate in vivo localization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings provide in vivo evidence that Pol IV aids in maintaining genomic stability not only by bypassing DNA lesions but also by participating in the restoration of stalled replication forks.

An investigation of bacterial diversity in compost was performed using molecular chronometer in order to reveal its phylogeny. Thirty-three bacterial isolates isolated from compost were analyzed by 16S rRNA gene sequencing which revealed phylogenetic lineage of class Bacilli, γ, β-Proteobacteria, and Actinobacteria. Among these lineages, isolates belonging to class Bacilli consisted of species from genera Staphylococcus, Bacillus, Terribacillus, and Lysinibacillus. From phylum Actinobacteria: Microbacterium barkeri and Kocuria sp. were identified. Other bacterial groups had phylogenetic linkage with genera Comamonas and Acidovorax (class β-Proteobacteria); Serratia, Klebsiella, and Enterobacter (class γ-Proteobacteria). Similar isolates were analyzed through ARDRA. Amplified product of 16S rRNA gene from each isolates was subjected to cleavage by enzymes HpaII, HinfI, and MspI in separate reaction tubes. HpaII generated 2–6 bands ranging from 90–688 bp, HinfI generated 2–5 bands of 71–1,038 bp, and MspI 2–7 bands of 69–793 bp. The restriction patterns from HpaII, HinfI, and MspI were normalized separately and combined by means of pattern recognition software “Diversity Database.” HpaII had highest discrimination index (0.72) than HinfI (0.68) and MspI (0.65), and the combination of all three showed discrimination index (0.69). Numerical analysis of ARDRA patterns demonstrated sufficient phylogenetic information for characterizing bacterial diversity. Phylogenetic relationship obtained among isolates through ARDRA was compared with 16S rRNA gene sequence and ARDRA results showed sufficiently similar 16S rRNA gene sequence analysis, but not an overlapping. It has been observed that ARDRA technique facilitates the identification of bacteria in less than 36 h as compared to traditional 16S rRNA gene sequencing.

Arsenic is one of the most important global environmental pollutants. In the present study, fifty one clinical strains of Yersinia enterocolitica biovar 1A showed high resistance to arsenite and arsenate. The minimum inhibitory concentration (MIC) of arsenite (0.625–20 mM) was lower than arsenate (10–80 mM). Growth of Y. enterocolitica in 2 mM arsenite led to 2–8 fold increase in MICs of the five antibiotics (amikacin, ciprofloxacin, gentamycin, kanamycin and tetracycline), suggesting expression of arsenite-induced multiple antibiotic resistance among the strains. Proteomic analysis of Y. enterocolitica revealed differential expression of certain proteins following arsenite exposure, which included a putative outer membrane porin (OmpA) and a putative amino acid transporter protein. In conclusion, modulation of membrane permeability may be involved in the induction of arsenite–mediated expression of multiple antibiotic resistance in Y. enterocolitica. (© 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

To evaluate whole cell protein profiling vis-à-vis genotyping to discern phylogenetic relationships among strains of Y. enterocolitica biovar 1A. Whole cell protein profiling of Y. enterocolitica biovar 1A strains was performed using SDS-PAGE. Twenty-one distinct protein profile types were obtained among a collection of 81 strains isolated from clinical and nonclinical sources. Whole cell protein profiling exhibited discriminatory index (DI) of 0·80 and clustered the strains into two distinct clonal groups. The clinical and the aquatic serotype O:6,30-6,31 strains were clustered into two discrete subgroups. Whole cell protein profiling displayed sufficient diversity among strains of Y. enterocolitica biovar 1A, and the phylogenetic relationships obtained were in good agreement with those established earlier by genotyping techniques. Whole cell protein profiling was as discriminatory as some of the genotyping methods and has the potentiality to be used as an adjunct tool to study epidemiology of Y. enterocolitica.

Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE) and multilocus restriction typing (MLRT) using six loci each. Such studies may reveal associations between the genotypes of the strains and their sources of isolation.

Background: The presence of β-lactamases in Y. enterocolitica has been reported to vary with serovars, biovars and geographical origin of the isolates. An understanding of the β-lactamases in other related species is important for an overall perception of antibiotic resistance in yersiniae. The objective of this work was to study the characteristics of β-lactamases and their genes in strains of Y. intermedia and Y. frederiksenii, isolated from clinical and non-clinical sources in India. Results: The enzymes, Bla-A (a constitutive class A penicillinase) and Bla-B (an inducible class C cephalosporinase) were found to be present in all the clinical and non-clinical strains of Y. intermedia and Y. frederiksenii by double disc diffusion method. The results showed differential expression of Bla-A as indicated by presence/absence of synergy whereas expression of Bla-B was quite consistent. The presence of these enzymes was also reflected in the high minimum inhibitory concentrations, MIC₅₀ (126–1024 mg/L) and MIC₉₀ (256–1024 mg/L) of β-lactam antibiotics against these species. Restriction fragment length polymorphism (RFLP) revealed heterogeneity in both blaA and blaB genes of Y. intermedia and Y. frederiksenii. The blaA gene of Y. intermedia shared significant sequence identity (87–96%) with blaA of Y. enterocolitica biovars 1A, 1B and 4. The sequence identity of blaA of Y. frederiksenii with these biovars was 77–79%. The sequence identity of blaB gene of Y. intermedia and Y. frederiksenii was more (85%) with that of Y. enterocolitica biovars 1A, 1B and 2 compared to other species viz., Y. bercovieri, Y. aldovae and Y. ruckeri. Isoelectric focusing data further revealed that both Y. intermedia and Y. frederiksenii produced Bla-A (pI 8.7) and "Bla-B like" (pI 5.5–7.1) enzymes. Conclusion: Both Y. intermedia and Y. frederiksenii showed presence of blaA and blaB genes and unequivocal expression of the two β-lactamases. Limited heterogeneity was detected in blaA and blaB genes as judged by PCR-RFLP. Phylogenetic relationships showed that the two species shared a high degree of identity in their bla genes. This is the first study reporting characteristics of β-lactamases and their genes in strains of Y. intermedia and Y. frederiksenii isolated from Asian region.

The β-lactamase genes blaA and blaB were detected by PCR amplification in strains of Yersinia enterocolitica biovar 1A isolated from India, Germany,