Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant

Sachin Kumar Gupta,신한섭,한덕기,허호길,Tatsuya Unno 한국미생물학회 2018 The journal of microbiology Vol.56 No.6

The increased antibiotic resistance among microorganisms has resulted into growing interest for investigating the wastewater treatment plants (WWTPs) as they are reported to be the major source in the dissemination of antibiotic resistance genes (ARGs) and heavy metal resistance genes (HMRGs) in the environment. In this study, we investigated the prevalence and persistence of ARGs and HMRGs as well as bacterial diversity and mobile genetic elements (MGEs) in influent and effluent at the WWTP in Gwangju, South Korea, using high-throughput sequencing based metagenomic approach. A good number of broad-spectrum of resistance genes (both ARG and HMRG) were prevalent and likely persistent, although large portion of them were successfully removed at the wastewater treatment process. The relative abundance of ARGs and MGEs was higher in effluent as compared to that of influent. Our results suggest that the resistance genes with high abundance and bacteria harbouring ARGs and MGEs are likely to persist more through the treatment process. On analyzing the microbial community, the phylum Proteobacteria, especially potentially pathogenic species belonging to the genus Acinetobacter, dominated in WWTP. Overall, our study demonstrates that many ARGs and HMRGs may persist the treatment processes in WWTPs and their association to MGEs may contribute to the dissemination of resistance genes among microorganisms in the environment.

Comparison of de‑novo assembly tools for plasmid metagenome analysis

Sachin Kumar Gupta,Shahbaz Raza,Tatsuya Unno 한국유전학회 2019 Genes & Genomics Vol.41 No.9

Background With the advent of next-generation sequencing techniques, culture-independent metagenome approaches have now made it possible to predict possible presence of genes in the environmental bacteria most of which may be non-cultivable. Short reads obtained from the deep sequencing can be assembled into long contigs some of which include plasmids. Plasmids are the circular double stranded DNA in bacteria and known as one of the major carriers of antibiotic resistance genes. Objective Metagenomic analyses, especially focused on plasmids, could help us predict dissemination mechanisms of antibiotic resistance genes in the environment. However, with the availability of a myriad of metagenomic assemblers, the selection of the most appropriate metagenome assembler for the plasmid metagenome study might be challenging. Therefore, in this study, we compared five open source assemblers to suggest most effective way of plasmid metagenome analysis. Methods IDBA-UD, MEGAHIT, SPAdes, SOAPdenovo2, and Velvet are compared for conducting plasmid metagenome analyses using two water samples. Results Our results clearly showed that abundance and types of antibiotic resistance genes on plasmids varied depending on the selection of assembly tools. IDBA-UD and MEGAHIT demonstrated the overall best assembly statistics with high N50 values with higher portion of longer contigs. Conclusion These two assemblers also detected more diverse plasmids. Among the two, MEGAHIT showed more memory efficient assembly, therefore we suggest that the use of MEGAHIT for plasmid metagenome analysis may offer more diverse plasmids with less computer resource required. Here, we also summarized a fundamental plasmid metagenome work flow, especially for antibiotic resistance gene investigation.

CYP1A1 Gene Polymorphisms: Modulator of Genetic Damage in Coal-Tar Workers

Giri, Shiv Kumar,Yadav, Anita,Kumar, Anil,Dev, Kapil,Gulati, Sachin,Gupta, Ranjan,Aggarwal, Neeraj,Gautam, Sanjeev Kumar Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.7

Aim: It is well known that polycyclic aromatic hydrocarbons (PAHs) such as benzo (a) pyrene have carcinogenic properties and may cause many types of cancers in human populations. Genetic susceptibility might be due to variation in genes encoding for carcinogen metabolizing enzymes, such as cytochrome P-450 (CYP450). Our study aimed to investigate the effect of genetic polymorphisms of CYP1A1 (m1 and m2) on genetic damage in 115 coal-tar workers exposed to PAHs at their work place. Methods: Genetic polymorphisms of CYP1A1 were determined by the PCR-RFLP method. Comet and buccal micronucleus assays were used to evaluate genetic damage among 115 coal tar workers and 105 control subjects. Results: Both CYP1A1 m1 and CYP1A1 m2 heterozygous and homozygous (wt/mt+mt/mt) variants individually as well as synergistically showed significant association (P<0.05) with genetic damage as measured by tail moment (TM) and buccal micronuclei (BMN) frequencies in control and exposed subjects. Conclusion: In our study we found significant association of CYP1A1 m1 and m2 heterozygous (wt/mt)+homozygous (mt/mt) variants with genetic damage suggesting that these polymorphisms may modulate the effects of PAH exposure in occupational settings.

Is long term storage of cryopreserved stem cells for hematopoieticstem cell transplantation a worthwhile exercise in developingcountries?

Santhosh Kumar Devadas,Minal Khairnar,Sumathi S Hiregoudar,Shashank Ojha,Sachin Punatar,Alok gupta,Anant Gokarn,Pallavi Bhole,Sadhana Kannan,Navin Khattry 대한혈액학회 2017 Blood Research Vol.51 No.4

Background: Stem cell units (SCUs) that are cryopreserved prior to both autologous and allogeneic hematopoietic stem cell transplants (for donor lymphocyte infusion) remain unused or partially used several times, and become an increased burden to blood banks/SCU repositories. Because of the scarcity of data regarding the duration for which the storage is useful, there is no general consensus regarding disposal of SCUs. Methods: We conducted a retrospective audit of SCU utilization in 435 patients who planned to undergo either autologous stem cell transplantation (auto-SCT) (N=239) or allogeneic stem cell transplantation (allo-SCT) (N=196) at a tertiary cancer care center between November 2007 to January 2015. Results: Our cohort consisted of 1,728 SCUs stored for conducting auto-SCT and 729 SCUs stored for conducting donor lymphocyte infusions (DLIs) after allo-SCT. Stem cells were not in-fused in 12.5% of patients who had planned to undergo auto-SCT, and 80% of patients who underwent allo-SCT never received DLI. Forty-one percent of SCUs intended for use in auto-SCT remained unutilized, with a second auto-SCT being performed only in 4 patients. Ninety-four percent of SCUs intended for carrying out DLIs remained unused, with only minimal usage observed one year after undergoing allo-SCT. Conclusion: The duration of storage of unused SCUs needs to be debated upon, so that a consensus can be reached regarding the ethical disposal of SCU.

Modeling of Micro-Scale Fiber Laser Hardening Process and Optimization via Statistical Approximation of the Engineering Models

Neeraj Gupta,Sachin Bhimrao Ahirrao,Santanu Paul,Ramesh Kumar Singh 한국정밀공학회 2015 International Journal of Precision Engineering and Vol. No.

Laser transformation hardening is effective technique used for selective hardening of components such as turbine blade, camshafts and gears. Laser hardening provides benefits over other selective hardening processes in terms of thermal distortion, control of process and appearance of component. The fiber laser is relatively recent development. The single/low mode fiber lasers have good beam quality, high wall plug efficiency, fiber delivery and powers up to few hundred watts. The beam quality of single mode fiber lasers enable it to be focused to a spot size of few tens of mm which can yield hardened tracks of 100 to 500 mm. These fiber lasers can be extremely useful in localized micro-scale surface hardening to create hardened patterns for improving the wear resistance. This paper is focused on developing analytical thermal model of moving heat sources and integrating it with kinetic hardening model to capture the metallurgical changes induced by fiber lasers. An ideal surface hardening technique should give widest hardened track at minimum case depth. To address this issue, an optimization methodology based on statistical approximation of the physics-based engineering models has been developed.

Modeling of Micro-Scale Fiber Laser Hardening Process and Optimization via Statistical Approximation of the Engineering Models

Neeraj Gupta,Sachin Bhimrao Ahirrao,Santanu Paul,Ramesh Kumar Singh 한국정밀공학회 2015 International Journal of Precision Engineering and Vol.16 No.13

Laser transformation hardening is effective technique used for selective hardening of components such as turbine blade, camshafts and gears. Laser hardening provides benefits over other selective hardening processes in terms of thermal distortion, control of process and appearance of component. The fiber laser is relatively recent development. The single/low mode fiber lasers have good beam quality, high wall plug efficiency, fiber delivery and powers up to few hundred watts. The beam quality of single mode fiber lasers enable it to be focused to a spot size of few tens of mm which can yield hardened tracks of 100 to 500 mm. These fiber lasers can be extremely useful in localized micro-scale surface hardening to create hardened patterns for improving the wear resistance. This paper is focused on developing analytical thermal model of moving heat sources and integrating it with kinetic hardening model to capture the metallurgical changes induced by fiber lasers. An ideal surface hardening technique should give widest hardened track at minimum case depth. To address this issue, an optimization methodology based on statistical approximation of the physics-based engineering models has been developed.

Is long term storage of cryopreserved stem cells for hematopoieticstem cell transplantation a worthwhile exercise in developingcountries?

Santhosh Kumar Devadas,Minal Khairnar,Sumathi S Hiregoudar,Shashank Ojha,Sachin Punatar,Alok gupta,Anant Gokarn,Pallavi Bhole,Sadhana Kannan,Navin Khattry 대한혈액학회 2017 Blood Research Vol.52 No.4

Background: Stem cell units (SCUs) that are cryopreserved prior to both autologous and allogeneic hematopoietic stem cell transplants (for donor lymphocyte infusion) remain unused or partially used several times, and become an increased burden to blood banks/SCU repositories. Because of the scarcity of data regarding the duration for which the storage is useful, there is no general consensus regarding disposal of SCUs. Methods: We conducted a retrospective audit of SCU utilization in 435 patients who planned to undergo either autologous stem cell transplantation (auto-SCT) (N=239) or allogeneic stem cell transplantation (allo-SCT) (N=196) at a tertiary cancer care center between November 2007 to January 2015. Results: Our cohort consisted of 1,728 SCUs stored for conducting auto-SCT and 729 SCUs stored for conducting donor lymphocyte infusions (DLIs) after allo-SCT. Stem cells were not in-fused in 12.5% of patients who had planned to undergo auto-SCT, and 80% of patients who underwent allo-SCT never received DLI. Forty-one percent of SCUs intended for use in auto-SCT remained unutilized, with a second auto-SCT being performed only in 4 patients. Ninety-four percent of SCUs intended for carrying out DLIs remained unused, with only minimal usage observed one year after undergoing allo-SCT. Conclusion: The duration of storage of unused SCUs needs to be debated upon, so that a consensus can be reached regarding the ethical disposal of SCU.

Comparative analysis of VMT genes/proteins in selected plant species with emphasis on bread wheat (Triticum aestivum L.)

Sharma Hemant,Shayaba,Kumar Rahul,Kumar Jitendra,Bhadana Deepa,Batra Ritu,Singh Rakhi,Kumar Sachin,Roy Joy K,Balyan Harindra S.,Gupta Pushpendra K. 한국유전학회 2023 Genes & Genomics Vol.45 No.11

Background In recent years, the study of molecular basis of uptake, transport and utilization of grain Fe/Zn (GFe/GZn) in wheat has been an active area of research. As a result, it has been shown that a number of transporters are involved in uptake and transport of Fe. In a recent study, knockout of a transporter gene OsVMT (VACUOLAR MUGINEIC ACID TRANSPORTER) in rice was shown to be involved in Fe homoeostasis. Objective In this study, we analysed VMT genes among six monocots and three dicots with major emphasis on wheat VMT genes (TaVMTs), taking OsVMT gene as a reference. Methods and results Using OsVMT gene as a reference, VMT genes were identified and sequence similarities were examined among six monocots and three dicots. Each VMT protein carried one functional domain and 7 to 10 distinct motifs (including 9 novel motifs). The qRT-PCR analysis showed differential expression by all the six TaVMT genes in pairs of contrasting wheat genotypes with high (FAR4 and WB02) and low (K8027 and HD3226) GFe/GZn at two different grain filling stages (14 DAA and 28 DAA). TaVMT1 genes showed up-regulation in high GFe/Zn genotypes relative to low GFe/Zn genotypes, whereas the TaVMT2 genes showed down-regulation or nonsignificant up-regulation in a few cases. Conclusions At 14 DAA, each of the six TaVMT genes exhibited higher expression in wheat genotypes with high GFe and GZn relative to those with low GFe and GZn, suggesting major role of VMT genes in improvement of grain Fe/Zn homoeostasis, thus making TaVMT genes useful for improvement in Fe/Zn in wheat grains.