Biology subjects

Kaushik, A.

Publications and source records attributed to Kaushik, A..

23 records · Page 2Linked to original sources

bioRxiv2019

Disruption of the coordination between host circadian rhythms and malaria parasite development alters the duration of the intraerythrocytic cycle

Malaria parasites complete their intra-erythrocytic developmental cycle (IDC) in multiples of 24 hours (depending on the species), suggesting a circadian basis to the asexual cell cycle, but the mechanism controlling this periodicity is unknown. Combining in vivo and in vitro approaches using rodent and human malaria parasites, we reveal that: (i) 57% of Plasmodium chabaudi genes exhibit 24 h \"circadian\" periodicity in transcription; (ii) 58% of these genes lose transcriptional rhythmicity when the IDC is out-of-synchrony with host rhythms; (iii) 9% of Plasmodium falciparum genes show circadian transcription under free-running conditions; (iv) Serpentine receptor 10 (SR10) has a circadian transcription profile and disrupting it in rodent malaria parasites shortens the IDC by 2-3 hours; (v) Multiple processes including DNA replication and the ubiquitin and proteasome pathways are affected by loss of coordination with host rhythms and by disruption of SR10. Our results show that malaria parasites are at least partly responsible for scheduling their IDCs explaining the fitness benefits of coordination with host rhythms.

genomics↗

bioRxiv2019

New β-Lactamase Inhibitors Nacubactam and Zidebactam Improve the In Vitro Activity of β-Lactam Antibiotics Against Mycobacterium abscessus Complex Clinical Isolates

The new diazabicyclooctane-based {beta}-lactamase inhibitors avibactam and relebactam improve the in vitro activity of {beta}-lactam antibiotics against Mycobacterium abscessus complex (MABC). Here, we evaluated the in vitro activity of two newer diazabicyclooctane-based {beta}-lactamase inhibitors in clinical development, nacubactam and zidebactam, with {beta}-lactams against clinical isolates of MABC. Both inhibitors lowered the MICs of their partner {beta}-lactams, meropenem (eight-fold) and cefepime (two-fold), and those of other {beta}-lactams, similar to prior results with avibactam and relebactam.

microbiology↗

bioRxiv2019

ApicoTFdb: The comprehensive web repository of apicomplexan transcription factors and regulators.

Despite significant progress in apicomplexans genome sequencing and genomics, the current list of experimentally validated TFs in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and TAFs. We have performed systematic bioinformatics aided prediction of TFs and TAFs in apicomplexan genomes, and developed ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TAFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1310 TFs, out of which 833 are novel and computationally predicted TFs, representing 22 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, CCAAT, HTH, Cupin/Jumonji, winged-helix, and FHA family proteins, not reported earlier in the genomes. Apart from TFs, ApicoTFdb also classifies TAFs into three main subclasses-TRs, CRRs and RNARs, representing 3047 TAFs in 14 apicomplexan species are analyzed in this study. The database is equipped with a set of useful tools for comparative analysis of a user-defined list of the proteins. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.

bioinformatics↗

bioRxiv2019

Activity of a long-acting injectable bedaquiline formulation in a paucibacillary mouse model of latent tuberculosis infection

The potent anti-tuberculosis activity and long half-life of bedaquiline make it an attractive candidate for long-acting/extended release formulations for treatment of latent tuberculosis infection (LTBI). Our objective was to evaluate a long-acting injectable (LAI) bedaquiline formulation in a validated paucibacillary mouse model of LTBI. Following immunization with Mycobacterium bovis rBCG30, BALB/c mice were challenged by aerosol infection with M. tuberculosis H37Rv. Treatment began 13 weeks after challenge infection with one of the following regimens: untreated negative control; positive controls of daily rifampin (10 mg/kg), once-weekly rifapentine (15 mg/kg) and isoniazid (50 mg/kg), or daily bedaquiline (25 mg/kg); test regimens of one, two, or three monthly doses of LAI bedaquiline at 160 mg/dose (BLAI-160); and test regimens of daily bedaquiline at 2.67 (B2.67), 5.33 (B5.33), or 8 (B8) mg/kg to deliver the same total bedaquiline as one, two, or three doses of BLAI-160, respectively. All drugs were administered orally, except for BLAI-160 (intramuscular injection). The primary outcome was the decline in M. tuberculosis lung CFU counts during 12 weeks of treatment. The negative and positive control regimens performed as expected. One, two, and three doses of BLA-160 resulted in decreases of 2.9, 3.2, and 3.5 log10 CFU/lung, respectively by week 12. Daily oral dosing with B2.67, B5.33, and B8 decreased lung CFU counts by 1.6, 2.8, and 4.1 log10, respectively. One dose of BLAI-160 exhibited activity for at least 12 weeks. The sustained activity of BLAI-160 indicates promise as a short-course LTBI treatment requiring few patient encounters to ensure treatment completion.

microbiology↗

bioRxiv2018

In vitro activity of the new β-lactamase inhibitors relebactam and vaborbactam in combination with β-lactams against Mycobacterium abscessus complex clinical isolates

Pulmonary disease due to infection with Mycobacterium abscessus complex (MABC) is notoriously difficult to treat, in large part due to MABCs intrinsic resistance to most antibiotics, including {beta}-lactams. MABC organisms express a broad-spectrum {beta}-lactamase that is resistant to traditional {beta}-lactam-based {beta}-lactamase inhibitors but inhibited by a newer non-{beta}-lactam-based {beta}-lactamase inhibitor, avibactam. Consequently, the susceptibility of MABC to some {beta}-lactams is increased in the presence of avibactam. Therefore, we hypothesized that two new non-{beta}-lactam-based {beta}-lactamase inhibitors, relebactam and vaborbactam, would also increase susceptibility of MABC to {beta}-lactams. The objective of the present study was to evaluate the in vitro activity of various marketed {beta}-lactams alone and in combination with either relebactam or vaborbactam against multidrug-resistant MABC clinical isolates. Our data demonstrate that both {beta}-lactamase inhibitors significantly improved the anti-MABC activity of many carbapenems (including imipenem and meropenem) and cephalosporins (including cefepime, ceftaroline, and cefuroxime). As a meropenem/vaborbactam combination is now marketed and an imipenem/relebactam combination is currently in phase III trials, these fixed combinations may become the {beta}-lactams of choice for the treatment of MABC infections. Furthermore, given the evolving interest in dual {beta}-lactam regimens, our results identify select cephalosporins, such as cefuroxime, with superior activity in the presence of a {beta}-lactamase inhibitor, deserving of further evaluation in combination with these carbapenem/{beta}-lactamase inhibitor products.

microbiology↗