Biology subjects

Thakkar, R.

Publications and source records attributed to Thakkar, R..

7 recordsLinked to original sources

bioRxiv2025

The effect of particle size on wheat bran fermentation by human gut microbiota

0.Dietary fibers within whole grains reach the large intestine where they shape the microbial composition. However, the bioavailability of these dietary nutrients to the microbiota is likely limited due to entrapment within the grain particle and requires liberation by microbial enzymes. Here, we used batch fecal fermentation from mixed donors on a range of sizes of wheat particles generated by cyclone milling from a single source to identify bacterial taxa and genomic signatures that are responsive to differences in wheat bran fine structures. We present evidence that different taxa within the same genus colonize wheat bran particles of different sizes. Further, neutral sugar content varied across wheat bran particles despite originating from the same batch, suggesting different polysaccharide structures and nutritional niches. In line with the taxonomic and compositional differences, specific short chain fatty acids varied across particle sizes; in fine wheat bran particle fermentations propionate was high and butyrate low. To identify relevant genomic features implicated in bran colonization, we took a metagenomic approach. From this, we linked genes associated with polysaccharide fermentation to wheat bran particles independent of size, however, within one well-distributed taxon, Lachnospiraceae, genes related to motility were linked to large and medium wheat bran particles. Overall, these results suggest that differences in fine structures and resource availability, as generated through milling, can drive compositional changes in the gut microbiota in an organism-specific manner, mediated through its genomic capacity. IMPORTANCECereal brans comprise a large fraction of the dietary fiber consumption. Although it is well-known that dietary fibers influence the metabolic output and taxonomic composition of the gut microbiota, relatively little is known regarding whether the fine structures and resource availability of milled whole grains exert any influence on the microbial makeup. Our data suggest that the sugar content varies across bran milled from a single source to different sizes. These differences in composition may result in colonization differences by related, but unique, taxa, mediated by genes related to polysaccharide fermentation, thus leading to differences in metabolic output. Furthermore, our data suggest that genes related to motility might influence the capacity of microorganisms to colonize particles. Taken together, our data suggest that physical context can influence gut microbiota composition in turn impacting metabolic output. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/654185v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1b3b95corg.highwire.dtl.DTLVardef@4e5432org.highwire.dtl.DTLVardef@79d317org.highwire.dtl.DTLVardef@119ba9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

A genome-wide cytotoxicity screen of Cluster F1 mycobacteriophage Girr reveals novel inhibitors of Mycobacterium smegmatis growth

Over the past decade, thousands of bacteriophage genomes have been sequenced and annotated. A striking observation from this work is that known structural features and functions cannot be assigned for >65% of the encoded proteins. One approach to begin experimentally elucidating the function of these uncharacterized gene products is genome-wide screening to identify phage genes that confer phenotypes of interest like inhibition of host growth. This study describes the results of a screen evaluating the effects of overexpressing each gene encoded by the temperate Cluster F1 mycobacteriophage Girr on the growth of the host bacterium Mycobacterium smegmatis. Overexpression of 29 of the 102 Girr genes ([~]28% of the genome) resulted in mild to severe cytotoxicity. Of the 29 toxic genes described, 12 have no known function (NKF) and are predominately small proteins of <125 amino acids. Overexpression of the majority of these 12 cytotoxic NKF proteins resulted in moderate to severe growth reduction and represent novel antimicrobial products. The remaining 17 toxic genes have predicted functions, encoding products involved in phage structure, DNA replication/modification, DNA binding/gene regulation, or other enzymatic activity. Comparison of this dataset with prior genome-wide cytotoxicity screens of mycobacteriophages Waterfoul and Hammy reveals some common functional themes, though several of the predicted Girr functions associated with cytotoxicity in our report, including genes involved in lysogeny, have not been described previously. This study, completed as part of the HHMI-supported SEA-GENES project, highlights the power of parallel, genome-wide overexpression screens to identify novel interactions between phages and their hosts.

microbiology↗

bioRxiv2021

Selective Laser Sintering of a Photosensitive Drug: Impact of Processing and Formulation Parameters on Degradation, Solid-State, and Quality of 3D Printed Dosage Forms

This research study utilized a light-sensitive drug, nifedipine (NFD), to understand the impact of processing parameters, and formulation composition on drug degradation, crystallinity, and quality attributes (dimensions, hardness, disintegration time) of selective laser sintering (SLS) based 3D printed dosage forms. Selective laser sintering (SLS), in most cases, uses an ultraviolet laser source, and drugs tend to absorb radiation at varying intensities around this wavelength (455 nm). This phenomenon may lead to chemical degradation, and solid-state transformation, which was assessed for nifedipine in formulations with varying amounts of vinyl pyrrolidone-vinyl acetate copolymer (Kollidon(R) VA 64) and potassium aluminum silicate-based pearlescent pigment (Candurin(R)), processed under different SLS conditions in the presented work. After preliminary screening Candurin(R), surface temperature (ST), and laser speed (LS) were identified as the significant independent variables. Further, using the identified independent variables a 17-run, randomized, Box-Behnken design was developed to understand the correlation trends and quantify the impact on degradation (%), crystallinity, quality attributes (dimensions, hardness, disintegration time) employing qualitative and quantitative analytical tools. The design of experiments (DoE) and statistical analysis observed that LS and Candurin(R) (%wt) had a strong negative correlation on drug degradation, hardness, and weight, whereas ST had a strong positive correlation with, drug degradation, amorphous conversion, and hardness of the 3D printed dosage form. From this study, it can be concluded that formulation and processing parameters have a critical impact on stability and performance; hence these parameters should be evaluated and optimized before exposing light-sensitive drugs to the SLS processes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/439089v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1e3dd02org.highwire.dtl.DTLVardef@c2bfaforg.highwire.dtl.DTLVardef@1b6b712org.highwire.dtl.DTLVardef@ad35fd_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2021

Synergistic application of continuous granulation and selective laser sintering 3D printing for the development of pharmaceutical dosage forms with enhanced dissolution rates and physical properties

This study demonstrated the first case of combining novel continuous granulation with powder-based pharmaceutical 3-dimensional (3D) printing processes to enhance the dissolution rate and physical properties of a poorly water-soluble drug. Powder bed fusion (PBF) and binder jetting 3D printing processes have gained much attention in pharmaceutical dosage form manufacturing in recent times. Although powder bed-based 3D printing platforms have been known to face printing and uniformity problems due to the inherent poor flow properties of the pharmaceutical physical mixtures (feedstock). Moreover, techniques such as binder jetting currently do not provide any solubility benefits to active pharmaceutical ingredients (APIs) with poor aqueous solubility (>40% of marketed drugs). For this study, a hot-melt extrusion-based versatile granulation process equipped with UV-Vis process analytical technology (PAT) tools for the in-line monitoring of critical quality attributes (i.e., solid-state) of indomethacin was developed. The collected granules with enhanced flow properties were mixed with vinylpyrrolidone-vinyl acetate copolymer and a conductive excipient for efficient sintering. These mixtures were further characterized for their bulk properties observing an excellent flow and later subjected to a PBF-3D printing process. The physical mixtures, processed granules, and printed tablets were characterized using conventional as well as advanced solid-state characterization. These characterizations revealed the amorphous nature of the drug in the processed granules and printed tablets. Further, the in vitro release testing of the tablets with produced granules as a reference standard depicted a notable solubility advantage (100% drug released in 5 minutes at >pH 6.8) over the pure drug and the physical mixture. Our developed system known as DosePlus combines innovative continuous granulation and PBF-3D printing process which can potentially improve the physical properties of the bulk drug and formulations in comparison to when used in isolation. This process can further find application in continuous manufacturing of granules and additive manufacturing of pharmaceuticals to produce dosage forms with excellent uniformity and solubility advantage. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/430988v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@29c7caorg.highwire.dtl.DTLVardef@fbae3eorg.highwire.dtl.DTLVardef@16c8de1org.highwire.dtl.DTLVardef@1d6b088_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2020

Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses

Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity to the human coronaviruses (HCoV) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 and other HCoV peptides that can be used to detect asymptomatic, mild and, severe SARS-CoV-2 infections, and may enable the discovery of biomarkers for immunity following infection or vaccination.

microbiology↗

bioRxiv2019

Identification of immunoreactive linear epitopes of Borrelia miyamotoi

Borrelia miyamotoi is an emerging tick-borne spirochete transmitted by Ixodid ticks. Current serologic assays for B. miyamotoi are impacted by genetic similarities to other Borrelia and limited understanding of optimal antigenic targets. In this study, we employed the TBD-Serochip, a peptide array platform, to identify new linear targets for serologic detection of B. miyamotoi. We examined a wide range of suspected B. miyamotoi antigens and identified 352 IgM and 91 IgG reactive peptides, with the majority mapping to variable membrane proteins. These included peptides within conserved fragments of variable membrane proteins that may have greater potential for differential diagnosis. We also identified reactive regions on FlaB, and demonstrate crossreactivity of B. burgdorferi C6 with a B. miyamotoi C6-like peptide. The panel of linear peptides identified in this study can be used to enhance serodiagnosis of B. miyamotoi.

microbiology↗

bioRxiv2018

Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection

Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980s. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance.

genomics↗