Biology subjects

Gulati, M.

Publications and source records attributed to Gulati, M..

6 recordsLinked to original sources

bioRxiv2025

Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease

Interstitial lung disease (ILD) is present in over 60% of patients with systemic sclerosis (SSc) and is the leading cause of SSc-related deaths. Profibrotic monocyte-derived alveolar macrophages (MoAM) play a causal role in the pathogenesis of pulmonary fibrosis in animal models where their persistence in the niche requires signaling through Colony Stimulating Factor 1 Receptor (CSF1R). We hypothesized that the presence and proportion of MoAM in bronchoalveolar lavage (BAL) fluid from patients with SSc-ILD may be a biomarker of ILD severity. To test this hypothesis, we analyzed BAL fluid from 9 prospectively enrolled patients with SSc-ILD and 13 healthy controls using flow cytometry and single-cell RNA sequencing. Patients with SSc-ILD had more MoAM and interstitial macrophages in BAL fluid than healthy controls, and their abundance was associated with lung fibrosis severity. We identified changes in the MoAM transcriptome as a function of treatment with mycophenolate, an effective therapy for SSc-ILD. In SSc-ILD lung explants, spatial transcriptomics identified an expanded population of interstitial macrophages spilling into the alveolar space. Our findings suggest that the proportion of profibrotic MoAM and interstitial macrophages in BAL fluid may serve as a biomarker of SSc-ILD and credential them as possible targets for therapy.

immunology↗

bioRxiv2025

Processing Ergativity in Compound Light Verb Constructions: Electrophysiological Evidence from Hindi

Ergativity marks subject arguments as agents of a transitive event and thereby signals verbal transitivity and influences language comprehension. We report here on an event-related brain potentials (ERP) study in Hindi, in which we investigated this interconnection to ascertain whether the ergative case as a processing cue and its ERP correlates can be generalized across and within ergative languages. The case marking on the subject argument (ergative or nominative case) in our study either matched or mismatched with the transitivity of the light verb (transitive or intransitive) in compound light verb constructions. Ergative case violations due to an intransitive light verb evoked an N400 effect, whereas nominative case violations due to a transitive light verb elicited a P600 effect. The results reveal neurophysiological differences in the processing of ergative and nominative case alignment modulated by the transitivity of the light verbs. The findings highlight the need for cross-linguistic research to aim beyond universality and elucidate the mechanism underlying the processing of language-specific structural variations.

neuroscience↗

bioRxiv2022

Plate-Q: A Frugal Microplate-Reader for Bacterial Signal Quantification

Microplate readers are laboratory instruments used to measure biological properties and reactions within a microplate. A microplate consists of small wells in which separated reactions take place. These reactions convert the progression of biochemical processes into optical signals. A microplate reader detects these signals and quantifies a parameter of interest. Most lab-grade microplate readers can cost up to $20,000, making them unaffordable for underfunded labs and developing countries. In light of this, we developed Plate-Q, a $150 frugal microplate reader capable of quantifying green fluorescence protein and optical density of bacterial samples from 96-hole microplates. Rather than using optical sensors found in laboratory microplate readers, Plate-Q takes advantage of a Raspberry-Pi camera to capture images of a microplate and manually extract brightness values using computer vision algorithms. Plate-Q utilizes 440nm excitation lights with a 510nm emission filter to measure GFP expression and 600nm lights for optical density readings. However, camera-based technologies have three main problems: lens distortion, signal interference, and brightness calculations. Plate-Q addresses these problems through camera movement over the well-plate, image optimization, 3D printed well-plate covers and mathematical regression algorithms. In testing with fusarium dual-plasmid biosensors, Plate-Q showed comparable accuracy to commercial microplate readers with an average error of .034 and a root mean squared error of .012 for fluorescence and an average error of .045 and root mean squared error of .023 error for optical density. Users can scan for other fluorescent proteins by changing the light source and filter for different wavelengths. With all aspects of Plate-Q being open source, labs worldwide can quantify samples in an affordable and time-efficient manner.

bioengineering↗

bioRxiv2020

Evolution of the complex transcription network controlling biofilm formation in Candida species

We examine how a complex transcription network composed of seven "master" regulators and hundreds of target genes evolved over a span of approximately 70 million years. The network controls biofilm formation in several Candida species, a group of fungi that are present in humans both as constituents of the microbiota and as opportunistic pathogens. The ability to form biofilms is crucial for microbial colonization of different host niches, particularly when an implanted medical device is present. We examined and compared the network underlying biofilm formation across four Candida species (C. albicans, C. dubliniensis, C. tropicalis, and C. parapsilosis), all of which form biofilms composed of multiple cell types. To describe the salient features of the network across different species, we employed four approaches: (1) we phenotypically characterized the biofilms formed by these species using a variety of methods; (2) we knocked out -- one by one -- the master regulators identified in C. albicans in the four species and monitored their effect on biofilm formation; (3) we identified the target genes of 18 master regulator orthologs across the four species by performing ChIP-seq experiments; and (4) we carried out transcriptional profiling across each species during biofilm formation. Additional network information was obtained by analyzing an interspecies hybrid formed between the two most closely related species, C. albicans and C. dubliniensis. We observed two major types of changes that have occurred in the biofilm circuit since the four species last shared a common ancestor. Master regulator "substitutions" occurred over relatively long evolutionary times, resulting in different species having overlapping, but different sets of master regulators of biofilm formation. Second, massive changes in the connections between the master regulators and their target genes occurred over much shorter timescales. Both types of change are crucial to account for the structures of the biofilm networks in extant species. We believe this analysis is the first detailed, empirical description of how a complex transcription network has evolved.

evolutionary biology↗

bioRxiv2020

Combination of antifungal drugs and protease inhibitors prevent Candida albicans biofilm formation and disrupt mature biofilms

Biofilms formed by the fungal pathogen Candida albicans are resistant to many of the antifungal agents commonly used in the clinic. Previous reports suggest that protease inhibitors, specifically inhibitors of aspartyl proteases, could be effective antibiofilm agents. We screened three protease inhibitor libraries, containing a total of 80 compounds for the abilities to prevent C. albicans biofilm formation and to disrupt mature biofilms. The compounds were screened individually and in the presence of subinhibitory concentrations of the most commonly prescribed antifungal agents for Candida infections: fluconazole, amphotericin B, or caspofungin. Although few of the compounds affected biofilms on their own, seven aspartyl protease inhibitors inhibited biofilm formation when combined with amphotericin B or caspofungin. Furthermore, nine aspartyl protease inhibitors disrupted mature biofilms when combined with caspofungin. These results suggest that the combination of standard antifungal agents together with specific protease inhibitors may be useful in the prevention and treatment of C. albicans biofilm infections. ImportanceCandida albicans is one of the most common pathogens of humans. C. albicans forms biofilms, structured communities of cells several hundred microns thick, on both biotic and abiotic surfaces. These biofilms are typically resistant to antifungal drugs at the concentrations that are normally effective against free-floating cells, thus requiring treatment with higher drug concentrations that often have significant side effects. Here, we show that certain combinations of existing antifungal agents with protease inhibitors, including several drugs already commonly used to treat HIV patients, are effective at inhibiting biofilm formation by C. albicans and/or at disrupting mature C. albicans biofilms.

microbiology↗

bioRxiv2018

The bacillithiol pathway is required for biofilm formation in Staphylococcus aureus

Staphylococcus aureus is a major human pathogen that can cause infections that range from superficial skin and mucosal infections to life threatening disseminated infections. S. aureus can attach to medical devices and host tissues and form biofilms that allow the bacteria to evade the host immune system and provide protection from antimicrobial agents. To counter host-generated oxidative and nitrosative stress mechanisms that are part of the normal host responses to invading pathogens, S. aureus utilizes low molecular weight (LMW) thiols, such as bacillithiol (BSH). Additionally, S. aureus synthesizes its own nitric oxide (NO), which combined with its downstream metabolites may also protect the bacteria against specific host responses. We have previously shown that LMW thiols are required for biofilm formation in Mycobacterium smegmatis and Pseudomonas aeruginosa. Our data show that the bshC mutant, which is defective in the last step of the bacillithiol pathway and lacks BSH, is impaired in biofilm formation. We also identify a putative S-nitrosobacillithiol reductase (BSNOR), similar to a S-nitrosomycothiol reductase found in M. smegmatis, and show that the BSNOR mutant has reduced levels of BSH and decreased biofilm formation. Our studies also show that NO plays an important role in biofilm formation and that acidified sodium nitrite severely reduces biofilm thickness. These studies provide insight into the roles of oxidative and nitrosative stress mechanisms on biofilm formation and indicate that bacillithiol and nitric oxide are key players in normal biofilm formation in S. aureus.\n\nImportanceStaphylococcus aureus is the most frequent cause of biofilm-associated infections in hospital settings. The biofilm mode of growth allows the pathogen to escape the host immune response and is extremely difficult to combat, as biofilms are highly resistant to physical and chemical stressors. As outbreaks of antibiotic-resistant bacterial strains become more commonplace, it is essential to understand the pathways involved in biofilm formation in order to target this important virulence factor. Low molecular weight thiols enable S. aureus to combat oxidative and nitrosative stress mechanisms that are used by host cells to defend against infection. Our findings indicate that bacillithiol and nitric oxide, which are produced by S. aureus to combat these host generated stressors, are important for biofilm development, and that disruption of these pathways results in biofilm defects. In the long term, this work may lead to new solutions to eradicate S. aureus biofilms in the clinic.

microbiology↗