Biology subjects

Irfan, S.

Publications and source records attributed to Irfan, S..

5 recordsLinked to original sources

bioRxiv2024

Soil bacteria may be the natural reservoirs of drug resistance genes

Soil bacteria are the main source of antibiotics because they produce them naturally to get territorial advantage. We collected deep soil samples and characterized cultivable microbes. We used morphological and cultural characters, biochemical reactions, 16s RNA PCR and DNA sequencing to identify the isolates. The isolates included Pseudomonas spp (12), Shigella spp (2), E. coli (1), Klebsiella/Citrobacter spp (1), Micrococcus spp (2), unidentified Bacillus spp.(18), Bacillus paramycoides (3), Paenibacillus lautus (2), Bacillus pacificus (2), and Lysinibacillus pakistanensis (1). Out of these 44 isolates, 33 (75%) were multi-drug resistant. Clinically relevant and clinically irrelevant bacteria had similar drug resistance patterns (88.9% and 88.0%, 88.9% and 88.0%, 100 and 96.0%, 61.1% and 92%, 83.3% and 96%, 33.3% and 36%, 55.6% and 68.0%, and 83.3% and 60%) towards Ampicillin, Amoxicillin, Oxacillin, Azithromycin, Streptomycin, Gentamicin, Ceftriaxone and Sulfamethoxazole respectively. The observation that bacteria which cannot colonize humans/animals and therefore cannot enter the horizontal drug resistance gene transfer cycle in clinical settings also have a large and similar arsenal of drug resistance genes, may indicate that they are actually the natural reservoirs. Because they are more dynamic in their ability to survive in different conditions, they provide better fitness for maintenance of these reservoirs. Impact StatementWe think this study has raised interesting questions and further probing at a larger scale and a greater depth will provide new insight that may be very helpful for understanding the phenomenon of spread of drug resistance among bacteria which is one of the paramount challenges for humanity.

microbiology↗

bioRxiv2024

The ventral CA2 region of the hippocampus and its differential contributions to social memory and social aggression

Although it is well-known that the hippocampus mediates declarative memory (the repository of information of people, places, things and events) and influences behavior, the differential contributions of the dorsal and ventral hippocampus to specific forms of memory and behavior remain largely unknown. Studies to date show that the dorsal hippocampal CA1 region is important for cognitive and spatial tasks whereas the ventral CA1 region is associated with affective or emotional processing. Whether other regions and forms of hippocampal-dependent memory and behavior show a similar distinction remains unclear. Here we examine how social memory and related social behaviors are encoded across the dorso-ventral axis of the hippocampus. Although recent studies show that the dorsal hippocampal CA2 region is required for social memory and acts to promote social aggression, the behavioral role of ventral CA2 remains unknown. Indeed, whether a defined CA2 region extends throughout ventral hippocampus is controversial. Here, we report that a molecularly, anatomically and electrophysiologically defined CA2 region extends to the extreme ventral pole of hippocampus, with both similarities and important differences in its projection patterns and synaptic impact compared to dorsal CA2. Of particular importance, we find that ventral CA2 is not required for social memory but is critical for promoting social aggression. These results support the view that the ventral region of hippocampus is more generally tuned for emotionally-related behaviors compared to the cognitively-tuned dorsal hippocampus.

neuroscience↗

bioRxiv2023

LEF1 isoforms regulate cellular senescence and aging

BackgroundThe study of aging and its mechanisms, such as cellular senescence, has provided valuable insights into age-related pathologies, thus contributing to their prevention and treatment. The current abundance of high throughput data combined with the surge of robust analysis algorithms has facilitated novel ways of identifying underlying pathways that may drive these pathologies. MethodsWith the focus on identifying key regulators of lung aging, we performed comparative analyses of transcriptional profiles of aged versus young human subjects and mice, focusing on the common age-related changes in the transcriptional regulation in lung macrophages, T cells, and B immune cells. Importantly, we validated our findings in cell culture assays and human lung samples. ResultsWe identified Lymphoid Enhancer Binding Factor 1 (LEF1) as an important age-associated regulator of gene expression in all three cell types across different tissues and species. Follow-up experiments showed that the differential expression of long and short LEF1 isoforms is a key regulatory mechanism of cellular senescence. Further examination of lung tissue from patients with Idiopathic Pulmonary Fibrosis (IPF), an age-related disease with strong ties to cellular senescence, we demonstrated a stark dysregulation of LEF1. ConclusionsCollectively, our results suggest that the LEF1 is a key factor of aging, and its differential regulation is associated with human and murine cellular senescence.

genomics↗

bioRxiv2023

Evidence for conservation of a primordial 12-hour ultradian gene program in humans

While circadian rhythms are entrained to the once daily light-dark cycle of the sun, many marine organisms exhibit [~]12h ultradian rhythms corresponding to the twice daily movement of the tides. Although human ancestors emerged from circatidal environment millions of years ago, direct evidence of [~]12h ultradian rhythms in humans is lacking. Here, we performed prospective, temporal transcriptome profiling of peripheral white blood cells and identified robust [~]12h transcriptional rhythms from three healthy participants. Pathway analysis implicated [~]12h rhythms in RNA and protein metabolism, with strong homology to the circatidal gene programs previously identified in Cnidarian marine species. We further observed [~]12h rhythms of intron retention events of genes involved in MHC class I antigen presentation, synchronized to expression of mRNA splicing genes in all three participants. Gene regulatory network inference revealed XBP1, and GABP and KLF transcription factor family members as potential transcriptional regulators of human [~]12h rhythms. These results suggest that human [~]12h biological rhythms have a primordial evolutionary origin with important implications for human health and disease.

systems biology↗

bioRxiv2022

The geometry of hippocampal CA2 representations enables abstract coding of social familiarity and identity

Social recognition consists of multiple memory processes, including the detection of familiarity - the ability to rapidly distinguish familiar from novel individuals - and recollection - the effortful recall of where a social episode occurred and who was present. At present, the neural mechanisms for these different social memory processes remain unknown. Here, we investigate the population code for novel and familiar individuals in mice using calcium imaging of neural activity in a region crucial for social memory, the dorsal CA2 area of the hippocampus. We report that familiarity changes CA2 representations of social encounters to meet the different demands of social memory. While novel individuals are represented in a low-dimensional geometry that allows for rapid generalization, familiar individuals are represented in a higher-dimensional geometry that supports high-capacity memory storage. The magnitude of the change in dimensionality of CA2 representations for a given individual predicts the performance of that individual in a social recognition memory test, suggesting a direct relationship between the representational geometry and memory-guided behavior. Finally, we show that familiarity is encoded as an abstract variable with neural responses generalizing across different identities and spatial locations. Thus, through the tuning of the geometry of structured neural activity, CA2 is able to meet the complex demands of multiple social memory processes.

neuroscience↗