Biology subjects

Darvish, M.

Publications and source records attributed to Darvish, M..

3 recordsLinked to original sources

bioRxiv2026

Region-specific Bmal1 deletion in the dorsal striatum alters alcohol consumption in a sex-specific manner

BackgroundCircadian disruption is strongly associated with alcohol use disorder (AUD), but insight into the underlying brain-region and sex-specific mechanisms is limited. The function of the circadian clock gene Bmal1 within the striatum has been linked to alcohol drinking, yet its role within functionally distinct striatal subregions has not been systematically examined. MethodsWe deleted Bmal1 in medium spiny neurons of the dorsomedial striatum (DMS) or dorsolateral striatum (DLS). Male and female mice were tested for anxiety-like behavior, depressive-like behavior, and motor coordination. Voluntary alcohol intake was measured with an intermittent two-bottle choice paradigm, followed by sucrose preference and quinine-adulterated alcohol tests. To assess hormonal contributions, a subset of female mice underwent ovariectomy before behavioral testing. ResultsDeletion of Bmal1 in the DLS did not alter alcohol intake, alcohol preference, or quinine-adulterated alcohol intake in either sex. In contrast, DMS Bmal1 deletion significantly reduced alcohol consumption and alcohol preference in female mice, with no effect in males. These effects were not accompanied by changes in depressive-like behavior or motor coordination and were not explained by generalized reward changes, as sucrose preference was unaffected. Ovariectomy eliminated the effect of DMS Bmal1 deletion on alcohol intake, indicating dependence on ovarian hormones. ConclusionsThe DMS is a critical site at which Bmal1 regulates alcohol consumption in a sex-specific manner. These findings support an interaction between local circadian mechanisms and ovarian hormones in controlling alcohol drinking and highlight a potential target for sex-specific therapeutics in AUD.

neuroscience↗

bioRxiv2022

Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries

Searching sequences in large, distributed databases is the most widely used bioinformatics analysis done. This basic task is in dire need for solutions that deal with the exponential growth of sequence repositories and perform approximate queries very fast. In this paper, we present a novel data structure: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it has the potential to serve as the underlying engine for many applications. We show that the HIBF is superior in build time, index size and search time while achieving a comparable or better accuracy compared to other state-of-the art tools (Mantis and Bifrost). The HIBF builds an index up to 211 times faster, using up to 14 times less space and can answer approximate membership queries faster by a factor of up to 129. This can be considered a quantum leap that opens the door to indexing complete sequence archives like the European Nucleotide Archive or even larger metagenomics data sets.

bioinformatics↗

bioRxiv2020

Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences

We present Raptor, a tool for approximately searching many queries in large collections of nucleotide sequences. In comparison with similar tools like Mantis and COBS, Raptor is 12-144 times faster and uses up to 30 times less memory. Raptor uses winnowing minimizers to define a set of representative k-mers, an extension of the Interleaved Bloom Filters (IBF) as a set membership data structure, and probabilistic thresholding for minimizers. Our approach allows compression and a partitioning of the IBF to enable the effective use of secondary memory.

bioinformatics↗