Biology subjects

Pokharel, D.

Publications and source records attributed to Pokharel, D..

4 recordsLinked to original sources

bioRxiv2026

Paw Preference in Rats Across Tests, Strains, Sex, and Age: A PRISMA-Compliant Systematic Review and Meta-Analysis

Paw preference in rats is widely used to study hemispheric lateralization, but many individual studies are underpowered and employ inconsistent methods, leading to conflicting reports of population-level bias. We conducted a PRISMA-compliant systematic review and meta-analysis to determine whether rats consistently display paw preference at the individual and population levels, and to evaluate the influence of behavioral test type, strain, sex, and age. Studies published between 1930 and 2025 were identified through PubMed, Google Scholar, and ScienceDirect. Data were extracted on strain, age, sex, behavioral paradigm, and paw-preference classification. Random-effects models were used to estimate pooled prevalence, with subgroup analyses for key variables. Forty studies (n = 1,609 rats) met inclusion criteria. At the individual level, 84% of rats displayed consistent paw preference (95% CI: 78-89%, p < 0.0001), demonstrating robust individual-level lateralization. However, population-level analyses showed no universal directional bias, right paw use occurred in 48% of rats (95% CI: 43-54%) and left paw use in 39% (95% CI: 34-44%). Ambidextrous classification thresholds were standardized across studies to ensure comparability. Subgroup analyses indicated modest strain- and test-dependent effects, with Sprague Dawley rats tending toward balanced paw use, while other strains showed slight rightward bias. Skilled-reaching tasks produced slightly stronger asymmetry than the Collins test. Sex- and age-related differences were subtle and inconsistent. Overall, rats exhibit reliable individual-level paw preference without species-wide directional asymmetry, distinguishing them from humans. Standardized testing protocols and balanced cohort designs will enhance reproducibility and translational relevance in lateralization research.

neuroscience↗

bioRxiv2026

Rigorous Validation of Paw Preference Using Three Complementary Behavioral Assays in Sprague Dawley Rats

Paw preference, or handedness, is a widely studied behavioral trait used to assess lateralization and motor function in rodents. This study aimed to determine the consistency and reliability of three commonly used behavioral tests to rigorously assess paw preference: the Collins Test, the Staircase Test, and the Pawedness Trait Test. Thirty Sprague Dawley rats (12-48 weeks; 20 females, 10 males) were subjected to all three behavioral tests. Paw uses were recorded, and the laterality index was calculated for each test. Additional cohorts of younger rats (6-9 weeks; 45 females, 45 males) and older rats (12-48 weeks; 38 females, 45 males) were tested to assess the effects of age and sex on paw preference. ANOVA, Fleiss and pairwise Cohens Kappa were used for statistical analysis. All three tests yielded comparable measures of paw preference (ANOVA, p = 0.801). Substantial inter-test agreement was demonstrated by Fleiss kappa ({kappa} = 0.761, p = 3.93 x 10{square}12). Paw preference did not significantly vary by age or sex, and the distribution of left, right, and ambidextrous preference categories aligned with existing literature. The Collins, Staircase, and Pawedness Trait Tests provide consistent, reliable assessments of paw preference in Sprague Dawley rats. These validated behavioral assays can serve as essential tools for preclinical research, including but not limited to models of motor asymmetry observed in stroke, cerebral palsy, traumatic brain injury, and language lateralization, as well as neurodegenerative diseases. HighlightsO_LIRigorously validated paw preference in Sprague Dawley rats using three commonly used behavioral tests. C_LIO_LIDemonstrated strong inter-test agreement across Collins, Staircase, and PaTRaT ({kappa} = 0.761) C_LIO_LIShowed that paw preference remains stable across age and sex in large cohorts C_LIO_LIApplied standardized LI thresholds to enable cross-test comparability C_LI

neuroscience↗

bioRxiv2024

A bifunctional antibody conjugate marks the location of DNA binding proteins on deproteinized DNA fibers.

Immunofluorescent foci of DNA Damage Response (DDR) proteins serve as surrogates for DNA damage and are frequently interpreted as denoting specific lesions. For example, Double Strand Breaks (DSBs) are potent inducers of the DDR, whose best-known factor is the phosphorylated histone variant H2AX ({gamma}-H2AX). The association with DSBs is so well established that the reverse interpretation that {gamma}-H2AX invariably implies DSBs is routine. However, this conclusion is inferential and has been challenged. The resolution of this question has been hampered by the lack of methods for distinguishing the location of DDR proteins relative to DSBs caused by sequence indifferent agents. Here, we describe an approach for marking the location of DDR factors in relation to DSBs on DNA fibers. We synthesized a two-arm "Y" conjugate containing biotin and trimethylpsoralen (TMP) coupled to a secondary antibody. After exposure to a DNA breaker, permeabilized mammalian cells were incubated with a primary antibody against the DDR factor followed by binding of the secondary antibody in the conjugate to the primary antibody. Exposure to longwave UV light covalently linked the psoralen to the DNA. DNA fibers were spread, and the immunofluorescence of the biotin tag denoted the location of the target protein. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/609705v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@15eaf5corg.highwire.dtl.DTLVardef@14ade70org.highwire.dtl.DTLVardef@51c83forg.highwire.dtl.DTLVardef@131cb58_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

biochemistry↗

bioRxiv2020

DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain

Duplication of mammalian genomes requires replisomes to overcome numerous impediments during passage through open (eu) and condensed (hetero) chromatin. Typically, studies of replication stress characterize mixed populations of challenged and unchallenged replication forks, averaged across S phase, and model a single species of "stressed" replisome. However, in cells containing potent obstacles to replication, we find two different lesion proximal replisomes. One is bound by the DONSON protein and is more frequent in early S phase, in regions marked by euchromatin. The other interacts with the FANCM DNA translocase, is more prominent in late S phase, and favors heterochromatin. The two forms can also be detected in unstressed cells. CHIP-seq of DNA associated with DONSON or FANCM confirms the bias of the former towards regions that replicate early and the skew of the latter towards regions that replicate late.

molecular biology↗