Biology subjects

Khan, F. A.

Publications and source records attributed to Khan, F. A..

8 recordsLinked to original sources

bioRxiv2026

Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs

B-cell leukemia/lymphoma 11B (BCL11B), despite its name, is a key regulator of T-cell development, specification, and T-cell malignancies. BCL11B contains a bipartite DNA binding domain composed of two C2H2 zinc finger arrays: low-affinity ZF2-3 and high affinity ZF4-6. These arrays function as homotypic modules that recognize similar six-nucleotide motifs, TG(O_SCPLOWNC_SCPLOW)CC(O_SCPLOWCC_SCPLOWO_SCPCAP/C_SCPCAPO_SCPLOWTC_SCPLOWO_SCPCAP/C_SCPCAPO_SCPLOWAC_SCPLOW), as seven of the eight DNA base-contacting residues are conserved between them. The most conserved interactions involve GG dinucleotides, contacted by arginine and lysine residues at key base-interacting positions in ZF3 and ZF5. The two ZF arrays are connected by a long [~]300-residue linker that provides flexibility in how the arrays engage DNA, allowing ZF2-3 and ZF4-6 binding to the same or opposite strands with variable orientation, spacing and positioning along the DNA. This extended linker is enriched in serine/threonine, acidic residues (aspartate/glutamate), and structural residues (glycine/proline), providing additional layers of transcriptional regulation possibly through post-translational modification, electrostatic modulation, and/or condensate formation. We also examined six missense mutations in base-interacting residues, that are associated with neurodevelopmental disorders. Substitutions replacing bulky, positively charged arginine or lysine with smaller or hydrophobic residues likely reduce DNA-binding affinity and/or specificity, whereas substitutions between asparagine and lysine may alter base recognition preferences.

biochemistry↗

bioRxiv2024

Sex-specific brain effective connectivity patterns associated with negative emotions

Sex differences in effective brain connectivity in emotional intelligence, emotional regulation, and stimuli-induced negative emotions have been highlighted in previous research. However, to our knowledge, no research has yet investigated the sex-specific effective connectivity related to negative emotions in healthy population during resting-state. The goal of this study is to find the association between sex-specific resting-state effective brain connectivity and basic negative emotions. For this, we have employed the NIH emotion battery of the three self-reported, basic negative emotions -- anger-affect, fear-affect, and sadness which we divided into high, moderate, and low emotion scores in each. The dataset comprises 1079 subjects (584 females) from HCP Young Adults. We selected large-scale resting-state brain networks important for emotional processing namely default mode, executive, and salience networks. We employed subject-level analysis using spectral dynamic causal modelling and group-level association analyses using parametric empirical Bayes. We report association of the self-connection of left hippocampus in females in high anger-affect, fear-affect, and sadness, whereas in males we found involvement of dorsal anterior cingulate cortex (dACC) in all three negative emotions - association of right amygdala to dACC in high anger-affect, association of the self-connection of dACC in high fear-affect, and association of dACC to left hippocampus in high sadness. Our findings primarily revealed the effective brain connectivity that is related to the higher levels of negative emotions that may lead to psychiatric disorders if not regulated. Sex-specific therapies and interventions that target psychopathology can be more beneficial when informed by the sex-specific resting-state effective connectivity.

neuroscience↗

bioRxiv2023

Relationship between luteal size and plasma progesterone concentration in pregnant and non-pregnant Indian crossbred dairy cows

The relationship between luteal size and plasma progesterone concentration in purebred cows has been investigated previously. However, there is limited information on this topic in Indian crossbred cows. This study aimed to evaluate the relationship between luteal size parameters (diameter and area) and plasma progesterone concentration in healthy pregnant and non-pregnant Indian crossbred cows. Fifty healthy lactating crossbred cows were artificially inseminated after estrus detection and retrospectively classified into pregnant (n=29) and non-pregnant (n=21) based on the results of ultrasonographic pregnancy diagnosis. Data on luteal diameter, luteal area, and plasma progesterone concentration collected on Days 7, 14, and 20 in non-pregnant cows and on Days 7, 14, 20, 25, 30, 35, 40, and 60 in pregnant cows were analyzed. Spearmans correlation test was used to evaluate the association between the corpus luteum size parameters and the plasma progesterone concentration. Luteal area was positively correlated with plasma progesterone concentration in both pregnant ({rho}=0.48, P<0.001) and non-pregnant ({rho}=0.43, P=0.001) cows. Luteal diameter had a relatively weaker correlation with plasma progesterone concentration in both pregnant ({rho}=0.45, P<0.001) and non-pregnant ({rho}=0.24, P=0.058) cows. These results suggest that luteal area is a better indicator of CL function than luteal diameter in healthy Indian crossbred cows.

physiology↗

bioRxiv2023

Comparative evaluation of straight and curved extension dialysis catheters for continuous renal replacement therapy in dogs with acute kidney injury

A patent dual lumen dialysis catheter is one of the basic requirements for efficient extracorporeal (EC) therapy. The objective of this study was to measure resistance to blood flow offered by straight and curved extension dual lumen dialysis catheters used for continuous renal replacement therapy (CRRT). Twenty dogs suffering from acute kidney injury (AKI) were subjected to CRRT. The dogs were allocated randomly to Group-I (Curved extension catheter, n=12) or Group-II (Straight extension catheter, n=8), based on the type of dual-lumen catheter used in CRRT. The catheter outflow and inflow pressures were recorded at blood pump speeds of 50 mL/min and 99-100 mL/min. Data were tested for normality and differences in mean inflow and outflow catheter resistances were evaluated for statistical significance using independent samples t tests. Straight extension catheters offered lower inflow resistance than curved extension catheters at both 50 mL/min (41.50 {+/-} 5.84 mm Hg and 63.75 {+/-} 6.88 mm Hg, respectively; P=0.03) and 99-100 mL/min (63.00 {+/-} 8.11 mm Hg and 86.92 {+/-} 7.02 mm Hg, respectively; P=0.04) blood flow rates. Straight extension catheters also offered lower outflow resistance than curved catheters at 99-100 mL/min (-94.12 {+/-} 7.91 mm Hg and -128.25 {+/-} 7.56 mm Hg, respectively; P=0.01; the negative signs only indicate the direction of blood flow). These findings suggest that straight extension dual lumen dialysis catheters would likely perform better than the curved model in extracorporeal renal replacement therapy.

pathology↗

bioRxiv2023

Development of Nature-Based Insect-Repellent Surface Coating Using ZnO Nanoparticles and Plant Extracts for Mosquito Control

Mosquitos have been a malice and source of many diseases in humans. Later on, humans understood they learned that plants also possess mosquito-repellent properties. Different insectrepellent coatings are present in the market which are chemically prepared and can be harmful to humans and the environment. Different plants have insect-repellent properties which have been utilized in this research to make a nature-based insect-repellent surface coating. Moringa oleifera L. and Mentha piperita L. are naturally insect-repellent plants. Nanoparticles increase the surface area and efficiency of extracts of plants. Thus, ZnONP of Moringa oliefera L. and Mentha piperita L. plants were made characterization was done through UV-vis spectroscopy, FTIR, and PSA. The UV-visible spectrum showed absorption peaks for ZnO nanoparticles at 350nm for Mentha piperita L. and 356nm for Moringa oleifera L. The particle size analysis indicated the variable sizes of ZnONPs for both plants. FTIR showed vibration peaks from 3341 to 650cm-1 for Moringa oleifera L. and 3393 to 700 cm-1 for Mentha piperita L. ZnONPs were used in paint along with water extracts of plants to make the paint insect-repellent in nature. Mosquito repellent activity of paint formulations was also tested against Aedes aegypti.

animal behavior and cognition↗

bioRxiv2022

Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis

The application of high throughput technologies has enabled unravelling of unique differences between healthy mares and mares with endometritis at transcriptomic and proteomic levels. However, differences in the uterine microbiome are yet to be investigated. The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis. Low-volume lavage (LVL) samples were collected from the uterus of 30 mares classified into healthy (n=15) and endometritis (n=15) based on their reproductive history, intrauterine fluid accumulation, gross appearance of LVL samples, endometrial cytology, and bacterial culture. The samples were subjected to metagenomic analysis using 16S rRNA sequencing. Notable differences in the uterine microbiome were observed between healthy mares and mares with endometritis at various taxonomic levels. In healthy mares, the most abundant phylum, class, order, and family were Firmicutes, Bacilli, Bacillales, and Paenibacillaceae, respectively. In contrast, the most abundant corresponding taxonomic levels in mares with endometritis were Proteobacteria, Gammaproteobacteria, Enterobacterales, and Enterobacteriaceae, respectively. At the genus level, Brevibacillus and Paenibacillus were more abundant in healthy mares, whereas Escherichia, Salmonella, and Klebsiella were more abundant in mares with endometritis. In healthy mares, Brevibacillus brevis was the most abundant species, followed by Brevibacillus choshinensis and Paenibacillus sp JDR-2. However, in mares with endometritis, Escherichia coli was the most abundant species, followed by Salmonella enterica and Klebsiella pneumoniae. These results indicate novel differences in the uterine microbiome between healthy mares and mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.

genomics↗

bioRxiv2021

Single Unit Analysis and Wide-Field Imaging Reveal Alterations in Excitatory andInhibitory Neurons in Glioma

Several studies have attributed the development of tumor-associated seizures to an excitatory-inhibitory imbalance, highlighting the importance of resolving the spatiotemporal interplay of different neuronal populations within the peritumoral microenvironment. We combined methods for microelectrode array recordings and single unit analysis during ictal events with wide-field optical mapping of pyramidal neurons in an ex vivo acute slice model of diffusely infiltrating glioma in Thy1-GCaMP6f mice. This approach allowed for characterization of excitatory and inhibitory populations across an extended peritumoral cortical region. As expected, measures of excitability were increased in tumor-bearing slices compared to control. This was accompanied by marked functional alterations in single units classified as fast-spiking interneurons, including reduced firing, altered timing with respect to excitatory firing, and deficits in surround inhibition. Inhibiting mTOR with AZD8055 reversed these glioma-induced changes to excitatory and inhibitory neuronal populations, suggesting a prominent role for functional mechanisms linked to mTOR activation.

cancer biology↗

bioRxiv2019

Volumetric Segmentation of Cell Cycle Markers in Confocal Images

I.AO_SCPCAPBSTRACTC_SCPCAPUnderstanding plant growth processes is important for many aspects of biology and food security. Automating the observations of plant development - a process referred to as plant phenotyping - is increasingly important in the plant sciences, and is often a bottleneck. Automated tools are required to analyse the data in images depicting plant growth. In this paper, a deep learning approach is developed to locate fluorescent markers in 3D timeseries microscopy images. The approach is not dependant on marker morphology; only simple 3D point location annotations are required for training. The approach is evaluated on an unseen timeseries comprising several volumes, capturing growth of plants. Results are encouraging, with an average recall of 0.97 and average F-score of 0.78, despite only a very limited number of simple training annotations. In addition, an in-depth analysis of appropriate loss functions is conducted. To accompany [the finally-published] paper we are releasing the 4D point annotation tool used to generate the annotations, in the form of a plugin for the popular ImageJ (Fiji) software. Network models will be released online.

plant biology↗