Biology subjects

Ahmed, B.

Publications and source records attributed to Ahmed, B..

At least 19 recordsLinked to original sources

bioRxiv2026

A solid-state heater-imager for quantitative evaluation of colorimetric isothermal nucleic acid amplification on paper

Maintaining precise isothermal conditions in portable nucleic acid amplification tests (NAATs) is critical for reproducible results but remains challenging with conventional single-sided thin-film heaters, which exhibit temperature gradients and strong dependence on ambient conditions. To close this gap, we engineered ThermiQuant VitroMini, a dual-sided heater design that achieves volumetric-level temperature uniformity using thin-film heaters while preserving optical transparency for real-time colorimetric loop-mediated isothermal amplification (LAMP) analysis on microfluidic paper-based analytical devices ({micro}PADs). The device integrates two independently regulated indium tin oxide (ITO) heaters (8 {Omega} each) controlled by independent proportional-integral-derivative (PID) algorithms. Heaters were evaluated under controlled ambient environments of 4 {degrees}C (refrigerated), 23 {degrees}C (room temperature), and 50 {degrees}C (oven). Analytical tests were performed using a colorimetric LAMP assay targeting the SARS-CoV-2 orf7ab gene on {micro}PADs preloaded with dried LAMP reagents, with time-lapse images (30 seconds interval) analyzed via Amplimetrics software. VitroMini maintained 65 {+/-} 0.5 {degrees}C across 4 to 50 {degrees}C ambient conditions and achieved a limit of detection of 34 copies/reaction (4.5 copies/{micro}L) and limit of quantification of 1000 copies/reaction (133 copies/{micro}L), with quantification time (Tq) linearly correlated with log10 DNA concentration. Dual-sided heating eliminated temperature bias, condensation artifacts, and ambient-dependent variability while preserving optical transparency for real-time quantitative LAMP reaction. ThermiQuant VitroMini bridges the gap between benchtop volumetric heaters and portable diagnostic devices, offering a compact, low-power platform for quantitative colorimetric molecular analysis on paper with potential for decentralized and field-deployable applications.

bioengineering↗

bioRxiv2026

Deterministic abiotic filtering and halophilic core microbiomes shape bacterial communities in costal salt flats (Sabkha) of southern Morocco

Coastal salt flats, locally known as Sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistently alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical Correspondence Analysis identified electrical conductivity (EC), Na2O, K2O and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria and Marinococcus, with 66% of ASVs shared across compartments. Host identity played a secondary role, as environmental filtering overshadawed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, mainly, Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium and Bac illus, tolerating up to 25% NaCl. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shalped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions. ImportanceCoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.

microbiology↗

bioRxiv2026

ThermiQuant(TM) MegaScan: High-throughput isothermal reactor with quantitative colorimetric readout for paper-based nucleic acid amplification tests

Isothermal nucleic acid amplification tests (NAATs), such as loop-mediated isothermal amplification (LAMP) implemented on microfluidic paper-based analytical devices ({micro}PADs), enable inexpensive and rapid ([≤]60 min) colorimetric molecular diagnostics; however, no existing instrument supports high-throughput (>100 reactions) quantitative analysis of colorimetric isothermal assays on paper substrates under controlled laboratory conditions. To address this gap, we developed ThermiQuant MegaScan, a scanner- and water-bath-based platform that accommodates a 160-reaction {micro}PAD cartridge, maintains uniform incubation at 65 {+/-} 0.5 {degrees}C, and enables real-time imaging every 30 s. We also developed accompanying software, Amplimetrics, for automated {micro}PAD detection and kinetic colorimetric analysis. Using paper-based colorimetric LAMP targeting the SARS-CoV-2 orf7ab region, the assay achieved a limit of detection at 95% probability (LOD95) of 34 copies per reaction (5 copies/{micro}L) and a limit of quantification (LOQ) of 250 copies per reaction (33 copies/{micro}L) using purified synthetic DNA targets, and achieved 72% sensitivity and 100% specificity relative to digital PCR (dPCR) for diluted human nasopharyngeal (NP) swab virus samples. We further evaluated the effects of viral and universal transport media (VTM/UTM) on assay performance and found that linear calibration derived from synthetic targets do not reliably translate to clinical samples in these media. Together, these results establish ThermiQuant MegaScan as a high-throughput laboratory research platform for standardized evaluation, optimization, and benchmarking of paper-based colorimetric nucleic acid amplification assays.

bioengineering↗

bioRxiv2025

Recapitulating Patient-to-Patient Colorectal Cancer Tumor Heterogeneity Using Patient-Derived Xenograft Cells in an Engineered Tissue Model

Establishing in vitro cancer models that more closely recapitulate patient tumor microenvironmental heterogeneity, including variations in stromal cells and mechanical properties that influence colorectal cancer (CRC) progression, is crucial for advancing CRC research. This study evaluated the ability of 3D engineered CRC-PDX (3D-eCRC-PDX) tissues to recapitulate the heterogeneity found between patient-derived xenograft (PDX) tumors from three CRC patients (stage II, III-B, and IV). To form the 3D-eCRC-PDX tissues, CRC-PDX tumor cells were encapsulated in PEG-fibrinogen hydrogels and maintained for 29 days in vitro. 3D-eCRC-PDX tissues recapitulated key patient-specific tumor characteristics. During long-term culture, 3D-eCRC-PDX tissues mimicked the patient-specific growth rates of the originating CRC-PDX tumors. Importantly, tumor cellular subpopulations, including the ratio of human cancer cells to mouse stromal cells and the ratios of proliferative human cancer cells and CK20+ cells were maintained in 3D-eCRC-PDX tissues, unlike in 2D cell culture. Differences in mechanical stiffness between the originating CRC-PDX tumors were also recapitulated by the 3D-eCRC-PDX tissues. Principal component analysis of transcriptomic data clustered 3D-eCRC-PDX tissues and CRC-PDX tumors together by patient, indicating similar gene expression profiles. These findings highlight the potential of 3D-eCRC-PDX tissues as a promising tool for CRC research, capable of maintaining patient-specific tumor microenvironment heterogeneity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/693817v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@16c19baorg.highwire.dtl.DTLVardef@d3a75org.highwire.dtl.DTLVardef@79026forg.highwire.dtl.DTLVardef@8ede45_HPS_FORMAT_FIGEXP M_FIG C_FIG Statement of SignificanceThis study establishes engineered colorectal cancer tissues formed using PEG-fibrinogen and patient-derived xenograft (PDX) tumor cells for modeling inter-patient tumor heterogeneity. In vitro models that preserve patient tumors biological and structural heterogeneity are central to the development of more predictive and reproducible preclinical cancer models. Here engineered tissues replicated patient-specific tumor growth dynamics, sustained key cancer and stromal cell subpopulations, recapitulated originating PDX tumor stiffness, and sustained patient-specific patterns of gene expression. This work demonstrates the long-term culture of cells from patient xenografts in engineered colorectal cancer tissues, enabling sustained preservation of critical patient tumor-specific microenvironmental characteristics in vitro.

bioengineering↗

bioRxiv2025

Super-resolution microscopy reveals distinct epigenetic states regulated by estrogen receptor activity

Changes in gene expression regulated by ligand-dependent transcription factors such as estrogen receptor- (ER) involves the recruitment of coactivators including p300 that acetylates histone H3 at lysine 27 (H3K27ac). While H3K27ac marks active enhancers, the detailed chromatin architecture of enhancers remains unclear. Using super-resolution microscopy, we reveal distinct structural states of H3K27ac modified chromatin in response to ER activation. In estradiol (E2)-treated cells, H3K27ac modified chromatin adopts open, elongated structures, while ER inhibition induces compact, spherical H3K27ac modified chromatin conformations. Using MED1, a core subunit of the Mediator complex that bridges transcription factors with RNA polymerase II (Pol II), we demonstrate that larger H3K27ac structures are preferentially associated with active enhancers, whereas more compact structures show reduced MED1 association, consistent with a less active or inactive state. A constitutively active ER mutation linked to endocrine therapy resistance in breast cancer maintains open chromatin states independent of ligand, suggesting sustained transcriptional activity. Our findings provide the first direct visualization of H3K27ac associated chromatin structural dynamics, challenging the assumption that H3K27ac modification alone is sufficient to lead to enhancer activation. By demonstrating that H3K27ac architecture is dynamically regulated by ER, we establish a new paradigm for understanding epigenetic regulation and highlight potential therapeutic targets for endocrine therapy resistant cancers.

cancer biology↗

bioRxiv2025

Lack of synergy between AR targeted therapies and PARP inhibitors in homologous recombination-proficient prostate cancer

Recent clinical trials have explored the combination of androgen receptor (AR) pathway inhibitors and poly (ADP-ribose) polymerase (PARP) inhibitors as a potential treatment for castration-resistant prostate cancer. This combination treatment is based on the premise that AR directly regulates expression of DNA repair genes, leading to synergy between PARP and AR inhibition. Despite some promising preclinical evidence, this combination therapy has shown limited efficacy in patients with homologous recombination (HR)-proficient tumors. To investigate this discrepancy between preclinical and clinical results, we profiled the effects of PARP inhibition in prostate cancer models in the presence or absence of AR inhibition. Surprisingly, AR inhibition impaired response to PARP inhibitors in castration-sensitive cells and had no effect on response in castration-resistant cells. AR inhibition also did not regulate DNA repair in either the castration-resistant or castration-sensitive setting. Instead, we find that cell cycle progression is required for response to PARP inhibition in homologous-recombination proficient prostate cancer. STATEMENT OF SIGNIFICANCEAndrogen deprivation does not inhibit DNA repair and does not synergize with PARP inhibition in prostate cancer with intact homologous recombination repair.

cancer biology↗

bioRxiv2025

Frequency and Characterization of Rare Histologic Subtypes in Canine Invasive Urothelial Carcinoma

The histologic and molecular heterogeneity of human muscle-invasive bladder cancer (MIBC) is a major contributor to poor treatment outcomes. While most cases of MIBC are diagnosed as conventional urothelial carcinoma (UC), there is growing recognition of histologic subtypes and divergent differentiation within conventional UC. This is clinically significant, as some require modification of therapy and some are associated with more aggressive behavior. Spontaneously occurring UC in dogs has been shown to exhibit histologic and molecular features that closely resemble those of human MIBC. In this study, we evaluated 31 canine UC tumor samples for histologic subtypes and divergent differentiation. Slides were reviewed by a human uropathologist and three board-certified veterinary pathologists and assessed for expression of uroplakin III and E-cadherin. All tumors were classified as high-grade UC. Fifteen cases were identified as conventional UC. Among the remainder, eight displayed glandular differentiation, four were classified as sarcomatoid UC, two showed squamous differentiation, and one case each was classified as large nested and tubular and microcystic subtypes. In summary, this study found a higher frequency of certain histologic subtypes and divergent differentiation in canine UC--particularly sarcomatoid UC and UC with glandular differentiation--compared to previous reports in both canine UC and human MIBC. ConclusionThe relatively high prevalence of the sarcomatoid UC subtype in dogs observed in this study suggests that canine UC may serve as a valuable translational model for evaluating novel therapeutic agents, particularly for this rare and aggressive variant in humans.

pathology↗

bioRxiv2024

Deep Neural Networks Explain Spiking Activity in Auditory Cortex

For static stimuli or at gross ([~]1-s) time scales, artificial neural networks (ANNs) that have been trained on challenging en gineering tasks, like image classification and automatic speech recognition, are now the best predictors of neural responses in primate visual and auditory cortex. It is, however, unknown whether this success can be extended to spiking activity at fine time scales, which are particularly relevant to audition. Here we address this question with ANNs trained on speech audio, and acute multi-electrode recordings from the auditory cortex of squirrel monkeys. We show that layers of trained ANNs can predict the spike counts of neurons responding to speech audio and to monkey vocalizations at bin widths of 50 ms and below. For some neurons, the ANNs explain close to all of the explain able variance--much more than traditional spectrotemporal- receptive-field models, and more than untrained networks. Non-primary neurons tend to be more predictable by deeper layers of the ANNs, but there is much variation by neuron, which would be invisible to coarser recording modalities.

neuroscience↗

bioRxiv2024

Transcriptional Responses and Microbiome Shifts in Pea Roots Under High pH Stress

High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlight the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA-seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.

plant biology↗

bioRxiv2024

Anatomical circuits for flexible spatial mapping by single neurons in posterior parietal cortex

Primate lateral intraparietal area (LIP) is critical for cognitive processing. Its contribution to categorization and decision-making has been causally linked to neurons spatial sensorimotor selectivity. We reveal the intrinsic anatomical circuits and neuronal responses within LIP that provide the substrate for this flexible generation of motor responses to sensory targets. Retrograde tracers delineate a loop between two distinct operational compartments, with a sensory-like, point-to-point projection from ventral to dorsal LIP and an asymmetric, more widespread projection in reverse. Neurophysiological recordings demonstrate that especially more ventral LIP neurons exhibit motor response fields that are spatially distinct from its sensory receptive field. The different associations of response and receptive fields in single neurons tile visual space. These anatomical circuits and neuronal responses provide the basis for the flexible allocation of attention and motor responses to salient or instructive visual input across the visual field.

neuroscience↗

bioRxiv2024

Genome-wide identification of MAPK gene family and comparative transcriptional profiling among different organ and stress response in two jute species

Mitogen activated protein kinase (MAPK) cascade is evolutionary conserved universal signal transduction module that plays central role in the growth and development of plants as well as in biotic and abiotic stress response. Although, MAPKs have been investigated in several model plants, no systematic analysis has been conducted in jute species (Corchorus olitorius and C. capsularis) even though, their genome sequencing has been completed. In the present study we identified 11 and 12 putative MAPKs in C. olitorius and C. capsularis using their genomic database, respectively. Here we provide a comprehensive bioinformatics analysis of the MAPK family from both Corchorus species including identification and nomenclature, chromosomal localization, sequence alignment, domain and Motif, gene structure, phylogenetic, functional analysis and investigation of expression analysis in response to abiotic stress and fiber cell development. The phylogenetic analysis of predicted MAPKs were clustered into four different clades and assigned with specific name based on their orthology based evolutionary relationship with Arabidopsis. Structural analysis of the MAPK genes revealed that there was a large variation among the exon number in both Corchorus species ranged from 2 to 11 but genes with the same clade had similar exon-intron structure. The sequence alignment analysis concede the presence of several conserved domain and motif including crucial signature phosphorylation motif TDY or TEY where first one is harbor in group D sequence and rest of the sequence contain TEY motif in their activation loop. Transcriptome analysis against salinity, drought along with fiber cell formation showed that MAPK4-1 genes in both jute genome highly expressed and may play a potential role in jute on adverse condition as well as jute fiber formation. These findings yielded new insights into the transcriptional control of MAPK gene expression, provide an improved understanding of abiotic stress responses and signaling transduction in jute, that lead to potential applications in the genetic improvement of jute cultivars.

molecular biology↗

bioRxiv2024

GENOME-WIDE IDENTIFICATION, CHARACTERIZATION AND EXPRESSION ANALYSIS OF NA+/H+ EXCHANGER GENE FAMILY IN TWO CORCHORUS SPECIES

Na+/H+ exchangers (NHXs) are secondary ion transporter to exchange H+ and transfer Na+ or K+ across membrane plays crucial role in cellular pH and Na+ and K+ homeostasis in plant. In the present study, we have performed genomewide identification, characterization and comparative analysis of NHXs genes in two cultivated jute species and found seven Co and Cc NHXs in each genome. Subsequently phylogenetic analysis demonstrated that Co and Cc NHXs have three sub-group that correlate with other plant species containing 10-12 transmembrane helices (TMH) and a hydrophilic C-terminal domain in the cytoplasmic region, the TMH compose a hollow cylinder to provide the channel for Na+ and H+ transport. Promoter profiling of both species NHXs genes revealed in enrichment of cis element involved in stress responsiveness reflecting their potential involvement against abiotic stress. Transcriptome data and real time PCR of Co and Cc NHXs gene expression analysis under saline and drought condition showed significant differences, which suggest their potential role in abiotic stress conditions. This is the first comprehensive analysis providing baseline information of Co and Cc NHXs genes in abiotic stress condition which can be used for the development of abiotic stress tolerant jute variety.

bioinformatics↗

bioRxiv2023

Implementation and testing of a biohybrid transitionmicroelectrode array for neural recording and modulation

Recent advances in microtissue engineered neural networks have opened avenues for the fabrication of biohybrid intracortical brain implants. To date, however, the experimental validation of these biohybrid implants has been restricted to singularly positioned electrodes, with the functionality confined to optical neuromodulation and neural recording. We present for the first time a biohybrid transition microelectrode array (TMEA) comprising a 4x4 matrix of biohybrid electrodes. These electrodes are expected to project axons into the brain, thereby establishing synaptic connections for electrical readout and excitation. Our device thus offers a promising pathway to leverage organic, endogenous materials in intracortical implants to enhance their biocompatibility as well as their functionality. In particular with respect to functionality, we assume that the spatiotemporal resolution of recorded neural signals may be significantly increased using this technology owing to the size ratios of these biohybrid microelectrodes compared to abiotic ones. Future investigations will therefore focus on the exploitation of the electrode density to further advance brain-computer interface technology.

neuroscience↗

bioRxiv2023

Monorhinal and Birhinal Odor Processing in Humans: an fMRI investigation

The olfactory nerve, also known as cranial nerve I, is known to have exclusive ipsilateral projections to primary olfactory cortical structures. It is still unclear whether these projections also correspond to functional pathways of odor processing. In an olfactory functional magnetic resonance imaging (fMRI) study of twenty young healthy subjects with a normal sense of smell, we tested whether nostril specific stimulation with phenyl ethyl alcohol (PEA), a pure olfactory stimulant, asymmetrically activates primary or secondary olfactory-related brain structures such as primary olfactory cortex, entorhinal cortex, and orbitofrontal cortex. The results indicated that without a challenging olfactory task, passive (no sniffing) and active (with sniffing) nostril-specific PEA stimulation did not produce asymmetrical fMRI activation in olfactory cortical structures.

neuroscience↗

bioRxiv2021

Molecular evolution and genetic analysis of Mesta yellow vein mosaic virus and associated betasatellites

Mesta yellow vein mosaic disease (MYVMD), one of the major diseases circulating mesta growing regions of Indian sub-continent, is responsible for serious yield loss in mesta crops. A complex of monopartite begomovirus, Mesta yellow vein mosaic virus (MYVMV) and associated betasatellite, is reported in several studies as the causal agent of MYVMD. However, all-inclusive molecular evolutionary analysis of so far available MYVMVs and associated betasatellites disseminating in this region is still lacking. In this study, by estimating and analyzing various indexes of population genetics and evolutionary parameters, we discussed the sources of genetic variations, population dynamics and different forces acting on the evolution of MYVMVs and associated betasatellites. The study finds recombination as a vital force in the evolution and diversification of begomovirus complexes in different geographic locations however, betasatellites were found to be exposed to more diverse recombination events compared to MYVMVs. Indian isolates are reported to have high frequency of polymorphism in this study which suggests a balancing selection or expansion occurring in Indian populations of begomoviruses. Higher degree of genetic differentiation and lower rate of gene flow calculated between the viral populations of Bangladesh and Pakistan is justified by the relatively far geographical distance between these two countries. Although the study detects overall purifying selection, the degrees of constraints acting on individual gene tested are found different. Coat protein (AV1) is estimated with very high nucleotide substitution rate which is very likely to result from the strongest purifying selection pressure (dN/dS = 0.131) calculated in this study on coat protein. The findings of this study on different evolutionary forces that shape the emergence and diversification of MYVMVs and associated betasatellites may provide directions towards future evolutionary trend analysis and development of comprehensive disease control strategies for begomoviruses.

evolutionary biology↗

bioRxiv2021

Evaluation of solubility and histological effect of 11-keto-β-Boswellic acid on the diabetic mice liver using FTIR-PCA analysis and microscopy

This study was designed to develop a rapid, sensitive, accurate, and inexpensive Fourier Transform Infrared Reflectance (FT-IR) Spectroscopy coupled with Principle Component Analysis (PCA) as a detection technique to evaluate the solubility of 11-Keto-{beta}-Boswellic acid (KBA), from the gum resin extracted from the Omani frankincense, (Boswellia sacra) in the liver of STZ induced diabetic mice. This study also investigated the effect of KBA on the histological changes of hepatocytes of diabetic mice. Liver tissue samples from three groups of mice included normal control group, diabetic control group and diabetic group treated IP with KBA were scanned with FT-IR spectrophotometer in the reflection mode. FT-IR Spectra were collected in the wavenumber range from 400 to 4000cm-1 using ATR accessorry. The results of FT-IR Spectra were analyzed by using multivariate method Principle Component Analysis. The PCA score plot is an exploratory multivariate method indicated that there was a complete segregation among the three groups of liver samples based on change in variation of position of wavenumber in FT-IR spectra, which revealed that there is a clear effect of KBA solubility on treatments. The histological features showed an improvement in the liver tissues with normal structures of hepatocytes with exhibiting mild vacuolations in their cytoplasm. In conclusion, reflectance FT-IR spectroscopy coupled with PCA could be deployed as a new detection method for rapid, low cost and non-destructive method for evaluating of treatment effects in diseased liver tissue based on the solubility of KBA. Histological findings demonstrated the protective effective of KBA on improving the morphology of liver tissue in diabetic mice which resulted in complete recovery to the damage observed in diabetic control group. Summary StatementReflectance FT-IR spectroscopy coupled with PCA has been deployed as a new rapid, inexpensive and non-destructive detection method to examine the solubility of 11-keto-{beta}-Boswellic acid (KBA) in streptozotocin (STZ) induced-diabetes mice liver tissue following intraperitoneal treatment. Moreover, microscopic study of liver tissue histopathology revealed that KBA has a protecting effect against STZ damage.

developmental biology↗

bioRxiv2019

Behavioral flexibility is associated with changes in structure and function distributed across a frontal cortical network in macaques

One of the most influential accounts of central orbitofrontal cortex- that it mediates behavioral flexibility - has been challenged by the finding that discrimination reversal in macaques -the classic test of behavioral flexibility -is unaffected when lesions are made by excitotoxin injection rather than aspiration. This suggests the critical brain circuit mediating behavioral flexibility in reversal tasks lies beyond the central orbitofrontal cortex. To determine its identity a group of nine macaques were taught discrimination reversal learning tasks and its impact on grey matter was measured. Magnetic resonance imaging scans were taken before and after learning and compared with scans from two control groups each comprising ten animals. One control group learned similar discrimination tasks but which lacked any reversal component and the other control group engaged in no learning. Grey matter changes were prominent in posterior orbitofrontal cortex/anterior insula but also were found in three other frontal cortical regions: lateral orbitofrontal cortex (12o), cingulate cortex, and lateral prefrontal cortex. In a second analysis, neural activity in posterior orbitofrontal cortex/anterior insula was measured at rest and its pattern of coupling with the other frontal cortical regions was assessed. Activity coupling increased significantly in the reversal learning group in comparison to controls. In a final set of experiments we used similar structural imaging procedures and analyses to demonstrate that aspiration lesion of central orbitofrontal cortex, of the type known to affect discrimination learning, affected structure and activity in the same frontal cortical circuit. The results identify a distributed frontal cortical circuit associated with behavioral flexibility.

neuroscience↗

bioRxiv2018

Intact extrastriate visual network without primary visual cortex in a Rhesus macaque with naturally occurring Blindsight

Lesions of primate primary visual cortex (V1) lead to loss of conscious visual perception, and are often devastating to those affected. Understanding the neural consequences of such damage may aid the development of rehabilitation methods. In this rare case of a Rhesus macaque (monkey S), likely born without V1, we investigated the brain structures underlying residual visual abilities using multimodal magnetic resonance imaging. In-group behaviour was unremarkable. Compared to controls, visual structures outside of monkey Ss lesion appeared normal. Visual stimulation under anaesthesia with checkerboards activated lateral geniculate nucleus of monkey S, but not the pulvinar, while full-field moving dots activated the pulvinar. Functional connectivity analysis revealed a network of bilateral dorsal visual areas temporally correlated with V5/MT, consistent across lesion and control animals. Overall, we found an intact network of visual cortical areas even without V1, but little evidence for strengthened subcortical input to V5/MT supporting residual visual function.

neuroscience↗