Biology subjects

Kohli, S.

Publications and source records attributed to Kohli, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Sex-specific weighting of shoal size and movement speed but no evidence of asymmetric dominance effect in zebrafish shoal-size preference

Social decisions often require animals to integrate information across multiple attributes of potential partners. Using biological motion stimuli, point-displays generated from tracked live shoals, we tested how adult zebrafish (Danio rerio) weigh shoal size and movement speed during social preference, and whether these preferences are susceptible to contextual manipulation by an asymmetrically placed alternative. In Experiment 1, we established a multi-attribute indifference point by presenting males and females with dichotomous contrasts in which shoal size and movement speed were traded off. Both sexes showed no preference when a larger, slower shoal (4 fish at 0.75x speed) was pitted against a smaller, faster shoal (2 fish at 1.25x speed), but preferred the smaller, faster shoal when the speed difference was greater (4 fish at 0.5x versus 2 fish at 1.25x), indicating that zebrafish are sensitive to graded differences in movement speed relative to numerical cues. In Experiment 2, unidimensional tests confirmed that both sexes preferred larger shoals when speed was held constant but revealed sex-based differences in speed sensitivity: males preferred faster-moving shoals at both shoal sizes tested, whereas females showed no significant speed preference. Male shoal size preferences were stronger at higher movement speeds, suggesting that speed modulates the strength of size preference. In Experiment 3, we tested the asymmetric dominance effect in males, the only sex sensitive to both dimensions, using the indifferent contrast from Experiment 1 as the primary options and four decoy shoals asymmetrically placed along either the size or speed dimension, under counterbalanced presentation orders. No decoy shifted male preference significantly from chance under any condition. These results indicate that zebrafish weigh social cues in a sex-specific manner, and that asymmetric decoy options do not induce preference biases in males when shoals vary along the dimensions of movement speed and size.

animal behavior and cognition↗

bioRxiv2026

Identifying Phelan-McDermid-Like Electrophysiological Subtypes in Autism Using EEG and Machine Learning

BackgroundPhelan McDermid syndrome (PMS), caused by SHANK3 haploinsufficiency, is a genetic form of autism spectrum disorder (ASD) that provides a genetically defined model for studying ASD-related circuit dysfunction. SHANK3 mutations disrupt synaptic organization and cortical synchrony, leading to attenuated gamma-band auditory steady-state responses (ASSRs). We investigated whether PMS-related electrophysiological signatures could be identified using machine learning and whether similar patterns are present in a subset of individuals with idiopathic ASD (iASD). MethodsEEG recorded during a 40-Hz ASSR paradigm was collected from 123 participants (42 TD aged 2-30, 56 iASD aged 3-31, 25 PMS aged 2-26). We extracted time-series, ERSP, FOOOF-derived spectral, and intertrial phase coherence (ITPC) features. XGBoost models with leave-one-out cross-validation classified PMS versus TD; the best age/sex-adjusted ITPC model was then applied to iASD participants to derive a Synchrony Atypicality Index (SAI). Unsupervised clustering of high-dimensional ITPC features was also performed. ResultsITPC-based models showed the strongest discrimination between TD and PMS participants (AUROC = 0.83). When applied to iASD participants, 35.7% exhibited elevated SAI, indicating a PMS-like gamma-band phase-locking profile. Classification of iASD versus PMS performed poorly in the full sample but improved markedly after excluding high-SAI iASD individuals, consistent with substantial heterogeneity within iASD. Unsupervised clustering of ITPC features identified PMS-enriched clusters that also captured high-SAI iASD participants. Results were consistent after controlling for age in sensitivity analyses. ConclusionsReduced 40-Hz ITPC is a mechanistically interpretable electrophysiological signature of PMS and identifies a biologically meaningful PMS-like subgroup within iASD, supporting biomarker-guided stratification.

neuroscience↗

bioRxiv2025

Anterior thalamic nucleus inputs to the retrosplenial cortex are unperturbed in the hAPP-J20 mouse model of Alzheimer's disease

Alzheimers disease (AD) is a neurodegenerative condition characterised by progressive loss of memory and general decline in cognitive function. Although research has traditionally focused on the hippocampus and entorhinal cortex, other regions important for memory and spatial navigation, such as the anterior thalamic nuclei (ATN) and retrosplenial cortex (RSC), are also affected. The RSC is an important brain region for both memory and spatial navigation, and displays dysfunction in humans during prodromal phases of AD. The ATN provide a major input to RSC, with loss of this input to RSC causing a dramatic reduction in the expression of the immediate early gene product c-Fos. The ATN to RSC connection may thus present a new target for therapeutic intervention in AD. Here, we set out to determine whether AD-like pathology perturbed projections from ATN to RSC using the hAPP-J20 amyloidopathy mouse model, using optogenetic activation of thalamic inputs combined with ex vivo patch clamp electrophysiology. We found that RSC displayed an age-dependent decline in basal c-Fos activity, with no additional effect of amyloid pathology on c-Fos expression. At all time points (3, 6 and 9 months) measured, we found no evidence of impairments in the synaptic strength or efficacy of the ATN projections to either granular or dysgranular subdivisions of RSC. We conclude that, in the hAPP-J20 mouse model, this pathway is unaffected by amyloid-{beta} overexpression.

neuroscience↗

bioRxiv2025

Unraveling Genomic Signatures of lncRNA Expression in Zebrafish Caudal Fin Regeneration: Bridging Regenerative Potential and Positional Memory.

Zebrafish (Danio rerio) is an essential model organism for tissue regeneration, but the function of long non-coding RNAs (lncRNAs) in tissue regeneration is not well understood. Identifying important regeneration-associated lncRNAs may allow for cross-species applications, improving tissue repair in other organisms. However, few studies and a lack of functional validation complicate our understanding of their mechanistic functions. This research explores novel lncRNAs associated with caudal fin regeneration and positional memory, aiming to identify those that are evolutionarily important across species and may hold universal significance. RNA-seq data deposited in the NCBI database were compared at various important time points (0h post-amputation (hpa), 12 hpa, 1 day post-amputation (dpa), two dpa, three dpa, and seven dpa) and fin parts (proximal, middle, and distal) to uncover major regulatory lncRNAs. Using HISAT2, StringTie, FEELnc, Conservation Analysis and WGCNA (Weighted Gene Co-expression Network Analysis), we found 107 lncRNAs related to regeneration time points and 229 about positional memory during regeneration. Overlapping analysis identified 13 common genomic regions that are complete or partial lncRNAs, indicating a functional connection between regeneration and positional identity and expressed differently in each time point and each position. Additionally, a comparison with regeneration-associated mRNAs revealed that these 13 regions play critical roles in both processes, providing insights into the molecular mechanisms of regenerative precision. Following validation by RT-PCR, the results further suggest that these overlapping regions are differentially expressed across distinct positions within the same tissue, despite a consistent injury pattern. This positional variation in expression may indicate potential roles in both evolutionary adaptation and the regulation of regenerative processes across multiple tissues.

genomics↗

bioRxiv2025

Limb-on-a-Chip: An All-Hydrogel Platform for Scalable and Reproducible Engineering of Neuromuscular Tissues

Diseases or injuries that impact neuromuscular tissues have a severe negative impact on human health, mobility, and quality-of-life, motivating the development of tissue engineered in vitro models of the motor control system. Current neuromuscular organoids and organ-on-a-chip platforms either rely on stochastic self-assembly that limits reproducibility or require complex microfabrication processes that preclude high-resolution imaging and scalable functional analysis. We have developed a Limb-on-a-Chip platform that addresses key challenges of current model systems by enabling reproducible and scalable manufacturing of neuromuscular tissues compartmentalized into "spinal cord" and "limb" chambers, while promoting biochemical crosstalk between cell types. Our fabrication method leverages 3D printed molds to perform 1-step micropatterning of an all-hydrogel chip containing precise features to guide muscle fiber alignment and motor neuron axonal outgrowth. We demonstrate the ability to co-culture motor neurons and skeletal muscles within this hydrogel platform, enabling tissue-wide readouts of muscle force as well as single cell-resolution measurements of muscle fiber calcium activity. Our accessible method for fabricating reproducible in vitro neuromuscular models that are compatible with high-resolution imaging and functional readouts provides a powerful new tool for investigating the neuromuscular interface in health and disease.

bioengineering↗

bioRxiv2025

Biohybrid tendons enhance the power-to-weight ratio and modularity of muscle-powered robots

Biohybrid robots powered by tissue engineered skeletal muscle have historically relied on architectures in which muscle actuators are placed directly on skeletons, thus limiting the accessible design space for such machines. By contrast, native musculoskeletal architecture relies on tendons to bridge the interface between muscles and skeletons, enabling precise, space-efficient, and energy-efficient force transmission. In this study, we use a mathematical model of the muscle-tendon-skeleton interface to design a biohybrid muscle-tendon unit composed of tissue engineered muscle coupled to adhesive tough hydrogel tendons. We show how tuning tendon stiffness and pre-tension modulates actuator performance, measure fatigue characteristics of our actuators over >7000 cycles, and tune skeleton stiffness to increase force transmission muscles to skeletons by [~]29X. Furthermore, we demonstrate an [~]11X improvement in power-to-weight ratio of muscle-tendon units as compared to previous demonstrations of robots powered by muscles alone. This work validates a robust approach for designing, manufacturing, and deploying muscle-tendon actuators that promises to enhance the modularity and efficiency of biohybrid robots.

bioengineering↗

bioRxiv2025

Delayed forebrain excitatory and inhibitory neurogenesis inSTRADA-related megalencephaly via mTOR hyperactivity

Biallelic pathogenic variants in STRADA, an upstream regulator of the mechanistic target of rapamycin (mTOR) pathway, result in megalencephaly, drug-resistant epilepsy, and severe intellectual disability. This study explores how mTOR pathway hyperactivity alters cell fate specification in dorsal and ventral forebrain development using STRADA knock-out human stem cell derived brain organoids. In both dorsal and ventral forebrain STRADA knock-out organoids, neurogenesis is delayed, with a predilection for progenitor renewal and proliferation and an increase in outer radial glia. Ventrally, interneuron subtypes shift to an increase in neuropeptide-Y expressing cells. Inhibition of the mTOR pathway with rapamycin results in rescue for most phenotypes. When mTOR pathway variants are present in all cells of the developing brain, overproduction of interneurons and altered interneuron cell fate may underlie mechanisms of megalencephaly, epilepsy, and cognitive impairment. Our findings suggest mTOR inhibition during fetal brain development as a potential therapeutic strategy in STRADA deficiency.

neuroscience↗

bioRxiv2025

Dissection of retrosplenial cortex inputs: ubiquitous drive from anterior thalamus

The retrosplenial cortex (RSC) is a highly interconnected brain region involved in spatial navigation and associative learning. It forms extensive, reciprocal connections with sensory, hippocampal, parahippocampal, prefrontal, and thalamic areas. RSC comprises granular (gRSC) and dysgranular (dRSC) subdivisions with distinct connectivity and functions. Despite its emerging role in behaviour and its implication in memory-related disorders such as Alzheimers disease, the nature of its synaptic inputs remains poorly understood. Here, we combined viral anatomical tracing, optogenetic stimulation, and patch-clamp electrophysiology to investigate inputs from the anterior cingulate cortex (ACC), dorsal subiculum (dSub), and anterior thalamic nuclei (ATN) to gRSC and dRSC. Strikingly, all recorded RSC pyramidal neurons received ATN input, regardless of subdivision or cortical layer. Activation of ATN inputs evoked significantly larger post-synaptic responses than those from dSub or ACC, though both regions maintained substantial connectivity with RSC. While dSub projections appeared denser in gRSC, synaptic responses were larger in dRSC, albeit with lower input probability. Notably, NMDA receptor-mediated components of RSC excitatory inputs were weaker than expected, potentially explaining the reported inability to induce long-term potentiation in RSC in ex vivo neurophysiology experiments. This is the first study to characterise the synaptic properties of retrosplenial afferents. Our findings highlight the dominant influence of ATN inputs and raise important questions about how RSCs long-range connectivity supports its roles in memory and spatial navigation.

neuroscience↗

bioRxiv2024

Discovery of Novel Long Non-Coding RNAs That May Potentially Play a Role in Zebrafish Brain Regeneration Post Traumatic Injury

Understanding brain regeneration mechanisms is vital for treating neurological conditions. Zebrafish (Danio rerio) are an excellent model due to their genetic similarity to humans and strong regenerative abilities. In this study, we identified novel long non-coding RNAs (lncRNAs) in the regenerating zebrafish brain following traumatic brain injury (TBI). RNA sequencing data of the zebrafish telencephalon from the BioStudies database was analyzed for novel long non-coding RNA expression (lncRNA) at control, one day post-lesion (early wound healing), three days post-lesion (cell proliferation), and 14 days post-lesion (differentiation). We identified 689 potential lncRNAs using HISAT2, StringTie, FEELnc, and PhastCon analysis tools. Principal component analysis (PCA) of identified lncRNAs revealed a distinct expression profile at 1-day post-lesion, indicating their significant role in early wound healing. Weighted Gene Co-expression Network Analysis (WGCNA) identified two modules (brown and turquoise) showing unique expression patterns critical to brain regeneration. Pathway enrichment analysis linked brown module lncRNAs to peptide biosynthesis, cellular amide metabolism, and ribosome biogenesis. In contrast, turquoise module lncRNAs were associated with ion transmembrane transport and cell adhesion pathways. qPCR validation confirmed co-expression patterns of selected lncRNAs and correlated genes, emphasizing their regulatory roles. This study demonstrates that lncRNAs play crucial roles in zebrafish brain regeneration by modulating gene expression during the early wound healing stage. These insights offer potential therapeutic applications of lncRNAs in neuroregenerative medicine.

bioinformatics↗

bioRxiv2024

2.5D Actuating Substrates Enable Decoupling the Mechanical and Biochemical Effects of Muscle Exercise on Motor Neurons

Emerging in vivo evidence suggests that exercise impacts peripheral nerves, but the difficulty of isolating and studying the muscle-specific impact on motor neurons in vivo, as well as the inability to decouple the biochemical and mechanical impacts of exercise in this setting, motivate investigating this phenomenon in vitro. In this study, we show that tuning the mechanical properties of fibrin hydrogels can generate stable 2.5D motor neuron and contractile skeletal muscle cultures that enable long-term efficient secretome harvesting from exercised tissues. Motor neurons stimulated with muscle-secreted cytokines significantly upregulate neurite outgrowth and migration, with an effect size dependent on exercise intensity. Actuating magnetic microparticles embedded within 2.5D substrates enabled us to dynamically stretch motor neurons and non-invasively mimic the mechanical effects of exercise, revealing that dynamic stretch has an equally significant impact on axonogenesis. RNA sequencing revealed different transcriptomic signatures between groups, with biochemical stimulation having a significantly greater impact on cell signaling related to axon growth and development, neuron projection guidance, and neuron-muscle synapse maturation. Our study thus leverages 2.5D actuating substrates to robustly validate a hypothesized role for muscle exercise in regulating motor neuron growth and maturation through both mechanical and biochemical signaling.

bioengineering↗

bioRxiv2023

Differential encoding of odor and place in mouse piriform and entorhinal cortex

The integration of olfactory and spatial information is critical for guiding animal behavior. The lateral entorhinal cortex (LEC) is reciprocally interconnected with cortical areas for olfaction and the hippocampus and thus ideally positioned to encode odor-place associations. Here, we used mini-endoscopes to record neural activity in the mouse piriform cortex (PCx) and LEC. We show that in head-fixed mice, odor identity could be decoded from LEC ensembles, but less accurately than from PCx. In mice freely navigating a linear track, LEC ensemble activity at the odor ports was dominated by spatial information. Spatial position along the linear track could be decoded from LEC and PCx activity, however, PCx but not LEC exhibited strong behavior-driven modulation of positional information. Together, our data reveal that information about odor cues and spatial context is differentially encoded along the PCx-LEC axis. Significance statementFor most animals, the sense of smell is essential for successfully navigating the environment to find food, shelter, and mates. However, how olfactory and spatial information is integrated in the brain to support olfactory-guided behaviors remains poorly understood. In mammals, candidate brain regions thought to support odor-place associations include the olfactory (piriform, PCx) cortex, entorhinal cortex, and hippocampus. We here characterize the activity of cells in the PCx and lateral entorhinal cortex (LEC) of freely moving mice in response to odor cues presented in a linear track. Using mini-endoscope microscopy and population coding analyses, we find that information about odors, spatial location, and behavior is differentially encoded along the PCx-LEC axis.

neuroscience↗

bioRxiv2023

Multiplex Base Editing to Protect from CD33-Directed Therapy: Implications for Immune and Gene Therapy

On-target toxicity to normal cells is a major safety concern with targeted immune and gene therapies. Here, we developed a base editing (BE) approach exploiting a naturally occurring CD33 single nucleotide polymorphism leading to removal of full-length CD33 surface expression on edited cells. CD33 editing in human and nonhuman primate (NHP) hematopoietic stem and progenitor cells (HSPCs) protects from CD33-targeted therapeutics without affecting normal hematopoiesis in vivo, thus demonstrating potential for novel immunotherapies with reduced off-leukemia toxicity. For broader applications to gene therapies, we demonstrated highly efficient (>70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in NHPs. In vitro, dual gene-edited cells could be enriched via treatment with the CD33 antibody-drug conjugate, gemtuzumab ozogamicin (GO). Together, our results highlight the potential of adenine base editors for improved immune and gene therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/529353v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@70c99dorg.highwire.dtl.DTLVardef@c46ef4org.highwire.dtl.DTLVardef@505fd2org.highwire.dtl.DTLVardef@c30b8c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Moxifloxacin-mediated killing of Mycobacterium tuberculosis involves respiratory downshift, reductive stress, and ROS accumulation

Moxifloxacin is central to treatment of multidrug-resistant tuberculosis. Effects of moxifloxacin on Mycobacterium tuberculosis redox state were explored to identify strategies for increasing lethality and reducing the prevalence of extensively resistant tuberculosis. A non-invasive redox biosensor and an ROS-sensitive dye revealed that moxifloxacin induces oxidative stress correlated with M. tuberculosis death. Moxifloxacin lethality was mitigated by supplementing bacterial cultures with an ROS scavenger (thiourea), an iron chelator (bipyridyl), and, after drug removal, an antioxidant enzyme (catalase). Lethality was also reduced by hypoxia and nutrient starvation. Moxifloxacin increased the expression of genes involved in the oxidative stress response, iron-sulfur cluster biogenesis, and DNA repair. Surprisingly, and in contrast with Escherichia coli studies, moxifloxacin decreased expression of genes involved in respiration, suppressed oxygen consumption, increased the NADH/NAD+ ratio, and increased the labile iron pool in M. tuberculosis. Lowering the NADH/NAD+ ratio in M. tuberculosis revealed that NADH-reductive stress facilitates an iron-mediated ROS surge and moxifloxacin lethality. Treatment with N-acetyl cysteine (NAC) accelerated respiration and ROS production, increased moxifloxacin lethality, and lowered the mutant prevention concentration. Moxifloxacin induced redox stress in M. tuberculosis inside macrophages, and co-treatment with NAC potentiated the anti-mycobacterial efficacy of moxifloxacin during nutrient starvation, inside macrophages, and in mice where NAC restricted the emergence of resistance. Thus, oxidative stress, generated in a novel way, contributes to moxifloxacin-mediated killing of M. tuberculosis. The results open a way to make fluoroquinolones more effective anti-tuberculosis agents and provide a mechanistic basis for NAC-mediated enhancement of fluoroquinolone lethality in vitro and in vivo. Author Summary A new paradigm was revealed for stress-mediated bacterial death in which moxifloxacin treatment of M. tuberculosis decreases respiration rate (respiration increases in E. coli). Although moxifloxacin-induced, ROS-mediated bacterial death was observed, it derived from elevated levels of NADH and iron, a phenomenon not seen with antibiotic-treated E. coli. Nevertheless, stimulation of respiration and ROS by N-acetyl cysteine (NAC) enhanced moxifloxacin-mediated killing of M. tuberculosis, thereby reinforcing involvement of ROS in killing. NAC stimulation of moxifloxacin-mediated killing of M. tuberculosis and restriction of the emergence of resistance in a murine model of infection emphasize the importance of lethal action against pathogens. The work, plus published benefits of NAC to TB patients, encourage studies of NAC-based enhancement of fluoroquinolones.

microbiology↗

bioRxiv2022

No evidence from complementary data sources of a direct projection from the mouse anterior cingulate area to the hippocampal formation

The connectivity and interplay between the prefrontal cortex and hippocampus underpin a number of key cognitive processes, with changes in these interactions being implicated in both neurodevelopmental as well as neurodegenerative conditions. Understanding the precise cellular connections through which this circuit is organised is, therefore, vital for understanding these same processes. Overturning earlier findings, a recent study described a novel excitatory projection from anterior cingulate cortex to hippocampus. We sought to validate this unexpected finding using multiple, complementary methods: anterograde and retrograde anatomical tracing, using both anterograde and retrograde AAVs and monosynaptic rabies tracing. Additionally, an extensive data search of the Allen Projection Brain Atlas database was conducted to find the stated projection within any of the deposited anatomical studies, as an independent verification of our own results. However, we failed to find any evidence of a direct, monosynaptic projection from mouse anterior cingulate cortex to the hippocampus proper.

neuroscience↗

bioRxiv2021

Hippocampal CA1 pyramidal cells do not receive monosynaptic input from thalamic nucleus reuniens

The prefrontal - hippocampal - entorhinal system is perhaps the most widely-studied circuit in cognitive and systems neuroscience, due to its role in supporting cognitive functions such as working memory and decision-making. Disrupted communication within this circuit is a key feature of disorders such as schizophrenia and dementia. Nucleus reuniens (NRe) is a midline thalamic nucleus that sits at the nexus of this circuit, linking these regions together. As there are no direct projections from prefrontal cortex to hippocampus, the accepted model is that the NRe mediates prefrontal drive of hippocampal activity, although these connections are poorly defined at the cellular and synaptic level. Using ex vivo optogenetics and electrophysiology, alongside monosynaptic circuit-tracing, we sought to test the mechanisms through which NRe could drive hippocampal activity. Unexpectedly, we found no evidence that pyramidal cells in CA1 receive input from NRe, with midline thalamic input to hippocampus proper appearing selective for GABAergic interneurons. In other regions targeted by NRe, we found that pyramidal cells in prosubiculum and subiculum received synaptic inputs from NRe that were at least an order of magnitude weaker than those in prefrontal or entorhinal cortices. We conclude that, contrary to widely-held assumptions in the field, the hippocampal pyramidal cells are not a major target of nucleus reuniens.

neuroscience↗

bioRxiv2021

Reversal of the renal hyperglycemic memory by targeting sustained tubular p21 expression

A major therapeutic obstacle in diabetes mellitus is the metabolic or hyperglycemic memory: the persistence of impaired organ function despite improvement of blood glucose. Therapies reversing the hyperglycemic memory and thus improving already established organ-dysfunction are lacking, but urgently needed considering the increasing prevalence of diabetes mellitus worldwide. Here we show that glucose-mediated changes in gene expression largely persist in diabetic kidney disease (DKD) despite reversing hyperglycemia. The senescence-associated cyclin-dependent kinase inhibitor p21 (Cdkn1a) was the top hit among genes persistently induced by hyperglycemia and was associated with sustained induction of the p53-p21 pathway. Persistent p21 induction was confirmed in various animal models, in several independent human samples and in in vitro models. Tubular p21 expression and urinary p21-levels were associated with DKD severity and remained elevated despite improved blood glucose levels in humans, suggesting that p21 may be a biomarker indicating persistent ("memorized") kidney damage. Glucose-mediated p21 induction and tubular senescence were enhanced in mice with reduced levels of the disease resolving protease activated protein C (aPC). Mechanistically, glucose-induced and sustained tubular p21 expression is linked with demethylation of its promoter and reduced DNMT1 expression. aPC reverses already established p21 expression independent of its anticoagulant function through receptor signaling. Accordingly, new pharmacological approaches specifically mimicking aPC signaling (3K3A-aPC, parmodulin-2) enabled the reversal of glucose-mediated sustained tubular p21 expression, tubular senescence, and DKD. Thus, p21-dependent tubular senescence contributes to the hyperglycemic memory but can be therapeutically targeted. Single sentence summaryaPC signaling targets persistent p21 expression and tubular senescence and reverses the hyperglycemic memory in diabetic kidney disease.

molecular biology↗

bioRxiv2021

Chemogenetic activation of midline thalamic nuclei fails to ameliorate memory deficits in two mouse models of Alzheimer's disease

One of the main features of Alzheimers disease is the progressive loss of memory, likely due to pathological changes within brain regions such as the hippocampus and entorhinal cortex. These structures are embedded within the extended memory circuit, an interconnected set of brain regions that are essential for episodic memory. The anterior thalamic nuclei (ATN) and thalamic nucleus reuniens (NRe) are both extensively and reciprocally connected with these important memory regions, so we sought to test the hypothesis that chemogenetically-enhancing neurotransmission through NRe and ATN would ameliorate memory deficits in two mechanistically-distinct mouse models of Alzheimers disease. Using the hAPP-J20 mouse model of amyloidopathy and the Tg4510 mouse model of tauopathy, we carried out stereotaxic injections of viral vectors to transduce hM3Dq (Gq)_mCherry into NRe or the anterio-dorsal/anterio-ventral nuclei of ATN, using mCherry as a control. At nine months (hAPP-J20) or six months (Tg4510) of age, mice underwent a behaviour battery of open field (OF), novel object recognition (NOR) and radial arm maze (RAM), with DREADD agonist 21 administered 30min prior to each behaviour test. Tissue was collected post-behaviour to confirm injection site and virus expression. Both Tg4510 and hAPP-J20 mice show marked hyperactivity in the OF, significant deficits in recognition memory, and a significant impairment in spatial reference and spatial working memory. Unexpectedly, chemogenetic activation of ATN or NRe did not significantly improve spatial memory impairments or reduce the observed hyperactivity, although NRe activation did modestly rescue recognition memory in J20 mice. This may be due to compensation elsewhere within the memory circuit, or that the pathological changes are too far advanced for behaviour reversal.

neuroscience↗

bioRxiv2020

Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: A model for genomic Imprinting

In mealybugs, transcriptional inactivation of the entire paternal genome in males, due to genomic imprinting, is closely correlated with sex determination. The sequencing, de-novo assembly and annotation of the mealybug, Maconellicoccus hirsutus genome and its comparison with Planococcus citri genome strengthened our gene identification. The expanded gene classes, in both genomes relate to the high pesticide and radiation resistance; the phenotypes correlating with increased gene copy number rather than the acquisition of novel genes. The complete repertoire of genes for epigenetic regulation and multiple copies of genes for the core members of polycomb and trithorax complexes and the canonical chromatin remodelling complexes are present in both the genomes. Phylogenetic analysis with Drosophila shows high conservation of most genes, while a few have diverged outside the functional domain. The proteins involved in mammalian X-chromosome inactivation are identified in mealybugs, thus demonstrating the evolutionary conservation of factors for facultative heterochromatization. The transcriptome analysis of adult male and female M.hirsutus indicates the expression of the epigenetic regulators and the differential expression of metabolic pathway genes and the genes for sexual dimorphism. The depletion of endosymbionts in males during development is reflected in the significantly lower expression of endosymbiont genes in them. Author summaryThe mealybug system offers a unique model for genomic imprinting and differential regulation of homologous chromosomes that pre-dates the discovery of dosage compensation of X chromosomes in female mammals. In the absence of robust genetics for mealybugs, we generated and analysed the genome and transcriptome profile as primary resources for effective exploration. The expanded gene classes in the mealybugs relate to their unique biology; the expansion of pesticide genes, trehalose transporter, SETMAR and retrotransposons correlate with pesticide, desiccation and radiation resistance, respectively. The similarity in the genomic profile of two species of mealybugs strengthens our gene prediction. All the known epigenetic modifiers and proteins of the primary complexes like the PRC1,2 and the trithorax are conserved in mealybugs, so also the homologues of mammalian proteins involved in X chromosome inactivation. The high copy number of genes for many partners in these complexes could facilitate the inactivation of a large part of the genome and raise the possibility of formation of additional non-canonical complexes for sex specific chromosome inactivation. In adult males and females, the status of epigenetic regulation is likely to be in a maintenance state; therefore, it is of interest to analyze the expression of epigenetic regulators during development.

genomics↗