Biology subjects

Jones, S.

Publications and source records attributed to Jones, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Increased Quadriceps Intermuscular Adipose Tissue in Chronic Liver Disease is Associated with an Altered Muscle Transcriptome compared with Healthy Age Matched Controls.

Muscle fat infiltration (i.e., myosteatosis) is an important index of muscle health and pathology in disease states, such as chronic liver disease (CLD). However, it is unknown whether myosteatosis differs due to anatomical location. Further, the mechanistic implications of divergent intermuscular adipose tissue (IMAT) deposition remains unknown in patients with CLD. 33 patients with CLD (55.0{+/-}10.5years) and 17 healthy controls (HC) (49.6{+/-}15.4years) were recruited. Quadriceps IMAT was estimated between 20-80% of muscle length and psoas IMAT at L3 via MRI. Body composition, muscle strength and habitual activity were assessed. Fasted vastus lateralis muscle biopsies were collected and subjected to RNA sequencing analysis. https://ClinicalTrials.gov identifier: NCT04734496. IMAT was greater in CLD compared with HC in both quadriceps and psoas (P<0.0001). Quadriceps IMAT positively correlated with BMI (r=0.62), body fat (r=0.65), age (r=0.36) and negatively correlated with maximal knee extensor strength (r=-0.45) and habitual physical activity (r=-0.50) in CLD and HC. 169 differentially expressed genes (DEGs) were identified in low IMAT CLD vs HC, and 178 DEGs were identified in high IMAT CLD vs HC. CLD patients with high and low IMAT exhibited defined expression profiles, with only 39 DEGs (representing 12.7%) in common. Pathway analysis of DEGs revealed enrichment of atrophic and pro-inflammatory pathways in the high IMAT group. IMAT is greater in patients with CLD compared to HC, irrespective of anatomical location and is associated with reductions in muscle function and may be exacerbated by physical inactivity. IMAT appears to alter the muscle transcriptome in COLD, potentially exacerbating muscle loss.

physiology↗

bioRxiv2025

A New Aneurysm Rupture-Prone Marfan Mouse Model with FBN1Q2467X Nonsense Mutation Reveals Adventitial Inflammation

Marfan syndrome (MFS) is a genetic disorder caused by mutations in fibrillin-1(FBN1), which encodes FBN1, a key structural component of the extracellular matrix. Mutations in FBN1 influence the severity of aortic disease and therapeutic responses, with aortic aneurysm being the leading cause of mortality in patients with MFS. To investigate the mechanisms driving aneurysm progression, we generated a mouse model (Fbn1Q2469X/+) carrying the FBN1Q2467X nonsense mutation identified in MFS patients. This mutation results in FBN1 deficiency. Although Fbn1Q2469X/+ mice appear normal, showing only mild, nonprogressive dilation of the aortic root and ascending aorta with minor reductions in blood pressure, homozygous Fbn1Q2469X/Q2469X mice develop spontaneous thoracic aortic aneurysms (TAA) that progress to rupture between 10 and 25 days of age, with 100% penetrance. Histopathology shows progressive vessel wall degeneration characterized by disorganized vascular smooth muscle cells, collagen loss, and elastic fiber fragmentation from early to late stages. RNA-seq analysis identifies inflammation as the dominant process in late-stage aneurysms. Immunofluorescence assay reveals inflammatory cells prominently localized to the adventitia near rupture sites, linking adventitial inflammation to aneurysm progression. This genetically modified Fbn1Q2469X/Q2469X mouse model consistently develops progressive aortic aneurysms and provides a reliable, cost-effective platform to investigate the molecular mechanisms of aneurysm progression and to evaluate therapeutic strategies in aneurysm diseases, including Marfan syndrome and related disorders.

genetics↗

bioRxiv2025

Carnosinylation of Cardiac Antigens Attenuates Immunogenic Responses and Improves Function in Failing Hearts

ObjectiveTo investigate the effects of carnosine on heart failure and to examine whether this is associated with reduced immunogenicity of oxidatively-generated aldehyde modified proteins. BackgroundHeart failure is associated with the accumulation of lipid derived aldehydes that form immunogenic protein adducts. However, the pathological impact of these aldehydes and aldehyde-modified proteins in heart failure has not been assessed. Histidyl dipeptides, such as carnosine found in the heart, bind to aldehydes, and their protein adducts. However, the effects of carnosine on heart failure or the antigenicity of aldehyde modified proteins have not been studied. MethodsMale, wild type C57BL/6J mice were subjected to either sham or transverse aortic constriction (TAC) surgery. To increase carnosine levels, they were placed on drinking water with or without {beta}-alanine prior to surgery, and for the remainder of the study. Cardiac function was evaluated by echocardiography, and the levels of histidyl dipeptides, immune cell populations, and CD4+ T cell activation were assessed via LC-MS/MS and flow cytometry, respectively. ResultsMyocardial levels of histidyl dipeptides decreased at both 3- and 8-weeks post-TAC. Supplementation with {beta}-alanine increased myocardial histidyl dipeptide levels, attenuated adverse cardiac remodeling, and reduced aldehyde stress. Carnosine formed covalent bond with protein-bound aldehydes in the failing heart, reducing their antigenic potential and decreasing activation of dendritic cells and CD4+ T cells in vitro. {beta}-alanine supplementation decreased the population of CD11b+CD64-Ly6G+ neutrophils and CD4+ CD44+ effector T cells in the failing heart. ConclusionsIncreasing myocardial carnosine levels reduces aldehyde stress, dampens maladaptive immune responses, and preserves cardiac function during heart failure. HIGHLIGHTSO_LILevels of endogenous dipeptide carnosine are depleted in failing hearts, while supplementation of the carnosine precurson {beta}-alanine increases myocardial carnosine and preserves cardiac function during heart failure. C_LIO_LIHeart failure is associated with increased activation and infiltration of CD4+ T cells and generation of aldehyde modified protein adducts in failing hearts. C_LIO_LIThe free aldehyde moiety of aldehyde modified protein adducts activates CD4+ T cells through dendritic cell presentation and capping this moiety with carnosine diminishes their antigencity. C_LIO_LIIncreasing myocardial carnosine levels diminishes aldehyde stress and activation of CD4+ T cells during heart failure. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/671840v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@28fc7corg.highwire.dtl.DTLVardef@d851ccorg.highwire.dtl.DTLVardef@1e24a5dorg.highwire.dtl.DTLVardef@18023b6_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Co-Electrospinning Extracellular Matrix with Polycaprolactone Enables a Modular Approach to Balance Bioactivity and Mechanics of a Multifunctional Bone Wrap

Decellularized tissue possesses significant regenerative potential, yet fabricating complex extracellular matrix (ECM) scaffolds remains challenging. Blending with synthetic polymers can aid ECM fabrication but often relies on digested ECM and encapsulation within the synthetic matrix can limit cell-ECM interactions. We recently developed a suspension electrospinning platform to facilitate ECM scaffold fabrication without the need for digestion or polymer-carriers. Its integration into a co- electrospinning system enables modular design of composite scaffolds to combine the regenerative potential of ECM with the advantages of synthetic polymers. This study directly compares co- electrospinning and blend electrospinning of polycaprolactone and small intestinal submucosa (SIS) for use as a bone wrap to augment membrane durability, sustain infection control, and enhance vascularity in Masquelets induced membrane technique. Co-spun wraps demonstrated improved handling properties as compared to ECM wraps and solvent welding was used to achieve target suture retention standards without diminishing SIS content. Unlike the blended wraps, the co-spun wraps supported full-thickness cell infiltration within 4 weeks, released gentamicin at a bactericidal concentration for 6 weeks, and demonstrated enhanced angiogenic properties. Collectively, these findings highlight the functionality of a co-electrospinning modular design and demonstrate the efficacy of using a co-spun wrap in bone tissue engineering applications.

bioengineering↗

bioRxiv2025

Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents

The transfer of antimicrobial resistance genes (ARGs) from environmental microbes to pathogens is a critical but underexplored One Health driver of antimicrobial resistance (AMR). Here, we evaluate freshwater snails, which are geographically widespread aquatic invertebrates, as environmental reservoirs of ARGs. We collected faeces from eight gastropod genera at 15 freshwater locations across Malawi, Uganda, Zanzibar, and the United Kingdom, and conducted the first freshwater snail faecal metagenomics study. We detected putative ARGs predicted to confer resistance to 13 antibiotic classes, including carbapenems in all countries. All ARGs that could be assembled into metagenome-assembled genomes (MAGs) were found within Proteobacteria, which dominated the faecal microbiomes and were strongly associated with the total ARG load. In Malawi, we linked blaOXA-181 (blaOXA-48-like), a previously mobilised carbapenemase gene, to Shewanella xiamenensis, the genes known progenitor. We detected another blaOXA-48-like gene by read-mapping from a sample in the United Kingdom. We identified mobile colistin resistance (mcr)-like genes at 11 of 15 locations, with two mcr-7-like genes being found in an Aeromonas jandaei MAG in Uganda. Our findings highlight freshwater snail faeces as a One Health-relevant environmental reservoir of clinically important ARGs. Data SummaryShort reads from all samples sequenced in this study have been deposited in the Sequence Read Archive (SRA) under BioProject PRJNA1211045, with accession numbers SRX27371064 - SRX27371078. Data and code used to carry out analyses in R are available at https://github.com/amoreo71/freshwater_snail_faecal.

microbiology↗

bioRxiv2025

Cardiac diffusion kurtosis imaging in the human heart in vivo using 300mT/m gradients

PurposeDiffusion tensor imaging (DTI) is commonly used in cardiac diffusion magnetic resonance imaging (dMRI). However, the tissues microstructure (cells, membranes, etc.) restricts the movement of the water molecules, making the spin displacements deviate from Gaussian behaviour. This effect may be observed with diffusion kurtosis imaging (DKI) using sufficiently high b-values (b > 450 s/mm2), which are presently outside the realm of routine cardiac dMRI due to the limited gradient strength of clinical scanners. The Connectom scanner with Gmax = 300 mT/m enables high b-values at echo times (TE) similar to DTI on standard clinical scanners, therefore facilitating cardiac DKI in humans. MethodsCardiac-gated, second-order motion-compensated dMRI was performed with bmax = 1350 s/mm2 in 10 healthy volunteers on a 3T MRI scanner with Gmax = 300 mT/m. The signal was fitted to a cumulant expansion up to and including the kurtosis term and diffusion metrics such as fractional anisotropy (FA), mean diffusivity (MD), mean kurtosis (MK), axial kurtosis (AK), and radial kurtosis (RK) were calculated. ResultsWe demonstrate deviation of the signal from monoexponential decay for b-values > 450 s/mm2 (MK = 0.32 {+/-} 0.03). Radial kurtosis (RK = 0.35 {+/-} 0.04) was observed slightly larger than axial kurtosis (AK = 0.27 {+/-} 0.02), and the difference is statistically significant (RK - AK = 0.08 {+/-} 0.04, p = 2e - 4). ConclusionThis work demonstrates the feasibility of quantifying kurtosis effect in the human heart in vivo (at an echo time shorter than typical TEs reported for cardiac DTI), using high-performance gradient systems (which are 4-8 times stronger than on standard clinical scanners). Our work lays the foundation for exploring new biomarkers in cardiac dMRI beyond DTI.

biophysics↗

bioRxiv2025

Cis-regulatory Mutations Drive Tissue-specific Subfunctionalization of sRNA loci Regulating Soybean Seed Color During Domestication

Gene duplication and structural rearrangements have played a pivotal role in plant genome evolution, enabling functional divergence and the development of novel traits. In soybeans (Glycine max), the I locus, which regulates seed color through tissue-specific subfunctionalization of sRNA loci, offers an example of these mechanisms. Using long-read sequencing, we investigated structural variations underlying four major alleles (I, ii, ik, and i) at the I locus. Our study revealed that large-scale rearrangements, including duplications, inversions, and deletions, within a 180-kb CHS repeat-rich region drive allele-specific RNA silencing through small interfering RNAs (siRNAs). The dominant I allele contains a cis-regulatory region of DnaJ upstream of CHS genes, while the ii and ik alleles feature subtilisin- and P450-driven siRNA loci, respectively. The recessive i allele lacks siRNA production due to deletions or inversions disrupting CHS gene clusters. Phenotypic analyses and RNA-seq confirmed allele-specific, tissue-dependent expression of siRNAs correlating with seed coat pigmentation patterns. This study highlights the evolutionary role of repeat-rich regions in generating regulatory innovations and phenotypic diversity. Our findings underscore the importance of structural rearrangements in domestication traits and demonstrate the power of long-read sequencing for resolving complex genomic regions, advancing both evolutionary biology and crop improvement. SIGNIFICANCE{square} Naturally occurring mutations in the soybean seed coat have revealed the evolution of sRNA genes and their subfunctionalization, resulting in tissue-specific gene expression. {square}Non-homologous recombination of repetitive sequences drives cis-regulatory region rearrangements, leading to the subfunctionalization of sRNA loci that regulates one of domestication traits.

plant biology↗

bioRxiv2025

Plakophilin-2 Coordinates Energy Metabolism and Contractility in Cardiomyocytes, Revealing Its Roles beyond Desmosomes

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial cardiac disease associated with ventricular arrhythmias and an increased risk of sudden cardiac death. Mutations in the desmosome gene Plakophilin-2, PKP2, lead to reduction in PKP2 protein and collapse of desmosomes that is known to compromise contractility and electrical stability of cardiomyocytes. Our previous studies demonstrated the efficacy of adeno-associated virus 9 (AAV9)-mediated restoration of PKP2 expression in a cardiac specific knock-out mouse model of Pkp2 and revealed profound changes in mRNA signatures of metabolic enzymes that were reversed by the gene replacement approach. In this study, we used PKP2-deficient mouse hearts and human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) to identify changes in steady-state metabolite levels associated with impaired lipid homeostasis, glycolysis, and glucose oxidation. These metabolic phenotypes align with human ARVC metabolic data and reflect an intrinsic impairment of cellular energy metabolism. Here we showed for the first time that these intracellular metabolic defects were associated specifically with poor contractility of cardiomyocytes. AAV9:PKP2 restored contractility, improved electrophysiological properties and Ca2+ transients. In contrast, we observed that treating PKP2-deficient cardiomyocytes pharmacologically with small molecule metabolic enhancers improved contractility but not electrophysiological properties and Ca2+ transients, suggesting differential sensitivity of structure-mediated functions in response to metabolic perturbance. Our study modeled and revealed a direct intracellular connection between compromised PKP2 function and metabolic impairment. We proposed that an increased risk of decoupling energy-responsive contractility from less energy-responsive electrical activities can be a new arrhythmogenic mechanism, potentially responsible for exercise-triggered cardiac adversity in ARVC disease development and progression.

cell biology↗

bioRxiv2024

Dysfunctional oscillatory bursting patterns underlie working memory deficits in adolescents with ADHD

Identifying neural markers of clinical symptom fluctuations is prerequisite to developing more precise brain-targeted treatments in psychiatry. We have recently shown that working memory (WM) in healthy adults is dependent on the rise and fall interplay between alpha/beta and gamma bursts within frontoparietal regions, and that deviations in these patterns lead to WM performance errors. However, it is not known whether such bursting deviations underlie clinically relevant WM-related symptoms or clinical status in individuals with WM deficits. In adolescents (n=27) with attention deficit hyperactivity disorder (ADHD), we investigated WM-related dynamics between alpha/beta and gamma bursts in relation to clinical status fluctuations. Participants repeatedly completed a visual Sternberg spatial working memory task during EEG recording as part of their participation in two research studies (n=224 person-sessions). Source localizing EEG data to each participants structural MRI, the rate and volume of alpha, beta, and gamma bursts were examined within the dorsolateral prefrontal cortex (DLPFC) and posterior parietal cortex (PPC). Alpha/beta and gamma bursts at the DLPFC and PPC displayed complimentary roles in WM processes. Alpha/beta bursting decreased during stimuli encoding and increased during the delay, while gamma bursting was elevated during encoding and decreased during the delay. Deviations in bursting patterns were associated with WM errors and clinical symptoms. We conclude that dysfunctional alpha/beta and gamma burst dynamics within the frontoparietal region underlie both intra-individual WM performance and WM symptom fluctuations in adolescents with ADHD. Such burst dynamics reflect a novel target and biomarker for WM-related treatment development.

neuroscience↗

bioRxiv2024

The association between oscillatory burst features and deviations during human working memory

Oscillatory power across multiple frequency bands has been associated with distinct working memory (WM) processes. Recent research has shown that previous observations based on averaged power are driven by the presence of transient, oscillatory burst-like events, particularly within the alpha, beta, and gamma bands. However, the interplay between different burst events in human WM is not well understood. The current EEG study aimed to investigate the dynamics between alpha (8-12 Hz)/beta (15-29 Hz) and high frequency activity (HFA; 55-80 Hz) bursts in human WM, particularly burst features and error-related deviations during the encoding and maintenance of WM in healthy adults. Oscillatory burst features within the alpha, beta and HFA bands were examined at frontal and parietal electrodes in healthy young adults during a Sternberg working memory task. Averaged power dynamics were driven by oscillatory burst features, most consistently the burst rate and burst power. Alpha/beta and HFA bursts displayed complementary roles in WM processes, in that alpha and beta bursting decreased during encoding and increased during delay, while HFA bursting had the opposite pattern, i.e., increased during encoding and decreased during the delay. Critically, weaker variation in burst dynamics across stages was associated with incorrect responses and impaired overall task performance. Together, these results indicate that successful human WM is dependent on the rise and fall interplay between alpha/beta and HFA bursts, with such burst dynamics reflecting a novel target for the development of treatment in clinical populations with WM deficits.

neuroscience↗

bioRxiv2024

Hippocampal CA2 neurons disproportionately express AAV-delivered genetic cargo

Hippocampal area CA2 is unique in many ways, largely based on the complement of genes expressed there. We and others have observed that CA2 neurons exhibit a uniquely robust tropism for adeno-associated viruses (AAVs) of multiple serotypes and variants. In this study, we aimed to systematically investigate the propensity for AAV tropism toward CA2 across a wide range of AAV serotypes and variants, injected either intrahippocampally or systemically, including AAV1, 2, 5, 6, 8, 9, DJ, PHP.B, PHP.eB, and CAP-B10. We found that most serotypes and variants produced disproportionally high expression of AAV-delivered genetic material in hippocampal area CA2, although two serotypes (AAV6 and DJ) did not. In an effort to understand the mechanism(s) behind this observation, we considered perineuronal nets (PNNs) that ensheathe CA2 pyramidal cells and, among other functions, buffer diffusion of ions and molecules. We hypothesized that PNNs might attract AAV particles and maintain them in close proximity to CA2 neurons, thereby increasing exposure to AAV particles. However, genetic deletion of PNNs from CA2 had no effect on AAV transduction. Next, we next considered the AAV binding factors and receptors known to contribute to AAV transduction. We found that the AAV receptor (AAVR), which is critical to transduction, is abundantly expressed in CA2, and knockout of AAVR nearly abolished expression of AAV-delivered material by all serotypes tested. Additionally, we found CA2 enrichment of several cell-surface glycan receptors that AAV particles attach to before interacting with AAVR, including heparan sulfate proteoglycans, N-linked sialic acid and N-linked galactose. Indeed, CA2 showed the highest expression of AAVR and the investigated glycan receptors within the hippocampus. We conclude that CA2 neurons are endowed with multiple factors that make it highly susceptible to AAV transduction, particularly to the systemically available PHP variants, including CAP-B10. Given the curved structure of hippocampus and the relatively small size of CA2, systemic delivery of engineered PHP or CAP variants could all but eliminate the need for intrahippocampal AAV injections, particularly when injecting recombinase-dependent AAVs into animals that express recombinases in CA2.

neuroscience↗

bioRxiv2024

Relationships between migraine and interoception: normal accuracy but altered sensibility and behaviour

BackgroundMigraine is typically precipitated by unaccustomed changes in ones internal state and/or external environment. Migraine symptoms largely involve increased, noxious, awareness of bodily changes and external stimuli. Links have been proposed between migraine and interoception (sensing and interpreting internal states), but direct evidence is limited. MethodsUnmedicated, otherwise healthy, age-matched female participants were grouped by migraine tendency: control (no unprovoked headaches, n=19); low-frequency (<=3 migraines/month, n=20); high-frequency (>=4 migraines/month, n=19). Interoception was assessed, interictally, with standardised questionnaires such as MAIA-2 and a widely used heartbeat counting task. ResultsThe notable significant questionnaire-based difference was in the noticing, not distracting domain of the MAIA-2; controls were least likely to continue activities despite experiencing physical discomfort, and high-frequency migraineurs most likely. Follow-up questioning clarified that this behaviour related predominantly to migraine-related symptoms. The heartbeat task found no differences in accuracy, but lower confidence in the low-frequency migraine group than the control and high-frequency groups. ConclusionsWe suggest that low interoceptive confidence is a risk factor for migraine, whilst amplification of interoceptive signals caused by migraine restores this confidence, but at the price of migraines disabling symptoms. Self-reported tendency to deliberately ignore physical discomfort, including that caused by migraine, may result in more migraine attacks.

neuroscience↗

bioRxiv2024

Noradrenergic and Pavlovian underpinnings of compulsive versus adaptive coping strategies

BackgroundLoss of control over coping strategies can result in the development of impulsive/compulsive spectrum disorders (ICSDs) such as obsessive-compulsive disorder or trichotillomania. Rats, like humans, show individual differences in their tendency to engage in and maintain control over coping behaviours. While most rats exposed to a schedule-induced polydipsia (SIP) procedure develop controlled, moderate, polydipsic coping, some vulnerable individuals engage in excessive, compulsive drinking, or hyperdipsia. The development of hyperdipsia depends in part on noradrenergic mechanisms, as it is prevented by the noradrenaline reuptake inhibitor, atomoxetine in highly impulsive vulnerable rats. However, whether noradrenergic mechanisms also underlie the expression of well-established hyperdipsia, or if other traits, such as the ICSD-relevant sign-tracking, confer vulnerability to its development, are unknown. MethodsIn two longitudinal studies in male Sprague-Dawley rats, we investigated whether well-established hyperdipsia is influenced by atomoxetine and whether its development is predicted by sign-tracking. ResultsSign-tracking was associated with faster acquisition of SIP and the development of high or compulsive levels of SIP. Chronic atomoxetine both exacerbated hyperdipsia and increased the mRNA levels of the markers of cellular activity and plasticity c-fos and zif268, across the dorsal striatum, as revealed by qPCR assays. Atomoxetine also altered the transcriptomic landscape of the nucleus accumbens shell and the pattern of cFos and zif268 expression in the amygdalo-striatal system. ConclusionsThese results provide new insight into the biobehavioural basis of compulsive behaviours, revealing a differential noradrenergic control of the development and expression of compulsive coping, the latter involving recruitment of distinct striatal processes.

animal behavior and cognition↗

bioRxiv2024

Neuronal plasticity at puberty in hypothalamic neurons controlling fertility in female mice

Puberty is a critical transition period to achieve fertility and reproductive capacity in all mammalian species. At puberty, the hypothalamic-pituitary-gonadal (HPG) is activated by neuroendocrine changes in the brain. Central to this are Kiss1 neurons that produce kisspeptin, a neuropeptide which is a potent stimulator of gonadotropin releasing hormone (GnRH) secretion. Kiss1 neurons in the arcuate region of the hypothalamus (Kiss1ARC) increase pulsatile secretion of GnRH at puberty. Other developmental maturational changes in the brain are often accompanied by neuronal plasticity changes but this has not been studied in Kiss1 neurons. Electrophysiological characterisation of Kiss1ARC neurons from female mice shows that these neurons undergo profound intrinsic plasticity at puberty with a critical window between 3 and 4 weeks. Immature Kiss1ARC neurons cannot sustain depolarisation-evoked firing for even 500 ms and instead fire a brief burst of high frequency spikes before falling silent. This would make them unsuitable for the sustained activity that is needed to activate GnRH neurons and trigger LH secretion in the HPG axis. After puberty, sustained firing can be maintained, which endows post-puberty Kiss1ARC neurons with a mature physiological phenotype that is amenable to neuropeptide modulation for generation of burst firing and pulsatile release of kisspeptin. There is a corresponding decrease in the threshold for action potential initiation, a more hyperpolarised post-spike trough and a larger medium after-hyperpolarisation (mAHP). Gene expression analysis showed a significant decrease in Scn2a (Nav1.2 channel), Kcnq2 (Kv7.2 channel) and Lrrc55 (BK channel auxiliary {gamma}3-subunit) expression and an increase in Hcn1 (hyperpolarization activated cyclic nucleotide-gated potassium channel) expression which may contribute to the observed electrophysiological changes. Ovariectomy and {beta}-estradiol replacement defined a window of estrogen-dependent plasticity of action potential firing at puberty, such that post-puberty Kiss1ARC neurons achieve a mature physiological phenotype for activation of the HPG axis.

neuroscience↗

bioRxiv2024

Is there a ubiquitous spectrolaminar motif of local field potential power across primate neocortex?

Mendoza-Halliday, Major et al.1 (referred to as "Mendoza-Halliday et al." for brevity), advocate for a local field potential (LFP)-based approach to functional identification of cortical layers during "laminar" (simultaneous recordings from all cortical layers) multielectrode recordings in nonhuman primates (NHPs). They describe a "ubiquitous spectrolaminar motif" in the primate neocortex: 1) 75-150 Hz power peaks in the supragranular layers, 2) 10-19 Hz power peaks in the infragranular layers and 3) the crossing point of their laminar power gradients identifies Layer 4 (L4). Identification of L4 is critical in general, but especially for Mendoza-Halliday et al. as the "motif" discovery is couched within a framework whose central hypothesis is that gamma activity originates in the supragranular layers and reflects feedforward activity, while alpha-beta activity originates in the infragranular layers and reflects feedback activity. In an impressive scientific effort, Mendoza-Halliday et al. analyzed laminar data from 14 cortical areas in 2 prior macaque studies and compared them to marmoset, mouse, and human data to further bolster the canonical nature of the motif. Identification of such canonical principles of brain operation is clearly a topic of broad scientific interest. Similarly, a reliable online method for L4 identification would be of broad scientific value for the rapidly increasing use of laminar recordings using numerous evolving technologies. Despite Mendoza-Halliday et al.s papers strengths, and its potential for scientific impact, a series of concerns that are fundamental to the analysis and interpretation of laminar activity profile data in general, and local field potential (LFP) signals in particular, led us to question its conclusions. Here, we address four key questions: Q1) Is the spectrolaminar motif ubiquitous, i.e. "found everywhere" or "universal"? Q2) Do features of the motif reliably identify Layer (L) 4? Q3) Are Mendoza-Halliday et al.s newly introduced methods (FLIP and vFLIP) reliable? And Q4) Are the proposed biophysical mechanisms underlying the motif well justified? We used new sets of data comprised of stimulus-evoked laminar response profiles from primary and higher-order auditory cortices (A1 and belt cortex), and primary visual cortex (V1) to test these questions. The rationale for using these areas as a test bed for new methods is that, in contrast to higher-order cortical areas, their laminar anatomy and physiology have already been extensively characterized by prior studies, and there is general agreement across laboratories on key matters like L4 identification. In short, we find that Mendoza-Halliday et al.s findings do not generalize well to these cortical areas. Specifically, regarding Q1: Though we can find a spectrolaminar gradient that is qualitatively consistent with Mendoza-Halliday et al., it is quantifiable in only 61-64% of our recordings, indicating that the motif is common but by no means universal (see "Evaluation of the FLIP method [...]" and "Evaluation of vFLIP [...]"). Regarding Q2: The motifs high/low frequency gradient cross point identified L4 in only 29-33% of our recordings. Regarding Q3: FLIP and vFLIP exhibit marked variability across studies, across brain areas, and spuriously detect cortical layer inversions (see "FLIPs fitting process [...]" and "Evaluation of vFLIP [...]"). Regarding Q4: the biophysical modeling findings cited to support Mendoza-Hallidays conclusions (see "Going forward - in silico [...]") do not reproduce the LFP data trends. While our findings are in many respects at odds with those of Mendoza-Halliday et al., the paper already has, and will continue to spark debate and further experimentation. Hopefully this countervailing presentation will lead to robust collegial efforts to define optimal strategies for applying laminar recording methods in future studies.

neuroscience↗

bioRxiv2024

Variations in human trigeminal and facial nerve branches and foramina identified by dissection and microcomputed tomography

The aim of this study was to identify branches of the trigeminal and facial nerves relevant to surgical incisions and injections and the scalp block techniques in the frontotemporal region, and to determine their relationships with superficial vascular structures and bony landmarks. Half-heads from consenting embalmed donors (6 male, 2 female, mean age at death 78.4 years) were used in this study. Detailed dissection was carried out to identify the position of the auriculotemporal nerve (ATN) relative to the superior temporal artery (STA) and the facial nerve (FN) in six subjects (5 male, 1 female). The results provide a minimum safe distance of 5 mm between the STA and the frontotemporal branches of the FN at the level of the low edge of zygoma and 8mm between the low edge of zygoma and the FN trunk, providing a pre-auricular triangle of safety for incisions and injections. Variability between subjects was up to 60%. Microcomputed tomography (microCT) scans were taken from all eight subjects and the three-dimensional reconstructions were used to identify the supraorbital notch (SON), the zygomaticotemporal foramen (ZTF) and the zygomaticofacial foramen (ZFF). The volume and relative locations of these foramina were calculated for 5-8 subjects. The closest distance between ZTF and the FZS ranged from 9 to 21mm (26% variation); 3 subjects had a single ZTF while 5 subjects had two ZTF. The angle at the centre of the orbit between ZFF and the FZS ranged from 156 to 166 degrees (2.5% variation). These findings demonstrate that both traditional cadaveric dissection methods as well as contemporary microCT methods can be used to investigate the relative locations of nerves or their foramina in the human head. The findings provide anatomical considerations for fronto-temporal incisions and local anaesthesia.

neuroscience↗

bioRxiv2024

Nanopore-based native RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between RNA regulatory features

The identification and functional characterization of chemical modifications on an mRNA molecule, in particular N6-methyladenosine (m6A) modification, significantly broadened our understanding of RNA function and regulation. While interactions between RNA modifications and other RNA features have been proposed, direct evidence showing correlation is limited. Here, using Oxford Nanopore long-read direct RNA sequencing (dRNA-seq), we simultaneously interrogate the transcriptome and epitranscriptome of a human leukemia cell line to investigate the correlation between m6A modifications, mRNA abundance, polyA tail length and alternative splicing. We demonstrated that high quality dRNA-seq is critically important for unbiased and large-scale correlative analyses of these RNA features. The genome wide landscape of RNA methylation was captured with single nucleotide and individual isoform resolution. The length of polyA tails were ascribed to individual transcripts and genes, allowing for unprecedent measurement of polyA tail length distribution. Global analysis indicated negative association between polyA tail length and mRNA abundance while uncovering pathway-specific responses upon depletion of m6A forming enzyme METTL3. Overall, our study presented a rich dRNA-seq data resource which has been validated and can be further exploited to inquire into the complexity of RNA modifications and potential interplays between RNA regulatory elements.

genomics↗

bioRxiv2024

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence SummaryChimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.

evolutionary biology↗