Miracle-dz/UniFAR-FTUs huggingface dataset:
Hurricane-induced demographic changes in a nonhuman primate population

Major disturbance events can have large impacts on the demography and dynamics of animal populations. Hurricanes are one example of an extreme climatic event, predicted to increase in frequency due to climate change, and thus expected to be a considerable threat to population viability. However, little is understood about the underlying demographic mechanisms shaping population response following these extreme disturbances. Here, we analyze 45 years of the most comprehensive free-ranging nonhuman primate demographic dataset to determine the effects of major hurricanes on the variability and maintenance of long-term population fitness. For this, we use individual-level data to build matrix population models and perform perturbation analyses. Despite reductions in population growth rate mediated through reduced fertility, our study reveals a demographic buffering during hurricane years. As long as survival does not decrease, our study shows that hurricanes do not result in detrimental effects at the population level, demonstrating the unbalanced contribution of survival and fertility to population fitness in long-lived animal populations.
A Phelipanche ramosa KAI2 Protein Perceives enzymatically Strigolactones and Isothiocyanates

Phelipanche ramosa is an obligate root-parasitic weed threatening major crops in central Europe. For its germination, it has to perceive various structurally diverging host-exuded signals, including isothiocyanates (ITCs) and strigolactones (SLs). However, the receptors involved are still uncharacterized. Here, we identified five putative SL receptors in P. ramosa, of which PrKAI2d3 is involved in seed germination stimulation. We established the high plasticity of PrKAI2d3, allowing interaction with different chemicals, including ITCs. The SL perception mechanism of PrKAI2d3 is similar to that of endogenous SLs in non-parasitic plants. We provide evidence that the PrKAI2d3 enzymatic activity confers hypersensitivity to SLs. Additionally, we demonstrated that methylbutenolide-OH binds PrKAI2d3 and stimulates P. ramosa germination with a bioactivity comparable to that of ITCs. This study highlights that P. ramosa has extended its signal perception system during evolution, a fact to be considered in the development of specific and efficient biocontrol methods.
Effects of D1 agonist on working memory and cognitive flexibility in a zebrafish model of aging

Part of the natural aging process is a decline in memory and executive function, even in the absence of disease. The dopaminergic system has been implicated in age associated alterations in cognitive flexibility and working memory. Here we examine the relationship between cognitive performance and dopamine function of young-adult and aging zebrafish (Danio rerio). We reveal an age-related decrease in working memory and cognitive flexibility when faced with a negative feedback loop for informing search strategies in the Free-Movement Pattern (FMP) Y-maze. We additionally found a selective role for dopamine D1-like receptor activation, by treatment with partial D1/D5 receptor agonist SKF-38393, for enhancing working memory performance in aged zebrafish, but not for restoring behavioural flexibility. We additionally noted that baseline performance levels were critical to the effect of SKF-38393 on cognitive flexibility. This reduction in behavioural plasticity was accompanied by a down-regulation of the dopamine transporter (dat) and a decrease in metabolic activity. Together, these findings suggest a selective role for cognitive enhancement via dopamine D1 receptors; however, beneficial effects are dependent on behavioural task and baseline performance, emphasising the need for caution when treating cognitive deficits with dopamine agonists to improve cognitive impairment of some tasks. This study further supports the use of zebrafish as a model of aging and cognitive decline.
Temporal expectation modulates the neural dynamics of delayed responses to working memory representations

Temporal expectation can induce anticipatory attention to enhance perceptual processing and optimise behaviours. However, it remains unexplored whether temporal expectation benefits delayed responses to information maintained in working memory (WM) and the underlying neural dynamics that support the benefits. Here we addressed these issues in behavioural and electroencephalography (EEG) experiments. Participants performed a rotation discrimination WM task. Temporal expectation was manipulated by varying the predictability for when a test probe would occur after a delay interval. We first demonstrated that temporal predictability benefited WM performance. Our EEG results showed decreased alpha power over the left posterior brain regions during the delay interval for high than low predictability trials. Importantly, we found earlier enhancement of the lateralised alpha power and the lateralised readiness potential for high than low predictability trials when WM contents were accessed for responses during the probe period. Finally, we found concurrent selection and preparation for responses when the probe onset was predictable but motor preparation lagged behind response selection when the probe onset was more variable. Together, this study provides new insights into the proactive, dynamic nature of the anticipatory deployment of attention in guiding WM maintenance and delayed responses.
Functional synchronization between hippocampal sEEG, parietal ECoG and scalp EEG during a verbal working memory task

Background The maintenance of items in working memory (WM) relies on a widespread network of brain areas where synchronization between electrophysiological recordings may reflect functional coupling. While the coupling from hippocampus to scalp EEG is well established, we provide here direct cortical recordings for a fine-grained analysis. Methods A patient performed a WM task where a string of letters was presented all at once, thus separating the encoding period from the maintenance period. We recorded sEEG from the hippocampus, temporo-parietal ECoG from a 64-contact grid electrode, and scalp EEG. Results Power spectral density (PSD) showed a clear task dependence: PSD in the posterior parietal lobe (10 Hz) and in the hippocampus (20 Hz) peaked towards the end of the maintenance period. Inter-area synchronization was characterized by the phase locking value (PLV). WM maintenance enhanced PLV between hippocampal sEEG and scalp EEG specifically in the theta range [6 7] Hz. PLV from hippocampus to parietal cortex increased during maintenance in the [9 10] Hz alpha and the 20 Hz range. When analyzing the information flow to and from auditory cortex by Granger causality, the flow was from auditory cortex to hippocampus with a peak in the [8 18] Hz range while letters were presented, and this flow was subsequently reversed during maintenance, while letters were maintained in memory. Conclusions The increased functional interaction between hippocampus and cortex through synchronized oscillatory activity and the directed information flow provide physiological basis for reverberation of memory items during maintenance. This points to a network for working memory that is bound by coherent oscillations involving cortical areas and hippocampus. SIGNIFICANCE STATEMENT Hippocampal activity is known for its role in cognitive tasks involving episodic memory or spatial navigation, but its role in working memory and its sensitivity to workload is still under debate. Here, we investigated hippocampal and cortical activity while a subject maintained sets of letters in verbal working memory for a few seconds to guide action. After confirming the coupling between hippocampal oscillations and oscillations on the scalp, we found during maintenance that hippocampal oscillations increased coupling differentially to several areas of cortex by recording directly from the cortex. During encoding of the letters, information flow was from auditory cortex to hippocampus and subsequently reversed during maintenance, thus providing a physiological basis for memory encoding and maintenance. This demonstrates a network for working memory that is bound by coherent oscillations that underlie the functional connectivity between cortical areas and hippocampus.
Donor-derived mitochondrial DNA variant peptides elicit allo-specific immune response in transplant patients

In stem cell transplant, mitochondrial DNA (mtDNA) nonsynonymous single nucleotide variants (SNVs) between donor and recipient (D-R) trigger alloimmune responses and transplant rejection. Whether similar alloimmune responses occurs in solid-organ transplantation remains unknown, particularly with the presence of human leukocyte antigen mismatches. This study characterized mtDNA SNVs between D-R of 163 human lung transplant pairs, and then, post-transplantation, assessed alloimmune responses against donor-derived mitochondrial peptides using ELISpot to measure interferon gamma (IFNγ) release from recipient’s monocytes. We identified a median of 6 nonsynonymous mtDNA SNVs (Interquartile Range = 4 – 9) per D-R pair. SNVs were predominantly located at MT-CYB, MT-ATP6, and MT-ND3 genes. The number of SNVs was higher in D-R race non-concordant pairs than in race-concordant pairs. Donor-derived mitochondrial peptides triggered a 19.8-fold higher IFNγ release compared to recipient-derived peptide. These findings were validated in heart transplantation and show that donor-derived mitochondrial peptides trigger allo-specific immune responses after transplantation.
Altered small-world functional network topology in patients with optic neuritis: A resting- state fMRI study

Purpose This study investigated changes in small-world topology and brain functional connectivity in patients with optic neuritis (ON) by resting-state functional magnetic resonance imaging (rs-fMRI) and based on graph theory. Methods A total of 21 patients with ON (8 males and 13 females) and 21 matched healthy control subjects (8 males and 13 females) were enrolled at the First Affiliated Hospital of Nanchang University and underwent rs-fMRI. Data were preprocessed and the brain was divided into 116 regions of interest. Small-world network parameters and area under the integral curve (AUC) were calculated from pairwise brain interval correlation coefficients. Differences in brain network parameter AUCs between the 2 groups were evaluated with the independent sample t-test, and changes in brain connection strength between ON patients and control subjects were assessed by network-based statistical analysis. Results In the sparsity range from 0.08 to 0.48, both groups exhibited small-world attributes. Compared to the control group, global network efficiency, normalized clustering coefficient, and small-world value were higher whereas the clustering coefficient value was lower in ON patients. There were no differences in characteristic path length, local network efficiency, and normalized characteristic path length between groups. In addition, ON patients had lower brain functional connectivity strength among the rolandic operculum, medial superior frontal gyrus, insula, median cingulate and paracingulate gyri, amygdala, superior parietal gyrus, inferior parietal gyrus, supramarginal gyrus, angular gyrus, lenticular nucleus, pallidum, superior temporal gyrus, cerebellum_Crus1_L, and left cerebellum_Crus6_L compared to the control group (P < 0.05). Conclusion The brain network in ON has a small-world attributes but shows reduced and abnormal connectivity compared to normal subjects. These findings provide a further insight into the neural pathogenesis of ON and reveal specific fMRI findings that can serve as diagnostic and prognostic indices.
Properties of Glial Cell at the Neuromuscular Junction Are Incompatible with Synaptic Repair in the SOD1G37R ALS Mouse Model

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting motoneurons (MNs) in a motor-unit (MU)-dependent manner. Glial dysfunction contributes to numerous aspects of the disease. At the neuromuscular junction (NMJ), early alterations in perisynaptic Schwann cell (PSC), glial cells at this synapse, may impact their ability to regulate NMJ stability and repair. Indeed, muscarinic receptors (mAChRs) regulate the repair phenotype of PSCs and are overactivated at disease-resistant NMJs [soleus muscle (SOL)] in SOD1G37R mice. However, it remains unknown whether this is the case at disease-vulnerable NMJs and whether it translates into an impairment of PSC-dependent repair mechanisms. We used SOL and sternomastoid (STM) muscles from SOD1G37R mice and performed Ca2+-imaging to monitor PSC activity and used immunohistochemistry to analyze their repair and phagocytic properties. We show that PSC mAChR-dependent activity was transiently increased at disease-vulnerable NMJs (STM muscle). Furthermore, PSCs from both muscles extended disorganized processes from denervated NMJs and failed to initiate or guide nerve terminal sprouts at disease-vulnerable NMJs, a phenomenon essential for compensatory reinnervation. This was accompanied by a failure of numerous PSCs to upregulate galectin-3 (MAC-2), a marker of glial axonal debris phagocytosis, on NMJ denervation in SOD1 mice. Finally, differences in these PSC-dependent NMJ repair mechanisms were MU type dependent, thus reflecting MU vulnerability in ALS. Together, these results reveal that neuron-glia communication is ubiquitously altered at the NMJ in ALS. This appears to prevent PSCs from adopting a repair phenotype, resulting in a maladapted response to denervation at the NMJ in ALS. SIGNIFICANCE STATEMENT Understanding how the complex interplay between neurons and glial cells ultimately lead to the degeneration of motor neurons and loss of motor function is a fundamental question to comprehend amyotrophic lateral sclerosis (ALS). An early and persistent alteration of glial cell activity takes place at the neuromuscular junction (NMJ), the output of motor neurons, but its impact on NMJ repair remains unknown. Here, we reveal that glial cells at disease-vulnerable NMJs often fail to guide compensatory nerve terminal sprouts and to adopt a phagocytic phenotype on denervated NMJs in SOD1G37R mice. These results show that glial cells at the NMJ elaborate an inappropriate response to NMJ degeneration in a manner that reflects motor-unit (MU) vulnerability and potentially impairs compensatory reinnervation.
Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species

Shellfish allergy affects up to 2% of the world’s population and persists for life in most patients. The diagnosis of a shellfish allergy, in particular shrimp, is however often challenging due to the similarity of allergenic proteins in other invertebrates. Despite the clinical importance, the complete allergen repertoire of allergy-causing shrimps remains unclear. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembled de novo from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). Trinity was used to assemble the transcriptome, and Transrate and BUSCO applied to verify the assembly. Blast search with the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. Salmon was utilised to measure their relative abundance, demonstrating sarcoplasmic calcium-binding protein, arginine kinase and myosin light chain as highly abundant allergens. In addition, the analyses revealed up to 40 unreported allergens in different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment, conducted in Jalview 2.1 with Clustal Omega, demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable genomic resource for investigating shellfish allergens, comparing invertebrate allergens and developing improved diagnostics and novel immunotherapeutics for food allergy.
Horizontal movement of seeds following tine and plough cultivation : implications for spatial dynamics of weed infestations

Summary Horizontal movement of seeds by different cultivators was investigated in three experiments. Seeds of barley (Hordeum vulgare L.), field bean (Vicia faba L.) and oilseed rape (Brassica napus L.) were positioned on the soil surface or buried 0.1 m deep prior to cultivation, Seed movement was assessed by counting germinated seedlings. The type of tine implement used significantly affected mean seed movement, with surface-sown seeds being moved significantly further than buried seeds. Primary cultivation with flexi- or spring-tine machines moved seeds further than straight-tine or power harrow implements. However, there was no overall difference between plough and flexi-tine mean seed movement. A single pass with a tine attached to a seed drili moved seeds less than the two passes with tine plus seed drill, but the first pass had the greatest effect. Small oilseed rape seeds moved significantly further than larger barley or field bean seeds. More than 84% of seeds moved ≤ 1m from the source: no seeds were observed>4.8m in a forward direction or >0.2m backwards from the source, In a fourth experiment, plots containing seeds of Sinapis arvensis L. were cultivated in alternate directions in successive years, The results broadly validated the findings of the previous experiments Quantifying the horizontal movement of weed seeds is important to the understanding of the spatial dynamics of weed patches and thus in the prediction of future weed distributions.
Variance in cortical depth across the brain surface

The distance between the surface of the scalp and the surface of the grey matter of the brain is a key factor in determining the effective dose of non-invasive brain stimulation for an individual person. The highly folded nature of the cortical surface means that the depth of a particular brain area is likely to vary between individuals. The question addressed here is: what is the variability of this measure of cortical depth? 94 anatomical MRI images were taken from the OASIS database. For each image, the minimum distance from each point in the grey matter to the scalp surface was determined. Transforming these estimates into standard space meant that the coefficient of variation could be determined across the sample. The results indicated that depth variability is high across the cortical surface, even when taking sulcal depth into account. This was true even for the primary visual and motor areas, which are often used in setting TMS dosage. The correlation of the depth of these areas and the depth of other brain areas was low. The results suggest that dose-setting of TMS based on visual or evoked potentials may offer poor reliability, and that individual brain images should be used when targeting non-primary brain areas.
Post-translational control is sufficient to coordinate membrane synthesis with growth in Escherichia coli

Every cell must produce enough membrane to contain itself. However, the mechanisms by which cells couple the rate of membrane synthesis with the rate of growth remain unresolved. By measuring precursors, intermediates, and enzymes of the fatty acid and phospholipid synthesis pathways of Escherichia coli, we show that while fatty acid and membrane synthesis capacities are maintained at a constant level across a 3-fold range of growth rates, the steady-state rate of phospholipid synthesis is principally mediated by allosteric control of a single enzyme, PlsB. Surprisingly, metabolic modelling indicates that PlsB activity also strongly influences flux into the synthesis pathway of lipopolysaccharide, the second-most abundant membrane component. In contrast to steady-state regulation, we find that responses to environmental perturbations are triggered directly via changes in acetyl-CoA concentrations, enabling rapid adaptation. Adaptations are further modulated by ppGpp, which regulates PlsB activity during slow growth and growth arrest. The strong reliance upon post-translational regulation for flux control ensures both robustness and responsiveness of membrane synthesis.
Wistar rats and C57BL/6 mice differ in their motivation to seek social interaction versus food in the Social versus Food Preference Test

Here we characterized the Social versus Food Preference Test, a behavioral paradigm designed to investigate the competition between the choice to seek social interaction versus the choice to seek food. We assessed how this competition was modulated by internal cues (social isolation, food deprivation), external cues (time-of-testing, stimulus salience), sex (males, females), age (adolescents, adults), and rodent model (Wistar rats, C57BL/6J mice). We found that changes in stimulus preference in response to the internal and external cue manipulations were similar across cohorts. Specifically, social over food preference scores were reduced by food deprivation and social familiarly in Wistar rats and C57BL/6J mice of both sexes. Interestingly, the degree of food deprivation-induced changes in stimulus investigation patterns were greater in adolescents compared to adults in Wistar rats and C57BL/6J mice. Strikingly, baseline stimulus preference and investigation times varied greatly between rodent models: across manipulations, Wistar rats were generally more social-preferring and C57BL/6J mice were generally more food-preferring. Adolescent Wistar rats spent more time investigating the social and food stimuli than adult Wistar rats, while adolescent and adult C57BL/6J mice investigated the stimuli a similar amount. Neither social isolation nor time-of-testing altered behavior in the Social versus Food Preference Test. Together, our results indicate that the Social versus Food Preference Test is a flexible behavioral paradigm suitable for future interrogations of the peripheral and central systems that can coordinate the expression of stimulus preference related to multiple motivated behaviors. HIGHLIGHTS Rats prefer social over food when sated, and this is attenuated by food deprivation. Mice have no preference when sated, and prefer food over social when food-deprived. Rats prefer a familiar social stimulus or a novel social stimulus over food. Mice prefer food over a familiar social stimulus. Adolescent rats investigate social and food stimuli longer than adult rats. GRAPHICAL ABSTRACT