Deterioration of brain capillary flow and architecture is a hallmark of aging and dementia. It remains unclear how loss of brain pericytes in these conditions contributes to capillary dysfunction. Here, we conduct cause-and-effect studies by optically ablating pericytes in adult and aged mice in vivo. Focal pericyte loss induces capillary dilation without blood-brain barrier disruption. These abnormal dilations are exacerbated in the aged brain, and result in increased flow heterogeneity in capillary networks. A subset of affected capillaries experience reduced perfusion due to flow steal. Some capillaries stall in flow and regress, leading to loss of capillary connectivity. Remodeling of neighboring pericytes restores endothelial coverage and vascular tone within days. Pericyte remodeling is slower in the aged brain, resulting in regions of persistent capillary dilation. These findings link pericyte loss to disruption of capillary flow and structure. They also identify pericyte remodeling as a therapeutic target to preserve capillary flow dynamics. | Make paid
A double -strand break (DSB) is one of the most deleterious forms of DNA damage. In eukaryotic cells, two main repair pathways have evolved to repair DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is the predominant pathway of repair in the unicellular eukaryotic organism, S. cerevisiae. However, during replicative aging the relative use of HR and NHEJ shifts in favor of end-joining repair. By monitoring repair events in the HO-DSB system, we find that early in replicative aging there is a decrease in the association of long-range resection factors, Dna2-Sgs1 and Exo1 at the break site and a decrease in DNA resection. Subsequently, as aging progressed, the recovery of Ku70 at DSBs decreased and the break site associated with the nuclear pore complex at the nuclear periphery, which is the location where DSB repair occurs through alternative pathways that are more mutagenic. End-bridging remained intact as HR and NHEJ declined, but eventually it too became disrupted in cells at advanced replicative age. In all, our work provides insight into the molecular changes in DSB repair pathway during replicative aging. HR first declined, resulting in a transient increase in the NHEJ. However, with increased cellular divisions, Ku70 recovery at DSBs and NHEJ subsequently declined. In wild type cells of advanced replicative age, there was a high frequency of repair products with genomic deletions and microhomologies at the break junction, events not observed in young cells which repaired primarily by HR. | Make paid
Calorie restriction (CR) promotes healthspan and extends the lifespan of diverse organisms, including mice, and there is intense interest in understanding the molecular mechanisms by which CR functions. Some studies have demonstrated that CR induces fibroblast growth factor 21 (FGF21), a hormone that regulates energy balance and that when overexpressed, promotes metabolic health and longevity in mice, but the role of FGF21 in the response to CR has not been fully investigated. We directly examined the role of FGF21 in the physiological and metabolic response to a CR diet by feeding Fgf21-/- and wild-type control mice either ad libitum (AL) diet or a 30% CR diet for 15 weeks. Here, we find that FGF21 is largely dispensable for CR-induced improvements in body composition and energy balance, but that lack of Fgf21 blunts CR-induced changes aspects of glucose regulation and insulin sensitivity in females. Surprisingly, despite not affecting CR-induced changes in energy expenditure, loss of Fgf21 significantly blunts CR-induced beiging of white adipose tissue in male but not female mice. Our results shed new light on the molecular mechanisms involved in the beneficial effects of a CR diet, clarify that FGF21 is largely dispensable for the metabolic effects of a CR diet, and highlight a sex-dependent role for FGF21 in the molecular adaptation of white adipose tissue to CR. | Make paid
Understanding microscale physiology and microstructural cellular features of the brain is key to understanding the mechanisms of neurodegenerative diseases and injury, as well as the prominent changes that neurons and glia in the brain undergo in development and aging which reflect functional state. Non-invasive imaging modalities sensitive to the microscale - especially diffusion magnetic resonance imaging (dMRI) - are extremely promising for three-dimensional mapping of cellular microstructure of brain tissues and brain connectivity via tractography; however, there is a need for robust validation techniques to verify and improve the biological accuracy of fiber orientation information derived from these techniques. Recent advances in dMRI acquisition and modeling have moved toward probing of the more complex grey matter architecture, challenging current validation techniques, which are largely based on ex vivo staining and microscopy and focused on white matter. Polarized light imaging (PLI) has been shown to be a successful technique for high resolution, direct, microstructural imaging and has been applied to dMRI validation with clear advantages over conventional staining and microscopy techniques. Conventionally, PLI is applied to thin, sectioned samples in transmission mode, but unlike histologic staining, PLI can be extended to operate with high sensitivity in reflectance mode and even extended to 3D imaging to bridge the gap toward in vivo validation of dMRI measurements of orientation features in both gray and white matter of the brain. In this report we investigate the use of backscattering Mueller Matrix polarimetry to characterize the microstructural content of intact Ferret brain specimens. The experimental results show that backscattering polarimetry can probe white matter fiber coherence and fiber orientation in whole brain specimens, and show promise for probing grey matter microstructure. Ultimately, these preliminary results motivate further study to fully understand how backscattering polarimetry can best be used for validation of in vivo microstructural imaging of the brain. | Make paid
Fibroblasts are spindle-shaped mesenchymal cells and an abundantly studied cell type that are easy to culture. Their adaptive response in culture conditions allows for use in many different cell biological experiments, including their utility in generating induced pluripotent stem cells. Despite extensive use of fibroblasts in cell and molecular biology and genetics experiments, fundamental evaluation of their resiliency and survival programs, in comparison with other cell types, is undetermined. Here, we demonstrate that fibroblasts exhibit remarkable survival capacity in post-mortem tissue decaying at room temperature and can be cultured from ear, tail tips, kidney, lung, fetal, and mammary tumor tissue after 12-hours of post-mortem tissue decay. Fibroblasts can be cultured from ear and lung tissue after 24-hours, and from ear after up to 120-hours of post-mortem tissue decay. Gene expression profiling of post-mortem lung tissue fibroblasts compared to fresh tissue cultured fibroblasts suggested a transition to a more quiescent phenotype with activation of nutrient scavenging pathways as evidenced by downregulation of genes associated with DNA replication, ribosomes, cell cycle, and spliceosomes as well as upregulation of genes associated metabolism, autophagy, and lysosomes. Measurement of light chain 3B (LC3B)-I/LC3B-II ratio and lysosomal-associated membrane protein (LAMP)-1 indicate that autophagy is increased in post-mortem fibroblasts, with evidence for potential increase in autolysosomes and senescence program. Our study provides evidence for the ability of normal fibroblasts to overcome extreme stress conditions and offers new insights into cell survival mechanisms and aging, with potential utility in tissue regeneration and repair. | Make paid
The Maillard reaction, a chemical reaction between amino acids and sugars, is exploited to produce flavorful food almost everywhere, from the baking industry to our everyday life. However, the Maillard reaction also takes place in all cells, from prokaryotes to eukaryotes, leading to the formation of Advanced Glycation End-products (AGEs). AGEs are a heterogeneous group of compounds resulting from the irreversible reaction between biomolecules and - dicarbonyls (-DCs), including methylglyoxal (MGO), an unavoidable byproduct of anaerobic glycolysis and lipid peroxidation. We previously demonstrated that Caenorhabditis elegans mutants lacking the glod-4 glyoxalase enzyme displayed enhanced accumulation of -DCs, reduced lifespan, increased neuronal damage, and touch hypersensitivity. Here, we demonstrate that glod-4 mutation increased food intake and identify that MGO-derived hydroimidazolone, MG-H1, is a mediator of the observed increase in food intake. RNA-seq analysis in glod-4 knockdown worms identified upregulation of several neurotransmitters and feeding genes. Suppressor screening of the overfeeding phenotype identified the tdc-1-tyramine-tyra-2/ser-2 signaling as an essential pathway mediating AGEs (MG-H1) induced feeding in glod-4 mutants. We also identified the elt-3 GATA transcription factor as an essential upstream factor for increased feeding upon accumulation of AGEs by partially regulating the expression of tdc-1 and tyra-2 genes. Further, the lack of either tdc-1 or tyra-2/ser-2 receptors suppresses the reduced lifespan and rescues neuronal damage observed in glod-4 mutants. Thus, in C. elegans, we identified an elt-3 regulated tyramine-dependent pathway mediating the toxic effects of MGO and associated AGEs. Understanding this signaling pathway is essential to modulate hedonistic overfeeding behavior observed in modern AGEs rich diets. | Make paid
The aging brain exhibits a decline in the regenerative populations of neural stem cells (NSCs), which may underlie age-associated defects in sensory and cognitive functions1-6. While mechanisms that restore old NSC function have started to be identified7-23, the role of lipids - especially complex lipids - in NSC aging remains largely unclear. Using lipidomic profiling by mass spectrometry, we identify age-related lipidomic signatures in young and old quiescent NSCs in vitro and in vivo. These analyses reveal drastic changes in several complex membrane lipid classes, including phospholipids and sphingolipids in old NSCs. Moreover, poly-unsaturated fatty acids (PUFAs) strikingly increase across complex lipid classes in quiescent NSCs during aging. Age-related changes in complex lipid levels and side chain composition are largely occurring in plasma membrane lipids, as revealed by lipidomic profiling of isolated plasma membrane vesicles. Experimentally, we find that aging is accompanied by modifications in plasma membrane biophysical properties, with a decrease in plasma membrane order in old quiescent NSCs in vitro and in vivo. To determine the functional role of plasma membrane lipids in aging NSCs, we performed genetic and supplementation studies. Knockout of Mboat2, which encodes a phospholipid acyltransferase, exacerbates age-related lipidomic changes in old quiescent NSCs and impedes their ability to activate. As Mboat2 expression declines with age, Mboat2 deficiency may drive NSC decline during aging. Interestingly, supplementation of plasma membrane lipids derived from young NSCs boosts the ability of old quiescent NSCs to activate. Our work could lead to lipid-based strategies for restoring the regenerative potential of NSCs in old individuals, which has important implications for countering brain decline during aging. | Make paid
Skin ageing has been widely associated with the formation and presence of increasing quantities of senescent cells, the presence of which are thought to reduce cell renewal. This study aimed to identify key factors influencing fibroblast and skin aging using RNA-seq data. Key differences in study designs included known sources of biological differences (sex, age, ethnicity), experimental differences, and environmental factors known to accelerate skin ageing (smoking, UV exposure) as well as study specific batch effects which complicated the analysis. To overcome these complications samples were stratified by these factors and differential expression assessed using Salmon and CuffDiff. Stratification of female fibroblast and skin samples combined with female specific normalisation of transcriptomic and methylation data sets increased functional enrichment and consistency across studies. The results identify the importance of considering environmental factors known to increase the rate of ageing (smoking status of donors, and UV-exposure status of skin and fibroblast samples) both independently and in combination for the identification of key ageing signatures. The results identified that in old (> 65) female skin decreases in the expression of transmembrane ion transporters coincide with increased methylation of oxidoreductases, and consequently reductions in respiration. This was further evidenced in old fibroblasts from smokers which identified reductions ion homeostasis, and the transcription of mitochondrial tRNAs, that were accompanied by reduced mitochondrial fission, reduced lipid catabolism and reduced immune signalling. These changes occurred in combination with reductions in cell proliferation, adhesion, ECM organisation, cell movement, cytoskeleton organisation and circulatory system development. Middle and old aged skin without environmental stratification's identified decreased expression of transmembrane ion transporters occurred alongside reductions in keratinisation, reduced mitochondrial fission, and this was associated with reduced metabolism (specifically carbohydrates), and consequently a reduction in the production of lipids (phospholipids for membranes and others) occured, exacerbating ion homeostasis issues at a keratinocyte level. Interestingly in skin the combined impacts of UV-exposure, smoking and ageing yielded different results, increased expression of calcium homeostasis genes, cell adhesion molecules (integrins), structural membrane constituents (loricrin, mucins, keratins and collagens), increased cornification, as well as structural cytoskeletal molecules (KRTAPs). This occurred alongside increased expression of genes involved in skin peeling (kalikriens), proliferation and differentiation, glycosylation, oxidative stress, autophagy, lactose metabolism, and lipid catabolism. Aged UV-exposed skin from smokers is on the whole more fibrous, with cells showing significant cell membrane and cytoskeletal structural changes, similar to those seen in skin cancers. Interestingly in non-UV-exposed skin from smokers most of these processes were reduced, and in within age group comparisons of smokers they were also reduced, suggesting that smoking reduced skin development and regeneration. Female specific analysis of smokers from different age groups enrichment results identified additional factors relating to tissue development, cell adhesion, vasculature development, peptide cross-linking, calcium homeostasis, cancer and senescence, leading to age related declines skin structure and function. Interestingly many diseases and infections with overlapping molecular consequences, (ER Calcium stress, reduced protein targeting to membranes) including human cytomegalovirus and herpes simplex virus are identified by the age only analysis, suggesting that viral infections and ageing have similar molecular consequences for cells. | Make paid
Sirt3, one of class III histone deacetylase, is mainly localized in mitochondria and plays a significant role in the control of the metabolic activity, senescence and death [1]. Recently, Sirt3 emerged as a novel member of anticancer. However, the role of Sirt3 in colorectal cancer (CRC) has never been explained exactly. In this study, we found that sirt3 is down-regulated after Bufalin treatment. We also found that AC-P53 is up-regulated which induces Bax translocation to mitochondrion and open the mitochondrial permeability transition (mPTP) pores result in the release of cytochrome C lead to the activation of caspase-dependent apoptosis pathway. Collectively, our data suggests that Sirt3 may play an important role in CRC development and progression and may be a promising therapeutic target for CRC. | Make paid
Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in the deep-sea hydrothermal vent and cold seep areas. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to the endemic environments. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, is remained to be investigated. Here we report a high-quality genome of R. piscesae collected at Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis revealed that that the high growth rates of vent-dwelling tubeworms might derive from small genome size. The small genome sizes of these tubeworms are attributed to the repeat content but not the number of genes and intron sizes. Additionally, four genes involved in cell proliferation were subject to positive selection in the genome of R. piscesae, suggesting that, besides apoptosis, cell proliferation is important for regulating growth rate in this species. | Make paid
Muller glia are a cellular source for neuronal regeneration in vertebrate retinas. However, the capacity for retinal regeneration varies widely across species. Understanding the mechanisms that regulate the reprogramming of Muller glia into progenitor cells is key to reversing the loss of vision that occurs with retinal diseases. In the mammalian retina, NFkB signaling promotes glial reactivity and represses the reprogramming of Muller glia into progenitor cells. Here we investigate different cytokines, growth factors, cell signaling pathways, and damage paradigms that influence NFkB-signaling in the mouse retina. We find that exogenous TNF and IL1b; potently activate NFkB-signaling in Muller glia in undamaged retinas, and this activation is independent of microglia. By comparison, TLR1/2 agonist indirectly activates NFkB-signaling in Muller glia, and this activation depends on the presence of microglia as Tlr2 is predominantly expressed by microglia, but not other types of retinal cells. Exogenous FGF2 did not activate NFkB-signaling, whereas CNTF, Osteopontin, WNT4, or inhibition of GSK3b; activated NFkB in Muller glia in the absence of neuronal damage. By comparison, dexamethasone, a glucocorticoid agonist, suppressed NFkB-signaling in Muller glia in damaged retinas, in addition to reducing numbers of dying cells and the accumulation of reactive microglia. Although NMDA-induced retinal damage activated NFkB in Muller glia, optic nerve crush had no effect on NFkB activation within the retina, whereas glial cells within the optic nerve were responsive. We conclude that the NFkB pathway is activated in retinal Muller glia in response to many different cell signaling pathways, and activation often depends on signals produced by reactive microglia. | Make paid
Cell senescence is a diverse phenotype and therapies often require combinatorial approaches. Here we have systematically collected transcriptomic data related to human fibroblasts to a total of 98 studies. We formed a database describing the relevant variables for each study which we have hosted online allowing users to filter the studies to select variables and genes of interest. Our own analysis of the database revealed 13 marker genes consistently downregulated in senescent cells compared to proliferating controls; however, we also found gene expression patterns that were highly specific and reliable for different senescence inducers, cell lines, and timepoint after induction, confirming several conclusions of existing studies based on single datasets, including differences in p53 and inflammatory signals between oncogene induced senescence (OIS) and DNA damage induced senescence (DDIS). We saw little evidence of an initial TGF-{beta}-centric SASP, but we did find evidence of a decrease in Notch signalling. Contrary to some early observations, both p16 and p21 mRNA levels appeared to rise quickly, depending on senescence type, and persist for at least 8-11 days. We concluded that while universal biomarkers of senescence are difficult to identify, the conventional senescence markers follow predictable profiles and construction of a framework for studying senescence could lead to more reproducible data. | Make paid
Global loss of DNA methylation in mammalian genomes occurs during aging and cancer, primarily in heterochromatin-associated Partially Methylated Domains (PMDs). It has previously been shown that local sequence context (100bp) has a strong influence on the rate of demethylation of individual CpG dinucleotides within PMDs. Here, we train a deep learning model to capture this sequence dependence, finding that methylation loss in healthy tissues and cancer can be predicted with high accuracy based on the 150bp surrounding a CpG. We use a published whole-genome map of the re-methylation rate of newly synthesized DNA during mitosis to show that CpGs with a "slow-loss" sequence context are efficiently re-methylated, while CpGs with a "fast-loss" sequence context are inefficiently re-methylated. Intriguingly, we find that the 10% most slow-loss CpGs lose almost no DNA methylation in healthy cell types, but lose significant DNA methylation in many cancer types. This finding suggests that loss of DNA methylation at slow-loss CpGs could underlie some cancer-specific transcriptional deregulation that has been linked to DNA hypomethylation, including the derepression of cancer antigens and transposable elements. | Make paid
Objective: To investigate the association of adherence to a healthy lifestyle with a panel of brain structural markers in middle-aged and older adults. Design: Cross-sectional and prospective study design. Setting: PolyvasculaR Evaluation for Cognitive Impairment and vaScular Events (PRECISE) study in China and UK Biobank (UKB). Participants: 2,413 participants in PRECISE and 19,822 participants in UKB. Exposures: A healthy lifestyle score (0-5) was constructed based on five modifiable lifestyle factors: healthy diet, physically active, non-current-smoking, non-alcohol consumption (in PRECISE)/moderate alcohol consumption (in UKB), and healthy body weight. Main Outcomes: Validated multimodal neuroimaging markers were derived from brain magnetic resonance imaging (MRI). Results : In the cross-sectional analysis of PRECISE, participants who adopted four or five low-risk lifestyle factors had larger total brain volume (TBV; {beta}= 0.12, 95%CI: -0.02, 0.26; p-trend = 0.048) and gray matter volume (GMV; {beta}= 0.16, 95%CI: 0.01, 0.30; p-trend = 0.047), smaller white matter hyperintensity volume (WMHV; {beta}= -0.35, 95%CI: -0.50, -0.20; p-trend <0.001) and lower odds of lacune (Odds Ratio [OR]=0.48, 95%CI: 0.22, 1.08; p-trend = 0.03), compared to those with zero or one low-risk factors. Meanwhile, in the prospective analysis in UKB (with a median of 7.7 years follow-up), similar associations were observed between the number of low-risk lifestyle factors (4-5 vs 0-1) and TBV ({beta}= 0.22, 95%CI: 0.16, 0.28; p-trend <0.001), GMV ({beta}= 0.26, 95%CI: 0.21, 0.32; p-trend < 0.001), white matter volume (WMV; {beta}= 0.08, 95%CI: 0.01, 0.15; p-trend = 0.001), hippocampus volume ({beta}= 0.15, 95%CI: 0.08, 0.22; p-trend = <0.001), and WMHV burden ({beta}= -0.23, 95%CI: -0.29, -0.17; p-trend < 0.001). Those with four or five low-risk lifestyle factors showed approximately 2.0-5.8 years of delay in aging of brain structure. Conclusion: Adherence to a healthier lifestyle was associated with a lower degree of neurodegeneration-related brain structural markers in middle-aged and older adults. | Make paid
Introduction: The ability to process sounds decreases with advancing age and the already high prevalence of people with hearing loss (HL) is estimated to increase further over the next decades. Hearing loss reduces speech identification which is important for day-to-day communication. In addition, it can lead to social isolation, depression, and lower quality of life. Current hearing rehabilitation strategies (eg, hearing aids) provide some benefits, but are not always accepted by hearing-impaired listeners and are less successful in real-life listening situations. Consequently, alternative rehabilitation strategies, such as the manipulation of cardiovascular (CV) health for the prevention and rehabilitation of HL, should be explored. Some research suggests that CV health and auditory functions are related, but the existence of such a link has not been systematically evaluated. This manuscript outlines the protocol for a systematic review of published research on the association between CV health and peripheral and central auditory functions across the adult lifespan and for all levels of hearing abilities. Method and analysis: The Preferred Reporting Items for Systematic reviews and Meta-Analyses Protocols (PRISMA-P) checklist will be followed. Studies included for analysis will be original peer-reviewed articles, measuring cardiovascular health and hearing abilities to explore their relationship. Participants will be aged [≥]18 years and will have various levels of hearing sensitivity and of CV health. Databases will be searched, using key words, to obtain evidence that meets the defined set of inclusion criteria. Data will be extracted and examined by two reviewers. Quality checks will occur, and, if appropriate, a meta-analysis will be performed. Data analysis will be completed and reported in a full systematic review, following the PRISMA guidelines. Ethics and dissemination: No ethical approval is needed for the systematic review as only published data will be analysed. Findings will be disseminated at conferences and in peer-reviewed journals. | Make paid
Understanding microscale physiology and microstructural cellular features of the brain is key to understanding the mechanisms of neurodegenerative diseases and injury, as well as the prominent changes that neurons and glia in the brain undergo in development and aging which reflect functional state. Non-invasive imaging modalities sensitive to the microscale - especially diffusion magnetic resonance imaging (dMRI) - are extremely promising for three-dimensional mapping of cellular microstructure of brain tissues and brain connectivity via tractography; however, there is a need for robust validation techniques to verify and improve the biological accuracy of fiber orientation information derived from these techniques. Recent advances in dMRI acquisition and modeling have moved toward probing of the more complex grey matter architecture, challenging current validation techniques, which are largely based on ex vivo staining and microscopy and focused on white matter. Polarized light imaging (PLI) has been shown to be a successful technique for high resolution, direct, microstructural imaging and has been applied to dMRI validation with clear advantages over conventional staining and microscopy techniques. Conventionally, PLI is applied to thin, sectioned samples in transmission mode, but unlike histologic staining, PLI can be extended to operate with high sensitivity in reflectance mode and even extended to 3D imaging to bridge the gap toward in vivo validation of dMRI measurements of orientation features in both gray and white matter of the brain. In this report we investigate the use of backscattering Mueller Matrix polarimetry to characterize the microstructural content of intact Ferret brain specimens. The experimental results show that backscattering polarimetry can probe white matter fiber coherence and fiber orientation in whole brain specimens, and show promise for probing grey matter microstructure. Ultimately, these preliminary results motivate further study to fully understand how backscattering polarimetry can best be used for validation of in vivo microstructural imaging of the brain. | Make paid
Infantile Neuroaxonal Dystrophy (INAD) is caused by recessive variants in PLA2G6 and is a lethal pediatric neurodegenerative disorder. Loss of the Drosophila homolog of PLA2G6, leads to ceramide accumulation, lysosome expansion, and mitochondrial defects. Here, we report that ceramide metabolism, the endolysosomal pathway, and mitochondrial morphology are affected in INAD patient-derived neurons. We show that in INAD mouse models the same features are affected and that glucosylceramides are elevated in dopaminergic neurons and Purkinje cells, arguing that the neuropathological mechanisms are evolutionary conserved and that ceramides can be used as biomarkers. We tested 20 drugs that target these pathways and found that Ambroxol, Desipramine, Azoramide, and Genistein alleviate neurodegenerative phenotypes in INAD flies and INAD patient-derived NPCs. We also develop an AAV-based gene therapy approach that delays neurodegeneration and prolongs lifespan in an INAD mouse model. | Make paid
Skin ageing has been widely associated with the formation and presence of increasing quantities of senescent cells, the presence of which are thought to reduce cell renewal. This study aimed to identify key factors influencing fibroblast and skin aging in European males using RNA-seq data. Key differences in study designs included known sources of biological differences (sex, age, ethnicity), experimental differences, and environmental factors known to accelerate skin ageing (smoking, UV exposure) as well as study specific batch effects which complicated the analysis. To overcome these complications samples were stratified by these factors and differential expression assessed using Salmon and CuffDiff. Functional enrichment and consistency across studies, stratification's and tools identified age related alterations in the transcriptomes of fibroblasts and skin. Functional enrichment of results identified alterations in protein targeting to membranes and the ER, and altered calcium homeostasis in aged fibroblasts. Extension to skin controlled for differences in fibroblast culturing methods confirming transient age related alterations in intracellular calcium homeostasis. In middle aged males (40-65) increased keratinisation, skin, epithelial and epidermal development was seen in conjunction with alterations to ER Calcium uptake, leading to the identification of related processes including; an unfolded protein response, altered metabolism, increased MMP expression, and altered Calcium handling, which were further exacerbated by UV-exposure. Interestingly the genes and processes subsequently decreased in old males (> 65), which exhibited signs of increased senescence. Extension to Illumina 450k array data from ageing skin uncovered evidence of epigenetic regulation; genes and isoforms with overlapping differentially methylated CpGs were differentially expressed. Smoking led to additional enrichment of genes relating to tissue development, cell adhesion, vasculature development, peptide cross-linking, calcium homeostasis, cancer and senescence. The results consistently identified alterations in ER and golgi Calcium uptake, which disrupt intracellular and extracellular calcium gradients that regulate metabolic and differentiation signalling in skin and fibroblasts, leading to age related declines skin structure and function. Interestingly many diseases and infections with overlapping molecular consequences, (ER Calcium stress, reduced protein targeting to membranes) including COVID-19 are identified by the analysis, suggesting that COVID-19 infection compounds pre-existing cellular stresses in aged males, which could help explain higher COVID-19 mortality rates in aged males, as well as highlighting potential ways to reduce them. | Make paid
Noisy galvanic vestibular stimulation has been shown to improve vestibular perception in healthy subjects. Here, we sought to obtain similar results using more natural stimuli consisting of small-amplitude motion perturbations of the whole body. Thirty participants were asked to report the perceived direction of antero-posterior sinusoidal motion on a MOOG platform. We compared the baseline perceptual thresholds with those obtained by applying small, stochastic perturbations at different power levels along the antero-posterior axis, symmetrically distributed around a zero-mean. At the population level, we found that the thresholds for all but the highest level of noise were significantly lower than the baseline threshold. At the individual level, the threshold was lower with at least one noise level than the threshold without noise in 87% of participants. Thus, small, stochastic oscillations of the whole body can increase the probability of detecting subthreshold vestibular signals, possibly due to stochastic resonance mechanisms. We suggest that, just as the external noise of the present experiments, also the spontaneous random oscillations of the body associated with standing posture are beneficial by enhancing vestibular thresholds with a mechanism similar to stochastic resonance. The results are also relevant from a clinical perspective, since they raise the possibility of improving motion perception in people with elevated thresholds due to aging or vestibulopathy by means of small-amplitude motion perturbations. | Make paid
The average human lifespan continues to increase with the increase in data flow and the advancement of related technological developments. However, this development brings with it many diseases, including immunological problems. Immunoglobulin varieties found in different organisms in the last 3-4 decades continue to be hope for many diseases. Interest has focused on the lesser weight but more mobile immunoglobulins found in camelids. Later, different types of these antibodies were tried to be made with biotechnological engineering and their effectiveness continues to be investigated. Disulfide bridges located on the immunoglobulin are one of the key points for the structure and function of the immunoglobulin. The interest of potassium hydroxide in disulfide bridges may enable us to damage or break these bonds. For this purpose, in this study, the relationship between disulfide bridges between light and heavy chains and potassium hydroxide was investigated. It was observed that the affinity of potassium hydroxide to disulfide bridges occurred exergonically. In the light of this information, it can be thought that lighter, more functional immunoglobulin fragments and nanobodies can be formed with potassium hydroxide compared to conventional immunoglobulin. | Make paid
The public-domain International Tree-Ring Data Bank (ITRDB) is an under-utilized dataset to improve existing estimates of global tree longevity. Since dendrochronologists have usually targeted the oldest trees in a stand, this public-domain resource is bound to offer better estimates of maximum tree age than those available from randomized plots or grid-based forest inventories. We used the longest continuous ring-width series of existing ITRDB collections as an index of maximum tree age for that species and site. Using a total of 3679 collections, we obtained longevity estimates for 236 unique tree species, 156 conifers and 80 angiosperms, distributed all over the world. More than half of the species (167) were represented by no more than 10 collections, and a similar number of species (144) reached longevity greater than 300 years. Maximum tree ages exceeded 1000 years for several species (22), all of them conifers, while angiosperm longevity peaked around 500 years. As new collections are constantly being added to the ITRDB, estimates of tree longevity may change slightly, mainly by adding new species to the database. Given the current emphasis on identifying human-induced impacts on global systems, detailed analyses of ITRDB holdings provide one of the most reliable sources of information for tree longevity as an ecological trait. | Make paid
Diverse mouse strains have different health and life spans, mimicking the diversity among humans. To capture conserved aging signatures, we studied long-lived C57BL/6J and short-lived NZO/HILtJ mouse strains by profiling transcriptomes and epigenomes of immune cells from peripheral blood and the spleen from young and old mice. Transcriptional activation of the AP-1 transcription factor complex, particularly Fos, Junb, and Jun genes, was the most significant and conserved aging signature across tissues and strains. ATAC-seq data analyses showed that the chromatin around these genes was more accessible with age and there were significantly more binding sites for these TFs with age across all studied tissues, targeting pro-inflammatory molecules including Il6. Age-related increases in binding sites of Jun/Fos factors were also conserved in human peripheral blood ATAC-seq data. Single-cell RNA-seq data from the mouse aging cell atlas Tabula Muris Senis showed that the expression of these genes increased with age in B, T, NK cells, and macrophages, with macrophages from old mice expressing these molecules more abundantly than other cells. Functional data showed that upon myeloid cell activation via poly(I:C), the levels of c-JUN protein and its binding activity increased more significantly in spleen cells from old mice compared to cells from young mice. In addition, upon activation, old cells produced more IL6 compared to young cells. In sum, we showed that the aging-related transcriptional activation of Jun/Fos members of the AP-1 complex is conserved across immune tissues and long- and short-living mouse strains, possibly contributing to increased inflammation with age. | Make paid
The establishment of aging clocks based on DNA methylation highlighted the strong link between epigenetic alterations and aging. However, the connection between DNA methylation changes at clock sites and their effect on cellular function remains unclear. We hypothesize that chromatin accessibility, a readout that integrates many epigenetic mechanisms, may connect epigenetic changes with their downstream effects. Here we generated chromatin accessibility profiles from peripheral blood mononuclear cells of 157 human donors and used them to construct a novel aging clock with a median absolute error on prediction of 5.69 years. Moreover, by comparing our chromatin accessibility data to matched transcriptomic profiles, we show that the genomic sites relevant for chromatin accessibility-based age predictions also undergo transcriptional changes during aging and that chromatin accessibility predicts age better than gene expression. This chromatin accessibility clock could therefore be used to investigate the direct effect of aged epigenetic states on cellular function. | Make paid
During a critical period of postnatal life, monocular deprivation (MD) of kittens by eyelid closure reduces the size of neurons in layers of the dorsal lateral geniculate nucleus (dLGN) connected to the deprived eye, and shifts cortical ocular dominance in favor of the non-deprived eye, modeling deprivation amblyopia in humans. Following long-term MD, temporary retinal inactivation of the non-deprived eye with microinjection of tetrodotoxin can promote superior recovery from MD, and at older ages, in comparison to conventional occlusion therapy. This suggests that monocular inactivation (MI) is a more potent approach to producing neural plasticity than occlusion. In the current study we assessed the modification of neuron size in the dLGN as a means of measuring the impact of a brief period of MI imposed at different ages during postnatal development. The biggest impact of inactivation was observed when it occurred at the peak of the critical period for ocular dominance plasticity. The effect of MI was evident in both the binocular and monocular segments of the dLGN, distinguishing it from MD that produces changes only within the binocular segment. With increasing age, the capacity for inactivation to alter postsynaptic cell size diminished but was still significant beyond the classic critical period. In comparison to MD, inactivation consistently produced effects that were about double in magnitude, and inactivation exhibited efficacy to produce neural modifications at older ages than MD. Notwithstanding the large neural alterations precipitated by inactivation, its anatomical effects were remediated with a short period of binocular visual experience, and vision through the previously inactivated eye fully recovered after washout of TTX. Our results demonstrate that MI is a potent means of modifying the visual pathway, and does so beyond the age at which occlusion is effective. The magnitude and longevity of inactivation to evoke neural modification highlights its potential to ameliorate disorders of the visual system such as amblyopia. | Make paid
Flexible neural electrodes improve the recording longevity and quality of individual neurons by promoting tissue-electrode integration. However, the intracortical implantation of flexible electrodes inevitably induces tissue damage. Understanding the longitudinal neural and vascular recovery following the intracortical implantation is critical for the ever-growing applications of flexible electrodes in both healthy and disordered brains. Aged animals are of particular interest because they play a key role in modeling neurological disorders, but their tissue-electrode interface remains mostly unstudied. Here we integrate in-vivo two-photon imaging and electrophysiological recording to determine the time-dependent neural and vascular dynamics after the implantation of ultraflexible neural electrodes in aged mice. We find heightened angiogenesis and vascular remodeling in the first two weeks after implantation, which coincides with the rapid increase in local field potentials and unit activities detected by electrophysiological recordings. Vascular remodeling in shallow cortical layers preceded that in deeper layers, which often lasted longer than the recovery of neural signals. By six weeks post-implantation vascular abnormalities had subsided, resulting in normal vasculature and microcirculation. Putative cell classification based on firing pattern and waveform shows similar recovery time courses in fast-spiking interneurons and pyramidal neurons. These results elucidate how structural damages and remodeling near implants affecting recording efficacy, and support the application of ultraflexible electrodes in aged animals at minimal perturbations to endogenous neurophysiology. | Make paid
The amyloid-tau-neurodegeneration (ATN) framework has led to an increased focus on Alzheimers disease (AD) biomarkers. The cost and invasiveness of obtaining biomarkers via cerebrospinal fluid has motivated efforts to develop sensitive blood-based biomarkers. Although AD is highly heritable, the biometric genetic and environmental etiology of blood-based biomarkers has never been explored. We therefore, analyzed plasma beta-amyloid (A{beta}40, A{beta}42, A{beta}42/40), total tau (t-tau), and neurofilament light (NFL) biomarkers in a sample of 1,050 men aged 60 to 73 years (m=68.2, SD=2.5) from the Vietnam Era Twin Study of Aging (VETSA). Unlike A{beta} and tau, NFL does not define AD; however, as a biomarker of neurodegeneration it serves as the N component in the ATN framework. Univariate estimates suggest that familial aggregation in A{beta}42, A{beta}42/40, t-tau, and NFL is entirely explained by additive genetic influences accounting for 40%-58% of the total variance. All remaining variance is associated with unshared or unique environmental influences. For A{beta}40, a additive genetic (31%), shared environmental (44%), and unshared environmental (25%) influences contribute to the total variance. In the more powerful multivariate analysis of A{beta}42, A{beta}40, t-tau, and NFL, heritability estimates range from 32% to 58%. A{beta}40 and A{beta}42 are statistically genetically identical (rg = 1.00, 95%CI = 0.92,1.00) and are also moderately environmentally correlated (re = 0.66, 95%CI = 0.59, 0.73). All other genetic and environmental associations were non-significant or small. Our results suggest that plasma biomarkers are heritable and that A{beta}40 and A{beta}42 share the same genetic influences, whereas the genetic influences on plasma t-tau and NFL are mostly unique and uncorrelated with plasma A{beta} in early old-age men. | Make paid
Trained immunity is the long-term functional reprogramming of innate immune cells following exposure to various insults that results in altered responses towards a secondary challenge. Indoxyl sulfate (IS) is a potent uremic stimulus associated with inflammation in chronic kidney disease (CKD). However, the impact of IS on trained immunity remains unknown. Here, we find that IS induces trained immunity in monocytes via epigenetic and metabolic reprogramming, resulting in augmented cytokine production upon LPS-stimulation. Further, the aryl hydrocarbon receptor contributes to IS-trained immunity by enhancing expression of arachidonic acid metabolism-related genes ALOX5 and ALOX5AP. Monocytes from end-stage renal disease (ESRD) patients have increased ALOX5 expression and healthy monocytes trained with uremic sera from ESRD patients exhibit increased TNF- and IL-6 production. Moreover, IS-trained mice have augmented TNF- production following LPS-stimulation. These results provide insight into the role of IS in trained immunity, which is critical during inflammatory responses in CKD patients. | Make paid
A nonlinear partial differential equation (PDE) based compartmental model of COVID-19 provides a continuous trace of infection over space and time. Finer resolutions in the spatial discretization, the inclusion of additional model compartments and model stratifications based on clinically relevant categories contribute to an increase in the number of unknowns to the order of millions. We adopt a parallel scalable solver allowing faster solutions for these high fidelity models. The solver combines domain decomposition and algebraic multigrid preconditioners at multiple levels to achieve the desired strong and weak scalability. As a numerical illustration of this general methodology, a five-compartment susceptible-exposed-infected-recovered-deceased (SEIRD) model of COVID-19 is used to demonstrate the scalability and effectiveness of the proposed solver for a large geographical domain (Southern Ontario). It is possible to predict the infections up to three months for a system size of 92 million (using 1780 processes) within 7 hours saving months of computational effort needed for the conventional solvers. | Make paid
Serology testing can identify past infection by quantifying the immune response of an infected individual providing important public health guidance. Individual immune responses are time-dependent, which is reflected in antibody measurements. Moreover, the probability of obtaining a particular measurement changes due to prevalence as the disease progresses. Taking into account these personal and population-level effects, we develop a mathematical model that suggests a natural adaptive scheme for estimating prevalence as a function of time. We then combine the estimated prevalence with optimal decision theory to develop a time-dependent probabilistic classification scheme that minimizes error. We validate this analysis by using a combination of real-world and synthetic SARS-CoV-2 data and discuss the type of longitudinal studies needed to execute this scheme in real-world settings. | Make paid
Globally, the number of obese patients has doubled due to sedentary lifestyles and improper dieting. The tremendous increase altered human genetics, and health. According to the world health organization, Life expectancy dropped from 80 to 75 years, as obese people struggle with different chronic diseases. This report will address the problems of obesity in children and adults using ML datasets to feature, predict, and analyze the causes of obesity. By engaging neural ML networks, we will explore neural control using diffusion tensor imaging to consider body fats, BMI, waist \& hip ratio circumference of obese patients. To predict the present and future causes of obesity with ML, we will discuss ML techniques like decision trees, SVM, RF, GBM, LASSO, BN, and ANN and use datasets implement the stated algorithms. Different theoretical literature from experts ML \& Bioinformatics experiments will be outlined in this report while making recommendations on how to advance ML for predicting obesity and other chronic diseases. | Make paid