title: Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes

abstract: Psoriasis is characterized by chronic inflammation, perpetuated by a Th17-dependent signaling loop between the immune system and keratinocytes that could involve phospholipase A2 (PLA2)-dependent eicosanoid release. A prior knowledge network supported by experimental observations was used to encode the regulatory network of psoriatic keratinocytes in a computational model for studying the mode of action of a cytosolic (c) PLA2 inhibitor. A combination of evidence derived from the computational model and experimental data suggests that Th17 cytokines stimulate pro-inflammatory cytokine expression in psoriatic keratinocytes via activation of cPLA2-PGE2-EP4 signaling, which could be suppressed using the anti-psoriatic calcipotriol. cPLA2 inhibition and calcipotriol showed overlapping and distinct modes of action. Model analyses revealed the immunomodulatory role of Th1 cytokines, the modulation of the physiological states of keratinocytes by Th17 cytokines, and how Th1 and Th17 cells together promote the development of psoriasis. Model simulations additionally suggest novel drug targets, including EP4 and PRKACA, for treatment that may restore a normal phenotype. Our work illustrates how the study of complex diseases can benefit from an integrated systems approach.

category: systems biology


title: Models of increased latent HIV reservoir turnover prior to cART initiation imply novel clearance strategies

abstract: CD4+ T cells with a naive or memory phenotype carrying a replication-competent HIV provirus are recognized as the major component of the persistent HIV reservoir. These cells only minimally express viral protein, reducing viral cytotoxicity effects and making them difficult targets for immune responses as well as every available antiretroviral drug. In patients on suppressive antiretroviral therapy, the half-life of these cells is approximately 4-5 years, balanced by clonal expansion of the cells resulting in an overall reservoir half-life in excess of 40 years. A recent study has shown that prior to the initiation of antiretroviral therapy, the half-life of these cells is instead on the order of two weeks. We present two models explaining the wide disparity in the on- and off-treatment half-lives of the quiescent infected T cells. In the first model, generalized (antigen non-specific) immune activation due to the high HIV viral loads explains the high latent reservoir turnover rates in the absence of treatment. If this mechanism dominates, we demonstrate that reduction of the latent reservoir size is possible, either through the administration of exogenous antigen or through the use of timed treatment interruptions. In the second model, direct killing of reservoir cells by HIV drives the increased turnover off-treatment. If this mechanism dominates, modulation of the reservoir size is not possible by the methods described above. Previously published models of the immune response to HIV show the possibility of inducing post-treatment control by reducing the latent reservoir size; by incorporating the same immune response dynamics in our first model, it is shown that it may be possible to induce post-treatment control using either exogenous antigen administration or timed treatment interruptions.


title: Lying in a 3T MRI Scanner Induces Neglect-Like Spatial Attention Bias

abstract: The static magnetic field of MRI scanners can induce a magneto-hydrodynamic stimulation of the vestibular organ (MVS). In common fMRI settings, this MVS effect leads to a vestibular ocular reflex (VOR). We asked whether - beyond inducing a VOR - putting a healthy subject in a 3T MRI scanner would also alter goal-directed spatial behavior, as is known from other types of vestibular stimulation. We investigated 17 healthy volunteers, all of which exhibited a rightward VOR inside the MRI-scanner as compared to outside-MRI conditions. More importantly, when probing the distribution of overt spatial attention inside the MRI using a visual search task, subjects scanned a region of space that was significantly shifted towards the right. An additional estimate of subjective straight-ahead orientation likewise exhibited an MVC-induced rightward shift. Hence, putting a subject in a 3T MRI-scanner induces a bias of spatial attention, which closely mimics that of stroke patients with spatial neglect.

category: neuroscience


title: A severe form of maternal separation in rat consisting of nineteen-day 6-hour daily separation at unpredictable times minimally affects behavior across lifespan and possibly confers protection against some maladaptive outcomes

abstract:
Maternal separation (MS), a type of early life stress, has been associated with adverse socioemotional and behavioral outcomes throughout the lifespan across multiple species. Comprehensive longitudinal biobehavioral characterization of MS in rats is sparse and conflicting, warranting more studies. We conducted an MS paradigm involving 6-hour daily separation at unpredictable start times from P2 to P21. We hypothesized this severe form of MS would lead to developmentally emerging maladaptive biobehavioral consequences from juvenile through adult periods compared to Controls (C), especially in social behaviors. We tested: (1) own dam odor preference shortly after weaning; (2) juvenile and adult anxiety-like, sociability, and play behaviors using the light-dark test, three-chambered social interaction test, and video-coded juvenile play behavior; and (3) adult coping behaviors and neuroendocrine response using the forced swim test and blood corticosterone responses. Our results show minimal effects on biobehavioral outcomes across the lifespan. Recently weaned MS male rats had a stronger preference for their dams odor. Juvenile MS females spent more time in rough-and-tumble play than C female rats. No differences in sociability were found in the juvenile or adult periods. MS promoted a decrease in anxiety-like behavior that persisted from juvenile to adult periods. Finally, MS led to deficits in coping behavior in male adults, but basal and reactive corticosterone levels were unaltered by MS. More studies are needed to validate our surprising findings and probe the neural mechanisms underlying some of the observed protective effects.

Significance StatementMaternal separation (MS), a type of early life stress, has been shown to lead to short and long-term adverse socioemotional consequences in humans and biobehavioral outcomes in rodents. Available data on MS exposed rats are sparse, conflicting, and often lack longitudinal outcomes. We designed a 6-hour unpredictable daily MS paradigm from postnatal day (P2) to P21 to severely disrupt normal dam-pup interactions. Our results show MS leads to increased preference for own dam odor, persisting reductions in anxiety-like behaviors from juvenile to adulthood, and no effects on sociability. Adverse effects on coping behaviors were uniquely identified in males. The present study warrants reevaluation of the central dogma that MS leads to maladaptive biobehavioral outcomes.


title: A severe form of maternal separation in rat consisting of nineteen-day 6-hour daily separation at unpredictable times minimally affects behavior across the lifespan


title: Immunoelectron microscopic characterization of vasopressin neurons in macaques by use of formaldehyde-fixed tissues stored for several years

abstract: Translational research often requires the testing of experimental therapies in primates, but research in non-human primates is now stringently controlled by law around the world. Tissues fixed in formaldehyde without glutaraldehyde have been thought to be inappropriate for use in electron microscopic analysis, particularly those of the brain. Here we report the immunoelectron microscopic characterization of arginine vasopressin (AVP)-producing neurons in macaque hypothalamo-pituitary axis tissues fixed with 4% formaldehyde and stored at -25{degrees}C for several years. The size difference of dense-cored vesicles between magnocellular and parvocellular AVP neurons was detectable in their cell bodies and perivascular nerve endings located, respectively, in the posterior pituitary and median eminence. Furthermore, glutamate and the vesicular glutamate transporter 2 were colocalized with AVP in perivascular nerve endings of both the posterior pituitary and the external layer of the median eminence, suggesting that both magnocellular and parvocellular AVP neurons are glutamatergic in primates. Both ultrastructure and immunoreactivity can therefore be sufficiently preserved in macaque brain tissues stored long-term for light microscopy. Taken together, these results suggest that this methodology could be applied to the human post-mortem brain and be very useful in translational research.


title: Microglial CX3CR1I249/M280 variant limits neurogenesis and remyelination in cuprizone-induced multiple sclerosis model

abstract: Microglia have been implicated in multiple sclerosis (MS) pathogenesis. The fractalkine receptor CX3CR1 regulates the activation of pathogenic microglia in models of MS and the human polymorphic CX3CR1I249/M280 (hCX3CR1I249/M280) variant increases MS disease progression. However, the role of hCX3CR1I249/M280 on microglial activation and central nervous system repair and regenerative mechanisms remain unknown. Therefore, using transgenic mice expressing the hCX3CR1I249/M280 variant, we aimed to determine the contribution of defective CX3CR1 signaling to remyelination and neurogenesis in the cuprizone model of focal demyelination. Here, we report that mice expressing hCX3CR1I249/M280 exhibit marked demyelination and microgliosis follow acute cuprizone treatment. Cuprizone-treated CX3CR1-deficient and fractalkine-deficient mice displayed a comparable phenotype. Nanostring gene expression analysis in demyelinated lesions showed that hCX3CR1I249/M280 upregulates genes associated with inflammation, oxidative stress and disease-associated microglia. In addition, gene expression analysis in the subgranular zone (SGZ) of the hippocampus in hCX3CR1I249/M280 mice was associated with a significant downregulation of gene networks linked to neurogenesis following acute demyelination. Confocal microscopy showed that hCX3CR1I249/M280 or loss of CX3CR1 signaling inhibits the generation of progeny from the neurogenic niche, including cells involved in myelin repair. These results provide evidence for the pathogenic capacity of hCX3CR1I249/M280 on microglia dysfunction and therapeutic targeting of CX3CR1 to promote CNS repair in MS.


title: Cardiac sympathovagal activity initiates a functional brain-body response to emotional processing

abstract:
A century-long debate on bodily states and emotions persists. While the involvement of bodily activity in emotion physiology is widely recognized, the specificity and causal role of such activity related to brain dynamics has not yet been demonstrated. We hypothesize that the peripheral neural monitoring and control of cardiovascular activity prompts and sustains brain dynamics during an emotional experience, so these afferent inputs are processed by the brain by triggering a concurrent efferent information transfer to the body. To this end, we investigated the functional brain-heart interplay under emotion elicitation in publicly available data from 62 healthy participants using a computational model based on synthetic data generation of EEG and ECG signals. Our findings show that sympathovagal activity plays a leading and causal role in initiating the emotional response, in which ascending modulations from vagal activity precede neural dynamics and correlate to the reported level of arousal. The subsequent dynamic interplay observed between the central and autonomic nervous systems sustains emotional processing. These findings should be particularly revealing for the psychophysiology and neuroscience of emotions.

SignificanceWe investigate the temporal dynamics of brain and cardiac activities in healthy subjects who underwent an emotional elicitation through videos. We demonstrate that, within the first few seconds, emotional stimuli modulate the heart activity, which in turn stimulate an emotion-specific cortical response in the brain. Then, the conscious emotional experience is sustained by a bidirectional brain-heart interplay and information exchange. Moreover, the perceived intensity of an emotional stimulus is predicted by the intensity of neural control regulating the heart activity. These findings may constitute the fundamental knowledge linking neurophysiology and psychiatric disorders, including the link between depressive symptoms and cardiovascular disorders.


title: NOCICEPTRA: Gene and microRNA signatures and their trajectories characterizing human iPSC-derived nociceptor maturation

abstract: Nociceptors are primary afferent neurons serving the reception of acute pain but also the transit into maladaptive pain disorders. Since native human nociceptors are hardly available for mechanistic functional research, and rodent models do not necessarily mirror human pathologies in all aspects, human iPSC-derived nociceptors (iDN) offer superior advantages as a human model system. Unbiased mRNA::microRNA co-sequencing, immunofluorescence staining and qPCR validations, revealed expression trajectories as well as miRNA target spaces throughout the transition of pluripotent cells into iDNs. mRNA and miRNA candidates emerged as regulatory hubs for neurite outgrowth, synapse development and ion channel expression. The exploratory data analysis tool NOCICEPTRA is provided as a containerized platform to retrieve experimentally determined expression trajectories, and to query custom gene sets for pathway and disease enrichments. Querying NOCICEPTRA for marker genes of cortical neurogenesis revealed distinct similarities and differences for cortical and peripheral neurons. The platform provides a public domain neuroresource to exploit the entire data sets and explore miRNA and mRNA as hubs regulating human nociceptor differentiation and function.


title: Cross-reactive TCR with alloreactivity for immunodominant HIV-1 epitope Gag TL9 with enhanced control of viral infection

abstract: Although both HLA B*81:01 and HLA B*42:01 are members of the B7 supertype and can present many of the same HIV-1 epitopes, the identification of a dual-reactive T-cell phenotype was unexpected, since structural data suggested that TL9 peptide binds to each allele in a distinct conformation. How the dual-reactive TCR recognizes these radically distinct p-MHC surfaces is revealed by our structural study, that the introduction of TCR T18A induces a molecular switch of the TL9 peptide in B4201 to approach its conformation in B8101. Most importantly, unique docking of CDR3{beta} towards MHC but not peptide ligand strengthens the peptide tolerance of T18A, extends the ability of TCR to adapt mutations. Moreover, the high affinity of dual-reactive TCR for WT and escape mutant TL9 highlights the functional advantage of the alloreactive phenotype.

category: immunology


title: Mutualistic interactions between B. subtilis and seeds dictate plant development

abstract: A tightly coordinated developmental program controls precise genetic and metabolic reprogramming that dictates efficient transition of the seeds from dormancy to metabolically active seedlings. Beneficial microbes are known to stimulate the germination of the seeds or adaptation of the seedlings; however, investigations of exact mechanisms mediating these interactions and the resulting physiological responses of the plants are only beginning. Bacillus subtilis is commonly detected in the plant holobiont and belongs to the group of microbes that provide multifaceted contribution to the health of the plants. The present study demonstrated that B. subtilis triggered genetic and physiological responses in the seeds that determined subsequent metabolic and developmental status of adult plants. Chemically diverse extracellular matrix of Bacillus was demonstrated to structurally cooperate in bacterial colonization of the seed storage tissues. Additionally, an amyloid protein and fengycin, which are two components of the extracellular matrix, targeted the oil bodies of the seed endosperm, provoking changes in lipid metabolism or accumulation of glutathione-related molecules that stimulated two different plant growth programs: the development of seed radicles or overgrowth and immunization of adult plants. We propose this mutualistic interaction is conserved in Bacilli and plant seeds containing storage oil bodies.

category: microbiology


title: 5-methylcytosine modification by Plasmodium NSUN2 stabilizes mRNA and mediates the development of gametocytes

abstract:
5-methylcytosine (m5C) is an important epitranscriptomic modification involved in mRNA stability and translation efficiency in various biological processes. However, it remains unclear if m5C modification contributes to the dynamic regulation of the transcriptome during the developmental cycles of Plasmodium parasites. Here, we characterize the landscape of m5C mRNA modifications at single nucleotide resolution in the asexual replication stages and gametocyte sexual stages of rodent (P. yoelii) and human (P. falciparum) malaria parasites. While different representations of m5C-modified mRNAs are associated with the different stages, the abundance of the m5C marker is strikingly enhanced in the transcriptomes of gametocytes. Our results show that m5C modifications confer stability to the Plasmodium transcripts and that a Plasmodium ortholog of NSUN2 is a major mRNA m5C methyltransferase in malaria parasites. Upon knock-out of P. yoelii nsun2 (pynsun2), marked reductions of m5C modification were observed in a panel of gametocytogenesis-associated transcripts. These reductions correlated with impaired gametocyte production in rodent and human malaria parasites. Restoration of the nsun2 gene in the knock-out parasites rescued the gametocyte production phenotype as well as m5C modification of the gametocytogenesis-associated transcripts. Together with the mRNA m5C profiles for two species of Plasmodium, our findings demonstrate a major role for NSUN2-mediated m5C modifications in mRNA transcript stability and sexual differentiation in malaria parasites.

SignificanceModifications of RNA including methylations of cytosine (m5C) and adenosine (m6A) have important roles in RNA metabolism, cellular responses to stress, and biological processes of differentiation and development. Here, we report on the profiles of m5C mRNA modifications in malaria parasites that infect rodents (Plasmodium yoelii) and humans (Plasmodium falciparum). These parasites have genes that encode homologs of human and plant NSUN2 methyltransferases (m5C "writers"). We show that one of these homologs, termed PyNSUN2, stabilizes mRNA transcripts in P. yoelii and mediates m5C-associated development of the parasite sexual stages (gametocytes). Further research on m5C and other epitranscriptomic modifications may yield new insights into molecular pathways of gametocyte development and mosquito infectivity that can be exploited to interrupt malaria transmission.


title: RNA polymerases from Low G+C Gram Positive Bacteria

abstract: The low G+C Gram positive bacteria represent some of the most medically and industrially important microorganisms. They are relied on for the production of food and dietary supplements, enzymes and antibiotics, as well as being responsible for the majority of nosocomial infections and serving as a reservoir for antibiotic resistance. Control of gene expression in this group is more highly studied than in any bacteria other than the Gram negative model Escherichia coli, yet until recently no structural information on RNA polymerase (RNAP) from this group was available. This review will summarise recent reports on the high resolution structure of RNAP from the model low G+C representative Bacillus subtilis, including the role of auxiliary subunits {delta} and {varepsilon}, and outline approaches for the development of antimicrobials to target RNAP from this group.

category: molecular biology


title: Insulin is expressed by enteroendocrine cells during human fetal development

abstract: Generation of beta cells via transdifferentiation of other cell types is a promising avenue for the treatment of diabetes. Here, we reconstruct a single cell atlas of enteroendocrine cells in the human fetal and neonatal small intestine. We identify a subset of fetal enteroendocrine K/L cells that express high levels of insulin and other beta cell genes. Our findings highlight a potential extra-pancreatic source of beta cells and exposes its molecular blueprint.

category: developmental biology


title: Resource-efficient pooled sequencing expands translational impact in solid tumors

abstract: Intratumoral genetic heterogeneity (ITH) poses a significant challenge to utilizing sequencing for decision making in the management of cancer. Although sequencing of multiple tumor regions can address the pitfalls of ITH, it does so at a significant increase in cost and resource utilization. We propose a pooled multiregional sequencing strategy, whereby DNA aliquots from multiple tumor regions are mixed prior to sequencing, as a cost-effective strategy to boost translational value by addressing ITH while preserving valuable residual tissue for secondary analysis. Focusing on kidney cancer, we demonstrate that DNA pooling from as few as two regions significantly increases mutation detection while reducing clonality misattribution. This leads to an increased fraction of patients identified with therapeutically actionable mutations, improved patient risk stratification, and improved inference of evolutionary trajectories with an accuracy comparable to bona fide multiregional sequencing. The same approach applied to non-small-cell lung cancer data substantially improves tumor mutational burden (TMB) detection. Our findings demonstrate that pooled DNA sequencing strategies are a cost-effective alternative to address intrinsic genetic heterogeneity in clinical settings.

category: genomics


title: Baby-brain phenomena is a subjective experience: absence of evidence for cognitive deficit in new mothers at one-year postpartum.

abstract: The experience and even existence of so-called "baby-brain" in the postpartum period is uncertain, with only a few scientific studies that have reported inconsistent results. Here we investigate cognition in 86 women (43 first-time mothers one year postpartum, and 43 non-mothers). Mothers and non-mothers showed no significant differences on measures of objective cognition (verbal memory, short-term memory, working memory, processing speed or theory of mind). Despite the absence of objective differences, mothers self-reported significantly worse subjective memory than non-mothers. To interpret the difference between objective and subjective measures of memory, we investigated relationships between subjective memory, objective memory, and wellbeing. Mothers, but not non-mothers, showed a positive correlation between subjective and objective measures of memory, indicating mothers are more  in-tune with their memory performance than non-mothers. Mothers also demonstrated a positive relationship between subjective memory and wellbeing (sleep, anxiety and depression), where better wellbeing correlated with higher subjective memory. This relationship was not apparent in non-mothers. The results suggest that poorer sleep, higher anxiety and higher depression are related to reports of poorer subjective memory in mothers. Our results refute the phenomena of "baby-brain" deficits at one year postpartum, with no evidence of cognitive differences between mothers and non-mothers.

category: animal behavior and cognition


title: Linking Parasitism to Network Centrality and the Impact of Sampling Bias in its Interpretation

abstract: Group living is beneficial for individuals, but also comes with costs. One such cost is the increased possibility of pathogen transmission because increased numbers or frequencies of social contacts are often associated with increased parasite abundance or diversity. The social structure of a group or population is paramount to patterns of infection and transmission. Yet, for various reasons, studies investigating the links between sociality and parasitism in animals, especially in primates, have only accounted for parts of the group (e.g., only adults), which is likely to impact the interpretation of results. Here, we investigated the relationship between social network centrality and an estimate of gastrointestinal helminth infection intensity in a whole group of Japanese macaques (Macaca fuscata). We then tested the impact of omitting parts of the group on this relationship. We aimed to test: (1) whether social network centrality - in terms of the number of partners (degree), frequency of interactions (strength), and level of social integration (eigenvector) - was linked to parasite infection intensity (estimated by eggs per gram of faeces, EPG); and, (2) to what extent excluding portions of individuals within the group might influence the observed relationship. We conducted social network analysis on data collected from one group of Japanese macaques over three months on Koshima Island, Japan. We then ran a series of knock-out simulations. General linear mixed models showed that, at the whole-group level, network centrality was positively associated with geohelminth infection intensity. However, in partial networks with only adult females, only juveniles, or random subsets of the group, the strength of this relationship - albeit still generally positive - lost statistical significance. Furthermore, knock-out simulations where individuals were removed but network metrics were retained from the original whole-group network, showed that this is partly a power issue and partly a real effect of incomplete network. Our study indicates that sampling bias can thus hamper our ability to detect real network effects involving social interaction and parasitism. In addition to supporting earlier results linking geohelminth infection to Japanese macaque social networks, this work introduces important methodological considerations for research into the dynamics of social transmission, with implications for infectious disease epidemiology, population management, and health interventions.


title: SE(3)-Equivariant Energy-based Models for End-to-End Protein Folding

abstract: Accurate prediction of protein structures is critical for understanding the biological function of proteins. Nevertheless, most structure optimization methods are built upon pre-defined statistical energy functions, which may be sub-optimal in formulating the conformation space. In this paper, we propose an end-to-end approach for protein structure optimization, powered by SE(3)-equivariant energy-based models. The conformation space is characterized by a SE(3)-equivariant graph neural network, with substantial modifications to embed the protein-specific domain knowledge. Furthermore, we introduce continuously-annealed Langevin dynamics as a novel sampling algorithm, and demonstrate that such process converges to native protein structures with theoretical guarantees. Extensive experiments indicate that SE(3)-Fold achieves comparable structure optimization accuracy, compared against state-of-the-art baselines, with over 1-2 orders of magnitude speed-up.

category: bioinformatics


title: A spatio-spectral approach for movement decoding from cortical and subcortical recordings in patients with Parkinson's disease

abstract: The application of machine learning to intracranial signal analysis has the potential to revolutionize deep brain stimulation (DBS) by personalizing therapy to dynamic brain states, specific to symptoms and behaviors. Most decoding pipelines for movement decoding in the context of adaptive DBS are based on single channel frequency domain features, neglecting spatial information available in multichannel recordings. Such features are extracted either from DBS lead recordings in the subcortical target and/or from electrocorticography (ECoG). To optimize the simultaneous use of both types of signals, we developed a supervised online-compatible movement decoding pipeline based on multichannel and multiple site recordings. We found that adding spatial information to the model has the potential to improve decoding. In addition, we demonstrate movement decoding from spatio-spectral features derived from cortical and subcortical oscillations. We demonstrate between-patients variability of the spatial neural maps and its relationship to feature decoding performance. This application of spatial filters to decode movement from combined cortical and subcortical recordings is an important step in developing machine learning approaches for intelligent DBS systems.


title: Movement decoding using spatio-spectral features of cortical and subcortical local field potentials


title: Interpersonal Comparison of Utility by Measuring Neural Activity

abstract: Aggregating welfare across individuals is a fundamental problem in our society. There is no rational aggregation procedure without interpersonally comparable utility (Arrows impossibility theorem). However, scientific methods for interpersonal comparison of utility have thus far not been available. Here, we have developed such a method based on brain signals that correlated with changes in expected utility weighted by subjective probability. The signal was larger for participants with lower household incomes than for those with higher household incomes and their ratio coincided with the estimates by "impartial spectators". These findings suggest that our interpersonal comparison method enables scientifically reasonable welfare aggregation.


title: Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing

abstract: We developed a method to tag telomeres and measure telomere length by nanopore sequencing in the yeast S. cerevisiae. Nanopore allows long read sequencing through the telomere, subtelomere and into unique chromosomal sequence, enabling assignment of telomere length to a specific chromosome end. We observed chromosome end specific telomere lengths that were stable over 120 cell divisions. These stable chromosome specific telomere lengths may be explained by stochastic clonal variation or may represent a new biological mechanism that maintains equilibrium unique to each chromosomes end. We examined the role of RIF1 and TEL1 in telomere length regulation and found that TEL1 is epistatic to RIF1 at most telomeres, consistent with the literature. However, at telomeres that lack subtelomeric Y sequences, tel1{Delta} rif1{Delta} double mutants had a very small, but significant, increase in telomere length compared to the tel1{Delta} single mutant, suggesting an influence of Y elements on telomere length regulation. We sequenced telomeres in a telomerase-null mutant (est2{Delta}) and found the minimal telomere length to be around 75bp. In these est2{Delta} mutants there were many apparent telomere recombination events at individual telomeres before the generation of survivors, and these events were significantly reduced in est2{Delta} rad52{Delta} double mutants. The rate of telomere shortening in the absence of telomerase was similar across all chromosome ends at about 5 bp per generation. This new method gives quantitative, high resolution telomere length measurement at each individual chromosome end, suggests possible new biological mechanisms regulating telomere length, and provides capability to test new hypotheses.


title: Insulin signaling couples growth and early maturation to cholesterol intake

abstract:
Nutrition is one of the most important influences on growth and the timing of developmental maturation transitions including mammalian puberty and insect metamorphosis. Childhood obesity is associated with precocious puberty, but the assessment mechanism that links body fat to early maturation is unknown. During development, intake of nutrients promotes signaling through insulin-like systems that govern the growth of cells and tissues and also regulates the timely production of the steroid hormones that initiate the juvenile-adult transition. We show here that the dietary lipid cholesterol, required as a component of cell membranes and as a substrate for steroid biosynthesis, also governs body growth and maturation in Drosophila via promoting the expression and release of insulin-like peptides. This nutritional input acts via the Niemann-Pick-type-C (Npc) cholesterol sensors/transporters in the glia of the blood-brain barrier and cells of the adipose tissue to remotely drive systemic insulin signaling and body growth. Furthermore, increasing intracellular cholesterol levels in the steroid-producing prothoracic gland strongly promotes endoreduplication, leading to accelerated attainment of a nutritional checkpoint that ensures that animals do not initiate maturation prematurely. These findings couple sensing of the lipid cholesterol to growth control and maturational timing, which may help explain both the link between cholesterol and cancer as well as the critical connection between body fat (obesity) and early puberty.

HIGHLIGHTSO_LIDietary cholesterol promotes developmental growth and leads to early maturation
C_LIO_LIInsulin signaling couples cholesterol intake with systemic growth
C_LIO_LICholesterol promotes insulin signaling and growth via glial and fat-tissue relays
C_LIO_LICholesterol sensing affects a nutritional checkpoint that prevents early maturation
C_LI

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/447368v1_ufig1.gif" ALT="Figure 1">
View larger version (26K):
org.highwire.dtl.DTLVardef@14e786borg.highwire.dtl.DTLVardef@c3eab5org.highwire.dtl.DTLVardef@6645c8org.highwire.dtl.DTLVardef@6f729a_HPS_FORMAT_FIGEXP  M_FIG GRAPHICAL ABSTRACT

C_FIG

category: cell biology


title: Modelling Porcine NAFLD by Deletion of Leptin and defining the role of AMPK in hepatic fibrosis

abstract: Liver fibrosis occurs during chronic liver disease. Advanced liver fibrosis results in cirrhosis, liver failure and often requires liver transplantation. However, due to the lack of human models, mechanisms underlining the pathogenesis of liver fibrosis remain unclear. Recent studies implicated a central role of deranged lipid metabolism in its pathogenesis. In this study, we generated LEPTIN-deficient (LEPTIN-/-) pigs using zinc finger nuclease technology to investigate the mechanisms of liver fibrosis associated with obesity. The LEPTIN-/- pigs showed increased body fat and significant insulin resistance by 12 months of age. To resemble non-alcoholic fatty liver disease (NAFLD) patients, LEPTIN-/- pig developed the phenotypic features of fatty liver, non-alcoholic steatohepatitis (NASH) and hepatic fibrosis with age. Meanwhile, LEPTIN absence reduced phosphorylation of JAK2-STAT3 and AMPK. The alteration of JAK2-STAT3 enhanced fatty acid {beta}-oxidation, whereas inactivation of AMPK led to mitochondrial autophagy, and both contributed to increased oxidative stress in hepatocytes. Although Leptin deletion in the rat liver altered JAK2-STAT3 phosphorylation, it activated the AMPK pathway and prevented liver fibrogenesis in contrast with the LEPTIN-/- pig. To our knowledge, the LEPTIN-/- pig provides the first model recapitulating the full pathogenesis of NAFLD and its progression toward liver fibrosis. The activity of AMPK signaling pathway suggests a potential target for development of new strategies for the diagnosis and treatment of NAFLD.


title: Natural selection promotes the evolution of recombination 2: during the selective process

abstract: The ubiquity of sex and recombination in nature has eluded unified explanation since the time of Darwin. Conditions that promote the evolution of recombination, broadly defined as any form of genetic mixing, are fairly well understood: it is favored when genomes tend to contain more selectively mismatched combinations of alleles than can be explained by chance alone. Yet, while a variety of theoretical approaches have been put forth to explain why such conditions would prevail in natural populations, each has turned out to be of limited scope and applicability. Here, we show, simply and surprisingly, that natural selection acting on standing heritable variation always creates conditions favoring the evolution of recombination, in expectation. Specifically, we find that, in expectation: 1) the mean selective advantage of recombinants is non-negative, 2) the mean selective advantage of a recombination-competent modifier is non-negative, and 3) the asymptotic frequency of a recombination-competent modifier is close to one and is independent of the strength of selection. Remarkably, these findings are independent of the distribution of genic fitnesses in the standing heritable variation upon which natural selection acts, implying that the source of this variation is immaterial. Taken together, our findings indicate that: 1) the evolution of recombination should be promoted in expectation wherever natural selection is operating, and 2) sex and recombination may have evolved more as a byproduct than as a catalyst of natural selection.

category: evolutionary biology


title: Natural selection promotes the evolution of recombination 2: during the process of natural selection


title: Natural selection promotes the evolution of recombination 1: among selected genotypes

abstract: Shuffling ones genetic material with another individual seems a risky endeavor more likely to decrease than to increase offspring fitness. This intuitive argument is commonly employed to explain why the ubiquity of sex and recombination in nature is enigmatic. It is predicated on the notion that natural selection assembles selectively well-matched combinations of genes that recombination would break up resulting in low-fitness offspring - a notion often stated in the literature as a self-evident premise. We show however that, upon closer examination, this premise is flawed: we find to the contrary that natural selection in fact has an encompassing tendency to assemble selectively mismatched gene combinations; recombination breaks up these selectively mismatched combinations (on average), assembles selectively matched combinations, and should thus be favored. The new perspective our findings offer suggests that sex and recombination are not so enigmatic but are instead unavoidable byproducts of natural selection.


title: Natural selection promotes the evolution of recombination 1: between the products of natural selection


title: Expansive and diverse phenotypic landscape of field Aedes aegypti larvae with differential susceptibility to temephos: beyond metabolic detoxification

abstract:
Arboviruses including dengue, Zika and chikungunya are amongst the most significant public health concerns worldwide and their control relies heavily on the use of insecticides to control the vector mosquito Aedes aegypti. The success of controlling these vector-pathogen systems is threatened by widespread insecticide resistance. The work presented here profiled the gene expression of the larvae from two field populations of Ae. aegypti with differential susceptibility to temephos. The contrasting phenotypes originated from two Colombian urban locations, Bello and Cucuta, that we have previously reported to have distinctive disease incidence, socioeconomics, and climate. The closeness of the geographical origin of the study populations was suspected to be highly influential in the profiling of the gene expression of resistance since the mosquitos resistance levels themselves are highly dependent upon environmental variables. We demonstrated that an exclusive field-to-lab (Ae. aegypti reference strain New Orleans) comparison generates an over estimation of differential gene expression (DGE) and that the inclusion of a geographically relevant field control, as used here, yields a more discrete, and likely, more specific set of genes. The composition of the obtained DGE profiles is varied, with commonly reported resistance associated genes such as detoxifying enzymes having only a small representation. We identify cuticle biosynthesis, ion exchange homeostasis, an extensive number of long non-coding RNAs, and chromatin modelling among the specifically and differentially expressed genes in field resistant Ae. aegypti larvae. It was also shown that temephos resistant larvae undertake further gene expression responses when temporarily exposed to this insecticide. The results from the sampling triangulation approach undertaken here contributes a discrete DGE profiling with reduced noise that permitted the observation of a greater gene diversity. This deeper gene granularity significantly increases the number of potential targets for the control of insecticide resistant mosquitoes and widens our knowledge base on the complex phenotypic network of the Ae. aegypti mosquito responses to insecticides.

Author SummaryAedes aegypti mosquitoes are vectors for several significant human viruses including dengue, Zika and chikungunya. The lack of widely available vaccines and specific antiviral treatments for these viruses means that the principal method for reducing disease burden is through controlling the vector mosquitoes. Mosquito control relies heavily on the use of insecticides and successful vector control is threatened by widespread insecticide resistance in Ae. aegypti. Here, we examined changes in gene expression that occur in temephos resistant populations of Ae. aegypti from two field populations in Colombia. We compare gene expression in resistant larvae from Cucuta with susceptible larvae from Bello and a susceptible laboratory strain of Ae. aegypti (New Orleans). We also compare mosquitoes from Cucuta with and without temephos exposure. We report several differentially expressed genes beyond those usually reported in resistant mosquitoes. We also demonstrate the over estimation in differential gene expression that can occur when field resistant populations are compared against lab susceptible populations only. The identification of new mechanisms involved in the development of insecticide resistance is crucial to fully understanding how resistance occurs and how best it can be reduced.

category: genetics


title: Evidence for a vocal signature in the rat and its reinforcing effects

abstract: While the term "language" is used for human and non-human primates, "vocal communication" is rather used for rodents or other species. The main difference is that there is, to date, no evidence for a vocal signature in the well-known 50- and 22-kHz ultrasonic vocalizations (USV) emitted by rats. Here, we show that rats can recognize the identity of the USV emitter since they self-administer preferentially playback of 50-kHz USV emitted by a stranger rat over those emitted by their cage-mate. In a second experiment, we show that the familiarity with the USV emitter also modulate the effect of USV playback during cocaine self-administration, since only stranger, but not familiar, 50-kHz USV decrease drug intake. Finally, to study the neurobiological substrate of those processes, we have tested the effects of the subthalamic nucleus (STN) lesion on these various conditions. STN-lesioned rats did not lever press much for any USV playback, whatever their emotional valence, nor did they seem able to differentiate familiar from stranger peer. Advocating for the existence of a vocal signature in rats, these results highlight the importance of ultrasonic communication in socio-affective influence of behavior, such as the influence of proximal social factors on drug consumption and confirm the role of the subthalamic nucleus on this influence.


title: ProCanBio: a database of manually curated biomarkers for Prostate Cancer

abstract:
BackgroundProstate Cancer is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of prostate cancer. However, information related to the biomarkers is widely scattered across numerous resources in complex textual format, which poses hindrance to understand the tumorigenesis of this malignancy and scrutinization of robust signature. To the best of authors knowledge, there is no resource that can consolidate the information contained in all the published literature.

ResultsHere, we present ProCanBio, a manually curated database that maintains detailed data on 2053 entries of potential prostate cancer biomarkers obtained from 412 publications in user friendly tabular format. Among them, 766 protein-based, 488 RNA-based, 157 genomic mutations, 261 miRNA-based, and 122 are metabolites-based biomarkers. To explore the information in the resource, a web-based interactive platform was developed with searching, and browsing facilities. ProCanBio is freely available and is compatible with most web browsers and devices. Eventually, we anticipated this resource will be highly useful for the research community involved in the area of prostate malignancy.

AvailabilityProCanBio is available at: https://webs.iiitd.edu.in/raghava/procanbio/

category: cancer biology


title: A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses

abstract: Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a datamine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to probe these via a new interactive web portal (http://toppcell.cchmc.org/ COVID-19). As examples, we develop three hypotheses: (1) a multicellular signaling cascade among alternatively differentiated monocyte-derived macrophages whose tasks include T cell recruitment and activation; (2) novel platelet subtypes with drastically modulated expression of genes responsible for adhesion, coagulation and thrombosis; and (3) a multilineage cell activator network able to drive extrafollicular B maturation via an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.


title: Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal


title: Neutralization against B.1.351 and B.1.617.2 with sera of COVID-19 recovered cases and vaccinees of BBV152

abstract: Recently, multiple SARS-CoV-2 variants have been detected across the globe. The recent emergence of B.1.617 lineage has created serious public health problem in India. The high transmissibility was observed with this lineage which has led to daily increase in the number of SARS-CoV-2 infections. Apparently, the sub-lineage B.1.617.2 has slowly dominated the other variants including B1617.1, B.617.3 and B.1.1.7. With this, World Health Organization has described B.1.617.2 as variant of concern. Besides this, variant of concern B.1.351 has been also reported from India, known to showreducedefficacyfor many approved vaccines. With the increasing threat of the SARS-CoV-2 variants, it is imperative to assess the efficacy of the currently available vaccines against these variants. Here, we have evaluated the neutralization potential of sera collected from COVID-19 recovered cases (n=20) and vaccinees with two doses of BBV152 (n=17) against B.1.351 and B.1.617.2 compared to the prototype B.1 (D614G) variant.The finding of the study demonstrated a reduction in neutralization titers with sera of COVID-19 recovered cases(3.3-fold and 4.6-fold) and BBV152 vaccinees (3. 0 and 2.7 fold) against B.1.351 and B.1.617.2 respectively.Although, there is reduction in neutralization titer, the whole-virion inactivated SARS-CoV-2 vaccine (BBV152) demonstrates protective response against VOC B.1351 and B.1.617.2.


title: FXR inhibition reduces ACE2 expression, SARS-CoV-2 infection and may improve COVID-19 outcome

abstract: Prevention of SARS-CoV-2 entry in cells through the modulation of viral host receptors, such as ACE2, could represent a new therapeutic approach complementing vaccination. However, the mechanisms controlling ACE2 expression remain elusive. Here, we identify the farnesoid X receptor (FXR) as a direct regulator of ACE2 transcription in multiple COVID19-affected tissues, including the gastrointestinal and respiratory systems. We demonstrate that FXR antagonists, including the over-the-counter compound z-guggulsterone (ZGG) and the off-patent drug ursodeoxycholic acid (UDCA), downregulate ACE2 levels, and reduce susceptibility to SARS-CoV-2 infection in lung, cholangiocyte and gut organoids. We then show that therapeutic levels of UDCA downregulate ACE2 in human organs perfused ex situ and reduce SARS-CoV-2 infection ex vivo. Finally, we perform a retrospective study using registry data and identify a correlation between UDCA treatment and positive clinical outcomes following SARS-CoV-2 infection, including hospitalisation, ICU admission and death. In conclusion, we identify a novel function of FXR in controlling ACE2 expression and provide evidence that this approach could be beneficial for reducing SARS-CoV-2 infection, thereby paving the road for future clinical trials.


title: In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR

abstract: A number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases - as seen with the B.1.1.7 variant - can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from -0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charite RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values observed with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.


title: In-vitro Reconstitution of Membrane Contact Sites between the Endoplasmic Reticulum and Lipid Droplets

abstract: Coordinated cell function requires inter-organelle communication across Membrane Contact Sites (MCS). Here we deposit ER-enriched microsomes purified from rat liver or from cultured cells on a coverslip in the form of a continuous planar membrane. We visualize real-time protein and lipid exchanges across MCS that form between this ER-mimicking membrane and lipid droplets purified from rat liver. An Optical trap is used to demonstrate physical tethering of individual lipid droplets to the ER-mimicking membrane at MCS, and to directly measure the strength of this tether. In-vitro MCS formation changes dramatically in response to metabolic state and immune activation in the animal. Surprisingly, we find that the Rab18 GTPase and Phosphatidic acid are common molecular factors to control both of these pathways. This assay could possibly be adapted to interrogate MCS formation between other membranes (e.g. mitochondria, peroxisomes, endosomes etc.), and abnormalities therein that cause neurological, metabolic and pathogenic diseases.


title: Complexin-1 regulated transition in the assembly of single neuronal SNARE complex

abstract: Neurotransmitter release is mediated by the synaptic vesicle exocytosis. Important proteins in this process have been identified including the molecular machine Synaptic-soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins, and other regulators. Complexin (Cpx) is one of the vital regulators in this process. The functions of Cpx are proposed to maintain a proper primed vesicle pool by preventing its premature depletion, which facilitates the vesicle fusion in the presence of Ca2+. However, the molecular mechanism remains unclear. Using dual-trap optical tweezers, we detected the interaction of complexin-1 (CpxI) with SNARE. We found that the CpxI stabilizes partially folded SNARE complexes by competing with C-terminal of Vamp protein and interacting with the C-terminal of t-SNARE complex.

category: biophysics


title: Dynamics and self-assembly of the SARS-CoV-2 spike transmembrane domain

abstract:
The spike (S) protein is a trimeric, membrane-anchored fusion protein that enables coronaviruses, such as the SARS-CoV-2, to recognize and fuse with their hosts cells. While the prefusion and postfusion structures of the ectomembrane domain of the spike protein are available, the corresponding organization of its transmembrane domain is obscure. Since the transmembrane and ectomembrane domains of fusion proteins are conformationally linked, an understanding of trimerization and transmembrane conformations in the viral envelope is a prerequisite to completely understand viral fusion by the spike protein. To address this, we computationally explored the self-assembly of the SARS-CoV-2 spike transmembrane domain, starting first by determining the membrane boundaries of the spike transmembrane helix. Using atomistic molecular dynamics simulations, we found the spike protein transmembrane domain to be plastic, and the transmembrane helix to be very dynamic. The observed movements of the helix changed the membrane embedded sequence, and thereby affected the conformational ensemble of the transmembrane assembly in Martini coarse grained simulations, even flipping the super-helical handedness. Analysis of the transmembrane organization of the spike transmembrane helix provided rich insights into the interfaces utilized to self-associate. Moreover, we identified two distinct cholesterol binding regions on the transmembrane helix with different affinities for the sterol. The cholesterol binding pockets overlapped with regions involved in the initiation of transmembrane protein-protein interaction. Together, the results from our multiscale simulations not only provide insight into understudied trimeric helical interfaces in biomembranes, but also enhance our understanding of the elusive transmembrane conformational dynamics of SARS-CoV-2 spike and more generally of viral fusion proteins. These insights should enable the inclusion of the conformations of the spike protein transmembrane domain into the prevalent models of virus fusion.

SignificanceEnveloped viruses rely on fusion proteins, called spike proteins in coronaviruses, to infect cells by fusing the virus envelope with the host cell membrane. The transmembrane domain (TMD) of the coronavirus spike protein is critically involved in successful viral fusion and other aspects of the virus lifecycle, but is poorly studied. Using multiscale molecular dynamics simulations of the SARS-CoV-2 spike TMD, we explore its conformational dynamics and self-assembly in different lipid environments. The results provided here improve our understanding of transmembrane stabilization of spike trimers, which are indispensable for viral infection. Exploiting this knowledge to destabilize spike trimers should facilitate design of transmembrane domain targeted viral fusion inhibitors.


title: Molecular classification reveals the diverse genetic features and prognosis of gastric cancer: a multi-omics consensus ensemble clustering

abstract:
BackgroundGastric cancer (GC) is the fifth most common tumor around the world, it is necessary to reveal novel molecular subtypes to guide the selection of patients who may benefit from specific target therapy.

MethodsMulti-omics data, including RNA-sequence of transcriptomics (mRNA, LncRNA, miRNA), DNA methylation and gene mutation of TCGA-STAD cohort was used for the clustering. Ten classical clustering algorithms were applied to recognize patients with different molecular features via the R package "MOVICS". The activated signaling pathways were evaluated using the single-sample gene set enrichment analysis. The difference distribution of gene mutations, copy number alterations and tumor mutation burden was compared, and potential response to immunotherapy and chemotherapy was assessed as well.

ResultsTwo molecular subtypes (CS1 and CS2) were recognized by ten clustering algorithms with further consensus ensembles. Patients in the CS1 group were found to contain a shorter average overall survival time (28.5 vs. 68.9 months, P = 0.016), and progression-free survival (19.0 vs. 63.9 months, P = 0.008) compared to the CS2 group. CS1 group contained more activation of extracellular associated biological process, while CS2 group displayed the activation of cell cycle associated pathways. The significantly higher total mutation numbers and neo antigens were observed in CS2 group, along with the specific mutation of TTN, MUC16 and ARID1A. Higher infiltration of immunocytes were also observed in CS2 group, reflected to the potential benefit from immunotherapy. Moreover, CS2 group also can response to 5-fluorouracil, cisplatin, and paclitaxel. The similar diverse of clinical outcome of CS1 and CS2 groups were successfully validation in external cohorts of GSE62254, GSE26253, GSE15459, and GSE84437.

ConclusionNovel insight into the GC subtypes was obtained via integrative analysis of five omics data by ten clustering algorithms, which can provide the idea to the clinical target therapy based on the specific molecular features.


title: TRIB1 regulates tumour growth via controlling tumour-associated macrophage phenotypes and is associated with breast cancer survival and treatment response

abstract:
Molecular mechanisms that regulate tumour-associated macrophage (TAM) phenotype and function are incompletely understood. Here, we show that the pseudokinase TRIB1 is highly expressed by TAMs in breast cancer and that its expression correlates with response to chemotherapy and patient survival. We used immune-competent murine models of breast cancer to characterise the consequences of altered (reduced or elevated) myeloid Trib1 expression on tumour growth and composition of stromal immune cells. We found that both overexpression and knockout of myeloid Trib1 promote tumour growth, albeit through distinct molecular mechanisms. Myeloid Trib1 deficiency resulted in an early accelearation of tumour growth, paired with a selective reduction in perivascular macrophage numbers in vivo and enhanced oncogenic cytokine expression in vitro. In contrast, elevated levels of Trib1 in myeloid cells led to an increase in mammary tumour volume at late stages, together with a reduction of NOS2 expressing macrophages and an overall reduction of these cells in hypoxic tumour regions. In addition, we show that myeloid Trib1 is a previously unknown, negative regulator of the anti-tumour cytokine IL-15 and that increased expression of myeloid Trib1 leads to reduced IL-15 levels in mammary tumours, with a consequent reduction in the number of T-cells, that are key to anti-tumour immune responses.

Together, these results define the different roles of TRIB1 in human breast cancer and provide a mechanistic understanding for the importance of myeloid TRIB1 expression levels in the development of this disease.

SignificanceTRIB1 expression is strongly associated with response to chemotherapy in breast cancer patients with aggressive tumours. This protein is also highly expressed by tumour-associated macrophages. Thus, we used myeloid-specific alterations of Trib1 expression in mice (Trib1mKO and Trib1mTg), and characterised consequent changes in the growth rate and tumour microenvironment of mammary tumours. Both Trib1mKO and Trib1mTg enhanced tumour growth, but at different stages of tumour growth and via distinct mechanisms. Trib1mKO significantly increased the expression of oncogenic cytokines, such as IL6, IL10, CCL20, PD-L1, and VEGF. In contrast, Trib1mTg accelerated at the later stage of tumour growth via inhibition of hypoxic TAMs in the TME, as well as by reduced IL-15 expression thus leading to impaired naive and cytotoxic T cell infiltration. These data define TRIB1 as a potential novel marker of therapeutic responses in breast cancer, as well as a key mechanistic regulator of the anti-tumour cytokine, IL-15 in myeloid cells.


title: Toxicity of 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NKK) in early development: a wide-scope metabolomics assay in zebrafish embryos

abstract: The tobacco-specific nitrosamine 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a carcinogenic and ubiquitous environmental pollutant which carcinogenic and cytotoxic activity has been thoroughly investigated in murine models and human tissues. However, its potential deleterious effects on vertebrate early development are yet poorly understood. In this work, we characterized the impact of NNK exposure during early developmental stages of zebrafish embryos, a known alternative model for mammalian toxicity studies. Embryos exposed to different NNK concentrations were monitored for lethality and for the appearance of malformations during the first five days after fertilization. LC/MS-based untargeted metabolomics was subsequently performed for a wide-scope assay of NNK-related metabolic alterations. Our results revealed the presence of not only the parental compound, but also of two NKK known metabolites, 4-Hydroxy-4-(3-pyridyl)-butyric acid (HPBA) and 4-(Methylnitrosamino)-1-(3-pyridyl-N-oxide)-1-butanol (NNAL-N-oxide) in exposed embryos likely resulting from active CYP450-mediated -hydroxylation and NNK detoxification pathways, respectively. This was paralleled by a disruption in purine and pyrimidine metabolisms and the activation of the base excision repair pathway. Our results confirm NNK as a harmful embryonic agent and demonstrate zebrafish embryos to be a suitable early development model to monitor NNK toxicity.

category: pharmacology and toxicology


title: BSCL2/Seipin Deficiency in Heart Causes Energy Deficit and Heart Failure via Inducing Excessive Lipid Catabolism

abstract: Heart failure (HF) is one of the leading causes of death world-wide and is associated with cardiac metabolic perturbations. Human Type 2 Berardinelli-Seip Congenital Lipodystrophy (BSCL2) disease is caused by mutations in the BSCL2 gene. Global lipodystrophic Bscl2-/- mice exhibit hypertrophic cardiomyopathy. Whether BSCL2 plays a direct role in regulating cardiac substrate metabolism and/or contractile function remains unknown. Here we show that mice with cardiac-specific deletion of Bscl2 (Bscl2cKO) developed dilated HF. Myocardial BSCL2 deletion led to elevated ATGL expression and FA oxidation (FAO) along with reduced cardiac lipid contents. Cardiac dysfunction in Bscl2cKO mice was independent of mitochondrial dysfunction and oxidative stress, but associated with decreased metabolic reserve and ATP levels. Importantly, heart failure in Bscl2cKO mice could be partially reversed by pharmacological inhibition of FAO, or prevented by high fat diet (HFD) feeding. Lipidomic analysis further identified markedly reduced glycerolipids, glycerophospholipids, NEFA and acylcarnitines in Bscl2cKO hearts, which were partially normalized by FAO inhibition or HFD. Our study reveals a new form of HF with excessive lipid catabolism, and identifies a crucial cardiomyocyte-specific role of BSCL2 in controlling cardiac lipid catabolism, energy state and contractile function. It also provides novel insights into metabolically treating energy-starved HF using FAO inhibitor or HFD.

category: physiology


title: Structural Variation and Polysaccharide Profiling of Intervessel Pit Membranes

abstract: Functional roles of intervessel pit membrane (PM) depend on its structure and polysaccharide composition, which are mostly unknown or lack of accurate information. This study uses grapevine as a model plant and an immunogold-scanning electron microscopy technique to simultaneously analyze structures and polysaccharide compositions of intervessel PMs in relation to their functions. Intervessel PMs with different structural integrity were found in functional xylem with about 90 % of them being intact with a smooth or relatively smooth surface and the rest 10 % with progressively degraded structures. The results also elucidated details of the removal process of wall materials from surface toward its depth during the natural intervessel PM degradation. Four groups of pectic and hemicellulosic polysaccharides were present in intervessel PMs but displayed differential spatial distributions and quantities: weakly methyl-esterified homogalacturonans abundant in the surficial layers, heavily methyl-esterified homogalacturonans and xylans mostly in deep layers, and fucosylated xyloglucans relatively uniform in presence at different depths of an intervessel PM. This information is crucial to reveal the polysaccharide profiling of primary cell wall and to understand intervessel PMs roles in the safety and regulation of water transport as well as the plant susceptibility to vascular diseases.

category: plant biology


title: Generation of star-shaped human induced astrocytes with a mature inflammatory phenotype for CNS disease modeling

abstract: Generating astrocytes from induced pluripotent stem cells has been hampered by either prolonged differentiation -spanning over two months -or by shorter protocols that generate immature astrocytes, devoid of salient inflammation-associated astrocytic traits pivotal for CNS neuropathological modeling. We directed human neural stem cells derived from induced pluripotent stem cells to astrocytic commitment and maturity by orchestrating an astrocytic-tuned culturing environment. In under 28 days, the generated cells express canonical and mature astrocytic markers, denoted by the expression of AQP4 and, remarkably, the expression and functionality of glutamate transporter EAAT2. We also show that this protocol generates astrocytes that encompass traits critical in CNS disease modeling, such as glutathione synthesis and secretion, upregulation of ICAM-1 and a cytokine secretion profile which is on par with primary astrocytes. This protocol generates a multifaceted astrocytic model suitable for CNS in vitro disease modeling and personalized medicine through brain-on-chip technologies.


title: Effects of early life adversity on immediate early gene expression: systematic review and 3-level meta-analysis of rodent studies

abstract: Early-life adversity (ELA) causes long-lasting structural and functional changes to the brain, rendering affected individuals vulnerable to the development of psychopathologies later in life. Immediate-early genes (IEGs) provide a potential marker for the observed alterations, bridging the gap between activity-regulated transcription and long-lasting effects on brain structure and function. Several heterogeneous studies have used IEGs to identify differences in cellular activity after ELA; systematically investigating the literature is therefore crucial for comprehensive conclusions. Here, we performed a systematic review on 39 pre-clinical studies in rodents to study the effects of ELA on IEG expression. Females and IEGs other than cFos were investigated in only a handful of publications. We meta-analyzed publications investigating specifically cFos expression. ELA increased cFos expression after an acute stressor only if the animals (control and ELA) had experienced multiple negative life events. At rest, ELA increased cFos expression irrespective of other life events, suggesting that ELA creates a phenotype similar to naive, acutely stressed animals. We present a conceptual theoretical framework to interpret the unexpected results. Overall, ELA likely alters IEG expression across the brain, especially in interaction with other negative life events. The present review highlights current knowledge gaps and provides guidance to aid the design of future studies.


title: Salt-inducible kinase (SIK) inhibition is protective in a mouse model of asthma

abstract: Interleukin-13 (IL-13) and other Th2 cytokines are important regulators of airway hyper-responsiveness, immune cell infiltration and inflammation in allergic asthma, and are produced when immune cells, such as type 2 innate lymphoid cells (ILC2s) and mast cells, are stimulated with IL-33. Here, we report that the IL-33-dependent secretion of IL-13 from ILC2s is prevented by inhibition of the salt-inducible kinases (SIKs), as we have shown previously in mast cells (Darling NJ et al., 2021, J. Biol. Chem. doi: 10.1016/j.jbc.2021.100428). We also report that a new SIK inhibitor with improved pharmacokinetic properties suppresses the recruitment of eosinophils to the lungs and serum immunoglobulin E (IgE) levels in the Alternaria alternata-induced model of allergic asthma. Our results suggest that drugs targeting SIK isoforms may have therapeutic potential for the treatment of asthma.


title: Hepatic miR-20b promotes nonalcoholic fatty liver disease by suppressing PPARα

abstract:
BackgroundNon-alcoholic fatty liver disease (NAFLD) is characterized by excessive lipid accumulation and imbalances in lipid metabolism in the liver. Although nuclear receptors (NRs) play a crucial role in hepatic lipid metabolism, the underlying mechanisms of NR regulation in NAFLD remain largely unclear.

MethodsUsing network analysis and RNA-seq to determine the correlation between NRs and microRNA in human NAFLD patients, we revealed that MIR20B specifically targets PPARA. MIR20B mimic and anti-MIR20B were administered to human HepG2 and Huh-7 cells and mouse primary hepatocytes as well as high fat diet (HFD)- or methionine-deficient diet (MCD)-fed mice to verify the specific function of MIR20B in NAFLD. We tested the inhibition of the therapeutic effect of a PPAR agonist, fenofibrate, by MIR20B and the synergic effect of combination of fenofibrate with anti-MIR20B.

ResultsWe revealed that MIR20B specifically targets PPARA through miRNA regulatory network analysis of nuclear receptor genes in NAFLD. The expression of MIR20B was upregulated in free fatty acid (FA)- treated hepatocytes and the livers of both obesity-induced mice and NAFLD patients. Overexpression of MIR20B significantly increased hepatic lipid accumulation and triglyceride levels. Furthermore, MIR20B significantly reduced FA oxidation and mitochondrial biogenesis by targeting PPARA. In MIR20B-introduced mice, the effect of fenofibrate to ameliorate hepatic steatosis was significantly suppressed. Finally, inhibition of MIR20B significantly increased FA oxidation and uptake, resulting in improved insulin sensitivity and a decrease in NAFLD progression. Moreover, combination of fenofibrate and anti-MIR20B exhibited the synergic effect on improvement of NAFLD in MCD-fed mice.

ConclusionsTaken together, our results demonstrate that the novel MIR20B targets PPARA, plays a significant role in hepatic lipid metabolism, and present an opportunity for the development of novel therapeutics for NAFLD.

FundingThis research was funded by Korea Mouse Phenotyping Project (2016M3A9D5A01952411), the National Research Foundation of Korea (NRF) grant funded by the Korea government (2020R1F1A1061267, 2018R1A5A1024340, NRF-2021R1I1A2041463, 2020R1I1A1A01074940), and the Future-leading Project Research Fund (1.210034.01) of UNIST.


title: Hepatic MIR20B promotes nonalcoholic fatty liver disease by suppressing PPARA


title: Single-molecule imaging reveals the coupling of translation and mRNA decay

abstract: The relationship between mRNA translation and decay is incompletely understood, with conflicting reports suggesting that translation can either promote decay or stabilize mRNAs. The effect of translation on mRNA decay has mainly been studied using ensemble measurements and global inhibitors of transcription and translation, which can mask the underlying mechanisms. We developed a single-molecule imaging approach to control the translation of a specific transcript that enabled simultaneous measurement of translation and mRNA decay. Our results demonstrate that mRNAs undergoing translation are degraded faster than non-translating ones, although with slower kinetics than translation-coupled degradation of transcripts targeted by NMD. Furthermore, our results indicate that miRNAs mediate efficient degradation of both translating and non-translating target mRNAs. Single-molecule measurements of translation and decay reveal a predominant role of mRNA decay in miRNA-mediated regulation. Simultaneous visualization of translation and decay on single mRNAs provides a framework to study how these processes are interconnected in cells.


title: A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

abstract: Regulation of subcellular components localization and motion is a critical theme in cell biology. Cells use the actomyosin cortex to regulate protein distribution on the plasma membrane, but the interplay between membrane binding, cortical movements and protein distribution remains poorly understood. In a polarizing one-cell stage Caenorhabditis elegans embryo, actomyosin flows transport PAR protein complexes into an anterior cortical domain to establish the anterior-posterior axis of the animal. Oligomerization of a key scaffold protein, PAR-3, is required for aPAR cortical localization and segregation. Although PAR-3 oligomerization is essential for polarization, it remains unclear how oligomer size contributes to aPAR segregation because PAR-3 oligomers are a heterogeneous population of many different sizes. To address this question, we engineered PAR-3 to defined sizes. We report that PAR-3 trimers are necessary and sufficient for PAR-3 function during polarization and later embryo development, while larger PAR-3 clusters are dispensable. Quantitative analysis of PAR-3 diffusion showed that PAR-3 clusters with three or more subunits are transported by frictional drag and experience extensive collisions with the actomyosin cortex. Our study provides a quantitative model for size-dependent protein transportation of membrane proteins by cortical flow.


title: Core and indicative bacterial and fungal taxa define characteristic soil communities of arable land, grassland, and forest

abstract: Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities over five years at thirty long-term soil monitoring sites from the three land-use types, arable land, permanent grassland, and forest. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use type associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.

category: ecology


title: Habitat percolation transition undermines sustainability in social-ecological agricultural systems

abstract: Steady increases in human population size and resource consumption are driving rampant agricultural expansion and intensification. Habitat loss caused by agriculture puts the integrity of ecosystems at risk, and threatens the persistence of human societies that rely on ecosystem services. We develop a spatially explicit model describing the coupled dynamics of an agricultural landscape and human population size to study the effect of different land-use management strategies, defined by agricultural clustering and intensification, on the sustainability of the social-ecological system. We show how agricultural expansion can cause natural habitat to undergo a percolation transition leading to abrupt habitat fragmentation that feedbacks on humans decision making, aggravating landscape degradation. We found that agricultural intensification to spare land from conversion is a successful strategy only in highly natural landscapes, and that clustering agricultural land is the most effective measure to preserve large connected natural fragments, avoid severe fragmentation, and thus, enhance sustainability.


title: Natural variation in the irld gene family affects insulin/IGF signaling and starvation resistance

abstract: Starvation resistance is a fundamental, disease-relevant trait, but the genetic basis of its natural variation is unknown. We developed a synthetic population-sequencing approach to measure starvation resistance for many wild C. elegans strains simultaneously. We identified three quantitative trait loci with variants in 16 insulin/EGF receptor-like domain (irld) family members. We show that four irld genes affect starvation resistance by regulating insulin/IGF signaling. We propose that IRLD proteins bind insulin-like peptides to modify signaling in the sensory nervous system thereby affecting organismal physiology. This work demonstrates efficacy of using population sequencing to dissect a complex trait, identifies irld genes that regulate insulin/IGF signaling, and shows that an expanded gene family modifies a deeply conserved signaling pathway to affect a fitness-proximal trait.


title: Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk

abstract: Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across several cell types. Genome-wide association studies (GWAS) have identified over 170 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-cell ATAC-seq to profile 28,316 cells across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants via quantitative trait locus and sequence-based predictive modeling. We identified a number of candidate mechanisms for smooth muscle cell transition states and identified putative binding sites for risk variants. We further employed CRE to gene linkage to nominate disease-associated key driver transcription factors such as PRDM16 and TBX2. This single cell atlas provides a critical step towards interpreting cis-regulatory mechanisms in the vessel wall across the continuum of CAD risk.


title: Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

abstract: The repetitive nature and complexity of multiple medically important genes make them intractable to accurate analysis, despite the maturity of short-read sequencing, resulting in a gap in clinical applications of genome sequencing. The Genome in a Bottle Consortium has provided benchmark variant sets, but these excluded some medically relevant genes due to their repetitiveness or polymorphic complexity. In this study, we characterize 273 of these 395 challenging autosomal genes that have multiple implications for medical sequencing. This extended, curated benchmark reports over 17,000 SNVs, 3,600 INDELs, and 200 SVs each for GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically important genes including CBS, CRYAA, and KCNE1. Our proposed solution improves variant recall in these genes from 8% to 100%. This benchmark will significantly improve the comprehensive characterization of these medically relevant genes and guide new method development.


title: Characterization of a recombinant plastid translocon co-chaperone

abstract: The transport of proteins into plastids is dependent on how the different translocon components work together. One translocon component, Tic40, possesses functional features found in other proteins such as co-chaperones and may thus work similarly in this capacity. To enhance the understanding of Tic40s mode of operation, a more basic characterization of the protein itself is required. This study was designed largely to examine the properties of recombinant Tic40 without the predicted transmembrane region. The properties of Tic40 revealed in this report are: 1) In plants, overall Tic40 levels can adjust to temperature; 2) Recombinant Tic40 proteins appear to display some level of functionality in the soluble form; and 3) Outside of a membranous context, the formation of complexes involving recombinant Tic40 can be influenced by temperature. The potential significance of these basic properties is discussed.

category: biochemistry


title: Cell culture-based production of defective interfering influenza A virus particles in perfusion mode using an alternating tangential flow filtration system

abstract:
Respiratory diseases including influenza A virus (IAV) infections represent a major threat to human health. While the development of a vaccine requires a lot of time, a fast countermeasure could be the use of defective interfering particles (DIPs) for antiviral therapy. IAV DIPs are usually characterized by a large internal deletion in one viral RNA segment. Consequentially, DIPs can only propagate in presence of infectious standard viruses (STVs), compensating the missing gene function. Here, they interfere with and suppress the STV replication and might act "universally" against many IAV subtypes. We recently reported a production system for purely clonal DIPs utilizing genetically modified cells. In the present study, we established an automated perfusion process for production of a DIP, called DI244, using an alternating tangential flow filtration (ATF) system for cell retention. Viable cell concentrations and DIP titers more than 10-times higher than for a previously reported batch cultivation were observed. Further, we investigated a novel tubular cell retention device for its potential for continuous virus harvesting into the permeate. Very comparable performances to typically used hollow fiber membranes were found during the cell growth phase. During the virus replication phase the tubular membrane, in contrast to the hollow fiber membrane, allowed 100% of the produced virus particles to pass through. To our knowledge, this is the first time a continuous virus harvest was shown for a membrane-based perfusion process. Overall, the process established offers interesting possibilities for advanced process integration strategies for next-generation virus particle and virus vector manufacturing.

Key pointsO_LIAn automated perfusion process for production of IAV DIPs was established
C_LIO_LIDIP titers of 7.40E+9 plaque forming units per mL were reached
C_LIO_LIA novel tubular cell retention device enabled continuous virus harvesting
C_LI

category: bioengineering


title: HistoClean: Open-source Software for Histological Image Pre-processing and Augmentation to Improve Development of Robust Convolutional Neural Networks

abstract: The growth of digital pathology over the past decade has opened new research pathways and insights in cancer prediction and prognosis. In particular, there has been a surge in deep learning and computer vision techniques to analyse digital images. Common practice in this area is to use image pre-processing and augmentation to prevent bias and overfitting, creating a more robust deep learning model. Herein we introduce HistoClean; user-friendly, graphical user interface that brings together multiple image processing modules into one easy to use toolkit. In this study, we utilise HistoClean to pre-process images for a simple convolutional neural network used to detect stromal maturity, improving the accuracy of the model at a tile, region of interest, and patient level. HistoClean is free and open-source and can be downloaded from the Github repository here: https://github.com/HistoCleanQUB/HistoClean.


title: Compensatory CSF2-driven macrophage activation promotes adaptive resistance to CSF1R inhibition in breast-to-brain metastasis

abstract: Tumor microenvironment-targeted therapies are emerging as promising treatment options for different cancer types. Tumor-associated macrophages and microglia (TAMs) represent an abundant non-malignant cell type in brain metastases and have been proposed to modulate metastatic colonization and outgrowth. We used an inhibitor of colony stimulating factor 1 receptor (CSF1R) to target TAMs at distinct stages of the metastatic cascade in preclinical breast-to-brain metastasis models and found that CSF1R inhibition leads to anti-tumor responses in prevention and intervention trials. However, in established brain metastases, compensatory CSF2Rb-STAT5-mediated pro-inflammatory TAM activation blunted the ultimate efficacy of CSF1R inhibition by inducing neuro-inflammation gene signatures in association with wound repair responses that fostered tumor recurrence. Consequently, combined blockade of CSF1R and STAT5 signaling led to sustained tumor control, a normalization of microglial activation states and amelioration of neuronal damage.


title: Systemic ligand-mimicking bioparticles cross the blood-brain barrier and reduce growth of intracranial triple-negative breast cancer using the human epidermal growth factor receptor 3 (HER3) to mediate both routes

abstract: Crossing the blood-brain barrier (BBB) and reaching intracranial tumors is a significant clinical challenge for targeted therapeutics and contributes to the poor prognosis for most patients with brain malignancies. Triple-negative breast cancer (TNBC) has a high propensity for metastasis to the brain and lacks cell surface markers that can be recognized by current targeted therapies used in the clinic, thus limiting therapeutic options. The human epidermal growth factor receptor HER3 (or ErbB3) has emerged as a biomarker of therapeutic resistance and metastasis in a growing range of tumor types and may serve as a possible therapeutic target for TNBC. Accordingly, we have developed HER3-targeted biological particles (bioparticles) that assume polyhedral capsid shapes when encapsulating nucleic acid cargo, forming nano-nucleocapsids (NNCs). The NNCs exhibit systemic homing to resistant and metastatic breast tumors, including TNBC, due to the high cell surface densities of HER3 on these tumors. Here we describe our discovery that HER3 is also prominently expressed on the brain endothelium and can mediate the passage of HER3-targeted NNCs across the BBB and into triple-negative breast tumors localized in the brain. Our findings show that HER3 is present at high levels on the vasculature (but not extravascular parenchyma) of both mouse and human adult brain specimens and associates with the extravasation of systemic HER3-targeted NNCs in mice and in a human model of the BBB (BBB chip). Furthermore, systemically delivered NNCs carrying tumoricidal agents reduced the growth of intracranial TNBC tumors in mice (representing metastatic breast tumors that have established in the brain) and exhibited improved therapeutic profile compared to current therapeutic interventions (liposomal doxorubicin) used in the clinic. This study addresses the major clinical problem of systemically delivering targeted therapeutics across the blood-brain barrier (BBB), and demonstrates a new route for not only accomplishing this but also for reaching tumors localized in the brain.


title: Applying automated patch-clamp to disease modeling: recapitulate phenotypes of Brugada syndrome using iPSC-CMs

abstract: Recently, there have been great advances in cardiovascular channelopathy modeling and drug safety pharmacology using human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). The automated patch-clamp (APC) technique overcomes the disadvantages of the manual patch-clamp (MPC) technique, which is labor intensive and gives low output. However, the application of the APC platform is still limited in iPSC-CM based research, due to the difficulty in maintaining the high quality of single iPSC-CMs during dissociation and recording. In this study, we improved the method for single iPSC-CM preparation by applying 2.5 M blebbistatin (BB, an excitation-contraction coupling uncoupler) throughout APC procedures (dissociation, filtration, storage, and recording). Under non-BB buffered condition, iPSC-CMs in suspension showed a severe bleb-like morphology. However, BB-supplement led to significant improvements in morphology and INa recording, and we even obtained several CMs that showed spontaneous action potentials with typical morphology. Furthermore, APC faithfully recapitulated the single-cell electrophysiological phenotypes of iPSC-CMs derived from Brugada syndrome patients, as detected with MPC. Our study indicates that APC is capable of replacing MPC in the modeling of cardiac channelopathies using human iPSC-CMs by providing high-quality data with higher throughput.


title: Blebbistatin protects iPSC-CMs from hypercontraction and facilitates automated patch-clamp based electrophysiological study


title: A biochemically-realisable model of the self-manufacturing cell

abstract: As shown by Hofmeyr, the processes in the living cell can be divided into three classes of efficient causes that produce each other, so making the cell closed to efficient causation, the hallmark of an organism. They are the enzyme catalysts of covalent metabolic chemistry, the intracellular milieu that drives the supramolecular processes of chaperone-assisted folding and self-assembly of polypeptides and nucleic acids into functional catalysts and transporters, and the membrane transporters that maintain the intracellular milieu, in particular its electrolyte composition. Each class of efficient cause can be modelled as a relational diagram in the form of a mapping in graph-theoretic form, and a minimal model of a self-manufacturing system that is closed to efficient causation can be constructed from these three mappings using the formalism of relational biology. This Fabrication-Assembly or (F,A)-system serves as an alternative to Robert Rosens replicative Metabolism-Repair or (M,R)-system, which has been notoriously problematic to realise in terms of real biochemical processes. A key feature of the model is the explicit incorporation of formal cause, which arrests the infinite regress that plagues all relational models of the cell. The (F,A)-system is extended into a detailed relational model of the self-manufacturing cell that has a clear biochemical realisation. This (F,A) cell model allows the interpretation and visualisation of concepts such as the metabolism and repair components of Rosens (M,R)-system, John von Neumanns universal constructor, Howard Pattees symbol-function split via the symbol-folding transformation, Marcello Barbieris genotype-ribotype-phenotype ontology, and Tibor Gantis chemoton.

category: systems biology


title: A biochemically-realisable relational model of the self-manufacturing cell


title: Treadmill exercise promotes retinal astrocyte plasticity and protects against retinal degeneration

abstract:
Exercise has been shown to be an effective neuroprotective intervention that preserves retinal function and structure in several animal models of retinal degeneration. However, retinal cell morphology and cell types governing exercise-induced retinal neuroprotection remain elusive. Previously, we found that the protective effects of exercise in animal models of retinal disease were accompanied by increased levels of circulating and retinal brain derived neurotrophic factor (BDNF) and required intact signal transduction with its high-affinity receptor, tropomyosin kinase B (TrkB). Studies of neurodegenerative diseases in the brain demonstrate that neurons and astrocytes express BDNF and TrkB. Additionally, astrocytes have been shown to alter their morphology in response to exercise. Here, we have investigated the role of retinal astrocytes as mediators of exercise-induced retinal neuroprotection in a light-induced retinal degeneration mouse model (LIRD). We found that treadmill exercise in both our dim (control maintenance light levels) and LIRD groups promote increased retinal astrocytic population, GFAP expression, branching and endpoints, dendritic complexity, and promotes BDNF-astrocyte interaction. In contrast, LIRD animals that were inactive had significant reductions in all measured parameters. Our findings indicate that exercise is sufficient to rescue retinal astrocyte morphology in a LIRD model maintaining branching and dendritic arborization similar to retinal astrocytes that are not undergoing degeneration. These studies provide essential information to current knowledge gaps in regards to exercise-induced neuroprotection and will additionally provide knowledge in exercise intervention optimization as a rehabilitative method.

Significance statementThis study represents an essential step in determining the cell-types governing and morphological alterations elicited from exercise which may provide neural repair and protection. Similar to astrocytes in the brain, retinal astrocytes alter their morphology in response to exercise. Our studies demonstrate exercise promotes increased interactions between retinal astrocytes and neural growth factors in healthy retinas as well as in retinas undergoing degeneration, which may ultimately protect dying retinal neurons. These studies provide insight into the potential neuroprotective role astrocytes play in neurodegenerative diseases.

category: neuroscience


title: Mitochondria decode firing frequency and coincidences of postsynaptic APs and EPSPs

abstract: Mitochondrial metabolism is critical for brain function. However, the mechanisms linking mitochondrial energy production to neuronal activity are elusive. Using whole-cell electrical recordings from Layer 5 pyramidal neurons in cortical slices and fluorescence imaging of cytosolic, mitochondrial Ca2+ indicators and endogenous NAD(P)H, we revealed ultra-fast, spike-evoked mitochondrial Ca2+ transients temporally similar to cytosolic Ca2+ elevations. We demonstrate that, whereas single or few spikes elicit the mitochondrial Ca2+ transients throughout the cell, their amplitude is differentially regulated in distinct neuronal compartments. Thus, these signals were prominent in the soma and apical dendrites and [~]3 times smaller in basal dendrites and axons. The spike firing frequency had a subtle effect on the amplitude of the cytosolic Ca2+ elevations but dramatically affected mitochondrial Ca2+ transients and NAD(P)H oxidation and recovery rates. Moreover, while subthreshold EPSPs alone caused no detectable Ca2+ elevation in dendritic mitochondria, the Hebbian coincidence of unitary EPSP and postsynaptic spike produced a localized, single mitochondrial Ca2+ elevation. These findings suggest that neuronal mitochondria are uniquely capable of decoding firing frequency and EPSP-to-spike time intervals for tuning the metabolic rate and triggering changes in synaptic efficacy.


title: Hypoxia is a dominant remodeler of the CD8+ T cell surface proteome relative to activation and regulatory T cell-mediated suppression

abstract: Immunosuppressive factors in the tumor microenvironment (TME) impair T cell function and limit the anti-tumor immune response. T cell surface receptors that influence interactions and function in the TME are already proven targets for cancer immunotherapy. However, surface proteome remodeling of primary human T cells in response to suppressive forces in the TME has never been characterized systematically. Using a reductionist cell culture approach with primary human T cells and SILAC-based quantitative cell surface capture glycoproteomics, we examined how two immunosuppressive TME factors, regulatory T cells (Tregs) and hypoxia, globally affect the activated CD8+ surface proteome (surfaceome). Surprisingly, the CD8+/Treg co-culture only modestly affected the CD8+ surfaceome, but did reverse several activation-induced surfaceomic changes. In contrast, hypoxia dramatically altered the CD8+ surfaceome in a manner consistent with both metabolic reprogramming and induction of an immunosuppressed state. The CD4+ T cell surfaceome similarly responded to hypoxia, revealing a novel hypoxia-induced surface receptor program. Our findings are consistent with the premise that hypoxic environments create a metabolic challenge for T cell activation, which may underlie the difficulty encountered in treating solid tumors with immunotherapies. Together, the data presented here provide insight into how suppressive TME factors remodel the T cell surfaceome and represent a valuable resource to inform future therapeutic efforts to enhance T cell function in the TME.

category: immunology