title: Cyclic constrained immunoreactive peptides from crucial P. falciparum proteins: potential implications in malaria diagnostics

abstract: Malaria is still a global challenge with significant morbidity and mortality, especially in the African, South-East Asian and Latin American region. Malaria diagnosis is a crucial pillar in the control and elimination efforts, often accomplished by administration of mass-scale Rapid diagnostic tests (RDTs). The inherent limitations of RDTs-failure of detection in low transmission settings, and deletion of one of the target proteins-Histidine rich protein (HRP) are evident from multiple reports; thus necessitating the need to explore novel diagnostic tools/targets. The present study used peptide microarray to screen potential epitopes from 13 antigenic proteins (CSP, EXP1, LSA1, TRAP, AARP, AMA1, GLURP, MSP1, MSP2, MSP3, MSP4, P48/45, HAP2) of P. falciparum. Three cyclic constrained immunoreactive peptides-C6 (EXP1), A8 (MSP2), B7 (GLURP) were identified from 5,458 cyclic constrained peptides (in duplicate) against P. falciparum infected sera. Peptides (C6, A8, B7-cyclic constrained) and (G11, DSQ, NQN-corresponding linear peptides) were fairly immunoreactive towards P. falciparum-infected sera in dot-blot assay. Using indirect ELISA, cyclic constrained peptides (C6 & B7) were found to be specific to P. falciparum infected sera and further, observed to be significantly reactive towards antibodies from field-collected P. falciparum infected sera. Notably, the structural location of the epitopes defines the reactivity, observed by the preferential recognition of cyclic constrained peptides vs linear peptides and corroborated by the homology modeling analysis of selected proteins. In conclusion, the study identified three cyclic constrained immunoreactive peptides (C6, B7 & A8) from P. falciparum secretory/surface proteins and two of them (C6 & B7) were validated for their diagnostic potential with field-collected P. falciparum infected sera samples.


title: Structural basis of mitochondrial protein import by the TIM complex

abstract: Mitochondria import nearly all their [~]1,000-2,000 constituent proteins from the cytosol across their double membrane envelope. Genetic and biochemical studies have shown that the conserved protein translocase, termed the TIM complex (also known as TIM23 complex), mediates import of presequence-containing proteins into the mitochondrial matrix and inner membrane. Among [~]10 different subunits of the complex, the essential multi-pass membrane protein Tim23, together with the evolutionarily related protein Tim17, has long been postulated to form a protein-conducting channel. However, the mechanism of TIM-mediated protein import remains uncertain due to a lack of structural information on the complex. Here, we have determined the cryo-EM structure of the core TIM complex (Tim17-Tim23-Tim44) from Saccharomyces cerevisiae. We show that, contrary to the prevailing model, Tim23 and Tim17 do not form a water-filled channel, but instead have separate, lipid-exposed concave cavities that face in opposite directions. Remarkably, our data suggest that the cavity of Tim17 itself forms the protein translocation path whereas Tim23 plays a structural role. We also show how the Tim17-Tim23 heterodimer associates with the scaffold protein Tim44 and J-domain proteins to mediate Hsp70-driven polypeptide transport into the matrix. Our work provides the structural foundation to understand the mechanism of TIM-mediated protein import and sorting, a central pathway in mitochondrial biogenesis.

category: biochemistry


title: Probiotic-guided CAR-T cells for universal solid tumor targeting

abstract: Synthetic biology enables the engineering of interactions between living medicines to overcome the specific limitations of any singular therapy. One major challenge of tumor-antigen targeting therapies like chimeric antigen receptor (CAR)-T cells is the identification of targetable antigens that are specifically and uniformly expressed on heterogenous solid tumors. In contrast, certain species of bacteria selectively colonize immune-privileged tumor cores and can be readily engineered as antigen-independent platforms for therapeutic delivery. Bridging these approaches, we develop a platform of probiotic-guided CAR-T cells (ProCARs), in which T cells are engineered to sense synthetic antigens (SA) that are produced and released by tumor-colonizing probiotic bacteria. We demonstrate increased CAR-T cell activation and tumor-cell lysis when SAs anchor to components of the extracellular matrix. Moreover, we show that ProCARs are intratumorally activated by probiotically-delivered SAs, receive further stimulation from bacterial TLR agonists, and are safe and effective in multiple xenograft models. This approach repurposes tumor-colonizing bacteria as beacons that guide the activity of engineered T cells, and in turn builds the foundation for communities of living medicines.

category: bioengineering


title: Subcellular localization of mutant P23H rhodopsin in an RFP fusion knockin mouse model of retinitis pigmentosa

abstract: The P23H mutation in rhodopsin (Rho), the visual pigment protein in rod photoreceptor neurons, is the most common genetic cause of autosomal dominant retinitis pigmentosa (adRP), a retinal disease that causes blindness. Despite multiple studies in animal models, the subcellular details of the fate of misfolded mutant Rho in rod photoreceptors have not been completely defined. We generated a new mouse model of adRP, in which the P23H-Rho mutant allele is fused to the fluorescent protein Tag-RFP-T (P23HhRhoRFP). In heterozygotes, outer segments formed, and WT rhodopsin was properly localized there, but mutant P23H-Rho protein was specifically mislocalized in the inner segments of rods. Despite this cellular phenotype, the P23HhRhoRFP heterozygous mice exhibited only slowly progressing retinal degeneration; in ERG recordings, scotopic a-wave amplitudes were reduced by 24% and 26% at 30 days and 90 days respectively, and the corresponding scotopic b-waves by 18% and 24%. Outer nuclear layer thickness was still 80% of WT at 90 days, but at 364 days had declined to 40% of WT. Transmission electron microscopy revealed greatly expanded membrane lamellae in the inner segment, and by fluorescence imaging, we determined that the mislocalized P23HhRhoRFP was contained in greatly expanded endoplasmic reticulum (ER) membranes. TUNEL staining revealed a slow pace of cell death involving chromosomal endonucleolytic degradation. Quantification of mRNA for markers of ER stress and the unfolded protein response revealed little or no increases in levels of messages encoding the proteins BiP, CHOP, ATF6, XBP1, PERK, Eif2 and Derlin-1, but a decreased level of total Rhodopsin (mouse + human) mRNA levels. The decline in the rate of cell death after an initial burst suggests that P23HhRhoRFP mutant rods undergo an adaptative process that prolongs survival despite gross P23HhRhoRFP protein accumulation in the ER. Because of its slowly progressing nature, and easy visualization of the mutant protein, the P23H-Rho-RFP mouse may represent a useful tool for the future study of the pathology and treatment of P23H-Rho and adRP.

category: neuroscience


title: CD47 cross-dressing by extracellular vesicles expressing CD47 inhibits phagocytosis without transmitting cell death signals

abstract: Transgenic CD47 overexpression is an encouraging approach to ameliorating xenograft rejection and alloresponses to pluripotent stem cells, and the efficacy correlates with the level of CD47 expression. However, CD47, upon ligation, also transmits signals leading to cell dysfunction or death, raising a concern that overexpressing CD47 could be harmful. Here, we unveiled an alternative source of cell surface CD47. We showed that extracellular vesicles (EVs), including exosomes (Exos), released from normal or tumor cells overexpressing CD47 (transgenic or native) can induce efficient CD47 cross-dressing on pig or human cells. Like the autogenous CD47, CD47 cross-dressed on cell surfaces is capable of interacting with SIRP to inhibit phagocytosis. However, ligation of the autogenous, but not cross-dressed, CD47 induced cell death. Thus, CD47 cross-dressing provides an alternative source of cell surface CD47 that may elicit its anti-phagocytic function without transmitting harmful signals to the cells. CD47 cross-dressing also suggests a previously unidentified mechanism for tumor-induced immunosuppression. Our findings should help to further optimize the CD47 transgenic approach that may improve outcomes by minimizing the harmful effects of CD47 overexpression.

category: immunology


title: Molecular assembly of measles and Nipah virus: specific lipid binding drives conformational change and matrix polymerization

abstract: Measles virus, Nipah virus, and multiple other paramyxoviruses cause disease outbreaks in humans and animals worldwide. The paramyxovirus matrix (M) protein mediates virion assembly and budding from host cell membranes. M is thus a key target for antivirals, but few high-resolution structures of paramyxovirus M are available, and we lack the clear understanding of how viral M proteins interact with membrane lipids to mediate viral assembly and egress needed to guide antiviral design. Here, we reveal that M proteins associate with phosphatidylserine and phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) at the plasma membrane. Using X-ray crystallography, electron microscopy, and molecular dynamics we demonstrate that PI(4,5)P2 binding induces conformational and electrostatic changes in the M protein surface that trigger membrane deformation, matrix layer polymerization, and virion assembly.

category: microbiology


title: Multiple nutritional and gut microbial factors associated with allergic rhinitis: the Hitachi Health Study

abstract: Several studies suggest the involvement of dietary habits and gut microbiome in allergic diseases. However, little is known about the nutritional and gut microbial factors associated with the risk of allergic rhinitis (AR). We recruited 186 apparently healthy workers with symptoms of AR and 106 controls at the Hitachi Health Care Center, Japan. The habitual consumption of 42 selected nutrients were examined using the brief-type self-administered diet history questionnaire. Faecal samples were collected and subjected to amplicon sequencing of the 16S ribosomal RNA gene hypervariable regions. Association analysis revealed that four nutrients (retinol, vitamin A, cryptoxanthin, and copper) were negatively associated with AR. Among 40 genera examined, relative abundance of Prevotella and Escherichia were associated with AR. Furthermore, significant statistical interactions were observed between retinol and Prevotella. The age- and sex-adjusted odds of AR were 25-fold lower in subjects with high retinol intake and high Prevotella abundance compared to subjects with low retinol intake and low Prevotella abundance. Our data provide insights into complex interplay between dietary nutrients, gut microbiome, and the development of AR.


title: Phage-encoded ribosomal protein S21 expression is linked to late stage phage replication

abstract: The ribosomal protein S21 (bS21) gene has been detected in diverse viruses with a large range of genome sizes, yet its in situ expression and potential significance have not been investigated. Here, we report five closely related clades of bacteriophages (phages) represented by 47 genomes (8 curated to completion and up to 331 kbp in length) that encode a bS21 gene. The bS21 gene is on the reverse strand within a conserved region that encodes the large terminase, major capsid protein, prohead protease, portal vertex proteins and some hypothetical proteins. These phages are predicted to infect Bacteroidetes species that inhabit a range of depths in freshwater lakes. Transcriptionally active bS21-encoding phages were sampled in the late-stage of replication, when core structural genes, bS21 and a neighboring gene of unknown function were highly expressed. Thus, our analyses suggest that bS21, which is involved in translation initiation, substitutes into the Bacteroidetes ribosomes and selects for phage transcripts during the late-stage replication when large-scale phage protein production is required for assembly of phage particles.


title: Catestatin selects for the colonization of antimicrobial-resistant gut bacterial communities

abstract: The gut microbiota is in continuous interaction with the innermost layer of the gut, namely the epithelium. One of the various functions of the gut epithelium, is to keep the microbes at bay to avoid overstimulation of the underlying mucosa immune cells. To do so, the gut epithelia secrete a variety of antimicrobial peptides, such as chromogranin A (CgA) peptide catestatin (CST: hCgA352-372). As a defense mechanism, gut microbes have evolved antimicrobial resistance mechanisms to counteract the killing effect of the secreted peptides. To this end, we treated wild-type mice and CST knockout (CST-KO) mice (where only the 63 nucleotides encoding CST have been deleted) with CST for 15 consecutive days. CST treatment was associated with a shift in the diversity and composition of the microbiota in the CST-KO mice. This effect was less prominent in WT mice. Levels of the microbiota-produced short-chain fatty acids, in particular, butyrate and acetate were significantly increased in CST-treated CST-KO mice but not the WT group. Both CST-treated CST-KO and WT mice showed a significant increase in microbiota-harboring phosphoethanolamine transferase-encoding genes, which facilitate their antimicrobial resistance. Finally, we show that CST was degraded by Escherichia coli via an omptin-protease and that the abundance of this gene was significantly higher in metagenomic datasets collected from patients with Crohns disease but not with ulcerative colitis. Overall, this study illustrates how the endogenous antimicrobial peptide, CST, shapes the microbiota composition in the gut and primes further research to uncover the role of bacterial resistance to CST in disease states such as inflammatory bowel disease.


title: Progressive protein aggregation in PRPF31 patient retinal pigment epithelium cells: the mechanism and its reversal through activation of autophagy

abstract:
Mutations in pre-mRNA processing factor 31 (PRPF31), a core protein of the spliceosomal tri-snRNP complex, cause autosomal-dominant retinitis pigmentosa (adRP). It has remained an enigma why mutations in ubiquitously expressed tri-snRNP proteins result in retina-specific disorders, and so far, the underlying mechanism of splicing factors-related RP is poorly understood. Here, we used iPSC technology to generate retinal organoids and RPE models from three patients with severe and very severe PRPF31-adRP, normal individuals and a CRISPR/Cas9-corrected isogenic control. To fully assess the impacts of PRPF31 mutations, quantitative proteomics analyses of retinal organoids and RPE cells was carried out showing RNA splicing, autophagy and lysosome, unfolded protein response (UPR) and visual cycle-related pathways to be significantly affected. Strikingly, the patient-derived RPE and retinal cells were characterised by the presence of large amounts of cytoplasmic aggregates containing the mutant PRPF31 and misfolded, ubiquitin-conjugated proteins including key visual cycle proteins, which accumulated progressively with time. Mutant PRPF31 variant was not incorporated into splicing complexes, but reduction of PRPF31 wildtype levels led to tri-snRNP assembly defects in Cajal bodies of PRPF31 patient retinal cells with reduced U4/U6 snRNPs and accumulation of U5, smaller nuclear speckles and reduced formation of active spliceosomes giving rise to global splicing dysregulation. Moreover, the impaired waste disposal mechanisms further exacerbated aggregate formation, and targeting these by activating the autophagy pathway using Rapamycin resulted in reduction of cytoplasmic aggregates and improved cell survival. Our data demonstrate that it is the progressive aggregate accumulation that overburdens the waste disposal machinery rather than direct PRPF31-initiated mis-splicing, and thus relieving the RPE cells from insoluble cytoplasmic aggregates presents a novel therapeutic strategy that can be combined with gene therapy studies to fully restore RPE and retinal cell function in PRPF31-adRP patients.

HighlightsO_LIPRPF31 RP mutations lead to formation of insoluble aggregates containing the mutant PRPF31 and misfolded, ubiquitin conjugated proteins including key visual cycle proteins (e.g. RLBP1) in RPE cells, which accumulate progressively with time and affect tight junctions and cell survival.
C_LIO_LIMutant PRPF31 is predominantly localised in cytoplasmic aggregates of patient specific RPE and retinal cells and is not able to be incorporated into splicing complexes to cause direct mis-splicing.
C_LIO_LIHigh-throughput quantitative proteomics identifies significantly altered RNA splicing, visual perception, retinoid metabolism, waste disposal and unfolded protein response pathways in patient RPE cells, and autophagy and lysosome, unfolded protein response (UPR) and visual cycle-related pathways in photoreceptor cells.
C_LIO_LIAccumulation of PRPF31 mutant variant as cytoplasmic aggregates reduces wildtype PRPF31 in the nucleus leading to tri-snRNP assembly defects, characterised by accumulation of U5 and reduction of U4/U6 snRNPs in Cajal bodies, altered morphology of nuclear speckles and consequently downregulation of active spliceosomes (Bact and C complexes) in PRPF31 patient RPE and retinal cells.
C_LIO_LIProteomic study of insoluble aggregates identifies other RP-linked splicing factors and multiple key retinal-specific proteins, whose variants are linked to retinitis pigmentosa, within the aggregates of patient RPE cells.
C_LIO_LIPRPF31 patient RPE cells have impaired waste disposal and proteasome mediated degradation, which together with the impaired autophagy pathway, further exacerbate aggregate formation.
C_LIO_LIPhagocytosis of photoreceptor outer segment fragments (POS) shed daily by RPE cells accelerates aggregation of key proteins indicating enhanced cytoplasmic aggregate formation under physiological conditions in patient RPE cells.
C_LIO_LIActivation of autophagy via administration of rapamycin results in reduction of cytoplasmic aggregates in RPE cells, correct localisation of mislocated and misfolded proteins to the nucleus, thereby improving cell survival.
C_LI

category: cell biology


title: A Multi-proxy assessment of the impact of climate change on Late Holocene (ca 4500-3800 BP) Native American villages of the Georgia coast

abstract: Circular shell rings along the Atlantic Coast of southeastern North America are the remnants of some of the earliest villages that emerged during the Late Archaic Period (5000 - 3000 BP). Many of these villages, however, were abandoned during the Terminal Late Archaic Period (ca 3800 - 3000 BP). Here, we combine Bayesian chronological modeling with multiple environmental proxies to understand the nature and timing of environmental change associated with the emergence and abandonment of shell ring villages on Sapleo Island, Georgia. Our Bayesian models indicate that Native Americans occupied the three Sapelo shell rings at varying times with some generational overlap. By the end of the complexs occupation, only Ring III was occupied before abandonment ca. 3845 BP. Ring III also consists of statistically smaller oysters (Crassostrea virginica) that people harvested from less saline estuaries compared to earlier occupations. These data, when integrated with recent tree ring analyses, show a clear pattern of environmental instability throughout the period in which the rings were occupied. We argue that as the climate became unstable around 4300 BP, aggregation at shell ring villages provided a way to effectively manage fisheries that are highly sensitive to environmental change. However, with the eventual collapse of oyster fisheries and subsequent rebound in environmental conditions ca. 3800 BP, people dispersed from shell rings, and shifted to non-marine subsistence economies and other types of settlements. This study provides the most comprehensive evidence correlations between large-scale environmental change and societal transformations on the Georgia coast during the Late Archaic period.

category: ecology


title: Rare instances of non-random dropout with the monochrome multiplex qPCR assay for mitochondrial DNA copy number

abstract:
Mitochondrial DNA copy number (mtDNA-CN) is a proxy for mitochondrial function and has been of increasing interest to the mitochondrial research community. There are a number of ways to measure mtDNA-CN, ranging from qPCR to whole genome sequencing [1]. A recent article in the Journal of Molecular Diagnostics [2] described a novel method for measuring mtDNA-CN that is both inexpensive and reproducible. After adapting the assay for use in our lab, we have found it to be reproducible and well-correlated with mtDNA-CN derived from whole genome sequencing. However, certain individuals show poor concordance between the two measures, particularly individuals with qPCR mtDNA-CN measurements >3 standard deviations below the sample mean, which corresponds to roughly 1% of assayed individuals (Figure 1). After examining whole genome sequencing data, this seems to be due to specific polymorphisms within the D-loop primer region, at positions MT 338, 340, 452, 457, 458, 460, 461, 466, and 467. All individuals with a variant in at least one of these positions have non-concordant mtDNA-CN measurements. Meanwhile, variants observed at other positions within the primer region do not appear to cause dropout.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/463983v1_fig1.gif" ALT="Figure 1">
View larger version (16K):
org.highwire.dtl.DTLVardef@134ca51org.highwire.dtl.DTLVardef@ce9196org.highwire.dtl.DTLVardef@1b82af6org.highwire.dtl.DTLVardef@c9701_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1.C_FLOATNO Discrepancy between the monochrome multiplex qPCR mtDNA-CN and the whole genome sequencing mtDNA-CN for 1,732 distinct individuals. Data are centered at 0 and scaled so that the standard deviation = 1. The dotted red line represents 3 standard deviations beneath the sample mean. Individuals in the U, L1, L4, and T haplogroups have a disproportionately higher risk of discordant measures between the two assays.

C_FIG

category: genetics


title: Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups

abstract: The rapid emergence of antimicrobial resistance (AMR) is a major concern for wildlife and ecosystem health globally. Genetic determinants of AMR have become indicators of anthropogenic pollution due to their greater association with humans and rarer presence in environments less affected by humans. The objective of this study was to determine the distribution and frequency of the class 1 integron, a genetic determinant of AMR, in both the faecal microbiome and in Escherichia coli isolated from neonates of three pinniped species. Australian sea lion (Neophoca cinerea), Australian fur seal (Arctocephalus pusillus doriferus) and long-nosed fur seal (Arctocephalus forsteri) pups from eight breeding colonies along the Southern Australian coast were sampled between 2016-2019. DNA from faecal samples (n=309) and from E. coli (n=795) isolated from 884 faecal samples were analysed for class 1 integrons using PCRs targeting the conserved integrase gene (intI) and the gene cassette array. Class 1 integrons were detected in A. p. doriferus and N. cinerea pups sampled at seven of the eight breeding colonies investigated in 4.85% of faecal samples (n=15) and 4.52% of E. coli isolates (n=36). Integrons were not detected in any A. forsteri samples. DNA sequencing of the class 1 integron gene cassette array identified diverse genes conferring resistance to four antibiotic classes. The relationship between class 1 integron carriage and the concentration of five trace elements and heavy metals was also investigated, finding no significant association. The results of this study add to the growing evidence of the extent to which antimicrobial resistant bacteria are polluting the marine environment. As AMR determinants are frequently associated with bacterial pathogens, their occurrence suggests that these pinniped species are vulnerable to potential health risks. The implications for individual and population health as a consequence of AMR carriage is a critical component of ongoing health investigations.


title: A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

abstract: The Klebsiella pneumoniae species complex (KpSC) is a set of seven Klebsiella taxa which are found in a variety of niches, and are an important cause of opportunistic healthcare-associated infections in humans. Due to increasing rates of multi-drug resistance within the KpSC, there is a growing interest in better understanding the biology and metabolism of these organisms to inform novel control strategies. We collated 37 sequenced KpSC isolates isolated from a variety of niches, representing all seven taxa. We generated strain-specific genome scale metabolic models (GEMs) for all 37 isolates and simulated growth phenotypes on 511 distinct carbon, nitrogen, sulphur and phosphorus substrates. Models were curated and their accuracy assessed using matched phenotypic growth data for 94 substrates (median accuracy of 96%). We explored species-specific growth capabilities and examined the impact of all possible single gene deletions on growth in 145 core carbon substrates. These analyses revealed multiple strain-specific differences, within and between species and highlight the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs, covering all seven taxa of the KpSC, provide a valuable resource to the Klebsiella research community.


title: The edible seaweed Laminaria japonica contains cholesterol analogues that inhibit Lipid Peroxidation and Cyclooxygenase Enzymes

abstract:
In this study, 5 sterols were isolated and purified from Laminaria japonica, commonly known as edible brown seaweed, and their structures were identified based on detailed chemical methods and spectroscopic analyses. Spectroscopic analyses characterized 5 sterols as 29-Hydroperoxy-stigmasta-5,24(28)-dien-3{beta}-ol, saringosterol (24-vinyl-cholest-5-ene-3{beta},24-diol), 24-methylenecholesterol, fucosterol (stigmasta-5,24-diene-3{beta}-ol), and 24-Hydroperoxy-24-vinyl-cholesterol. The bioactivities of these sterols were tested using lipid peroxidation (LPO) and cyclooxygenase (COX-1 and -2) enzyme inhibitory assays. Fucosterol exhibited the highest COX-1 and -2 enzyme inhibitory activities at 59 and 47%, respectively. Saringosterol, 24-methylenecholesterol and fucosterol showed higher LPO inhibitory activity at >50% than the other compounds. In addition, the results of molecular docking revealed that the 5 sterols were located in different pocket of COX-1 and -2 and fucosterol with tetracyclic skeletons and olefin methine achieved the highest binding energy (-7.85 and -9.02 kcal/mol) through hydrophobic interactions and hydrogen bond. Our results confirm the presence of 5 sterols in L. japonica and its significant anti-inflammatory and antioxidant activity.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/463984v1_ufig1.gif" ALT="Figure 1">
View larger version (21K):
org.highwire.dtl.DTLVardef@16c3f43org.highwire.dtl.DTLVardef@1ad7385org.highwire.dtl.DTLVardef@7b3c4borg.highwire.dtl.DTLVardef@b3675a_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LISterols 29-hydroperoxy-stigmasta-5,24(28)-dien-3{beta}-ol and 24-hydroperoxy-24-vinyl-cholesterol are identified for the first time in L. japonica.
C_LIO_LISaringosterol, 24-methylenecholesterol and fucosterol showed strong LPO inhibitory activity.
C_LIO_LIFucosterol showed highest binding affinity for COX-1 and -2 enzymes through hydrophobic interactions.
C_LI


title: Mouse model and human patient data suggest critical roles for Pten and p53 in suppressing POLE mutant tumor development

abstract: Mutations in the exonuclease domain of POLE are associated with tumors harboring very high mutation burdens. The mechanisms linking this significant mutation accumulation and tumor development remain poorly understood. Pole+/P286R;Trp53+/- mice showed accelerated cancer mortality compared to Pole+/P286R;Trp53+/+ mice. Cells from Pole+/P286R mice showed increased p53 activation, and subsequent loss of p53 permitted rapid growth, implicating canonical p53 loss of heterozygosity in POLE mutant tumor growth. Somewhat surprisingly, however, p53 status had no effect on tumor mutation burden or single base substitution signatures in POLE mutant tumors from mice or humans. Pten has important roles in maintaining genome stability. We find that PTEN mutations are highly enriched in human POLE mutant tumors, including many in POLE signature contexts. One such signature mutation, PTEN-F341V, was previously shown in a mouse model to specifically decrease nuclear Pten and lead to increased DNA damage. We found tumors in Pole+/P286R mice that spontaneously acquired PtenF341V mutations and were associated with significantly reduced nuclear Pten and elevated DNA damage. Taken together with recent published work, our results support the idea that POLE-mediated hypermutagenesis is necessary, but not entirely sufficient, for tumorigenesis. Disabling surveillance of nuclear DNA damage is a likely sufficient factor.

category: cancer biology


title: Resting brain activity emerges from wave propagating along spatiotemporal varying hyper-structural connectome

abstract: How spontaneous brain activities emerge from the structural connectivity (SC) has puzzled researchers for a long time. The underlying mechanism still remains largely unknown. Previous studies on modeling the resting-state human brain functional connectivity (FC) are normally based on the relatively static structural connectome directly and very few of them concern about the dynamic spatiotemporal variability of FC. Here we establish an explicit wave equation to describe the spontaneous cortical neural activities based on the high-order hypergraph representation of SC. Theoretical solution shows that the dynamic couplings between brain regions fluctuates in the form of an exponential wave regulated by the spatiotemporal varying Laplacian of the hyper-structural connectome (hSC), which orchestrates the cortical activities propagating in both space and time. Ultimately, we present a possible mechanism of how negative correlations emerge during the fluctuation of the hypergraph Laplacian of SC, which helps to further understand the fundamental role of SC in shaping the entire pattern of FC with a new perspective. Comprehensive tests on four connectome datasets with different resolutions confirm our theory and findings.


title: STAG2 promotes the myelination transcriptional program in oligodendrocytes

abstract: Cohesin folds chromosomes via DNA loop extrusion. Cohesin-mediated chromosome loops regulate transcription by shaping long-range enhancer-promoter interactions, among other mechanisms. Mutations of cohesin subunits and regulators cause human developmental diseases termed cohesinopathy. Vertebrate cohesin consists of SMC1, SMC3, RAD21, and either STAG1 or STAG2. To probe the physiological functions of cohesin, we created conditional knockout (cKO) mice with Stag2 deleted in the nervous system. Stag2 cKO mice exhibit growth retardation, neurological defects, and premature death, in part due to insufficient myelination of nerve fibers. Stag2 cKO oligodendrocytes exhibit delayed maturation and downregulation of myelination-related genes. Stag2 loss reduces promoter-anchored loops at downregulated genes in oligodendrocytes. Thus, STAG2-cohesin generates promoter-anchored loops at myelination-promoting genes to facilitate their transcription. Our study implicates defective myelination as a contributing factor to cohesinopathy and establishes oligodendrocytes as a relevant cell type to explore the mechanisms by which cohesin regulates transcription.

category: developmental biology


title: The structure of genotype-phenotype maps makes fitness landscapes navigable

abstract: Fitness landscapes are often described in terms of  peaks and  valleys, implying an intuitive low-dimensional landscape of the kind encountered in everyday experience. The space of genotypes, however, is extremely high-dimensional, which results in counter-intuitive properties of genotype-phenotype maps, such as the close proximity of one phenotype to many others. Here we investigate how common structural properties of high-dimensional genotype-phenotype maps, such as the presence of neutral networks, affect the navigability of fitness landscapes. For three biologically realistic genotype-phenotype map models--RNA secondary structure, protein tertiary structure and protein complexes--we find that, even under random fitness assignment, fitness maxima can be reached from almost any other phenotype without passing through a fitness valley. This in turn implies that true fitness valleys are very rare. By considering evolutionary simulations between pairs of real examples of functional RNA sequences, we show that accessible paths are also likely to be utilised under evolutionary dynamics.

category: evolutionary biology


title: Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites

abstract: The human genome contains roughly 1,600 transcription factors (TFs) (1), DNA-binding proteins recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX (2), and in vivo, using techniques including ChIP-seq (3, 4). We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. We will continue to expand the resource as ENCODE Phase IV data are released.

category: bioinformatics


title: HORmon: automated annotation of human centromeres

abstract: Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats (HORs)). Even though there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres, and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we demonstrate that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.


title: Multi-layer Regulation of Rubisco in Response to Altered Carbon Status in Synechococcus elongatus PCC 7942

abstract:
Photosynthetic organisms possess a variety of mechanisms to achieve balance between absorbed light (source) and the capacity to metabolically utilize or dissipate this energy (sink). While regulatory processes that detect changes in metabolic status/balance are relatively well-studied in plants, analogous pathways remain poorly characterized in photosynthetic microbes. Herein, we explore systemic changes that result from alterations in carbon availability in the model cyanobacterium Synechococcus elongatus PCC 7942 by taking advantage of an engineered strain where influx/efflux of a central carbon metabolite, sucrose, can be regulated experimentally. We observe that induction of a high-flux sucrose export pathway leads to depletion of internal carbon storage pools (glycogen), and concurrent increases in photosynthetic parameters. Further, a proteome-wide analysis and fluorescence reporter-based analysis revealed that upregulated factors following the activation of the metabolic sink are strongly concentrated on ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) and axillary modules involved in Rubisco maturation. Carboxysome number and Rubisco activity also increase following engagement of sucrose secretion. Conversely, reversing the flux of sucrose by feeding exogenous sucrose heterologously results in increased glycogen pools, decreased Rubisco abundance, decreased photosystem II quantum efficiency, and carboxysome reorganization. Our data suggest that Rubisco activity and organization are key outputs connected to regulatory pathways involved in metabolic balancing in cyanobacteria.

One sentence summaryRubisco activity and organization are key outputs involve in source-sink balancing in cyanobacteria.


title: Model-based ordination with constrained latent variables

abstract:
O_LIIn community ecology, unconstrained ordination can be used to predict latent variables from a multivariate dataset, which generated the observed species composition.
C_LIO_LILatent variables can be understood as ecological gradients, which are represented as a function of measured predictors in constrained ordination, so that ecologists can better relate species composition to the environment while reducing dimensionality of the predictors and the response data.
C_LIO_LIHowever, existing constrained ordination methods do not explicitly account for information provided by species responses, so that they have the potential to misrepresent community structure if not all predictors are measured.
C_LIO_LIWe propose a new method for model-based ordination with constrained latent variables in the Generalized Linear Latent Variable Model framework, which incorporates both measured predictors and residual covariation to optimally represent ecological gradients. Simulations of unconstrained and constrained ordination show that the proposed method outperforms CCA and RDA.
C_LI


title: Evolutionary Dynamics, Evolutionary Forces, and Robustness: A Nonequilibrium Statistical Mechanics Perspective

abstract: Any realistic evolutionary theory has to consider: (i) the dynamics of organisms that reproduce and possess heritable traits; (ii) the appearance of stochastic variations in these traits; and (iii) the selection of those organisms that better survive and reproduce. These elements shape the "evolutionary forces" that characterize the evolutionary dynamics. Here, we introduce a general model of reproduction-variation-selection dynamics. By treating these dynamics as a non-equilibrium thermodynamic process, we make precise the notion of the forces that characterize evolution. One of these forces, in particular, can be associated with the robustness of reproduction to variations. The emergence of this trait in our model--without any explicit selection for it--is an example of a general phenomenon, which can be called enaptation, distinct from the well-known and studied phenomena of adaptation and exaptation. Some of the detailed predictions of our model can be tested by quantitative laboratory experiments, similar to those performed in the past on evolving populations of proteins or viruses.


title: Whole genome sequence analysis of blood lipid levels in >66,000 individuals

abstract: Plasma lipids are heritable modifiable causal factors for coronary artery disease, the leading cause of death globally. Despite the well-described monogenic and polygenic bases of dyslipidemia, limitations remain in discovery of lipid-associated alleles using whole genome sequencing, partly due to limited sample sizes, ancestral diversity, and interpretation of potential clinical significance. Increasingly larger whole genome sequence datasets with plasma lipids coupled with methodologic advances enable us to more fully catalog the allelic spectrum for lipids. Here, among 66,329 ancestrally diverse (56% non-European ancestry) participants, we associate 428M variants from deep-coverage whole genome sequences with plasma lipids. Approximately 400M of these variants were not studied in prior lipids genetic analyses. We find multiple lipid-related genes strongly associated with plasma lipids through analysis of common and rare coding variants. We additionally discover several significantly associated rare non-coding variants largely at Mendelian lipid genes. Notably, we detect rare LDLR intronic variants associated with markedly increased LDL-C, similar to rare LDLR exonic variants. In conclusion, we conducted a systematic whole genome scan for plasma lipids expanding the alleles linked to lipids for multiple ancestries and characterize a clinically-relevant rare non-coding variant model for lipids.


title: Reverse engineering of metacognition

abstract: The human ability to introspect on thoughts, perceptions or actions - metacognitive ability - has become a focal topic of both cognitive basic and clinical research. At the same time it has become increasingly clear that currently available quantitative tools are limited in their ability to make unconfounded inferences about metacognition. As a step forward, the present work introduces a comprehensive framework and model of metacognition that allows for inferences about metacognitive noise and metacognitive biases during the readout of type 1 decision values or at the confidence reporting stage. The model assumes that confidence results from a continuous but noisy and potentially biased transformation of decision values, described by a confidence link function. A canonical set of metacognitive noise distributions is introduced which differ, amongst others, in their predictions about metacognitive sign flips of type 1 decision values. Successful recovery of model parameters is demonstrated and the model is validated on an empirical data set. In particular, it is shown that metacognitive noise and bias parameters correlate with conventional behavioral measures. Crucially, in contrast to these conventional measures, metacognitive noise parameters inferred from the model are shown to be independent of type 1 performance. This work is accompanied by a toolbox (ReMeta) that allows researchers to estimate key parameters of metacognition in confidence datasets.

category: systems biology


title: Assessing The Repeatability of Multi-Frequency Multi-Layer Brain Network Topologies Across Alternative Researchers Choice Paths

abstract: There is a growing interest in the neuroscience community on the advantages of multimodal neuroimaging modalities. Functional and structural interactions between brain areas can be represented as a network (graph) allowing us to employ graph-theoretic tools in multiple research directions. Researchers usually treated brain networks acquired from different modalities or different frequencies separately. However, there is strong evidence that these networks share complementary information while their interdependencies could reveal novel findings. For this purpose, neuroscientists adopt multilayer networks, which can be described mathematically as an extension of trivial single-layer networks. Multilayer networks have become popular in neuroscience due to their advantage to integrate different sources of information. We can incorporate this information from different modalities (multi-modal case), from different frequencies (multi-frequency case), or a single modality following a dynamic functional connectivity analysis (multi-layer,dynamic case). Researchers already used multi-layer networks to model brain disorders, to detect key hubs related to a specific function, to reveal structural-functional relationships, and to define more precise connectomic biomarkers related to brain disorders. However, the construction of a multilayer network depends on the selection of multiple preprocessing steps that can affect the final network topology. Here, we analyzed the fMRI dataset from a single human performing scanning over a period of 18 months (84 scans in total). We focused on assessing the reproducibility of multi-frequency multilayer topologies exploring the effect of two filtering methods for extracting frequencies from BOLD activity, three connectivity estimators, with or without a topological filtering scheme, and two spatial scales. Finally, we untangled specific combinations of researchers choices that yield repeatable topologies, giving us the chance to recommend best practices over consistent topologies.


title: Brain Data Standards Ontology: A data-driven ontology of transcriptomically defined cell types in the primary motor cortex

abstract: Large scale single cell omics profiling is revolutionising our understanding of cell types, especially in complex organs like the brain. This presents both an opportunity and a challenge for cell ontologies. Annotation of cell types in single cell  omics data typically uses unstructured free text, making comparison and mapping of annotation between datasets challenging. Annotation with cell ontologies is key to overcoming this challenge, but this will require meeting the challenge of extending cell ontologies representing classically defined cell types by defining and classifying cell types directly from data. Here we present the Brain Data Standards Ontology (BDSO), a data driven ontology that is built as an extension to the Cell Ontology (CL). It supports two major use cases: cell type annotation, and navigation, search, and organisation of a web application integrating single cell omics datasets for the mammalian primary motor cortex. The ontology is built using a semi-automated pipeline that interlinks cell type taxonomies and necessary and sufficient marker genes, and imports relevant ontology modules derived from external ontologies. Overall, the BDS ontology provides an underlying structure that supports these use cases, while remaining sustainable and extensible through automation as our knowledge of brain cell type expands.


title: Strategic Leadership Coaching supports Young Executives decision-making

abstract: Decision-making is central to daily function for executives in any organisation. Strategic leadership coaching (SLC) is an effective way to support complex decision-making, yet empirical neuroscientific data to support is lacking. The purpose of this study was to investigate the effects of SLC on young executives cortical arousal and their neural circuitry activation during the completion of computerized tasks which require activation of decision-making circuitry. We hypothesised SLC would improve cortical arousal when engaged with decision-making tasks, specifically increased electroencephalography (EEG) relative alpha band activity and improved neural circuitry engagement, measured as increased amplitude of event-related potential wave components. This study included thirty-one young male executives, of which eighteen underwent 8 sessions of SLC over two months. EEG records were collected thrice from those who underwent SLC (prior, post, and two months post), and twice from the control group (two months apart). The EEG recording session included completion of two decision-making tasks, an Iowa gambling task and Stroop colour-word conflict task. Finding, SLC increased alpha band activity over left frontal and central electrodes, and increased right parietal N170 amplitude and left parietal P300 amplitude. These findings support our hypothesis, as SLC improved cognitive cortical resources (enhanced alpha) which in turn permitted greater efficiency within decision-making circuitry (increased wave component amplitudes). This study provides the first and necessary neurobiological evidence to support and develop this line of research in SLC, and other forms of coaching, as it adds significant value.


title: Impact of hedonic value of stimuli on sampling dynamics during a preference test

abstract: The decision of whether to continue with a current action or to stop and consider alternatives is ever present in the life of an animal. Such continuous-time decision making lies at the heart of food preference tests whose outcomes are typically quantified by a single variable, the total amount consumed. However, the dynamics that give rise to such a quantity in terms of durations of bouts of sampling at a stimulus before pauses, and the impact of alternative stimuli on those bout durations and subsequent actions following a pause, can contain a richness of behavior that is not captured in a single palatability measure. Here we carry out multiple analyses of these dynamics, with a particular focus on assessing how the hedonic value of one taste stimulus impacts the behavior of a rat sampling a second taste stimulus during a preference test. We find evidence for an explicit competitive interaction between bout durations, such that the more palatable a stimulus the longer the bout durations when the rat samples the stimulus and the shorter the bout durations at the alternative. Such competition is reproduced in a model of a neural circuit that could underlie the continuous decision of when to end a sampling bout. We find that the competitive impact on bout durations is relatively short-lived whereas a competitive impact on the choice of which stimulus to approach following a pause persists. Such a discrepancy in the timescales for the decay of the impact of the alternative stimulus suggests different neural processes are involved in the choice of which stimulus to approach versus the choice of how long to sample from it. Since these two choices together combine to determine net consumption and therefore the inferred palatability or preference of a gustatory stimulus, our results suggest that palatability is not a unitary quantity but the result of at least two distinct, context-dependent neural processes.

category: animal behavior and cognition


title: A Novel Activation Maximization-based Approach for Insight into Electrophysiology Classifiers

abstract: Spectral analysis remains a hallmark approach for gaining insight into electrophysiology modalities like electroencephalography (EEG). As the field of deep learning has progressed, more studies have begun to train deep learning classifiers on raw EEG data, which presents unique problems for explainability. A growing number of studies have presented explainability approaches that provide insight into the spectral features learned by deep learning classifiers. However, existing approaches only attribute importance to different frequency bands. Most of the methods cannot provide insight into the actual spectral values or the relationship between spectral features that models have learned. Here, we present a novel adaptation of activation maximization for electrophysiology time-series that generates samples that indicate the features learned by classifiers by optimizing their spectral content. We evaluate our approach within the context of EEG sleep stage classification with a convolutional neural network, and we find that our approach is able to identify spectral patterns known to be associated with each sleep stage. We also find surprising results suggesting that our classifier may have prioritized the use of eye and motion artifact when identifying Awake samples. Our approach is the first adaptation of activation maximization to the domain of raw electrophysiology classification. Additionally, our approach has implications for explaining any classifier trained on highly dynamic, long time-series.


title: In-silico investigation of umami peptides with receptor T1R1/T1R3 for the discovering potential targets: A combined modeling approach

abstract: Umami, providing amino acids/peptides for animal growth, represents one of the major attractive taste modalities. The biochemical and umami properties of peptide are both important for scientific research and food industry. In this study, we did the sequence analysis of 205 umami peptides with 2-18 amino acids, sought the active sites of umami peptides by quantum chemical simulations and investigated their recognition residues with receptor T1R1/T1R3 by molecular docking. The results showed the peptides with 2-3 amino acids accounting for 44% of the total umami peptides. Residues D and E are the key active sites no matter where they in peptides (N-terminal, C-terminal or middle), when umami peptides contain D/E residues. N69, D147, R151, A170, S172, S276 and R277 residues in T1R1 receptor were deem to the key residues binding umami peptides. Finally, a powerful decision rule for umami peptides was proposed to predict potential umami peptides, which was convenient, time saving and efficiently.


title: Stably Accelerating Stiff Quantitative Systems Pharmacology Models: Continuous-Time Echo State Networks as Implicit Machine Learning

abstract: Quantitative systems pharmacology (QsP) may need to change in order to accommodate machine learning (ML), but ML may need to change to work for QsP. Here we investigate the use of neural network surrogates of stiff QsP models. This technique reduces and accelerates QsP models by training ML approximations on simulations. We describe how common neural network methodologies, such as residual neural networks, recurrent neural networks, and physics/biologically-informed neural networks, are fundamentally related to explicit solvers of ordinary differential equations (ODEs). Similar to how explicit ODE solvers are unstable on stiff QsP models, we demonstrate how these ML architectures see similar training instabilities. To address this issue, we showcase methods from scientific machine learning (SciML) which combine techniques from mechanistic modeling with traditional deep learning. We describe the continuous-time echo state network (CTESN) as the implicit analogue of ML architectures and showcase its ability to accurately train and predict on these stiff models where other methods fail. We demonstrate the CTESNs ability to surrogatize a production QsP model, a >1,000 ODE chemical reaction system from the SBML Biomodels repository, and a reaction-diffusion partial differential equation. We showcase the ability to accelerate QsP simulations by up to 56x against the optimized DifferentialEquations.jl solvers while achieving <5% relative error in all of the examples. This shows how incorporating the numerical properties of QsP methods into ML can improve the intersection, and thus presents a potential method for accelerating repeated calculations such as global sensitivity analysis and virtual populations.

category: pharmacology and toxicology


title: Decoding of human identity by computer vision and neuronal vision

abstract: Extracting meaning from a dynamic and variable flow of incoming information is a major goal of both natural and artificial intelligence. Computer vision (CV) guided by deep learning (DL) has made significant strides in recognizing a specific identity despite highly variable attributes1,2. This is the same challenge faced by the nervous system and partially addressed by the concept cells--neurons exhibiting selective firing in response to specific persons/places, described in the human medial temporal lobe (MTL)3-6. Yet, access to neurons representing a particular concept is limited due to these neurons sparse coding. It is conceivable, however, that the information required for such decoding is present in relatively small neuronal populations. To evaluate how well neuronal populations encode identity information in natural settings, we recorded neuronal activity from multiple brain regions of nine neurosurgical epilepsy patients implanted with depth electrodes, while the subjects watched an episode of the TV series "24". We implemented DL models that used the time-varying population neural data as inputs and decoded the visual presence of the main characters in each frame. Before training and testing the DL models, we devised a minimally supervised CV algorithm (with comparable performance against manually-labelled data7) to detect and label all the important characters in each frame. This methodology allowed us to compare "computer vision" with "neuronal vision"--footprints associated with each character present in the activity of a subset of neurons--and identify the brain regions that contributed to this decoding process. We then tested the DL models during a recognition memory task following movie viewing where subjects were asked to recognize clip segments from the presented episode. DL model activations were not only modulated by the presence of the corresponding characters but also by participants subjective memory of whether they had seen the clip segment, and by the associative strengths of the characters in the narrative plot. The described approach can offer novel ways to probe the representation of concepts in time-evolving dynamic behavioral tasks. Further, the results suggest that the information required to robustly decode concepts is present in the population activity of only tens of neurons even in brain regions beyond MTL.


title: Neuronal Dot1l is a broad mitochondrial gene-repressor associated with human brain aging via H3K79 hypermethylation

abstract: Methylation of histone 3 at lysine 79 (H3K79) and its catalyst, disrupter of telomeric silencing (Dot1l), have been coupled to multiple forms of stress like bioenergetic and ER challenges. However, studies on H3K79 methylation and Dot1l in the aging brain and neurons are very limited. This together with increasing evidence of a dynamic neuroepigenome made us wonder if H3K79 methylation and Dot1l could play unknown roles in brain aging and associated disorders. In aged humans, we found strong and consistent hypermethylation of H3K79 in neurons that accumulate lipofuscine, while neuronal Dot1l transcript abundance reacts to bioenergenic and oxidative challenges. Indeed, in dopaminergic neurons we found rapid global H3K79me turnover (<12h). While shortly after reduction of H3K79 methylation, synaptic transcripts decreased while mitochondrial genes, particularly respiratory chain transcripts increased. Strikingly, 6 months after reduction of Dot1l levels, almost solely a variety of mitochondrial genes linked to aging and Parkinsons disease remained increased. These profiles are in much detail inverse to those described in hallmark PD and aging studies and associate Dot1l and H3K79me with neuronal stress in the aging brain while putting Dot1l forward as dynamic master regulator of mitochondrial transcription in dopamine neurons.


title: Age-related intrinsic functional connectivity changes of locus coeruleus from childhood to older adults

abstract: The locus coeruleus is critical for selective information processing by modulating brains connectivity configuration. Increasingly studies have suggested that LC controls sensory inputs at the sensory gating stage. Furthermore, accumulating evidence has examined that young children and older adults are more prone to distraction and filter out irrelevant information less efficiently, possibly due to the impaired LC connectivity. However, the LC connectivity pattern across the life span is not fully examined yet, hampering our ability to understand the relationship between LC development and the distractibility. In this study, we examined the intrinsic network connectivity of the LC using resting-state fMRI from the enhanced NKI dataset with wide-range age samples. Based on LC-seed functional connectivity maps, we examined the age-related variation in the LC connectivity with a quadratic model. The analyses revealed two connectivity patterns explicitly. The sensory-related brain regions showed a positive quadratic age effect (u-shape), and the frontal regions for the cognitive control showed a negative quadratic age effect (inverted u-shape). Our results imply that such age-related distractibility is possibly due to the impaired sensory gating by the LC and the insufficient top-down controls by the frontal regions. We discuss the underlying neural mechanisms and limitations of our study.


title: Is there magnocellular facilitation of early neural processes underlying visual word recognition? Evidence from masked repetition priming with ERPs

abstract: An influential theory in the field of visual object recognition proposes that fast magnocellular (M) information facilitates neural processing of spatially more fine-grained but slower parvocellular (P) information. While written words can be considered as a special type of visual objects, it is unknown whether magnocellular facilitation also plays a role in reading. We used a masked priming paradigm that has been shown to result in neural facilitation in visual word processing and tested whether these facilitating effects are mediated by the magnocellular system. In two experiments, we manipulated the influence of magnocellular and parvocellular systems on visual processing of a contextually predictable target character by contrasting high versus low spatial frequency and luminance versus color contrast, respectively. In addition, unchanged (normal) primes were included in both experiments as a manipulation check. As expected, unchanged primes elicited typical repetition effects in the N1, N250 and P3 components of the ERP in both experiments. In the experiment manipulating spatial contrast, we obtained repetition effects only for the N1 component for both M- and P-biased primes. In the luminance versus color contrast experiment, repetition effects were found in N1 and N250 for both M- and P- biased primes. Furthermore, no interactions were found between M- vs. P-biased prime types and repetition. Together these results indicate that M- and P- information contributes jointly to early neural processes underlying visual word recognition.


title: Feature-based gating of cortical information transmission

abstract: In highly developed visual systems, spatial- and feature-based attentional modulation interact to prioritize relevant information and suppress irrelevant details. We investigated the specific role and integration of these two attentional mechanisms in visual cortical area MST of rhesus monkeys. We show that spatial attention acts as a gate for information processing by providing unimpeded high-gain pass-through processing for all sensory information from attended visual locations. Feature-based attentional enhancement does not only show the known dependency on a match between the attended feature and a given cells selectivity, but surprisingly is restricted to those features for which a given cell contributes to perception. This necessitates a refinement of the feature-similarity gain model of attention and documents highly optimized attentional gating of sensory information for cortical processing. This gating is shaped by neuronal sensory preferences, behavioral relevance, and the causal link to perception of neurons that process this visual input.


title: Parietal and Motor Cortical Dynamics Differentially Shape the Computation of Choice History Bias

abstract: AO_SCPLOWBSTRACTC_SCPLOWHumans and other animals tend to systematically repeat (or alternate) their previous choices, even when judging sensory stimuli presented in a random sequence. Choice history biases may arise from action preparation in motor circuits, or from perceptual or decision processing in upstream areas. Here, we combined source-level magnetoencephalographic (MEG) analyses of cortical population dynamics with behavioral modeling of a visual decision process. We disentangled two neural history signals in human motor and posterior parietal cortex. Gamma-band activity in parietal cortex tracked previous choices throughout the trial and biased evidence accumulation toward choice repetition. Action-specific beta-band activity in motor cortex also carried over to the next trial and biased the accumulation starting point toward alternation. The parietal, but not motor, history signal predicted the next trials choice as well as individual differences in choice repetition. Our results are consistent with a key role of parietal cortical signals in shaping choice sequences.


title: Effects of forest disturbance and regeneration on tree species composition and traits in DR Congo

abstract: Despite their key role in biodiversity conservation, forests of the Congo Basin are increasingly threatened by human activities. Whereas deforestation is very conspicuous, it remains challenging to monitor the impact of forest degradation under a more or less intact canopy. Likewise, the outcomes of forest regeneration following agricultural abandonment remain poorly studied in the Congo Basin. Here, we surveyed 125 vegetation quadrats across 25 forest inventory plots in the Yangambi region, and based on historical land-use maps. We aimed to assess both the impact of anthropogenic disturbance and forest recovery on tree species diversity, tree functional traits, community composition, canopy cover, and forest structure, as compared to undisturbed old-growth forest. We found that undisturbed old-growth forest harboured more tree individuals, particularly individuals with a smaller diameter, as well as species with a higher wood density when compared to both disturbed old-growth and regrowth forest. Moreover, species diversity was highest in disturbed old-growth forest. Tree species composition was significantly different between undisturbed old-growth forest and the other two forest categories. Our findings indicate that anthropogenic disturbance results in a degraded forest structure and may reduce the forests ability to store carbon. Whereas species diversity recovered 60 years after agricultural abandonment, species composition remained different from undisturbed old-growth forest. Our study illustrates the need for more extensive vegetation surveys in the Congo Basin in order to quantify the effects of human disturbance under a closed canopy.


title: Confirmation of fishers' local ecological knowledge of ciguatoxic fish species and ciguatera-prone hotspot areas in Puerto Rico using harmful benthic algae surveys and fish toxicity testing

abstract: Ciguatoxin fish poisoning (CFP) is caused by the consumption of tropical and subtropical fishes and other marine species with high levels of ciguatoxin (CTX) in their tissues. CTX is a polycyclic neurotoxin produced by single-celled, photosynthetic dinoflagellates in the Gambierdiscus and Fukuyoa genera which are found in close association with benthic autotrophs. CTX enters the food web when these dinoflagellates are inadvertently consumed by herbivores grazing on their preferred substrates. The toxin biomagnifies up the food chain to the top predators and if humans consume seafood with high levels of CTX it can cause a variety of flu-like symptoms. The best way to avoid CFP is to avoid toxic fishes. However, CTX is undetectable by physical inspection. This study investigated local fishers knowledge of ciguatera hotspots and coldspots along Puerto Rican coral reefs using toxic-dinoflagellate cell counts and by estimating fish toxicity in those sites using a cell-based Neuro-2a cytotoxicity assay. The fishers identified regions of high and low risk for CFP based on their local ecological knowledge (LEK) which were deemed hotspots and coldspots, respectively. There is a 35-fold difference in dinoflagellate cell counts of low-toxicity Gambierdiscus species in samples in the identified hotspot compared to the coldspot. Also, higher trophic level fishes (>3.4 ETL) had higher median estimates of CTX in their tissues at the hotspot than the same species in the coldspot. This study shows the effectiveness of LEK in identifying potential problem areas for ciguatera.


title: Universal Ontogenetic Growth without Fitting Parameters: Implications for Life History Invariants & Population Growth

abstract: Since the work of Von Bertalanffy (1957), several models have been proposed that relate the ontogenetic scaling of energy assimilation and metabolism to growth, being able to describe ontogenetic growth trajectories for living organisms and collapse them onto a single universal curve (West et al. 2001; Barnavar et al. 2002). Nevertheless, all these ontogenetic growth models critically depends on fitting parameters and on the allometric scaling of the metabolic rate. Using a new metabolic rate relation (Escala 2019) applied to a Bertalanffy-type ontogenetic growth equation, we find that ontogenetic growth can also be described by an universal growth curve for all studied species, but without the aid of any fitting parameters. We find that the inverse of the heart frequency fH, rescaled by the ratio of the specific energies for biomass creation and metabolism, defines the characteristic timescale for ontogenetic growth. Moreover, our model also predicts a generation time and lifespan that explains the origin of several  Life History Invariants (Charnov 1993) and predicts that the Mathusian Parameter should be inversely proportional to both the generation time and lifespan, in agreement with the data in the literature (Duncan et al. 1997; Dillingham et. al 2016; Hatton et al 2019). In our formalism, several critical timescales and rates (lifespan, generation time & intrinsic population growth rate) are all proportional to the heart frequency fH, thus their allometric scaling relations comes directly from the allometry of the heart frequency, which is typically fH{propto} M-0.25 under basal conditions.


title: Evolution of reduced dormancy during range expansions

abstract: There is increasing evidence that life-history traits can evolve rapidly during range expansion and that this evolution can impact the ecological dynamics of population spread. While dispersal evolution during range expansion has received substantial attention, dormancy (dispersal in time) has not. Here, we use an individual-based model to investigate the evolution of seed dormancy during range expansion. When a population is at spatial equilibrium our model produces results that are consistent with previous theoretical studies: seed dormancy evolves due to kin competition and the degree of dormancy increases as temporal environmental variation increases. During range expansions we consistently observe evolution towards reduced rates of dormancy at the front. Behind the front there is selection for higher rates of dormancy. Notably, the decreased dormancy towards the expanding margin reduces the regional resilience of recently expanded populations to a series of harsh years. We discuss how dormancy evolution during range expansion, and its consequences for spatial population dynamics, may impact other evolutionary responses to environmental change. We end with suggestions for future theoretical and empirical work.


title: Deep learning redesign of PETase for practical PET degrading applications

abstract: Plastic waste poses an ecological challenge1. While current plastic waste management largely relies on unsustainable, energy-intensive, or even hazardous physicochemical and mechanical processes, enzymatic degradation offers a green and sustainable route for plastic waste recycling2. Poly(ethylene terephthalate) (PET) has been extensively used in packaging and for the manufacture of fabrics and single-used containers, accounting for 12% of global solid waste3. The practical application of PET hydrolases has been hampered by their lack of robustness and the requirement for high processing temperatures. Here, we use a structure-based, deep learning algorithm to engineer an extremely robust and highly active PET hydrolase. Our best resulting mutant (FAST-PETase: Functional, Active, Stable, and Tolerant PETase) exhibits superior PET-hydrolytic activity relative to both wild-type and engineered alternatives, (including a leaf-branch compost cutinase and its mutant4) and possesses enhanced thermostability and pH tolerance. We demonstrate that whole, untreated, post-consumer PET from 51 different plastic products can all be completely degraded by FAST-PETase within one week, and in as little as 24 hours at 50 {degrees}C. Finally, we demonstrate two paths for closed-loop PET recycling and valorization. First, we re-synthesize virgin PET from the monomers recovered after enzymatic depolymerization. Second, we enable in situ microbially-enabled valorization using a Pseudomonas strain together with FAST-PETase to degrade PET and utilize the evolved monomers as a carbon source for growth and polyhydroxyalkanoate production. Collectively, our results demonstrate the substantial improvements enabled by deep learning and a viable route for enzymatic plastic recycling at the industrial scale.


title: scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model

abstract: Cell reprogramming offers a potential treatment to many diseases, by regenerating specialized somatic cells. Despite decades of research, discovering the transcription factors that promote cell reprogramming has largely been accomplished through trial and error, a time-consuming and costly method. A computational model for cell reprogramming, however, could guide the hypothesis formulation and experimental validation, to efficiently utilize time and resources. Current methods often cannot account for the heterogeneity observed in cell reprogramming, or they only make short-term predictions, without modelling the entire reprogramming process. Here, we present scREMOTE, a novel computational model for cell reprogramming that leverages single cell multiomics data, enabling a more holistic view of the regulatory mechanisms at cellular resolution. This is achieved by first identifying the regulatory potential of each transcription factor and gene to uncover regulatory relationships, then a regression model is built to estimate the effect of transcription factor perturbations. We show that scREMOTE successfully predicts the long-term effect of overexpressing two key transcription factors in hair follicle development by capturing higher-order gene regulations. Together, this demonstrates that integrating the multimodal processes governing gene regulation creates a more accurate model for cell reprogramming with significant potential to accelerate research in regenerative medicine.


title: GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation

abstract:
BackgroundOver the past three decades there have been numerous molecular biology developments that have led to an explosion in the number of gene expression studies being performed. Many of these gene expression studies publish their data to the public database GEO, making them freely available. By analysing gene expression datasets, researchers can identify genes that are differentially expressed between two groups. This can provide insights that lead to the development of new tests and treatments for diseases. Despite the wide availability of gene expression datasets, analysing them is difficult for several reasons. These reasons include the fact that most methods for performing gene expression analysis require programming proficiency.

ResultsWe developed the GEOexplorer software package to overcome several of the difficulties in performing gene expression analysis. GEOexplorer was therefore developed as a web application, that can perform interactive and reproducible microarray gene expression analysis, while producing a wealth of interactive visualisations to facilitate result exploration. GEOexplorer is implemented in R using the Shiny framework and is fully integrated with the existing core structures of the Bioconductor project. Users can perform the essential steps of exploratory data analysis and differential gene expression analysis intuitively and generate a broad spectrum of publication ready outputs.

ConclusionGEOexplorer is distributed as an R package in the Bioconductor project (http://bioconductor.org/packages/GEOexplorer/). GEOexplorer provides a solution for performing interactive and reproducible analyses of microarray gene expression data, empowering life scientists to perform exploratory data analysis and differential gene expression analysis on GEO microarray datasets.


title: Single cell micro-pillar-based characterization of endothelial and fibroblast cell mechanics

abstract: Mechanotransduction, the ability of cells to sense and respond to the mechanical cues from their microenvironment, plays an important role in numerous cellular processes, ranging from cell migration to differentiation. Several techniques have been developed to investigate the underlying mechanisms of mechanotransduction, in particular, force measurement-based techniques. However, we still lack basic single cell quantitative comparison on the mechanical properties of commonly used cell types, such as endothelial and fibroblast cells. Such information is critical to provide a precedent for studying complex tissues and organs that consist of various cell types. In this short communication, we report on the mechanical characterization of the commonly used endothelial and fibroblast cells at the single cell level. Using a micropillar-based assay, we measured the traction force profiles of these cells. Our study showcases differences between the two cell types in their traction force distribution and morphology. The results reported can be used as a reference and to lay the groundwork for future analysis of numerous disease models involving these cells.

category: biophysics


title: Cryo-electron microscopy revealed TACAN is extensively and specifically associated with membrane lipids

abstract: TACAN is not a mechanosensitive ion channel but significantly linked to the mechanical hyperalgesia. In this study, we show that the human TACAN is a homodimer with each monomer consisting of a body, a spring and a blade domains. The body domain contains six transmembrane helices that forms an independent channel. The spring domain adapts a loop-helix-loop configuration with the helix running within and parallel to the membrane. The blade domain is composed of two cytoplasmic helices. In addition, we found that all the helices of the body and the spring domains are specifically associated with membrane lipids. Particularly, a lipid core, residing within a cavity formed by the two body and spring domains, contacts with the helices from the body and spring domains and extends to reach two symmetrically arranged lipid clusters. These results extremely imply that the membrane lipids coordinate with the membrane-embedded protein to sense and transduce the mechanic signal.


title: Elevated transcriptional pausing of RNA polymerase II underlies acquired resistance to radiotherapy

abstract: As the mainstay modality for many malignancies, particularly inoperable solid tumors such as nasopharyngeal carcinoma (NPC), ionizing radiation (IR) induces a variety of lesions in genomic DNA, evoking a multipronged DNA damage response to interrupt many cellular processes including transcription. The turbulence in transcription, depending on the nature of DNA lesions, encompasses local blockage of RNA polymerase II (RNAPII) near the damage sites, as well as a less understood genome-wide alteration. How the transcriptional change influences the effectiveness of radiotherapy remains unclear. Using a panel of NPC and lung cancer cell lines, we observe increased phosphorylation at serine 5 (pS5) of the RNAPII after IR, indicating an accumulation of paused RNAPII. Remarkably, a similar increase of pS5 is seen in IR-resistant cells. ChIP-seq analysis of RNAPII distribution confirms this increased pausing both in IR-treated and IR-resistant NPC cells, notably on genes involved in radiation response and cell cycle. Accordingly, many of these genes show downregulated transcripts abundance in IR-resistant cells, and individual knockdown some of them such as TP53 and NEK7 endows NPC cells with varying degrees of IR-resistance. Decreasing pS5 of RNAPII and hence tuning down transcriptional pausing by inhibiting CDK7 reverses IR-resistance both in cell culture and xenograft models. Our results therefore uncover an unexpected link between elevated transcriptional pausing and IR-resistance. Given the recurrent NPC tissues display a steady increase in pS5 compared to the paired primary tissues, we suggest that CDK7 inhibitors can be used in combination with radiotherapy to increase sensitivity and thwart resistance.


title: Belemnite phylogeny and decline during the mid-Cretaceous

abstract: Belemnites are common fossil coleoid cephalopods of the Mesozoic. They began to diversify in the Triassic-Early Jurassic and maintained this diversity until the early Early Cretaceous. During the mid-Cretaceous, they declined in diversity and distribution, being restricted to only the Boreal and Austral Realm since the Turonian. Here, I present the first cladistic analysis of belemnite phylogeny, spanning taxa representative of the whole diversity and stratigraphic range of the group. This analysis shows that the usually applied subdivision of all belemnites into "Belemnitina" and "Belemnopseina" is not supported. A newly identified clade, the Pseudoalveolata, is suggested here. Pseudoalveolate belemnites represent the last remaining belemnites after the Aptian. Oceanic anoxia and warming are likely the main cause of the mid-Cretaceous belemnite decline, resulting in the Aptian-Albian dominance of the warm-adapted pseudoalveolate genus Neohibolites. The rise of teleost fish diversity during the mid-Cretaceous is discussed and its relevance for belemnite evolution. Some teleosts (e.g., Enchodus) might have taken over the mesopredator niches left by belemnites during the mid-Cretaceous, being better adapted to warming seas. Belemnites were not able to recover their earlier widespread distribution and diversity and the last remaining, disjunctly distributed families, the northern Belemnitellidae and southern Dimitobelidae, became extinct at the K/Pg-boundary.

category: paleontology


title: Somatic mutation detection in plants: a critical evaluation through simulations and reanalyses

abstract:
O_LIMutation, the source of genetic diversity, is the raw material of evolution; however, the mutation process remains understudied, especially in plants. Using both a simulation and reanalysis framework, we set out to test the performance of two types of variant callers, generic ones and those developed for cancer research, to detect de novo somatic mutations.
C_LIO_LIIn an in silico experiment, we generated Illumina-like sequence reads spiked with simulated mutations at different allele frequencies to compare the performance of seven commonly-used variant callers to recall them. More empirically, we then reanalyzed two of the largest datasets available for plants, both developed for identifying within-individual variation in long-lived pedunculate oaks.
C_LIO_LIEven in plants, variant callers developed for cancer research outperform generic callers regarding mutation recall and precision, especially at low allele frequency. Such variants at low allele frequency are typically expected for within-individual de novo plant mutations. Reanalysis of published oak data with the best-performing caller based on our simulations identified up to 7x more somatic mutations than initially reported.
C_LIO_LIOur results advocate the use of cancer research callers to boost de novo mutation research in plants, and to reconcile empirical reports with theoretical expectations.
C_LI

category: plant biology


title: Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks


title: Drosophila tachykininergic neurons modulate the activity of two groups of receptor-expressing neurons to regulate aggressive tone

abstract: Neuropeptides influence animal behaviors through complex molecular and cellular mechanisms, many of which are difficult to predict solely from synaptic connectivity. Here, we uncovered two separate downstream targets that are differentially modulated by the neuropeptide tachykinin, which promotes Drosophila aggression. Tachykinin from a single sexually dimorphic group of neurons recruits two separate downstream groups of neurons. One downstream group, synaptically connected to the tachykinergic neurons, expresses the receptor TkR86C and is necessary for aggression. Tachykinin supports the strength of cholinergic excitatory synaptic transmission between the tachykinergic and TkR86C downstream neurons. The other downstream group expresses the TkR99D receptor and is recruited primarily when tachykinin is over-expressed in the source neurons. This circuit reconfiguration correlates with the quantitative and qualitative enhancement of aggression observed when tachykinin is present in excess. Our data highlight how the amount of neuropeptide released from a small number of neurons can reshape the activity patterns of multiple downstream neural populations.


title: Global and Local Head Direction Coding in the Human Brain

abstract:
Orientation-specific head direction (HD) cells increase their firing rate to indicate ones facing direction in the environment. Rodent studies suggest HD cells in distinct areas of thalamus and retrosplenial cortex (RSC) code either for global (relative to the wider environment) or local (e.g., room-specific) reference frames. To investigate whether similar neuroanatomical dissociations exist in humans, we reanalysed functional magnetic resonance imaging data in which participants learned the orientation of unique images in separate local environments relative to distinct global landmarks (Shine, Valdes-Herrera, Hegarty, & Wolbers, 2016). The environment layout meant that we could establish two separate multivariate analysis models in which the HD on individual trials was coded relative either to global (North, South, East, West) or local (Front, Back, Right, Left) reference frames. Examining the data first in key regions of interest (ROI) for HD coding, we replicated our previous results and found that global HD was decodable in the thalamus and precuneus; the RSC, however, was sensitive only to local HD. Extending recent findings in both humans and rodents, V1 was sensitive to both HD reference frames. Additional small volume-corrected searchlight analyses supported the ROI results and indicated that the anatomical locus of the thalamic global HD coding was located in the medial thalamus, bordering the anterior thalamus, a region critical for global HD coding in rodents. Our findings elucidate further the putative neural basis of HD coding in humans, and suggest that distinct brain regions code for different frames of reference in HD.

Significance statementHead direction (HD) cells provide a neural signal as to ones orientation in the environment. HD can be coded relative to global or local (e.g., room-specific) reference frames, with studies suggesting that distinct areas of thalamus and retrosplenial cortex (RSC) code for this information. We reanalysed fMRI data where human participants associated images with global HDs before undergoing scanning. The design enabled us to examine both global and local HD coding. Supporting previous findings, global HD was decodable in thalamus, however the RSC coded only for local HD. We found evidence also for both reference frames in V1. These findings elucidate the putative neural basis of HD coding in humans, with distinct brain regions coding for different HD reference frames.


title: Additive, synergic and antagonistic interactions between maternal immune activation and peripubertal stress in cocaine addiction-like behaviour, morphofunctional brain parameters and striatal transcriptome.

abstract: Substance use disorders are more prevalent in schizophrenia, worsening its course and prognosis. Here, we used a double-hit rat model, combining maternal immune activation (MIA) and peripubertal stress (PUS), to study cocaine addiction and the underlying neurobehavioural alterations. We injected lipopolysaccharide or saline on gestational days 15 and 16 to pregnant rats. Their male offspring were then subjected to 5 episodes of unpredictable stress every other day during adolescence (from postnatal day 28 to 38). When rats reached adulthood, we studied cocaine addiction-like behaviour, impulsivity, conditioning processes and several aspects of brain structure and function by MRI, PET and RNAseq. MIA facilitated the acquisition of cocaine self-administration while PUS reduced cocaine intake, an effect that was reversed by MIA. MIA increased motivation for cocaine and reversed the effects of PUS during extended access. Incubation of seeking was unaffected. Neither hit alone nor their combination impacted Pavlovian or instrumental conditioning or impulsiveness. At the brain level, PUS reduced hippocampal volume and hyperactivated the dorsal subiculum. MIA+PUS altered the structure and function of the dorsal striatum increasing its volume and interfering with glutamatergic dynamics. MIA did not affect the gene expression of the nucleus accumbens but, when combined with PUS, modulated specific genes that could account for the restored cocaine intake. PUS had a profound effect on the dorsal striatal transcriptome however, this was obliterated when PUS occurred in animals with MIA. These results describe a complex interplay between MIA and stress on neurodevelopment and in the susceptibility to develop cocaine addiction.


title: C9orf72-derived poly-GA DPRs undergo endocytic uptake in iNPC-derived astrocytes and spread to motor neurons

abstract: Dipeptide repeat proteins (DPRs) are aggregation-prone polypeptides encoded by the pathogenic G4C2 repeat expansion in the C9orf72 gene, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). In this study, we focus on the role of poly-GA DPRs in disease spread. We demonstrate that recombinant poly-GA oligomers can directly convert into solid-like aggregates and form characteristic &[beta]-sheet fibrils in vitro. To dissect the process of cell-to-cell DPR transmission, we closely follow the fate of poly-GA DPRs in either their oligomeric or fibrillized form after administration in the cell culture medium. We observe that poly-GA DPRs are taken up via dynamin-dependent and - independent endocytosis, eventually converging at the lysosomal compartment and leading to axonal swellings in neurons. We then use a co-culture system to demonstrate astrocyte-to- motor neuron DPR propagation, showing that astrocytes may internalise and release aberrant peptides in disease pathogenesis. Overall, our results shed light on the mechanisms of poly- GA cellular uptake and cell-to-cell propagation, suggesting lysosomal impairment as a possible feature underlying the cellular pathogenicity of these DPR species.


title: FOXP4 differentially controls cold-induced beige adipocyte differentiation and thermogenesis

abstract: Beige adipocytes possess a discrete developmental origin and notable plasticity in thermogenic capacity in response to various environmental cues. But the transcriptional machinery controlling beige adipocyte development and thermogenesis remains largely unknown. By analyzing beige adipocyte-specific knockout mice, we identified a transcription factor, Forkhead Box P4 (FOXP4) that differentially governs beige adipocyte differentiation and activation. Depletion of Foxp4 caused a decline in the frequency of beige preadipocytes by switching their cell fate towards fibroblastic cells at the expense of beige adipocytes. However, we observed that ablation of Foxp4 in differentiated adipocytes profoundly potentiated their thermogenesis upon cold exposure. Of note, the outcome of Foxp4-deficiency on UCP1-mediated thermogenesis was confined to beige adipocytes, rather than to brown adipocytes. Taken together, we submit that FOXP4 primes beige adipocyte cell fate commitment and differentiation by potent transcriptional repression of the thermogenic program.


title: Intercellular alignment of apical-basal polarity coordinates tissue homeostasis and growth

abstract: Maintaining apicobasal polarity (ABP) is crucial for epithelial integrity and homeostasis during tissue development. Although recent studies have greatly advanced our understanding of intracellular mechanisms underlying ABP establishment, it remains largely unknown how the ABP is regulated at the tissue level. Here, we address intercellular mechanisms coordinating ABP using the Drosophila wing imaginal disc. By studying Scribble, a key ABP determinant, we show that ABP is regulated through intercellular alignment, which takes place either progressively or regressively in a context-dependent manner. Cells expressing wild type scribble progressively restore ABP in scribble hypomorphic mutant cells. In contrast, cells with conditional scribble knockdown instigate the regressive loss of polarity in abutting wild type cells. Our data reveal that genetic and physical interactions between Scribble, Septate junction complex and -Catenin appear to be key for sustaining intercellular network of ABP. Taken together, our findings indicate that the intercellular relay of the status of ABP contributes to the robustness of polarity across the tissue.


title: Stretch-induced endogenous electric fields drive neural crest directed collective cell migration in vivo

abstract: Directed collective cell migration (dCCM) is essential for morphogenesis1, 2. Cell clusters migrate in inherently complex in vivo environments composed of chemical, electrical, mechanical as well as topological features. While these environmental factors have been shown to allow dCCM in vitro, our understanding of dCCM in vivo is mostly limited to chemical guidance3. Thus, despite its wide biological relevance, the mechanisms that guide dCCM in vivo remain unclear. To address this, we study endogenous electric fields in relation to the migratory environment of the Xenopus laevis cephalic neural crest, an embryonic cell population that collectively and directionally migrates in vivo4, and whose migratory mode has been linked to cancer invasion and metastasis5. Combining bioelectrical, biomechanical and molecular tools, we show that endogenous electric fields drive neural crest dCCM via electrotaxis in vivo. Moreover, we identify the voltage-sensitive phosphatase 1 (Vsp1) as a key component of the molecular mechanism used by neural crest cells to transduce electric fields into a directional cue in vivo. Furthermore, Vsp1 function is specifically required for electrotaxis, being dispensable for cell motility and chemotaxis. Finally, we reveal that endogenous electric fields are mechanoelectrically established. Mechanistically, convergent extension movements of the neural fold generate membrane tension, which in turn opens stretch-activated channels to mobilise the ions required to fuel electric fields. Overall, our results reveal a mechanism of cell guidance, where electrotaxis emerges from the mechanoelectrical and molecular interplay between neighbouring tissues. More broadly, our data contribute to validate the, otherwise understudied, functions of endogenous bioelectrical stimuli in morphogenetic processes6.


title: Climate shapes flowering periods across plant communities

abstract:
AimClimate shapes the composition and function of plant communities globally, but it remains unclear how this influence extends to floral traits. Flowering phenology, or the time period in which a species flowers, has well-studied relationships with climatic signals at the species level but has rarely been explored at a cross-community and continental scale. Here, we characterise the distribution of flowering periods (months of flowering) across continental plant communities encompassing six biomes, and determine the influence of climate on community flowering period lengths.

LocationAustralia

TaxonFlowering plants

MethodsWe combined plant composition and abundance data from 629 standardised floristic surveys (AusPlots) with data on flowering period from the AusTraits database and additional primary literature for 2,983 species. We assessed abundance-weighted community mean flowering periods across biomes and tested their relationship with climatic annual means and the predictability of climate conditions using regression models.

ResultsCombined, temperature and precipitation (annual mean and predictability) explain 29% of variation in continental community flowering period. Plant communities with higher mean temperatures and lower mean precipitation have longer mean flowering periods. Moreover, plant communities in climates with predictable temperatures and, to a lesser extent, predictable precipitation have shorter mean flowering periods. Flowering period varies by biome, being longest in deserts and shortest in alpine and montane communities. For instance, desert communities experience low and unpredictable precipitation and high, unpredictable temperatures and have longer mean flowering periods, with desert species typically flowering at any time of year in response to rain.

Main conclusionsOur findings demonstrate the role of current climate conditions in shaping flowering periods across biomes, with implications under climate change. Shifts in flowering periods across climatic gradients reflect changes in plant strategies, affecting patterns of plant growth and reproduction as well as the availability of floral resources across the landscape.