title: Were Neoarchean atmospheric methane hazes and early Paleoproterozoic glaciations driven by the rise of oxygen in surface environments?

abstract: Geochemical evidence suggests methane was the predominant greenhouse gas in the Archean and early Proterozoic eons. Consequently, fluctuations in methane concentration in Earths atmosphere (i.e.,  methane hazes) would have contributed to climate change and influenced the flux of UV radiation reaching surface environments. If correct, understanding what factors (e.g., O2 and/or resource concentration) drove the biological methane cycle might shed light on the repetition of biological, atmospheric and climatic events preserved in the sedimentary rock record from ~2.8 to 2.0 BYA. To explore these interdependencies, we developed a novel dynamical model of microbial ecological interactions to investigate the conditions under which methane is preferentially released to the atmosphere. We found that the interplay between resource and O2 availability results in complex cyclic methane dynamics unrelated to the functional groups or efficiencies of microbial communities, to initial conditions, or to other model constraints. Based on these results, we propose that the cyclicity of methane haze events and glacial episodes in the Neoarchean and early Paleoproterozoic may have been linked to the progressive increase in oceanic and atmospheric O2 through the interval.

category: systems biology


title: Development of antibacterial compounds that block evolutionary pathways to resistance

abstract: Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC50 50-75 {micro}M against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3 resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC50) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which block evolutionary escape routes in pathogens.

category: biophysics


title: Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids

abstract: In mammals, circadian clocks are strictly suppressed during early embryonic stages as well as pluripotent stem cells, by the lack of CLOCK/BMAL1 mediated circadian feedback loops. During ontogenesis, the innate circadian clocks emerge gradually at a late developmental stage, then, with which the circadian temporal order is invested in each cell level throughout a body. Meanwhile, in the early developmental stage, a segmented body plan is essential for an intact developmental process and somitogenesis is controlled by another cell-autonomous oscillator, the segmentation clock, in the posterior presomitic mesoderm (PSM). In the present study, focusing upon the interaction between circadian key components and the segmentation clock, we investigated the effect of the CLOCK/BMAL1 on the segmentation clock Hes7 oscillation, revealing that the expression of functional CLOCK/BMAL1 severely interferes with the ultradian rhythm of segmentation clock in induced PSM and gastruloids. RNA sequencing analysis showed that the premature expression of CLOCK/BMAL1 affects the Hes7 transcription and its regulatory pathways. These results suggest that the suppression of CLOCK/BMAL1-mediated transcriptional regulation during the somitogenesis may be inevitable for intact mammalian development.

category: developmental biology


title: A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication

abstract: Most models of selection incorporate some notion of environmental degradation where the majority of the population becomes less fit with respect to a character resulting in pressure to adapt. Such models have been variously associated with an adaptation cost, the substitution load. Conversely, adaptative mutations that represent an improvement in fitness in the absence of environmental change have generally been assumed to be associated with negligible cost. However, such adaptations could represent a competitive advantage that diminishes resource availability for others and so induces a cost. This type of adaptation in the form of seedling competition has been suggested as a mechanism for increases in seed size during domestication, a trait associated with the standard stabilizing selection model. We present a novel cost framework for competitive selection that demonstrates significant differences in behaviour to environmental based selection in intensity, intensity over time and directly contrasts to the expectations of the standard model. Grain metrics of nine archaeological crops fit a mixed model in which episodes of competitive selection often emerge from shifting optimum episodes of stabilizing selection, highlighting the potential prevalence of the mechanism outlined here and providing a fundamental insight into the factors driving domestication.

category: evolutionary biology


title: Rhythmic modulation of visual perception by continuous rhythmic auditory stimulation

abstract:
At any given moment our sensory systems receive multiple, often rhythmic, inputs from the environment. Processing of temporally structured events in one sensory modality can guide both behavioural and neural processing of events in other sensory modalities, but whether this occurs remains unclear. Here, we used human electroencephalography (EEG) to test the cross-modal influences of a continuous auditory frequency-modulated (FM) sound on visual perception and visual cortical activity. We report systematic fluctuations in perceptual discrimination of brief visual stimuli in line with the phase of the FM sound. We further show that this rhythmic modulation in visual perception is related to an accompanying rhythmic modulation of neural activity recorded over visual areas. Importantly, in our task, perceptual and neural visual modulations occurred without any abrupt and salient onsets in the energy of the auditory stimulation and without any rhythmic structure in the visual stimulus. As such, the results provide a critical validation for the existence and functional role of cross-modal entrainment and demonstrates its utility for organising the perception of multisensory stimulation in the natural environment.

Significance StatementOur sensory environment is filled with rhythmic structures that are often multi-sensory in nature. Here we show that the alignment of neural activity to the phase of an auditory frequency-modulated sound has cross-modal consequences for vision: yielding systematic fluctuations in perceptual discrimination of brief visual stimuli that is mediated by accompanying rhythmic modulation of neural activity recorded over visual areas. These cross-modal effects on visual neural activity and perception occurred without any abrupt and salient onsets in the energy of the auditory stimulation and without any rhythmic structure in the visual stimulus. The current work shows that continuous auditory fluctuations in the natural environment can provide a pacing signal for neural activity and perception across the senses.

category: neuroscience


title: Neuroplasticity associated with changes in conversational turn-taking following a family-based intervention

abstract: Childrens early language environments are associated with linguistic, cognitive, and academic development, as well as concurrent brain structure and function. This study investigated neurodevelopmental mechanisms linking language input to development by measuring neuroplasticity associated with an intervention designed to enhance language environments of families primarily from lower socioeconomic backgrounds. Families of 52 4-to-6 year-old children were randomly assigned to a 9-week, interactive, family-based intervention or no-contact control group. Children completed pre- and post-assessments of verbal and nonverbal cognition (n=52), structural magnetic resonance imaging (n=45), and home auditory recordings of language exposure (n=39). Families who completed the intervention exhibited greater increases in adult-child conversational turns, and changes in turn-taking mediated intervention effects on language and executive functioning measures. Collapsing across groups, turn-taking changes were also positively correlated with cortical thickening in left inferior frontal and supramarginal gyri, the latter of which mediated relationships between changes in turn-taking and childrens language development. This is the first study of longitudinal neuroplasticity in response to changes in childrens language environments, and findings suggest that conversational turns support language development through cortical growth in language and social processing regions. This has implications for early interventions to enhance childrens language environments to support neurocognitive development.


title: Phylogenomics reveals that Asaia symbionts from insects underwent convergent genome reduction, preserving an insecticide-degrading gene

abstract:
The mosquito microbiota is composed by several lineages of microorganisms whose ecological roles and evolutionary histories have yet to be investigated in depth. Among these microorganisms, Asaia bacteria play a prominent role, given its abundance in the gut, reproductive organs and salivary glands of different mosquito species, while its presence has also been reported in several other insects. Notably, Asaia has great potential as a tool for the control of mosquito-borne diseases. Here, we present a wide phylogenomic analysis of Asaia strains isolated from different species of mosquito vectors and from different populations of the Mediterranean fruit fly (medfly) Ceratitis capitata, an insect pest of worldwide economic importance. We show that phylogenetically distant lineages of Asaia experienced independent genome reductions, despite following a common pattern, characterized by the early loss of genes involved in genome stability. This result highlights the role of specific metabolic pathways in the symbiotic relationship between Asaia and the insect host. Finally, we discovered that all but one of the Asaia strains included in the study possess the pyrethroid hydrolase gene. Phylogenetic analysis revealed that this gene is ancestral in Asaia, strongly suggesting that it played a role in the establishment of the symbiotic association between these bacteria and the mosquito hosts. We propose that this gene from the symbiont contributed to initial pyrethroid resistance in insects harboring Asaia, also considering the widespread production of pyrethrins by several plants.

ImportanceWe have studied genome reduction within several strains of the insect symbiont Asaia, isolated from different species/strains of mosquito and medfly. Phylogenetically distant strains of Asaia, despite following a common pattern involving the loss of genes related to genome stability, have undergone independent genome reductions, highlighting the peculiar role of specific metabolic pathways in the symbiotic relationship between Asaia and its host. We also show that the pyrethroid hydrolase gene is present in all the Asaia strains isolated except for the South American malaria vector An. darlingi, for which resistance to pyrethroids has never been reported, suggesting a possible involvement of Asaia in determining the resistance to insecticides.

category: microbiology


title: Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing

abstract: Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), viruses and hosts are each predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. Here, by coupling phenotypic and genomic analyses of coevolving populations of bacteriophage {lambda} and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet whole genome analyses did not. Rather than coevolution unfolding along a single trajectory, cryptic genetic variation emerges during initial virus-host coevolution. This variation is maintained across generations and eventually supplants dominant lineages. These observations constitute what we term  leapfrog coevolutionary dynamics, revealing weaknesses in the predictive power of standard coevolutionary models. The findings shed light on the mechanisms that structure coevolving ecological networks and reveal the limits of using phenotypic assays alone in characterizing coevolutionary dynamics.


title: Catestatin induces glycogenesis by stimulating phosphoinositide 3-kinase-AKT pathway

abstract:
AimDefects in hepatic glycogen synthesis contribute to postprandial hyperglycemia in type 2 diabetic (T2D) patients. Chromogranin A (CgA) peptide Catestatin (CST: hCgA352-372) has been shown to improve glucose tolerance in insulin-resistant mice. Here, we seek to determine whether CST also reduces hyperglycemia by increasing hepatic glycogen synthesis.

MethodsWe determined liver glycogen, glucose-6-phosphate (G6P), uridine diphosphate glucose (UDPG), and glycogen synthase (GYS2) activities; plasma insulin, glucagon, norepinephrine (NE), and epinephrine (EPI) levels in fed and fasted liver of lean and obese mice as well as in CST knockout (CST-KO) mice after treatments with saline, CST, or insulin. We also determined glycogen synthesis and glycogenolysis in primary hepatocytes. In addition, we analyzed phosphorylation signals of Insulin receptor (IR), insulin receptor substrate-1 (IRS-1), phosphatidylinositol dependent kinase-1 (PDK-1), GYS2, glycogen synthase kinase-3{beta} (GSK-3{beta}), AKT (an enzyme in AKR mouse that produces Thymoma)/PKB (protein kinase B) and mTOR (mammalian/mechanistic target of rapamycin) by immunoblotting.

ResultsCST stimulated glycogen accumulation in fed and fasted liver and in primary hepatocytes. CST reduced plasma NE and EPI levels, suggesting that CST promotes glycogenesis by inhibiting catecholamine-induced glycogenolysis. CST also directly stimulated glycogenesis and inhibited NE and EPI-induced glycogenolysis in hepatocytes. CST elevated the levels of UDPG and increased GYS2 activity, thus redirecting G6P to the glycogenic pathway. CST-KO mice had decreased liver glycogen that was restored by treatment with CST, reinforcing the crucial role of CST in hepatic glycogenesis. CST can improve insulin signals downstream of insulin receptor IR and IRS-1 by enhancing phospho-AKT signals through stimulation of PDK-1 and mTORC2 (mTOR complex 2) activities.

ConclusionsWe conclude that CST directly promotes the glycogenic pathway and reduces plasma glucose levels in insulin-resistant mice by (i) reducing glucose production, (ii) increasing glycogen synthesis from UDPG, and (iii) reducing glycogenolysis. This is achieved by enhancing downstream insulin signaling.

category: physiology


title: A eukaryote-wide perspective on the diversity and evolution of the ARF GTPase protein family

abstract:
The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARF GTPases that act in eukaryote-specific processes, including membrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a dataset of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor (LECA), nearly doubling the previously inferred ancient system complexity. Evidence for the wide occurrence and ancestral origin of Arf6, Arl13 and Arl16 is presented for the first time. Moreover, Arl17, Arl18 and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our dataset revealed a previously unsuspected diversity of membrane association modes and domain architectures within the ARF family. We detail the step-wise expansion of the ARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, our work fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.

SignificanceARF Family GTPases are crucial regulations of a diversity of cellular compartments and processes and as such the extent of this system in eukaryotes reflects both cellular complexity in modern eukaryotes and its evolution. Strikingly, a comprehensive comparative genomic analysis of the protein family is lacking, leaving its recent and ancient evolution poorly resolved. We performed a comprehensive molecular evolutionary analysis, reconstructing a highly complex ARF family complement in the Last Eukaryotic Common Ancestor, including a number of paralogs never before identified as such, and we find resolved relationships between the paralogs. This work has implications for cellular evolution from eukaryogenesis to cellular complexity in metazoans.


title: The genetic and ecological landscape of plasmids in the human gut

abstract:
Plasmids are mobile genetic elements that often carry key determinants of fitness, yet their diversity in natural systems is poorly understood. Here we trained a machine learning model on reference genomes to recognize the genetic architecture of plasmids. We applied our model to a global collection of human gut metagenomes to identify 68,350 non-redundant plasmids, which represent a 200-fold increase in the number of detectable plasmids in the human gut. This broad view of plasmid diversity revealed 1,169  plasmid systems, an evolutionary phenomenon where a backbone sequence with core plasmid functions, such as replication, is recombined with cargo functions, such as antibiotic resistance, depending on the environment. This work unearths the astonishing diversity of plasmids and provides a framework for studying their ecology and evolution.

One-Sentence SummaryNew computational methods enable a global search and reveal evolutionary principles of plasmids in the human gut microbiome.

category: bioinformatics


title: Natural isotope correction improves analysis of protein modification dynamics

abstract: Stable isotope labelling in combination with high resolution mass spectrometry approaches are increasingly used to analyse both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.


title: An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins

abstract: Intraviral protein-protein interactions are crucial for replication, pathogenicity, and viral assembly. Among these, virus assembly is a critical step as it regulates the arrangements of viral structural proteins and helps in the encapsulation of genomic material. SARS-CoV-2 structural proteins play an essential role in the self-rearrangement, RNA encapsulation, and mature virus particle formation. In SARS-CoV, the membrane protein interacts with the envelope and spike protein in Endoplasmic Reticulum Golgi Intermediate Complex (ERGIC) to form an assembly in the lipid bilayer, followed by membrane-ribonucleoprotein (nucleocapsid) interaction. In this study, we tried to understand the interaction of membrane proteins interaction with envelope, spike, and nucleocapsid proteins using protein-protein docking. Further, simulation studies performed up to 100 ns to examine the stability of protein-protein complexes of Membrane-Envelope, Membrane-Spike, and Membrane-Nucleocapsid. Prime MM-GBSA showed high binding energy calculations than the docked complex. The interactions identified in our study will be of great importance, as it provides valuable insight into the protein-protein complex, which could be the potential drug targets for future studies.


title: A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium.

abstract: SARS-CoV-2, causative agent of the COVID-19 pandemic, is thought to release its RNA genome at either the cell surface or within endosomes, the balance being dependent on spike protein stability, and the complement of receptors, co-receptors and proteases. To investigate possible mediators of pH-dependence, pKa calculations have been made on a set of structures for spike protein ectodomain and fragments from SARS-CoV-2 and other coronaviruses. Dominating a heat map of the aggregated predictions, 3 histidine residues in S2 are consistently predicted as destabilising in pre-fusion (all 3) and post-fusion (2 of 3) structures. Other predicted features include the more moderate energetics of surface salt-bridge interactions, and sidechain-mainchain interactions. Two aspartic acid residues in partially buried salt-bridges (D290 - R273 and R355 - D398) have pKas that are calculated to be elevated and destabilising in more open forms of the spike trimer. These aspartic acids are most stabilised in a tightly closed conformation that has been observed when linoleic acid is bound, and which also affects the interactions of D614. The D614G mutation is known to modulate the balance of closed to open trimer. It is suggested that D398 in particular contributes to a pH-dependence of the open/closed equilibrium, potentially coupled to the effects of linoleic acid binding and D614G mutation, and possibly also A570D mutation. These observations are discussed in the context of SARS-CoV-2 infection, mutagenesis studies, and other human coronaviruses.


title: Epigenetic regulation of epithelial dectin-1 through an IL-33-STAT3 axis in allergic disease

abstract: Allergic diseases arise in susceptible individuals in part because of decrements in protective pathways. The mechanism by which these anti-inflammatory molecules become repressed remains unclear. We have previously reported that epithelial dectin-1 prevents aberrant type 2 responses and is downregulated in the epithelium of allergic patients. Here we report that dectin-1 is constitutively expressed by the respiratory epithelium in humans, and that IL-33 specifically acts as a repressor of dectin-1. Mechanistically, this occurs via IL-33-dependent STAT3 activation and the subsequent repression of the dectin-1 gene, CLEC7A. We have identified a novel enhancer region upstream of the proximal promoter of CLEC7A that is only accessible in epithelial cells, but not in hematopoietic cells. Epigenetic repression of CLEC7A through this newly identified locus, downstream of an aberrant IL-33-STAT3 axis, occurs in the epithelium of allergic individuals. Collectively, our data identify a mechanism of epigenetic fine-tuning of dectin-1 expression in epithelial cells that may participate in allergenicity.

category: immunology


title: A non-olfactory shark adenosine receptor activates CFTR with unique pharmacology and structural features

abstract:
Adenosine receptors (ADORs) are G-protein coupled purinoceptors that have several functions including regulation of chloride secretion via CFTR in human airway and kidney. We cloned an ADOR from Squalus acanthias (shark) that likely regulates CFTR in the rectal gland. Phylogenic- and expression- analyses indicate that elasmobranch ADORs are non-olfactory, and appear to represent extant predecessors of mammalian ADORs. We therefore designate the shark ADOR as the A0 receptor. We co-expressed A0 with CFTR in Xenopus laevis oocytes and characterized the coupling of A0 to the chloride channel. Two electrode voltage clamping was performed and current-voltage (I-V) responses were recorded to monitor CFTR status. Only in A0- and CFTR- co-injected oocytes did adenosine analogs produce a significant concentration-dependent activation of CFTR consistent with its electrophysiological signature. A pharmacological profile for A0 was obtained for ADOR agonists and antagonists that differed markedly from all mammalian ADOR subtypes (agonists: R-PIA > S-PIA > CGS21680 > CPA > 2ClADO > CV1808 = DPMA > NECA) and (antagonists: DPCPX > PD115199 > 8PT > CGC > CGS15943). Structures of human ADORs permitted a high-confidence homology model of the shark A0 core which revealed unique structural features of ancestral receptors. We conclude: (1) A0 is a novel and unique adenosine receptor ancestor by functional and structural criteria; (2) A0 likely activates CFTR in vivo and this receptor activates CFTR in oocytes indicating an evolutionary coupling between ADORs and chloride secretion; and (3) A0 appears to be a non-olfactory evolutionary ancestor of all four mammalian ADOR subtypes.

Significance StatementWe have cloned and characterized an ancient adenosine receptor from sharks that is unlikely to be olfactory in function. The shark receptor, which we designate as A0, has a unique pharmacological profile, characteristic structural features, and is also highly likely to be the dominant ADOR regulator of the shark ancient ortholog of the Cystic Fibrosis chloride channel, called CFTR.

category: cell biology


title: Investigating age- and sex-specific effects of socialization on voluntary ethanol administration using a novel vapor paradigm

abstract:
IntroductionAdolescence is characterized as a transitional developmental period between childhood and adulthood that is associated with increased freedom and novel experiences that are frequently peer-influenced. Due to newfound independence, there is a higher prevalence of alcohol consumption, which is heightened by the rewarding effects of alcohol. However, the contributions of social interaction and sexual dimorphism to alcohol intake are not fully understood. Here we explore the use a novel self-administration ethanol (EtOH) vapor system to investigate the sexual dimorphic nature of socially facilitated ethanol exposure.

MethodsAdolescent and adult male and female Sprague-Dawley rats underwent a novel voluntary intermittent EtOH vapor paradigm. Nosepoke initiated self-administration vapor chambers administered 20mg/L of vaporized EtOH or air into the chamber following each nosepoke. Beginning on postnatal day 30 (PND30), during the onset of adolescence, or 70 (PND70), at the onset of adulthood, animals were placed in vapor chambers for 4hr every other day for 40 sessions. All animals underwent 10 sessions with their cagemate (social access) followed by 10 sessions in isolation (isolated access), a 10-day forced abstinence period, 10 sessions isolated access, and 10 sessions social access.

ResultsThese data reveal that despite low EtOH consumption across all groups, adolescent (PND30) and adult (PND70) female rats voluntarily self-administered more EtOH vapor per body weight than age-matched males, while male rats increased EtOH preference over sessions regardless of age. In addition, all rats regardless of sex or age voluntarily self-administered more EtOH vapor per body weight during the social access session than during the subsequent isolated access sessions.

ConclusionThese data demonstrate that under these experimental parameters, male and female rats regardless of age do not self-administer high quantities of EtOH vapor using this paradigm. Further work is required to determine whether the nose-poke EtOH vapor self-administration apparatus can be modified to promote high voluntary EtOH consumption that can be socially facilitated. These data demonstrate that with further investigation, the self-administration EtOH vapor system could be an effective alternative to other methods of voluntary EtOH administration to further our understanding of socially facilitated drinking.


title: Structural and functional plasticity in the dorsolateral geniculate nucleus of mice following bilateral enucleation

abstract: Within the nervous system, plasticity mechanisms attempt to stabilize network activity following disruption by injury, disease, or degeneration. Optic nerve injury and age-related diseases can induce homeostatic-like responses in adulthood. We tested this possibility in the thalamocortical (TC) neurons in the dorsolateral geniculate nucleus (dLGN) using patch-clamp electrophysiology, optogenetics, immunostaining, and single-cell dendritic analysis following loss of visual input via bilateral enucleation. We observed progressive loss of vGlut2-positive retinal terminals in the dLGN indicating degeneration post-enucleation that was coincident with changes in microglial morphology indicative of microglial activation. Consistent with the decline of vGlut2 puncta, we also observed loss of retinogeniculate (RG) synaptic function assessed using optogenetic activation of RG axons while performing whole-cell voltage clamp recordings from TC neurons in brain slices. Surprisingly, we did not detect any significant changes in the frequency of miniature post-synaptic currents (mEPSCs) or corticothalamic feedback synapses. Analysis of TC neuron dendritic structure from single-cell dye fills revealed a gradual loss of dendrites proximal to the soma, where TC neurons receive the bulk of RG inputs. Finally, analysis of action potential firing demonstrated that TC neurons have increased excitability following enucleation, firing more action potentials in response to depolarizing current injections. Our findings show that degeneration of the retinal axons/optic nerve and loss of RG synaptic inputs induces structural and functional changes in TC neurons, consistent with neuronal attempts at compensatory plasticity in the dLGN.


title: Preserved sensory processing but hampered conflict detection when stimulus input is task-irrelevant

abstract: Conflict detection in sensory input is central to adaptive human behavior. Perhaps unsurprisingly, past research has shown that conflict may even be detected in absence of conflict awareness, suggesting that conflict detection is an automatic process that does not require attention. To test the possibility of conflict processing in the absence of attention, we manipulated task relevance and response overlap of potentially conflicting stimulus features across six behavioral tasks. Multivariate analyses on human electroencephalographic data revealed neural signatures of conflict only when at least one feature of a conflicting stimulus was attended, regardless of whether that feature was part of the conflict, or overlaps with the response. In contrast, neural signatures of basic sensory processes were present even when a stimulus was completely unattended. These data reveal an attentional bottleneck at the level of objects, suggesting that object-based attention is a prerequisite for cognitive control operations involved in conflict detection.


title: A biophysical limit for quorum sensing in biofilms

abstract:
Bacteria grow on surfaces in complex immobile communities known as biofilms, which are composed of cells embedded in an extracellular matrix. Within biofilms, bacteria often interact with members of their own species, and cooperate or compete with members of other species via quorum sensing (QS). QS is a process by which microbes produce, secrete, and subsequently detect small molecules called autoinducers (AIs) to assess their local population density. We explore the competitive advantage of QS through agent-based simulations of a spatial model in which colony expansion via extracellular matrix production provides greater access to a limiting diffusible nutrient. We note a significant difference in results based on whether AI production is constitutive or limited by nutrient availability: If AI production is constitutive, simple QS-based matrix-production strategies can be far superior to any fixed strategy. However, if AI production is limited by nutrient availability, QS-based strategies fail to provide a significant advantage over fixed strategies. To explain this dichotomy, we derive a novel biophysical limit for the dynamic range of nutrient-limited AI concentrations in biofilms. This range is remarkably small (less than 10-fold) for the realistic case in which a growth-limiting diffusible nutrient is taken up within a narrow active growth layer. This biophysical limit implies that for QS to be most effective in biofilms, AI production should be a protected function not directly tied to metabolism.

Significance StatementBiofilms are a ubiquitous form of bacterial community. Within biofilms, bacteria communicate via chemical signals in a process called quorum sensing (QS). However, if signal production is nutrient-limited, then the nutrient-deficient interior of a biofilm cannot contribute to QS, which limits the ability of bacteria to assess their own population and behave accordingly. Numerical simulations of competitions among biofilm bacteria led us to discover a novel biophysical limit on the efficacy of nutrient-limited QS. In view of this limit, we conclude that to be most effective, QS signal production should be a prized function that is not metabolically slaved.


title: Conditional distribution modeling as an alternative method for covariates simulation: comparison with joint multivariate normal and bootstrap techniques

abstract: Clinical trial simulation (CTS) is a valuable tool in drug development. To obtain realistic scenarios, the subjects included in the CTS must be representative of the target population. Common ways of generating virtual subjects are based upon bootstrap (BS) procedures or multivariate normal distributions (MVND). Here, we investigated the performance of an alternative method based on conditional distributions (CD). Covariates data from a hypertension drug development program were used. The methods were evaluated based on the original dataset (internal evaluation) and on their ability to reproduce an older, unobserved population (extrapolation). Similar results were obtained in the internal evaluation for summary statistics, yet BS was able to preserve the correlation structure of the empirical distribution, which was not adequately reproduced by MVND; CD was in between BS and MVND. BS does not allow to extrapolate to an unobserved population. When the dataset used to inform the extrapolation was well approximated by a MVND, the results from CD and MVND were comparable. However, improved extrapolation performance was observed for CD when deviations from normality assumptions occurred. If CTS is used to simulate within the observed distribution, BS is the preferred method. When extrapolating to new populations, a parametric method like CD/MVND is needed. In case the empirical multivariate distribution is characterized by linearly related covariates and unimodal marginal distributions, MVND can be used because of the simpler statistical framework and well-established use; however, if uncertainty about the MVND assumptions exists, CD will increase the confidence in the simulations compared to MVND.

category: pharmacology and toxicology


title: A plausible mechanism for longitudinal lock-in of cortical microtubule array after light-induced reorientation

abstract: The light-induced reorientation of the cortical microtubule array in dark-grown A. thaliana hypocotyl cells is a striking example of the dynamical plasticity of the microtubule cytoskeleton. A consensus model, based on katanin-mediated severing at microtubule crossovers, has been developed that successfully describes the onset of the observed switch between a transverse and longitudinal array orientation. However, we currently lack an understanding of why the newly-populated longitudinal array direction remains stable for longer times and re-equilibration effects would tend to drive the system back to a mixed orientation state. Using both simulations and analytical calculations, we show that the assumption of a small orientation-dependent shift in microtubule dynamics is sufficient to explain the long term lock-in of the longitudinal array orientation. Furthermore, we show that the natural alternative hypothesis that there is a selective advantage in severing longitudinal microtubules, is neither necessary nor sufficient to achieve cortical array reorientation, but is able to accelerate this process significantly.

category: plant biology


title: Beyond linearity in neuroimaging: Capturing nonlinear relationships with application to longitudinal studies

abstract: The ubiquitous adoption of linearity for quantitative explanatory variables in statistical modeling is likely attributable to its advantages of straightforward interpretation and computational feasibility. The linearity assumption may be a reasonable approximation especially when the variable is confined within a narrow range, but it can be problematic when the variables effect is non-monotonic or complex. Furthermore, visualization and model assessment of a linear fit are usually omitted because of challenges at the whole brain level in neuroimaging. By adopting a principle of learning from the data in the presence of uncertainty to resolve the problematic aspects of conventional polynomial fitting, we introduce a flexible and adaptive approach of multilevel smoothing splines (MSS) to capture any nonlinearity of a quantitative explanatory variable for population-level neuroimaging data analysis. With no prior knowledge regarding the underlying relationship other than a parsimonious assumption about the extent of smoothness (e.g., no sharp corners), we express the unknown relationship with a sufficient number of smoothing splines and use the data to adaptively determine the specifics of the nonlinearity. In addition to introducing the theoretical framework of MSS as an efficient approach with a counterbalance between flexibility and stability, we strive to (a) lay out the specific schemes for population-level nonlinear analyses that may involve task (e.g., contrasting conditions) and subject-grouping (e.g., patients vs controls) factors; (b) provide modeling accommodations to adaptively reveal, estimate and compare any nonlinear effects of an explanatory variable across the brain, or to more accurately account for the effects (including nonlinear effects) of a quantitative confound; (c) offer the associated program 3dMSS to the neuroimaging community for whole-brain voxel-wise analysis as part of the AFNI suite; and (d) demonstrate the modeling approach and visualization processes with a longitudinal dataset of structural MRI scans.


title: A gain and dynamic range independent index to quantify spillover spread to aid panel design in flow cytometry

abstract: In conventional flowcytometry one detector (primary) is dedicated for one fluorochrome. However, photons usually end up in other detectors too (fluorescence spillover).  Compensation is a process that corrects the spillover signal from all detectors except the primary detector. Post  compensation, the photon counting error of spillover signals become evident as spreading of the data. The spreading induced by spillover impairs the ability to resolve stained cell population from the unstained one, potentially reducing or completely losing cell populations. For successful multi-color panel design, it is important to know the expected spillover to maximize the data resolution. The Spillover Spreading Matrix (SSM) can be used to estimate the spread, but the outcome is dependent on detector sensitivity. Simply, the same single stained sample produces different spillover spread values when detector(s) sensitivity is altered. Many researchers mistakenly use this artifact to "reduce" the spread by decreasing detector sensitivity. This can result in diminished capacity to resolve dimly expressing cell populations. Here, we introduce SQI (Spread Quantification Index), that can quantify the spillover spread independent of detector sensitivity and independent of dynamic range. This allows users to compare spillover spread between instruments having different types of detectors, which is not possible using SSM.


title: The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection

abstract: Inter-species comparisons of both morphology and gene expression within a phylum have revealed a period in the middle of embryogenesis with more similarity between species compared to earlier and later time-points. This  developmental hourglass pattern has been observed in many phyla, yet the evolutionary constraints on gene expression, and underlying mechanisms of how this is regulated, remains elusive. Moreover, the role of positive selection on gene regulation in the more diverged earlier and later stages of embryogenesis remains unknown. Here, using DNase-seq to identify regulatory regions in two distant Drosophila species (D. melanogaster and D. virilis), we assessed the evolutionary conservation and adaptive evolution of enhancers throughout multiple stages of embryogenesis. This revealed a higher proportion of conserved enhancers at the phylotypic period, providing a regulatory basis for the hourglass expression pattern. Using an in silico mutagenesis approach, we detect signatures of positive selection on developmental enhancers at early and late stages of embryogenesis, with a depletion at the phylotypic period, suggesting positive selection as one evolutionary mechanism underlying the hourglass pattern of animal evolution.


title: Population differentiation and structural variation in the genome of Manduca sexta across the United States

abstract: Many species that are extensively studied in the laboratory are less well characterized in their natural habitat, and laboratory strains represent only a small fraction of the variation in a species genome. Here we investigate genomic variation in three natural North American populations of an agricultural pest and a model insect for many scientific disciplines, the tobacco hornworm (Manduca sexta). We show that hornworms from Arizona, Kansas, and North Carolina are genetically distinct, with Arizona being particularly differentiated from the other two populations using Illumina whole-genome resequencing. Peaks of differentiation exist across the genome, but here we focus in on the most striking regions. In particular, we identify two likely segregating inversions found in the Arizona population. One inversion on the Z chromosome may enhance adaptive evolution of the sex chromosome. The larger, autosomal inversion contains a pseudogene may be involved in the exploitation of a novel hostplant in Arizona, but functional genetic assays will be required to support this hypothesis. Nevertheless, our results reveal undiscovered natural variation and provide useful genomic data for both pest management and evolutionary genetics of this insect species.


title: The epithelial splicing regulator ESRP2 is epigenetically repressed by DNA hypermethylation in Wilms tumour and acts as a tumour suppressor

abstract: Wilms tumour (WT), a childhood kidney cancer with embryonal origins, has been extensively characterised for genetic and epigenetic alterations, but a proportion of WTs still lack identifiable abnormalities. To uncover DNA methylation changes critical for WT pathogenesis, we compared the epigenome of fetal kidney with two WT cell lines, using methyl-CpG immunoprecipitation. We filtered our results to remove common cancer-associated epigenetic changes, and to enrich for genes involved in early kidney development. This identified four candidate genes that were hypermethylated in WT cell lines compared to fetal kidney, of which ESRP2 (epithelial splicing regulatory protein 2), was the most promising gene for further study. ESRP2 was commonly repressed by DNA methylation in WT, and this was shown to occur early in WT development (in nephrogenic rests). ESRP2 expression could be reactivated by DNA methyltransferase inhibition in WT cell lines. When ESRP2 was overexpressed in WT cell lines, it acted as an inhibitor of cellular proliferation in vitro, and in vivo it suppressed tumour growth of orthotopic xenografts in nude mice. RNA-seq of the ESRP2-expressing WT cell lines identified several novel splicing targets, in addition to well-characterised targets of ESRP2. We propose a model in which the mesenchymal to epithelial transition that is essential for early kidney development, can be disrupted in to generate WT, either by genetic abnormalities such as WT1 mutations, or by epigenetic defects, such as ESRP2 methylation.

category: cancer biology


title: Control of neurogenic competence in mammalian hypothalamic tanycytes.

abstract: Hypothalamic tanycytes, radial glial cells that share many features with neuronal progenitors, generate small numbers of neurons in the postnatal hypothalamus, but the identity of these neurons and the molecular mechanisms that control tanycyte-derived neurogenesis are unknown. In this study, we demonstrate that tanycyte-specific disruption of the NFI family of transcription factors (Nfia/b/x) robustly stimulates tanycyte proliferation and tanycyte-derived neurogenesis. Single-cell RNA- and ATAC-Seq analysis reveals that NFI factors repress Shh and Wnt signaling in tanycytes, and small molecule modulation of these pathways blocks proliferation and tanycyte-derived neurogenesis in Nfia/b/x-deficient mice. We show that Nfia/b/x-deficient tanycytes give rise to multiple mediobasal hypothalamic neuronal subtypes that can mature, integrate into hypothalamic synaptic circuitry, and selectively respond to changes in internal states. These findings identify molecular mechanisms that control tanycyte-derived neurogenesis, suggesting a new therapeutic approach to selectively remodel the hypothalamic neural circuitry that controls homeostatic physiological processes.


title: ATF-4 and hydrogen sulfide signalling mediate longevity from inhibition of translation or mTORC1

abstract: Inhibition of the master growth regulator mTORC1 (mechanistic target of rapamycin complex 1) slows ageing across phyla, in part by reducing protein synthesis. Various stresses globally suppress protein synthesis through the integrated stress response (ISR), resulting in preferential translation of the transcription factor ATF-4. Here we show in C. elegans that inhibition of translation or mTORC1 increases ATF-4 expression, and that ATF-4 mediates longevity under these conditions independently of ISR signalling. ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production. This H2S boost increases protein persulfidation, a protective modification of redox-reactive cysteines. The ATF-4/CTH-2/H2S pathway also mediates longevity and increased stress resistance from mTORC1 suppression. Increasing H2S levels, or enhancing mechanisms that H2S influences through persulfidation, may represent promising strategies for mobilising therapeutic benefits of the ISR, translation suppression, or mTORC1 inhibition.


title: Learning to live with Dale's principle: ANNs with separate excitatory and inhibitory units

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe units in artificial neural networks (ANNs) can be thought of as abstractions of biological neurons, and ANNs are increasingly used in neuroscience research. However, there are many important differences between ANN units and real neurons. One of the most notable is the absence of Dales principle, which ensures that biological neurons are either exclusively excitatory or inhibitory. Dales principle is typically left out of ANNs because its inclusion impairs learning. This is problematic, because one of the great advantages of ANNs for neuroscience research is their ability to learn complicated, realistic tasks. Here, by taking inspiration from feedforward inhibitory interneurons in the brain we show that we can develop ANNs with separate populations of excitatory and inhibitory units that learn just as well as standard ANNs. We call these networks Dales ANNs (DANNs). We present two insights that enable DANNs to learn well: (1) DANNs are related to normalization schemes, and can be initialized such that the inhibition centres and standardizes the excitatory activity, (2) updates to inhibitory neuron parameters should be scaled using corrections based on the Fisher Information matrix. These results demonstrate how ANNs that respect Dales principle can be built without sacrificing learning performance, which is important for future work using ANNs as models of the brain. The results may also have interesting implications for how inhibitory plasticity in the real brain operates.


title: New Insights from Old Data: Multimodal Classification of Schizophrenia using Automated Deep Learning Configurations

abstract: AO_SCPLOWBSTRACTC_SCPLOWSchizophrenia is a heterogeneous cognitive disorder where clinical classification is challenging because of the lack of well-established, non-invasive diagnoses biomarkers. There is, hence, a need for objective systems that can classify Schizophrenia despite challenges such as overlapping symptomatic factors, diverse internal clinical manifestations, and complex diagnostic process leading to delayed treatment. Thus, experimentation with automated machine learning architectural frameworks (AutoML) is presented in order to handle multimodal Functional Network Connectivity(FNC) and Source Based Morphometry(SBM) features based on functional magnetic resonance imaging(fMRI) and structural magnetic resonance imaging(sMRI) components respectively. On evaluating the resultant AutoML models with respect to approximately 280 machine learning architectures on the Overall AUC metric, the former outperforms the latter despite remarkable limitations including complex high dimensional feature space with very little data.


title: A global indicator of utilised wildlife populations: regional trends and the impact of management

abstract: The sustainable use of wildlife is a core aspiration of biodiversity conservation but is the subject of intense debate in the scientific literature as to how, and whether, species are best used and managed. While both positive and negative outcomes of sustainable use are known for specific taxa or local case studies, a global and regional picture of trends in wildlife populations in use is lacking. We use a global data set of over 11,000 time-series to derive indices of  utilised and  not utilised wildlife populations and assess global and regional changes, principally for mammals, birds and fishes. We also assess whether  management makes a measurable difference to wildlife population trends, especially for the utilised species populations. Our results show that wildlife population trends globally are negative, but with utilised populations tending to decline more rapidly, especially in Africa and the Americas. Crucially, where utilised populations are managed, using a variety of mechanisms, there is a positive impact on the trend. It is therefore true that use of species can both be a driver of negative population trends, or a driver of species recovery, with numerous species and population specific case examples making up these broader trends. This work is relevant to the evidence base for the IPBES Sustainable Use Assessment, and to the development of indicators of sustainable use of species under the post-2020 Global Biodiversity Framework being developed under the Convention on Biological Diversity.

category: ecology


title: Zinc-embedded fabrics inactivate SARS-CoV-2 and influenza A virus

abstract: Infections with respiratory viruses can spread via liquid droplets and aerosols, and cause diseases such as influenza and COVID-19. Face masks and other personal protective equipment (PPE) can act as barriers that prevent the spread of respiratory droplets containing these viruses. However, influenza A viruses and coronaviruses are stable for hours on various materials, which makes frequent and correct disposal of these PPE important. Metal ions embedded into PPE may inactivate respiratory viruses, but confounding factors such as absorption of viruses make measuring and optimizing the inactivation characteristics difficult. Here we used polyamide 6.6 (PA66) fibers that had zinc ions embedded during the polymerisation process and systematically investigated if these fibers can absorb and inactivate pandemic SARS-CoV-2 and influenza A virus H1N1. We find that these viruses are readily absorbed by PA66 fabrics and inactivated by zinc ions embedded into this fabric. The inactivation rate (pfu{middle dot}gram-1{middle dot}min-1) exceeds the number of active virus particles expelled by a cough and supports a wide range of viral loads. Moreover, we found that the zinc content and the virus inactivating property of the fabric remain stable over 50 standardized washes. Overall, these results provide new insight into the development of "pathogen-free" PPE and better protection against RNA virus spread.


title: The Mitochondrial Permeability Transition Pore Activates the Mitochondrial Unfolded Protein Response and Promotes Aging

abstract: Mitochondrial activity determines aging rate and the onset of chronic diseases. The mitochondrial permeability transition pore (mPTP) is a pathological pore in the inner mitochondrial membrane thought to be composed of the F-ATP synthase (complex V). OSCP, a subunit of F-ATP synthase, helps protect against mPTP formation. How the destabilization of OSCP may contribute to aging, however, is unclear. We have found that loss OSCP in the nematode Caenorhabditis elegans initiates the mPTP and shortens lifespan specifically during adulthood, in part via initiation of the mitochondrial unfolded protein response (UPRmt). Pharmacological or genetic inhibition of the mPTP inhibits the UPRmt and restores normal lifespan. Loss of the putative pore-forming component of F-ATP synthase extends adult lifespan, suggesting that the mPTP normally promotes aging. Our findings reveal how an mPTP/UPRmt nexus may contribute to aging and age-related diseases and how inhibition of the UPRmt may be protective under certain conditions.


title: Reciprocal lateral hypothalamic and raphe GABAergic projections promote wakefulness

abstract: The lateral hypothalamus (LH), together with multiple neuromodulatory systems of the brain, such as the dorsal raphe nucleus (DR), is implicated in arousal, yet interactions between these systems are just beginning to be explored. Using a combination of viral tracing, circuit mapping, electrophysiological recordings from identified neurons and combinatorial optogenetics in mice, we show that GABAergic neurons in the LH selectively inhibit GABAergic neurons in the DR resulting in increased firing of a substantial fraction of its neurons that ultimately promotes arousal. These DRGABA neurons are wake active and project to multiple brain areas involved in the control of arousal including the LH, where their specific activation potently influences local network activity leading to arousal from sleep. Our results show how mutual inhibitory projections between the LH and the DR promote wakefulness and suggest a complex arousal control by intimate interactions between long-range connections and local circuit dynamics.


title: Extensive and accurate benchmarking of DIA acquisition methods and software tools using a complex proteomic standard

abstract: Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1 - Sigma) at 8 different concentrations in an E. coli proteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline and Spectronaut) with or without the use of a DDA spectral library. Based on the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.


title: IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs

abstract: Missing values weaken the power of label-free quantitative proteomic experiments to uncover true quantitative differences between biological samples or experimental conditions. Match-between-runs (MBR) has become a common approach to mitigate the missing value problem, where peptides identified by tandem mass spectra in one run are transferred to another by inference based on m/z, charge state, retention time, and ion mobility when applicable. Though tolerances are used to ensure such transferred identifications are reasonably located and meet certain quality thresholds, little work has been done to evaluate the statistical confidence of MBR. Here, we present a mixture model-based approach to estimate the false discovery rate (FDR) of peptide and protein identification transfer, which we implement in the label-free quantification tool IonQuant. Using several benchmarking datasets generated on both Orbitrap and timsTOF mass spectrometers, we demonstrate superior performance of IonQuant with FDR-controlled MBR compared to MaxQuant (19-38 times faster; 6-18% more proteins quantified and with comparable or better accuracy). We further illustrate the performance of IonQuant, and highlight the need for FDR-controlled MBR, in two single-cell proteomics experiments, including one acquired with the help of high-field asymmetric ion mobility spectrometry (FAIMS) separation. Fully integrated in FragPipe computational environment, IonQuant with FDR-controlled MBR enables fast and accurate peptide and protein quantification in label-free proteomics experiments.


title: Disrupted visual cortical plasticity in early neurodegeneration

abstract:
Neurodegeneration is a hallmark of many dementias and is thought to underlie a progressive impairment of neural plasticity. How neurodegeneration affects plasticity in neural circuits is not known. We therefore characterised the impact of tau-driven neurodegeneration on plasticity in the visual system, where normal function is well understood. We studied a very simple form of visual plasticity that allowed us to track both long timescales (across days) and shorter timescales (over minutes). We recorded the local field potential in the primary visual cortex of rTg4510 transgenic mice, a mouse model of tauopathy, while animals were repeatedly exposed to the same stimulus over the course of 9 days. We studied animals at early stages of neurodegeneration (5 months old) and at a more advanced stage where pathology is evident (8 months). We found that both short- and long-term visual plasticity were already disrupted at early stages of neurodegeneration, and were further reduced in older animals, such that it was abolished in mice expressing the mutant tau. Additionally, we found that visually evoked behaviours were disrupted in both younger and older mice expressing the mutant tau. Our results show that visual cortical plasticity and visually evoked behaviours are disrupted in the rTg4510 model of tauopathy, even at early stages of neurodegeneration. This simple measure of neural plasticity may help understand how neurodegeneration disrupts neural circuits, and offers a translatable platform for detection and tracking of the disease.

HighlightsO_LIVisual plasticity is disrupted at early stages of neurodegeneration in rTg4510 mice
C_LIO_LIVisual plasticity is reduced in older animals, particularly during neurodegeneration
C_LIO_LIInstinctive visual behaviours are reduced in neurodegeneration
C_LIO_LIShort-term visual plasticity is reduced in neurodegeneration
C_LI


title: Synergistic Coding of Carbon Dioxide and a Human Sweat Odorant in the Mosquito Brain

abstract: The yellow fever mosquito Aedes aegypti employs olfaction to locate humans. We applied neural activity mapping to define the molecular and cellular logic of how the mosquito brain is wired to detect two human odorants that are attractive when blended together. We determined that the human breath volatile carbon dioxide (CO2) is detected by the largest unit of olfactory coding in the antennal lobe of the mosquito brain. Synergistically, CO2 detection gates pre-synaptic calcium signaling in olfactory sensory neuron axon terminals that innervate unique antennal lobe regions tuned to the human sweat odorant L-(+)-lactic acid. We propose that simultaneous detection of the signature human volatiles CO2 and L-(+)-lactic acid disinhibits a multimodal olfactory network for hunting humans in the mosquito brain.


title: The evolution of latitudinal ranges in reef-associated fishes: heritability, limits, and inverse Rapoport's rule

abstract:
AimVariation in the size and position of geographical ranges is a key variable that underlies most biogeographical patterns. However, relatively little is known in terms of general principles driving their evolution, particularly in the marine realm. In this study we explore several fundamental properties regarding the evolution of reef fish latitudinal ranges, namely the degree of similarity in range size between ancestor and descendant lineages (i.e. phylogenetic signal); the evolution of range limits; and the latitudinal distribution of range sizes, particularly with respect to Rapoports rule.

LocationGlobal.

TaxonReef-associated fishes.

MethodsWe integrate data on the latitudinal distribution and evolutionary history of 5,071 reef fish species with phylogenetic comparative methods to assess the level of phylogenetic signal in latitudinal range size, low- and high-latitude limits, and range midpoints, and to estimate rates of evolution of those traits. Finally, we test whether latitudinal ranges become smaller near the equator, as predicted by Rapoports rule, using phylogenetic generalized least squares.

ResultsThere were varying levels of phylogenetic signal in latitudinal range size, low- and high-latitude limits, and range midpoints. Despite these differences, latitudinal midpoints were consistently shown to have the highest phylogenetic signal among all measured geographic features. Interestingly, the position of high-latitude limits in general evolved at substantially faster rates than their low-latitude counterparts. Finally, we confirm for the first time the existence of an inverse Rapoports rule in reef-associated fishes using phylogenetic comparative methods. Indeed, mean latitudinal range size of tropical species is nearly twice the size of their temperate counterparts (2067{+/-}1431 km vs. 1168{+/-}725 km, respectively).

Main conclusionsWe uncovered several congruent patterns in phylogenetic signal and rates of evolution of latitudinal ranges, despite vastly disparate biogeographical distributions and ecological differences between the studied fish lineages. Such broad congruence across different taxa and oceans, as well as with previous data from terrestrial environments, suggests that the observed patterns might represent general principles governing geographical range evolution.


title: Human-in-the-Loop Weight Compensation in Upper Limb Wearable Robots Towards Total Muscles Effort Minimization

abstract: In this paper: (1) We present a novel human-in-the-loop adaptation method for whole arm muscles effort minimization by means of weight compensation in the face of an object with an unknown mass. (2) This adaptation rule can also be used as a cognitive model for the identification of mass value using EMG sensors. (3) This adaptation rule utilizes the activation (myoelectric) signal of only four muscles in the upper limb to minimize the whole muscles effort. We analytically discuss the stability, optimality, and convergence of the proposed method. The effectiveness of this method for whole muscles effort reduction is studied by simulations (OpenSim software) on a generic and realistic model of the human arm, a model with 7-DOF and 50 Hill-type-muscles. The simulation results show the presented methods performance and applicability for weight compensation and mass estimation in upper limb assistive robots. In addition, the simulations in OpenSim completely support that the suggested set of mono-articular muscles are sufficient for whole muscles effort reduction.

category: bioengineering


title: E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer

abstract: The loss of the intercellular adhesion molecule E-cadherin is a hallmark of the epithelial- mesenchymal transition (EMT), during which tumor cells transition into an invasive phenotype. Accordingly, E-cadherin has long been considered a tumor suppressor gene. Using novel multi-compartment spheroids and multiple in vivo models, we show that E-cadherin promotes a hyper-proliferative phenotype in breast cancer cells via interaction with the transmembrane receptor EGFR. This interaction results in the activation of the MEK/ERK signaling pathway, leading to a significant increase in proliferation via the activation of transcription factors including c-Fos. Pharmacological inhibition of MEK activity in E-cadherin positive breast cancer cells significantly decreases both tumor growth and macro-metastasis in vivo. This work provides evidence for a novel role of E-cadherin in breast tumor growth and identifies a potential new target to treat hyper-proliferative E-cadherin-positive breast tumors.


title: Strong and localized coupling controlsdimensionality of neural activity across brainareas

abstract: The brain contains an astronomical number of neurons, but it is their collective activity that underlies brain function. The number of degrees of freedom that this collective activity explores - its dimensionality - is therefore a fundamental signature of neural dynamics and computation (1-7). However, it is not known what controls this dimensionality in the biological brain - and in particular whether and how local synaptic networks play a role (8-10). Through analysis of high-density Neuropixels recordings (11), we argue that areas across the mouse cortex operate in a sensitive regime that gives these synaptic networks a very strong role in controlling dimensionality. Moreover, we show that this control is expressed through highly tractable features of these synaptic networks. We then analyze these key features via a massive synaptic physiology dataset (12). Quantifying these features in terms of cell-type specific network motifs, we find that the synaptic patterns that impact dimensionality are prevalent in both mouse and human brains. Thus local circuitry scales up systematically to help control the degrees of freedom that brain networks may explore and exploit.


title: Strong and localized recurrence controlsdimensionality of neural activity across brainareas


title: A genetically encoded, pH-sensitive mTFP1 biosensor for probing lysosomal pH

abstract: Lysosomes are important sites for macromolecular degradation, defined by an acidic lumenal pH of [~]4.5. To better understand lysosomal pH, we designed a novel, genetically encoded, fluorescent protein (FP) based pH biosensor called FIRE-pHLy (Fluorescence Indicator REporting pH in Lysosomes). This biosensor was targeted to lysosomes with lysosomal-associated membrane protein 1 (LAMP1) and reported lumenal pH between 3.5 and 6.0 with monomeric teal fluorescent protein 1 (mTFP1), a bright cyan pH sensitive FP variant with a pKa of 4.3. Ratiometric quantification was enabled with cytosolically oriented mCherry using high-content quantitative imaging. We expressed FIRE-pHLy in several cellular models and quantified the alkalinizing response to bafilomycin A1, a specific V-ATPase inhibitor. In summary, we have engineered FIRE-pHLy, a specific, robust and versatile lysosomal pH biosensor that has broad applications for investigating pH dynamics in aging and lysosome-related diseases, as well as in lysosome-based drug discovery.


title: Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

abstract: The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ~50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins. The measured median step sizes range between 20-40 nm at forces of 1.0-0.2 pN, respectively, comparable with the holocomplex size. These large steps show that, strikingly, condensin typically reels in DNA in very sizeable amounts with ~200 bp on average per single extrusion step at low force, and occasionally even much larger, exceeding 500 bp per step. Using Molecular Dynamics simulations, we demonstrate that this is due to the structural flexibility of the DNA polymer at these low forces. Using ATP-binding-impaired and ATP-hydrolysis-deficient mutants, we find that ATP binding is the primary step-generating stage underlying DNA loop extrusion. We discuss our findings in terms of a scrunching model where a stepwise DNA loop extrusion is generated by an ATP-binding-induced engagement of the hinge and the globular domain of the SMC complex.


title: Peeling Back the Layers: Complex Dynamics Shaping the Evolution of the Ledebouriinae (Scilloideae, Asparagaceae)

abstract: The Ledebouriinae (Scilloideae, Asparagaceae) are a widespread group of bulbous geophytes found predominantly throughout seasonal climates in sub-Saharan Africa, with a handful of taxa in Madagascar, the Middle East, India, and Sri Lanka. Phylogenetic relationships within the group have been historically difficult to elucidate. Here, we provide the first phylogenomic perspective into the Ledebouriinae. Using the Angiosperms353 targeted enrichment probe set, we consistently recovered four major clades (i.e., two Ledebouria clades, Drimiopsis, and Resnova). The two Ledebouria clades closely align with geography, either consisting almost entirely of sub-Saharan African taxa (Ledebouria Clade A), or East African and non-African taxa (Ledebouria Clade B). Our results suggest that the Ledebouriinae likely underwent a rapid radiation leading to rampant incomplete lineage sorting. We additionally find evidence for potential historical hybridization between Drimiopsis and a subclade within Ledebouria Clade A.


title: Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae)


title: Copy number-aware deconvolution of tumor-normal DNA methylation profiles

abstract: Aberrant methylation is a hallmark of cancer, but bulk tumor data is confounded by admixed normal cells and copy number changes. Here, we introduce Copy number-Aware Methylation Deconvolution Analysis of Cancers (CAMDAC; https://github.com/VanLoo-lab/CAMDAC), which outputs tumor purity, allele-specific copy number and deconvolved methylation estimates. We apply CAMDAC to 122 multi-region samples from 38 TRACERx non-small cell lung cancers profiled by reduced representation bisulfite sequencing. CAMDAC copy number profiles parallel those derived from genome sequencing and highlight widespread chromosomal instability. Deconvolved polymorphism-independent methylation rates enable unbiased tumor-normal and tumor-tumor differential methylation calling. Read-phasing validates CAMDAC methylation rates and directly links genotype and epitype. We show increased epigenetic instability in adenocarcinoma vs. squamous cell carcinoma, frequent hypermethylation at sites carrying somatic mutations, and parallel copy number losses and methylation changes at imprinted loci. Unlike bulk methylomes, CAMDAC profiles recapitulate tumor phylogenies and evidence distinct patterns of epigenetic heterogeneity in lung cancer.

category: genomics


title: A region-based method for causal mediation analysis of DNA methylation data

abstract: Exposure to environmental factors can affect DNA methylation at a CpG site or a genomic region, which can then affect an outcome. In other words, environmental effects on an outcome could be mediated by DNA methylation. To date, single CpG site-based mediation analysis has been employed extensively. More recently, however, there has been considerable interest on studying differentially methylated regions (DMRs), both because DMRs are more likely to have functional effects than single CpG sites and because testing DMRs reduces multiple testing. In this report, we propose a novel causal mediation approach under the counterfactual framework to test the significance of total, direct and indirect effects of predictors on response variable with a methylated region (MR) as the mediator (denoted as MR-Mediation). Functional linear transformation is used to reduce the possible high dimension of the CpG sites in a predefined methylated region and to account for their location information. In our simulation studies, MR-Mediation retained the desired Type I error rates for total, direct and indirect effect tests, for both continuous and binary outcomes. Furthermore, MR-Mediation had better power performance than testing mean methylation level as the mediator in most considered scenarios, especially for indirect effect (i.e., mediated effect) test, which could be more interesting than the other two effect tests. We further illustrate our proposed method by analyzing the methylation mediated effect of exposure to gun violence on total immunoglobulin E (IgE) or atopic asthma among participants in the Epigenetic Variation and Childhood Asthma in Puerto Ricans (EVA-PR) study.


title: Towards a Better Understanding of Reverse-Complement Equivariance for Deep Learning Models in Regulatory Genomics

abstract: Predictive models mapping double-stranded DNA to signals of regulatory activity should, in principle, produce analogous (or "equivariant") predictions whether the forward strand or its reverse complement (RC) is supplied as input. Unfortunately, standard neural networks can produce highly divergent predictions across strands, even when the training set is augmented with RC sequences. Two strategies have emerged to enforce equivariance: conjoined/"siamese" architectures, and RC parameter sharing or RCPS. However, the connections between the two remain unclear, comparisons to strong baselines are lacking, and neither has been adapted to base-resolution signal profile prediction. Here we extend conjoined & RCPS models to base-resolution signal prediction, and introduce a strong baseline: a standard model (trained with RC data augmentation) that is made conjoined only after training, which we call "post-hoc" conjoined. Through benchmarks on diverse tasks, we find post-hoc conjoined consistently performs best or second-best, surpassed only occasionally by RCPS, and never underperforms conjoined-during-training. We propose an overfitting-based hypothesis for the latter finding, and study it empirically. Despite its theoretical appeal, RCPS shows mediocre performance on several tasks, even though (as we prove) it can represent any solution learned by conjoined models. Our results suggest users interested in RC equivariance should default to post-hoc conjoined as a reliable baseline before exploring RCPS. Finally, we present a unified description of conjoined & RCPS architectures, revealing a broader class of models that gradually interpolate between RCPS and conjoined while maintaining equivariance.


title: Cross-species analysis between the maize smut fungi Ustilago maydis and Sporisorium reilianum highlights the role of transcriptional plasticity of effector orthologs for virulence and disease

abstract:
O_LIThe constitution and regulation of effector repertoires determines and shapes the outcome of the interaction with the host. Ustilago maydis and Sporisorium reilianum are two closely related smut fungi, which both infect maize, but cause distinct disease symptoms. Understanding how effector orthologs are regulated in these two pathogens can therefore provide insights to pathogen evolution and host adaption.
C_LIO_LIWe tracked the infection progress of U. maydis and S. reilianum in maize leaves, characterized two distinct infection stages for cross species RNA-sequencing analysis and identified 207 out of 335 one-to-one effector orthologs being differentially regulated during host colonization, while transcriptional plasticity of the effector orthologs correlated with the distinct disease development strategies.
C_LIO_LIBy using CRISPR-Cas9 mediated gene conversion, we identified two differentially expressed effector orthologs with conserved function between two pathogens. Thus, differential expression of functionally conserved genes contributes to species specific adaptation and symptom development. Interestingly, another differentially expressed orthogroup (UMAG_05318/Sr1007) showed diverged protein function during speciation, providing a possible case for neofunctionalization.
C_LIO_LICollectively, we showed the diversification of effector genes in related pathogens can be caused both by plasticity on the transcriptional level, as well as through functional diversification of the encoded effector proteins.
C_LI


title: Temporal pattern and synergy influence activity of ERK signaling pathways during L-LTP induction

abstract: Long-lasting long-term potentiation (L-LTP) is a cellular mechanism of learning and memory storage. Studies have demonstrated a requirement for extracellular signal-regulated kinase (ERK) activation in L-LTP produced by a diversity of temporal stimulation patterns. Multiple signaling pathways converge to activate ERK, with different pathways being required for different stimulation patterns. To answer whether and how different temporal patterns select different signaling pathways for ERK activation, we developed a computational model of five signaling pathways (including two novel pathways) leading to ERK activation during L-LTP induction. We show that calcium and cAMP work synergistically to activate ERK and that stimuli given with large inter-trial intervals activate more ERK than shorter intervals. Furthermore, these pathways contribute to different dynamics of ERK activation. These results suggest that signaling pathways with different temporal sensitivity facilitate ERK activation to diversity of temporal patterns.


title: Cave Thiovulaceae differ metabolically and genomically from marine species

abstract: Life in Movile Cave (Romania) relies entirely on carbon fixation by bacteria. The microbial community in the surface water of Movile Caves hypoxic air bells is dominated by large spherical-ovoid bacteria we identified as Thiovulum sp. (Campylobacterota). These form a separate phylogenetic cluster within the Thiovulaceae, consisting mostly of freshwater cave bacteria. We compared the closed genome of this Thiovulum to that of the marine strain Thiovulum ES, and to a genome we assembled from public data from the sulfidic Frasassi caves. The Movile and Frasassi Thiovulum were very similar, differing greatly from the marine strain. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, respectively. NO3-, is likely reduced to NH3 via dissimilatory nitrate reduction to ammonia using periplasmic nitrate reductase (Nap) and hydroxylamine oxidoreductase. Thus, Thiovulum, is likely important to both S and N cycles in sulfidic subterranean aquatic ecosystems. Additionally, we suggest that the short peritrichous flagella-like structures typical of Thiovulum are type IV pili, for which genes were found in all Thiovulum genomes. These pili may play a role in veil formation, connecting adjacent cells and the exceptionally fast swimming of these bacteria.


title: Developmental regulation of mitotic chromosome formation revealed by condensin reporter mice

abstract:
Withdrawal Note:

The authors have withdrawn their manuscript due to the discovery of artifacts that call into question key findings from the study. Both artifacts originate from cell-type differences that arose during sample processing, creating the impression that non-SMC subunits of condensin proteins were present at substantially higher levels in thymic T cells compared to bone marrow B cells or erythroblast cells. Based on data collected since the preprint was submitted, we no longer believe this to be true. The experimental artifacts do not affect the data contributed by the Papadopoulos laboratory (Figure 4).

The authors wish to make it clear that all data and experimental protocols in the original manuscript were accurately reported, and that the experimental artifacts which affect data interpretation were discovered during internal review, independently of peer review, and are being reported at the authors own instigation. They do not, to our knowledge, affect the interpretation of data from any other published work.

Due to the issues outlined above, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.


title: Spatial structure impacts adaptive therapy by shaping intra-tumoral competition

abstract: (1) Background: Adaptive therapy aims to tackle cancer drug resistance by leveraging intra-tumoral competition between drug-sensitive and resistant cells. Motivated by promising results in prostate cancer there is growing interest in extending this approach to other cancers. Here we present a theoretical study of intra-tumoral competition during adaptive therapy, to identify under which circumstances it will be superior to aggressive treatment; (2) Methods: We use a 2-D, on-lattice, agent-based tumour model to examine the impact of different microenvironmental factors on the comparison between continuous drug administration and adaptive therapy. (3) Results: We show that the degree of crowding, the initial resistance fraction, the presence of resistance costs, and the rate of tumour cell turnover are key determinants of the benefit of adaptive therapy, and we study in detail how these factors alter competition between cells. We find that intra-specific competition between resistant cells plays an unexpectedly important role in the ability to control resistance. To conclude we show how differences in resistance cost and turnover change the tumours spatial organisation and may explain differences in cycling speed observed in a cohort of 67 prostate cancer patients undergoing intermittent androgen deprivation therapy; (4) Conclusion: Our work provides insights into how adaptive therapy leverages inter- and intra-specific competition to control resistance, and shows that the tumours spatial architecture will likely be an important factor in determining the quantitative benefit of adaptive therapy in patients.


title: Osteosarcoma tumors maintain intra-tumoral heterogeneity, even while adapting to environmental pressures that drive clonal selection

abstract:
BackgroundTumors are complex tissues containing collections of phenotypically diverse malignant and non-malignant cells. We know little of the mechanisms that govern heterogeneity within tumor cells themselves and the role it plays in overcoming stresses, such as adaptation to a metastatic microenvironment. Osteosarcoma is an ideal model for studying these mechanisms--it exhibits widespread inter- and intra-tumoral heterogeneity, progresses with predictable patterns of metastasis, and lacks clear targetable driver mutations. Understanding the processes that facilitate adaptation to primary and metastatic microenvironments could inform the development of therapeutic strategies with potential to significantly impact clinical outcomes.

ResultsWe investigated single-cell RNA-sequencing profiles of 47,977 cells obtained from cell line and patient-derived xenograft models as osteosarcoma cells adapted to different environments. Tumor cells from almost all models maintained phenotypic heterogeneity as they adapted to the selective pressures imposed during bone and lung colonization. Subsets of cells identified within primary bone and metastatic lung tumors retained unique transcriptional phenotypes associated with distinct pathways, including heterogeneity in glucose metabolism that we validated using immunofluorescence staining. Finally, by leveraging concurrent lineage tracing and single-cell transcriptomics, we found that lung colonization enriches for clonal populations with diverse phenotypes, each of which conserves phenotype across cellular generations.

ConclusionsAdaptation to environmental stressors occurs through complex and dynamic phenotypic adaptations, although heterogeneity is maintained, even in conditions that enforce clonal selection. These findings likely reflect a retention of developmental processes that promote the robustness of a tumor cell population in the face of selective pressures.


title: The Correlation Of Substitution Effects Across Populations And Generations In The Presence Of Non-Additive Functional Gene Action

abstract: Allele substitution effects at quantitative trait loci (QTL) are part of the basis of quantitative genetics theory and applications such as association analysis and genomic prediction. In the presence of non-additive functional gene action, substitution effects are not constant across populations. We develop an original approach to model the difference in substitution effects across populations as a first order Taylor series expansion from a "focal" population. This expansion involves the difference in allele frequencies and second-order statistical effects (additive by additive and dominance). The change in allele frequencies is a function of relationships (or genetic distances) across populations. As a result, it is possible to estimate the correlation of substitution effects across two populations using three elements: magnitudes of additive, dominance and additive by additive variances; relationships (Neis minimum distances or Fst indexes); and assumed heterozygosities. Similarly, the theory applies as well to distinct generations in a population, in which case the distance across generations is a function of increase of inbreeding. Simulation results confirmed our derivations. Slight biases were observed, depending on the non-additive mechanism and the reference allele. Our derivations are useful to understand and forecast the possibility of prediction across populations and the similarity of GWAS effects.

category: genetics


title: Evolution of Antibody Immunity to SARS-CoV-2

abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected 78 million individuals and is responsible for over 1.7 million deaths to date. Infection is associated with development of variable levels of antibodies with neutralizing activity that can protect against infection in animal models. Antibody levels decrease with time, but the nature and quality of the memory B cells that would be called upon to produce antibodies upon re-infection has not been examined. Here we report on the humoral memory response in a cohort of 87 individuals assessed at 1.3 and 6.2 months after infection. We find that IgM, and IgG anti-SARS-CoV-2 spike protein receptor binding domain (RBD) antibody titers decrease significantly with IgA being less affected. Concurrently, neutralizing activity in plasma decreases by five-fold in pseudotype virus assays. In contrast, the number of RBD-specific memory B cells is unchanged. Memory B cells display clonal turnover after 6.2 months, and the antibodies they express have greater somatic hypermutation, increased potency and resistance to RBD mutations, indicative of continued evolution of the humoral response. Analysis of intestinal biopsies obtained from asymptomatic individuals 4 months after coronavirus disease-2019 (COVID-19) onset, using immunofluorescence, or polymerase chain reaction, revealed persistence of SARS-CoV-2 nucleic acids and immunoreactivity in the small bowel of 7 out of 14 volunteers. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence.


title: SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice

abstract: There is an urgent need for an accessible and low-cost COVID-19 vaccine suitable for low- and middle-income countries. Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed at high levels in yeast (Pichia pastoris), as a suitable vaccine candidate against COVID-19. After introducing two modifications into the wild-type RBD gene to reduce yeast-derived hyperglycosylation and improve stability during protein expression, we show that the recombinant protein, RBD219-N1C1, is equivalent to the wild-type RBD recombinant protein (RBD219-WT) in an in vitro ACE-2 binding assay. Immunogenicity studies of RBD219-N1C1 and RBD219-WT proteins formulated with Alhydrogel(R) were conducted in mice, and, after two doses, both the RBD219-WT and RBD219-N1C1 vaccines induced high levels of binding IgG antibodies. Using a SARS-CoV-2 pseudovirus, we further showed that sera obtained after a two-dose immunization schedule of the vaccines were sufficient to elicit strong neutralizing antibody titers in the 1:1,000 to 1:10,000 range, for both antigens tested. The vaccines induced IFN-{gamma}, IL-6, and IL-10 secretion, among other cytokines. Overall, these data suggest that the RBD219-N1C1 recombinant protein, produced in yeast, is suitable for further evaluation as a human COVID-19 vaccine, in particular, in an Alhydrogel(R) containing formulation and possibly in combination with other immunostimulants.


title: The translational landscape of SARS-CoV-2 and infected cells

abstract: SARS-CoV-2 utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2 infected model cell lines and primary airway cells grown at the air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We find that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy in comparison to HIV-1, suggesting utilization of distinct structural elements. In the highly permissive cell models, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokines, cytokines and interferon stimulated genes, many of these mRNAs were not translated efficiently. Impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.


title: Estimating latent positions in social and biological networks using Graph Neural Networks in R with GCN4R

abstract: Network analysis methods are useful to better understand and contextualize relationships between entities. While statistical and machine learning prediction models generally assume independence between actors, network-based statistical methods for social network data allow for dyadic dependence between actors. While numerous methods have been developed for the R statistical software to analyze such data, deep learning methods have not been implemented in this language. Here, we introduce GCN4R, an R library for fitting graph neural networks on independent networks to aggregate actor covariate information to yield meaningful embeddings for a variety of network-based tasks (e.g. community detection, peer effects models, social influence). We provide an extensive overview of insights and methods utilized by the deep learning community on learning on social and biological networks, followed by a tutorial that demonstrates some of the capabilities of the GCN4R framework to make these methods more accessible to the R research community.


title: Tracing production instability in a clonally-derived CHO cell line using single cell transcriptomics

abstract:
A variety of mechanisms including transcriptional silencing, gene copy loss and increased susceptibility to cellular stress have been associated with a sudden or gradual loss of monoclonal antibody (mAb) production in Chinese hamster ovary (CHO) cell lines. In this study, we utilised single cell RNA-seq (scRNA-seq) to study a clonally-derived CHO cell line that underwent production instability leading to a dramatic reduction of the levels of mAb produced. From the scRNA-seq data we identified sub clusters associated with variations in the mAb transgenes and observed that heavy chain gene expression was significantly lower than that of the light chain across the population. Using trajectory inference, the evolution of the cell line was reconstructed and was found to correlate with a reduction in heavy and light chain gene expression. Genes encoding for proteins involved in the response to oxidative stress and apoptosis were found to increase in expression as cells progressed along the trajectory. Future studies of CHO cell lines using this technology have the potential to dramatically enhance our understanding of the characteristics underpinning efficient manufacturing performance as well as product quality.

HighlightsO_LIA clonally-derived CHO cell line in our laboratory had undergone production instability - in that the amount of intact monoclonal antibody had reduced dramatically to levels at which reliable quantitation was no longer possible. We were, however, able to detect mAb heavy and light chain protein, as well as dimerised light chain species in the cell culture media.
C_LIO_LISingle cell RNA-seq was utilised to capture > 3,800 gene expression profiles from the cell line at 72hrs post seeding.
C_LIO_LIAnalyses of the scRNA-seq data uncovered transcriptional heterogeneity and revealed the presence of multiple intra cell line clusters. The heavy chain transcript was detected at a significantly lower level in comparison to light chain transcripts. Light chain gene expression was not only more abundant, but also expressed more uniformly across the cell population.
C_LIO_LIUsing unsupervised trajectory analysis, the emergence of heterogeneity in the cell population was traced from those cells most similar to the original isolated clone to those where transcription of the mAb heavy and light chain was undetectable.
C_LIO_LISubsequent analysis of CHO cell gene expression patterns revealed a correlation between the progression of cells along the trajectory and the upregulation of genes involved in the cellular response to oxidative stress.
C_LI


title: Exploring the relationship between functional structure and ecosystem multifunctionality requires intraspecific trait variability

abstract: The authors have withdrawn their manuscript whilst they conduct additional data analysis to confirm if some of their conclusions are affected by data analysis artefact or not. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.


title: Fin sweep angle does not determine flapping propulsive performance

abstract: The importance of the leading-edge sweep angle of propulsive surfaces used by unsteady swimming and flying animals has been an issue of debate for many years, spurring studies in biology, engineering, and robotics with mixed conclusions. In this work, we provide results from three-dimensional simulations of finite foils undergoing tail-like (pitch-heave) and flipper-like (twist-roll) kinematics for a range of sweep angles based on a large range of animal data while carefully controlling all other parameters. Our primary finding is the negligible 0.043 maximum correlation between the sweep angle and the propulsive force and power for both tail-like and flipper-like motions. This indicates that fish tails and mammal flukes with similar range and size can have a large range of potential sweep angles without significant negative propulsive impact. Although there is a slight benefit to avoiding large sweep angles, this is easily compensated by adjusting the fins motion parameters such as flapping frequency, amplitude and maximum angle of attack to gain higher thrust and efficiency.