title: CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing

abstract: Proper control of replication timing (RT) is of vital importance to maintain genome and epigenome integrity. However, the genome-wide sequence determinants regulating RT remain unclear. Here, we develop a new machine learning method, named CO_SCPLOWONCERTC_SCPLOW, to simultaneously predict RT from sequence features and identify RT-modulating sequence elements in a genome-wide manner. CO_SCPLOWONCERTC_SCPLOW integrates two functionally cooperative modules, a selector, which performs importance estimationbased sampling to detect predictive sequence elements, and a predictor, which incorporates bidirectional recurrent neural networks and self-attention mechanism to achieve selective learning of longrange spatial dependencies across genomic loci. We apply CO_SCPLOWONCERTC_SCPLOW to predict RT in mouse embryonic stem cells and multiple human cell types with high accuracy. The identified RT-modulating sequence elements show novel connections with genomic and epigenomic features such as 3D chromatin interactions. In particular, CO_SCPLOWONCERTC_SCPLOW reveals a class of RT-modulating elements that are not transcriptional regulatory elements but are enriched with specific repetitive sequences. As a generic interpretable machine learning framework for predicting large-scale functional genomic profiles based on sequence features, CO_SCPLOWONCERTC_SCPLOW provides new insights into the potential sequence determinants of RT.


title: Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms

abstract:
While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that extracellular filaments in archaea, such as Type IV pili, hami and cannulae, play a part in the formation of archaeal biofilms. We have used cryo-electron microscopy to determine the atomic structure of a previously uncharacterized class of archaeal surface filaments from hyperthermophilic Pyrobaculum calidifontis. These filaments, which we call archaeal bundling pili (ABP), assemble into highly ordered bipolar bundles. The bipolar nature of these bundles most likely arises from the association of filaments from at least two different cells. The component protein shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major component of the extracellular matrix in bacterial biofilms, contributing to biofilm stability. We show that ABP forms very stable filaments in a manner similar to the donor-strand exchange of bacterial TasA fibers and chaperone-usher pathway pili where a {beta}-strand from one subunit is incorporated into a {beta}-sheet of the next subunit. Our results reveal mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms, and suggest that there could be many other archaeal surface filaments that are as yet uncharacterized.

SignificanceBiofilms are communities of microbes where cells attach to each other as well as to surfaces, and bacterial biofilms have been intensively studied due to their importance in many infections. Much less has been known about archaeal biofilms, where archaea are a third domain of life. Using cryo-electron microscopy, we have determined the atomic structure of a surface filament in archaea that forms bi-polar bundles connecting cells. We show that this protein has common ancestry with a protein known to be an important component of bacterial biofilms. This adds to our understanding of the evolutionary relationship between bacteria and archaea and may provide new insights into bacterial biofilms.

category: biophysics


title: Active mechanics of sea star oocytes

abstract: Actomyosin is a canonical example of an active material, driven out of equilibrium in part through the injection of energy by myosin motors. This influx of energy allows actomyosin networks to generate cellular-scale contractility, which underlies cellular processes ranging from division to migration. While the molecular players underlying actomyosin contractility have been well characterized, how cellular-scale deformation in disordered actomyosin networks emerges from filament-scale interactions is not well understood. Here, we address this question in vivo using the meiotic surface contraction wave of Patiria miniata oocytes. Using pharmacological treatments targeting actin polymerization, we find that the cellular deformation rate is a nonmonotonic function of cortical actin density peaked near the wild type density. To understand this, we develop an active fluid model coarse-grained from filament-scale interactions and find quantitative agreement with the measured data. This model further predicts the dependence of the deformation rate on the concentration of passive actin crosslinkers and motor proteins, including the surprising prediction that deformation rate decreases with increasing motor concentration. We test these predictions through protein overexpression and find quantitative agreement. Taken together, this work is an important step for bridging the molecular and cellular length scales for cytoskeletal networks in vivo.


title: Membrane tension spatially organizes lysosomal exocytosis

abstract: Lysosomal exocytosis is involved in many key cellular processes but its spatio-temporal regulation is poorly known. Using total internal reflection fluorescence microscopy (TIRFM) and spatial statistics, we observed that lysosomal exocytosis is not random at the adhesive part of the plasma membrane of RPE1 cells but clustered at different scales. Although the rate of exocytosis is regulated by the actin cytoskeleton, neither interfering with actin or microtubule dynamics by drug treatments alters its spatial organization. Exocytosis events partially co-appear at focal adhesions (FAs) and their clustering is reduced upon removal of FAs. Changes in membrane tension following a hypo-osmotic shock or treatment with methyl-{beta}-cyclodextrin was found to increase clustering. To investigate the link between FAs and membrane tension, cells were cultured on adhesive ring-shaped micropatterns, which allows to control the spatial organization of FAs. By using a combination of TIRFM and fluorescence lifetime imaging microscopy (FLIM) microscopy, we revealed the existence of a radial gradient in membrane tension. By changing the diameter of micropatterned substrates, we further showed that this gradient as well as the extent of exocytosis clustering can be controlled. Together, our data indicate that the spatial clustering of lysosomal exocytosis relies on membrane tension patterning controlled by the spatial organization of FAs.


title: ACSS2 Regulates HIF-2α Degradation through the E3-Ubiquitin Ligase MUL1 in Clear Cell Renal Cell Carcinoma

abstract:
Clear cell renal cell carcinoma (ccRCC) is an aggressive kidney cancer driven by VHL loss and aberrant HIF-2 signaling. Acetate metabolism may contribute to this axis by ACSS2-dependent acetylation of HIF-2 and may provide opportunities to intervention. Here we tested the effects of pharmacological and genetic manipulation of ACSS2 on HIF-2, ccRCC cells, and tumors. ACSS2 inhibition led to HIF-2 degradation and suppressed ccRCC growth in vitro, in vivo, and in primary cell cultures of ccRCC patient tumors. This treatment resulted in reduced glucose and cholesterol metabolism, mitochondrial biogenesis and altered cristae deformation, that are consistent with loss of HIF-2. Mechanistically, HIF-2 protein levels are regulated through proteolytic degradation and we found, in parallel to VHL, HIF-2 stability was dependent on ACSS2 activity to prevent direct interaction with the E3 ligase MUL1. These findings highlight ACSS2 as a critical upstream regulator of HIF-2 that may be exploited to overcome resistance to HIF-2 inhibitor therapies.

STATEMENT OF SIGNIFICANCEWe have unveiled ACSS2 as a critical upstream regulator of HIF-2 in ccRCC. Targeting ACSS2 potently promotes HIF-2 degradation via MUL1 to effectively deplete mitochondrial activity and block ccRCC primary tumor models and growth models resistant to HIF-2 inhibitor therapy.

category: cancer biology


title: Genomic and transcriptomic landscape of advanced renal cell cancer to individualize treatment strategy

abstract: The genomic landscape of advanced renal cell cancer (RCC) was characterized for 91 patients to identify actionable targets and signatures by combining whole-genome sequencing (WGS) with matched RNA sequencing (RNA-Seq). WGS data were analyzed for somatic small variants, copy-number alterations (CNAs) and structural variants. Somatic aberrations were analyzed for driver genes, CNA drivers, mutational signatures, catastrophic events and fusion genes. For papillary and clear cell RCC, potential actionable drug targets were detected by WGS in 89% and 100% of the patients, respectively. RNA-Seq data of clear cell and papillary RCC were clustered according to a previously developed angio-immunogenic gene signature. WGS and RNA-Seq may improve therapeutic decision making for most patients with advanced RCC, including patients with non-clear cell RCC for whom no standard treatment is available to date. Prospective clinical trials are needed to evaluate the impact of genomic and transcriptomic diagnostics on survival outcome for advanced RCC patients.


title: A revised phylogenetic classification for Viola (Violaceae)

abstract: The genus Viola (Violaceae) is among the 40-50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then known 400 species were distributed among 14 sections and numerous unranked groups. Here we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Beckers classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We subdivide the 658 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Study on seed anatomy and morphology is required to understand the fossil record of the genus.

category: plant biology


title: Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment

abstract: The human gut microbiome has been associated with several metabolic disorders including type 2 diabetes. Understanding metabolic changes in the gut microbiome is important to elucidate the role of gut bacteria in regulating host metabolism. Here, we used available metagenomics data from a metformin study, together with genome-scale metabolic modelling of the key bacteria in individual and community-level to investigate the mechanistic role of the gut microbiome in response to metformin. Individual modelling predicted that species that are increased after metformin treatment have higher growth rates in comparison to species that are decreased after metformin treatment. Gut microbial enrichment analysis showed prior to metformin treatment pathways related to the hypoglycemic effect were enriched. Our observations highlight how the key bacterial species after metformin treatment have commensal and competing behavior, and how their cellular metabolism changes due to different nutritional environment. Integrating different diets showed there were specific microbial alterations between different diets. These results show the importance of the nutritional environment and how the dietary guidelines may improve drug efficiency through the gut microbiota.

category: systems biology


title: Chemogenetic disconnection between the orbitofrontal cortex and the rostromedial caudate nucleus disrupts motivational control of goal-directed action

abstract:
The orbitofrontal cortex (OFC) and its major downstream target within the basal ganglia--the rostromedial caudate nucleus (rmCD)--are involved in reward-value processing and goal-directed behavior. However, a causal contribution of the pathway linking these two structures to goal-directed behavior has not been established. Using the chemogenetic technology of Designer Receptors Exclusively Activated by Designer Drugs with a crossed inactivation design, we functionally and reversibly disrupted interactions between the OFC and rmCD in two male macaque monkeys. We injected an adeno-associated virus vector expressing an inhibitory designer receptor (hM4Di) into the OFC and contralateral rmCD, the expression of which was visualized in vivo by positron emission tomography (PET) and confirmed by post-mortem immunohistochemistry. Functional disconnection of the OFC and rmCD resulted in a significant and reproducible loss of sensitivity to the cued reward value for goal-directed action. This decreased sensitivity was most prominent when monkeys had accumulated a certain amount of reward. These results provide causal evidence that the interaction between the OFC and the rmCD is needed for motivational control of action on the basis of the relative reward value and internal drive. This finding extends current understanding of the physiological basis of psychiatric disorders in which goal-directed behavior is affected, such as obsessive-compulsive disorder.

Significance StatementIn daily life, we routinely adjust the speed and accuracy of our actions on the basis of the value of expected reward. Abnormalities in these kinds of motivational adjustments might be related to behaviors seen in psychiatric disorders such as obsessive-compulsive disorder. In the current study, we show that the connection from the orbitofrontal cortex to the rostromedial caudate nucleus is essential formotivational control of action in monkeys. This finding expands our knowledge about how the primate brain controls motivation and behavior and provides a particular insight into disorders like obsessive-compulsive disorder, in which altered connectivity between the orbitofrontal cortex and the striatum has been implicated.

category: neuroscience


title: Organization of the corticotropin-releasing hormone and corticotropin-releasing hormone-binding protein systems in the central nervous system of the sea lamprey Petromyzon marinus

abstract: The expression of the corticotropin-releasing hormone (PmCRH) and the CRH-binding protein (PmCRHBP) mRNAs was studied by in situ hybridization in the brain of prolarvae, larvae and adults of the sea lamprey Petromyzon marinus. We also generated an antibody against the PmCRH mature peptide to study the distribution of PmCRH-immunoreactive cells and fibers. PmCRH immunohistochemistry was combined with anti-tyrosine hydroxylase immunohistochemistry, PmCRHBP in situ hybridization or neurobiotin transport from the spinal cord. The most numerous PmCRH-expressing cells were observed in the magnocellular preoptic nucleus-paraventricular nucleus and in the superior and medial rhombencephalic reticular formation. PmCRH expression was more extended in adults than in larvae, and some cell populations were mainly (olfactory bulb) or only (striatum, ventral hypothalamus, prethalamus) observed in adults. The preopto-paraventricular fibers form conspicuous tracts coursing towards the neurohypophysis, but many immunoreactive fibers were also observed coursing in many other brain regions. Brain descending fibers in the spinal cord come from cells located in the isthmus and in the medial rhombencephalic reticular nucleus. The distribution of PmCRHBP-expressing neurons was different from that of PmCRH cells, with cells mainly present in the septum, striatum, preoptic region, tuberal hypothalamus, pretectum, pineal complex, isthmus, reticular formation, and spinal cord. Again, expression in adults was more extended than in larvae. PmCRH- and PmCRHBP-expressing cells are different, excluding colocalization of these substances in the same neuron. Present findings reveal a complex CRH/CRHBP system in the brain of the oldest extant vertebrate group, the agnathans, which shows similarities but important divergences with that of mammals.


title: Impaired immune response drives age-dependent severity of COVID-19

abstract:
SARS-CoV-2 is a highly contagious respiratory virus and the causative agent for COVID-19. The severity of disease varies from mildly symptomatic to lethal and shows an extraordinary correlation with increasing age, which represents the major risk factor for severe COVID-191. However, the precise pathomechanisms leading to aggravated disease in the elderly are currently unknown. Delayed and insufficient antiviral immune responses early after infection as well as dysregulated and overshooting immunopathological processes late during disease were suggested as possible mechanisms. Here we show that the age-dependent increase of COVID-19 severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) responses. To overcome the limitations of mechanistic studies in humans, we generated a mouse model for severe COVID-19 and compared the kinetics of the immune responses in adult and aged mice at different time points after infection. Aggravated disease in aged mice was characterized by a diminished IFN-{gamma} response and excessive virus replication. Accordingly, adult IFN-{gamma} receptor-deficient mice phenocopied the age-related disease severity and supplementation of IFN-{gamma} reversed the increased disease susceptibility of aged mice.

Mimicking impaired type I IFN immunity in adult and aged mice, a second major risk factor for severe COVID-192-4, we found that therapeutic treatment with IFN-{lambda} in adult and a combinatorial treatment with IFN-{gamma} and IFN-{lambda} in aged Ifnar1-/-mice was highly efficient in protecting against severe disease.

Our findings provide an explanation for the age-dependent disease severity of COVID-19 and clarify the nonredundant antiviral functions of type I, II and III IFNs during SARS-CoV-2 infection in an age-dependent manner. Based on our data, we suggest that highly vulnerable individuals combining both risk factors, advanced age and an impaired type I IFN immunity, may greatly benefit from immunotherapy combining IFN-{gamma} and IFN-{lambda}.

category: immunology


title: An Efficient Approach for SARS-CoV-2 Monoclonal Antibody Production via Modified mRNA-LNP Immunization

abstract: Throughout the COVID-19 pandemic, many prophylactic and therapeutic drugs have been evaluated and introduced. Among these treatments, monoclonal antibodies (mAbs) that bind to and neutralize SARS-CoV-2 virus have been applied as complementary and alternative treatments to vaccines. Although different methodologies have been utilized to produce mAbs, traditional hybridoma fusion technology is still commonly used for this purpose due to its unmatched performance record. In this study, we coupled the hybridoma fusion strategy with mRNA-lipid nanoparticle (LNP) immunization. This time-saving approach can circumvent biological and technical hurdles, such as difficult to express membrane proteins, antigen instability, and the lack of posttranslational modifications on recombinant antigens. We used mRNA-LNP immunization and hybridoma fusion technology to generate mAbs against the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein. Compared with traditional protein-based immunization approaches, inoculation of mice with RBD mRNA-LNP induced higher titers of serum antibodies. In addition, the mAbs we obtained can bind to SARS-CoV-2 RBDs from several variants. Notably, RBD-mAb-3 displayed particularly high binding affinities and neutralizing potencies against both Alpha and Delta variants. In addition to introducing specific mAbs against SARS-CoV-2, our data generally demonstrate that mRNA-LNP immunization may be useful to quickly generate highly functional mAbs against emerging infectious diseases.


title: A highly sensitive strand-specific multiplex RT-qPCR assay for quantitation of Zika virus replication

abstract:
Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is widely used to quantify viral RNA genomes for diagnostics and research, yet conventional RT-qPCR protocols are unable to accurately distinguish between the different viral RNA species that exist during infection. Here we show that false-priming and self-priming occur during reverse transcription with several published Zika virus (ZIKV) primer sets. We developed a RT-qPCR assay using tagged primers and thermostable reverse transcriptase, which greatly reduced the occurrence of nonspecific cDNA products. Furthermore, we optimized the assay for use in multiplex qPCR which allows for simultaneous quantitative detection of positive-strand and negative-strand ZIKV RNA along with an internal control from both human and mosquito cells. Importantly, this assay is sensitive enough to study early stages of virus infection in vitro. Strikingly, using this assay, we detected ZIKV negative-strand RNA as early as 3 h post-infection in mammalian cell culture, at a time point prior to the onset of positive-strand RNA synthesis. Overall, the strand-specific RT-qPCR assay developed herein is a valuable tool to quantify ZIKV RNA and to study viral replication dynamics during infection. The application of these findings has the potential to increase accuracy of RNA detection methods for a variety of viral pathogens.

HighlightsO_LISelf-primed cDNA is amplified by widely-used ZIKV qPCR primer sets
C_LIO_LIUse of tagged primers and thermostable RT increases strand-specificity for RT-qPCR
C_LIO_LIMultiplexed qPCR allows for simultaneous quantitation of (+) and (-) strand viral RNAs, and an internal control
C_LIO_LIStrand-specific RT-qPCR can detect fewer than one copy of viral RNA per cell in human and mosquito cells
C_LI

category: microbiology


title: Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.529 (Omicron)

abstract: The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. Here, we analyzed the S1/S2 cleavage site (also called "furin cleavage site") of the spike protein of SARS-CoV-2 B.1.529 (Omicron variant) in vitro, to assess the role of two key mutations (spike gene, N679K and P681H) compared to the ancestral B.1 virus. We observed significantly increased intrinsic cleavability with furin compared to an original B lineage virus (Wuhan-Hu-1) and two variants, B.1.1.7 (Alpha) and B.1.617 (Delta), that subsequently had wide circulation. Increased furin-mediated cleavage was attributed to the N679K mutation, which lies outside the conventional furin binding pocket. Our findings suggest that B.1.529 (Omicron variant) has gained genetic features linked to intrinsic furin cleavability, in line with its evolution within the population as the COVID-19 pandemic has proceeded.


title: Integrated optical device for Structured Illumination Microscopy

abstract: Structured Illumination Microscopy (SIM) is a key technology for high resolution and super-resolution imaging of biological cells and molecules. The spread of portable and easy-to-align SIM systems requires the development of novel methods to generate a light pattern and to shift it across the field of view of the microscope. Here we show a miniaturized chip that incorporates optical waveguides, splitters, and phase shifters, to generate a 2D structured illumination pattern suitable for SIM microscopy. The chip creates three point-sources, coherent and controlled in phase, without the need for further alignment. Placed in the pupil of a microscopes objective, the three sources generate a hexagonal illumination pattern on the sample, which is spatially translated thanks to thermal phase shifters. We validate and use the chip, upgrading a commercial inverted fluorescence microscope to a SIM setup and we image biological sample slides, extending the resolution of the microscope.

category: cell biology


title: Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

abstract:
BackgroundThe rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

ResultsHere, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1,059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming", which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

ConclusionsOverall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability.

category: ecology


title: The Free Fatty Acid-Binding Pocket is a Conserved Hallmark in Pathogenic β-Coronavirus Spike Proteins from SARS-CoV to Omicron

abstract:
As COVID-19 persists, severe acquired respiratory syndrome coronavirus-2 (SARS-CoV-2) Variants of Concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S receptor-binding domain (RBD) comprises a free fatty acid (FFA)-binding pocket. FFA-binding stabilizes a locked S conformation, interfering with virus infectivity. We provide evidence that the pocket is conserved in pathogenic {beta}-coronaviruses ({beta}-CoVs) infecting humans. SARS-CoV, MERS-CoV, SARS-CoV-2 and VOCs bind the essential FFA linoleic acid (LA), while binding is abolished by one mutation in common cold-causing HCoV-HKU1. In the SARS-CoV S structure, LA stabilizes the locked conformation while the open, infectious conformation is LA-free. Electron tomography of SARS-CoV-2 infected cells reveals that LA-treatment inhibits viral replication, resulting in fewer, deformed virions. Our results establish FFA-binding as a hallmark of pathogenic {beta}-CoV infection and replication, highlighting potential antiviral strategies.

One-Sentence SummaryFree fatty acid-binding is conserved in pathogenic {beta}-coronavirus S proteins and suppresses viral infection and replication.

category: biochemistry


title: SARS-CoV-2 spike variants differ in their allosteric response to linoleic acid

abstract: The SARS-CoV-2 spike protein contains a fatty acid binding site, also found in some other coronaviruses (e.g. SARS-CoV), which binds linoleic acid and is functionally important. When occupied by linoleic acid, it reduces infectivity, by  locking the spike in a less infectious conformation. Here, we use dynamical-nonequilibrium molecular dynamics (D-NEMD) simulations to compare the response of spike variants to linoleic acid removal. These simulations show that the fatty acid site is coupled to functional regions of the protein, some of them far from the site (e.g. in the receptor-binding motif, N-terminal domain, the furin cleavage site located in position 679-685 and the fusion peptide-surrounding regions) and identify the allosteric networks involved in these connections. Comparison of the response of the original ( Wuhan) spike with four variants: Alpha, Delta, Delta plus and Omicron BA.1 show that the variants differ significantly in their response to linoleic acid removal. The allosteric connections to the fatty acid site on Alpha are generally similar to the original protein, except for the receptor-binding motif and S71-R78 region which show a weaker link to the FA site. In contrast, Omicron is the most affected variant exhibiting significant differences in the receptor-binding motif, N-terminal domain, V622-L629 and the furin cleavage site. These differences in allosteric modulation may be of functional relevance, e.g. in differences in transmissibility and virulence. Experimental comparison of the effects of linoleic acid on different variants is warranted.


title: High-Throughput Global Phosphoproteomic Profiling Using Phospho Heavy-Labeled-Spiketide FAIMS Stepped-CV DDA (pHASED)

abstract: Global high-throughput profiling of oncogenic signaling pathways by phosphoproteomics is increasingly being applied to cancer specimens. Such quantitative unbiased phosphoproteomic profiling of cancer cells identifies oncogenic signaling cascades that drive disease initiation and progression; pathways that are often invisible to genomics sequencing strategies. Therefore, phosphoproteomic profiling has immense potential for informing individualized anti-cancer treatments. However, complicated and extensive sample preparation protocols, coupled with intricate chromatographic separation techniques that are necessary to achieve adequate phosphoproteomic depth, limits the clinical utility of these techniques. Traditionally, phosphoproteomics is performed using isobaric tagged based quantitation coupled with TiO2 enrichment and offline prefractionation prior to nLC-MS/MS. However, the use of isobaric tags and offline HPLC limits the applicability of phosphoproteomics for the analysis of individual patient samples in real-time. To address these limitations, here we have optimized a new protocol, phospho-Heavy-labeled-spiketide FAIMS Stepped-CV DDA (pHASED). pHASED maintained phosphoproteomic coverage yet decreased sample preparation time and complexity by eliminating the variability associated with offline prefractionation. pHASED employed online phosphoproteome deconvolution using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and internal phosphopeptide standards to provide accurate label-free quantitation data. Compared with our traditional tandem mass tag (TMT) phosphoproteomics workflow and optimized using isogenic FLT3-mutant acute myeloid leukemia (AML) cell line models (n=18/workflow), pHASED halved total sample preparation, and running time (TMT=10 days, pHASED=5 days) and doubled the depth of phosphoproteomic coverage in real-time (phosphopeptides = 7,694 pHASED, 3,861 TMT). pHASED coupled with bioinformatic analysis predicted differential activation of the DNA damage and repair ATM signaling pathway in sorafenib-resistant AML cell line models, uncovering a potential therapeutic opportunity that was validated using cytotoxicity assays. Herein, we optimized a rapid, reproducible, and flexible protocol for the characterization of complex cancer phosphoproteomes in real-time, highlighting the potential for phosphoproteomics to aid in the improvement of clinical treatment strategies.


title: The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells

abstract:
Human cancers often re-express germline factors, yet their mechanistic role in oncogenesis and cancer progression remains unknown. Here we demonstrate that DDX4, a germline factor and RNA helicase conserved in all multicellular organisms, contributes to epithelial mesenchyme transition (EMT)-like features and cisplatin resistance in small cell lung cancer (SCLC) cells. DDX4 depletion in H69AR and SHP77 cell lines decreased motility and resistance to cisplatin, whereas its overexpression increased these features. Proteomic analysis suggests that DDX4 upregulates metabolic protein expression related to DNA repair and immune/inflammatory response, suggesting its fundamental function may be in regulating cellular metabolism. Consistent with these trends in cell lines, DDX4 depletion compromised in vivo tumor development while its overexpression enhanced tumor growth even after cisplatin treatment in nude mice. Although the DDX4 expression level in somatic tumors is generally low compared to that in the germline, the relatively higher DDX4 expression in SCLC patients correlates with decreased survival and shows increased expression of EMT and cisplatin resistance markers. Taken together, we conclude that DDX4 influences the survival of SCLC patients by altering cellular metabolism in response to environmental cues such as drug treatments. This fundamental function of DDX4 as a germline factor might be applicable in other cancer types that express DDX4 and may serve as a key to combat specific tumors that are highly resistant to treatments.

HighlightsO_LIDDX4 contributes to cellular motility and drug resistance in SCLC cells.
C_LIO_LIDDX4-overexpression globally alters the proteome and suppresses cytokine production.
C_LIO_LIDDX4 promotes tumorigenesis and drug resistance in vitro and in vivo.
C_LIO_LIDDX4 expression correlates with survival in SCLC patients and with immune/inflammatory response both in cell lines and patient samples.
C_LI


title: Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer's Dementia

abstract: Despite significant advances in identifying genetic drivers of neurodegenerative disorders, the majority of affected individuals lack molecular genetic diagnosis, with somatic mutations proposed as one potential contributor to increased risk. Here, we report the first cell-type-specific map of somatic mosaicism in Alzheimers Dementia (AlzD), using 4,014 cells from prefrontal cortex samples of 19 AlzD and 17 non-AlzD individuals. We integrate full-transcript single-nucleus RNA-seq (SMART-Seq) with matched individual-level whole-genome sequencing to jointly infer mutational events and the cell-type in which they occurred. AlzD individuals show increased mutational burden, localized in excitatory neurons, oligodendrocytes, astrocytes and disease-associated "senescent" cells. High-mutational-burden cells showed mutational enrichment and similar single-cell expression profiles in AlzD cases versus non-AlzD individuals, indicating cellular-level genotype-to-phenotype correlation. Somatic mutations are specifically enriched for known AlzD genes, and implicate biologically meaningful cell-type specific processes, including: neuronal energy regulation, endocytic trafficking (NEFM), lipid metabolism (CNP, CRYAB), proteostasis (USP34), cytoskeleton, and microtubule dynamics (MACF1).


title: Synapses learn to utilize pre-synaptic noise for the prediction of postsynaptic dynamics

abstract: Synapses in the brain are highly noisy, which leads to a large trial-by-trial variability. Given how costly synapses are in terms of energy consumption these high levels of noise are surprising. Here we propose that synapses use their noise to represent uncertainties about the activity of the post-synaptic neuron. To show this we utilize the free-energy principle (FEP), a well-established theoretical framework to describe the ability of organisms to self-organize and survive in uncertain environments. This principle provides insights on multiple scales, from high-level behavioral functions such as attention or foraging, to the dynamics of single microcircuits in the brain, suggesting that the FEP can be used to describe all levels of brain function. The synapse-centric account of the FEP that is pursued here, suggests that synapses form an internal model of the somatic membrane dynamics, being updated by a synaptic learning rule that resembles experimentally well-established LTP/LTD mechanisms. This approach entails that a synapse utilizes noisy processes like stochastic synaptic release to also encode its uncertainty about the state of the somatic potential. Although each synapse strives for predicting the somatic dynamics of its neuron, we show that the emergent dynamics of many synapses in a neuronal network resolve different learning problems such as pattern classification or closed-loop control in a dynamic environment. Hereby, synapses coordinate their noise processes to represent and utilize uncertainties on the network level in behaviorally ambiguous situations.


title: Protein preference and elevated plasma FGF21 induced by dietary protein restriction is similar in both male and female mice

abstract:
Animals that are moderately protein restricted respond to this dietary stress by increasing consumption of protein-containing foods. This is true in many species, including rodents. Rodent models of protein restriction have typically relied on only male subjects, and there are plausible reasons why female rodents may respond differently to dietary protein restriction. To address this gap in knowledge, the current experiments examined protein preference after two weeks on a 5% protein diet or 20% protein control diet, in male and female mice. We found that female mice, like male mice, increase consumption of 4% casein (protein) relative to 4% maltodextrin (carbohydrate) when presented with both simultaneously. Interestingly, this increased consumption was due to more bursts in females and more licks per burst in males, indicating possible differences in mechanism by which increased intake is achieved. Stage of the estrous cycle did not affect female responses. Moreover, we measured plasma FGF21 - a hormone induced by protein restriction and necessary for protein preference - in male and female mice. Here, we found no statistical differences between protein-restricted males, females in diestrus, or females in proestrus. In non-restricted mice FGF21 levels were low, but significantly higher in females in proestrus than females in diestrus or males. Overall, these experiments highlight the importance of including female subjects in studies of food choice and macronutrient restriction.

Highlights- Protein-restricted male and female mice exhibit protein preference
- Estrous cycle stage does not influence protein preference
- Estrous cycle stage does not affect plasma FGF21 during protein restriction
- Non-restricted females in proestrus have higher FGF21 than those in diestrus or males


title: MME+ fibro-adipogenic progenitors are the dominant adipogenic population during fatty infiltration in human skeletal muscle

abstract:
Summary/Abstract

Fatty infiltration, the ectopic deposition of adipose tissue within skeletal muscle, is mediated via the adipogenic differentiation of fibro-adipogenic progenitors (FAPs). We used single-nuclei and single- cell RNA sequencing to characterize FAP heterogeneity in patients with fatty infiltration. We identified an MME+ FAP subpopulation which, based on ex vivo characterization as well as transplantation experiments, exhibits high adipogenic potential. MME+ FAPs are characterized by low activity of WNT, known to control adipogenic commitment, and are refractory to the inhibitory role of WNT activators. Using preclinical models for muscle damage versus fatty infiltration, we show that many MME+ FAPs undergo apoptosis during muscle regeneration and differentiate into adipocytes under pathological conditions, leading to their depletion. Finally, we utilized the varying fat infiltration levels in human hip muscles to show the depletion of MME+ FAPs in fatty infiltrated human muscle. Altogether, we have identified the dominant adipogenic FAP subpopulation in skeletal muscle.


title: Evolutionary conservation and divergence of the transcriptional regulation of bivalve shell secretion across life history stages

abstract: Adult molluscs produce shells with diverse morphologies and ornamentations, different colour patterns and microstructures. The larval shell however, is a phenotypically more conserved structure. How do developmental and evolutionary processes generate varying diversity at different life history stages? Using live-imaging, histology, scanning electron microscopy and transcriptomic profiling, we have described shell development in a heteroconchian bivalve the Antarctic clam, Laternula elliptica and compared it to adult shell secretion processes in the same species. Adult downstream shell genes, such as those encoding extracellular matrix proteins and biomineralisation enzymes, were largely not expressed during shell development, and instead, a development-specific downstream gene repertoire was expressed. Upstream regulatory genes such as transcription factors and signalling molecules were conserved between developmental and adult shell secretion. Comparing heteroconchian transcriptomic data with recently reported pteriomorphian larval shell proteome data suggests that, despite being phenotypically more conserved, the downstream effectors constituting the larval shell "tool-kit" may be as diverse as that of adults. Overall, our new data suggests that a larval shell formed using development-specific downstream effector genes is a conserved and ancestral feature of the bivalve lineage, and possibly more broadly across the molluscs.

category: evolutionary biology


title: SMURF: embedding single-cell RNA-seq data with matrix factorization preserving selfconsistency

abstract: The advance of single-cell RNA-sequencing (scRNA-seq) sheds light on cell-specific transcriptomic studies of cell developments, complex diseases, and cancers. Nevertheless, scRNA-seq techniques suffer from "dropout" events, and imputation tools are proposed to address the sparsity. Here, rather than imputation, we propose a tool, SMURF, to embed cells and genes into their latent space vectors utilizing matrix factorization with a mixture of Poisson-Gamma divergent as objective while preserving self-consistency. As for wet lab dataset evaluation, SMURF exhibited feasible cell subpopulation discovery efficacy with the latent vectors on all the eight-cell line mixtures. Furthermore, SMURF can embed the cell latent vectors into a 1D-oval and recover the time course of the cell cycle. SMURF can also serve as an imputation tool, the in silico data assessment shows that SMURF paraded the most robust gene expression recovery power with low root mean square error and high Pearson correlation. Moreover, SMURF recovers the gene distribution for the WM989 Drop-seq data. SMURF is available at https://github.com/deepomicslab/SMURF.

category: bioinformatics


title: Identifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?

abstract: AO_SCPLOWBSTRACTC_SCPLOWThere is still no consensus as to how to select models in Bayesian phylogenetics, and more generally in applied Bayesian statistics. Bayes factors are often presented as the method of choice, yet other approaches have been proposed, such as cross-validation or information criteria. Each of these paradigms raises specific computational challenges, but they also differ in their statistical meaning, being motivated by different objectives: either testing hypotheses or finding the best-approximating model. These alternative goals entail different compromises, and as a result, Bayes factors, cross-validation and information criteria may be valid for addressing different questions. Here, the question of Bayesian model selection is revisited, with a focus on the problem of finding the best-approximating model. Several model selection approaches were re-implemented, numerically assessed and compared: Bayes factors, cross-validation (CV), in its different forms (k-fold or leave-one-out), and the widely applicable information criterion (wAIC), which is asymptotically equivalent to leave-one-out cross validation (LOO-CV). Using a combination of analytical results and empirical and simulation analyses, it is shown that Bayes factors are unduly conservative. In contrast, cross-validation represents a more adequate formalism for selecting the model returning the best approximation of the data-generating process and the most accurate estimates of the parameters of interest. Among alternative CV schemes, LOO-CV and its asymptotic equivalent represented by the wAIC, stand out as the best choices, conceptually and computationally, given that both can be simultaneously computed based on standard MCMC runs under the posterior distribution.


title: IL-17A controls CNS autoimmunity by regulating gut microbiota and inducing regulatory T cells

abstract:
A disrupted equilibrium between IL-17A-producing CD4 T-cells (Th17) and CD4+CD25+FoxP3+ regulatory T cells (Tregs) play an important role in the pathobiology of Multiple sclerosis (MS). Gut bacteria help in maintaining immune homeostasis by regulating the balance between anti-inflammatory Tregs and pro-inflammatory Th17 cells. Although, both gut bacteria and Tregs can regulate Th17 cells, the impact of IL-17A on gut microbiota and Tregs is unclear. Utilizing HLA-DR3 transgenic mouse model of MS, we show that IL-17A deficiency (HLA-DR3.IL17A-/- mice) expands Treg-inducing gut bacteria such as Prevotella, Parabacteroides, and Bacteroides and consequently Tregs, resulting in a milder disease in an animal model of MS. Notably, IL-17A sufficient DR3 mice develop milder disease on cohousing with IL-17A-deficient mice, highlighting a dominant role for gut microbiota in inducing Treg and reducing disease severity. Further, we observed an enrichment of bacterial-specific Treg promoting short-chain-fatty-acid metabolic pathways and induction of tolerogenic dendritic cells in HLA-DR3.IL17A-/- mice. Thus, our study shows a novel role of IL-17A in immune homeostasis and inflammation through regulation of the gut microbiota-Treg axis which can be used for the development of gut bacteria as therapeutics for MS.

Significance of our workIL-17A a pro-inflammatory cytokine, is linked with pathobiology of multiple inflammatory diseases including multiple sclerosis (MS) and regulated by both gut microbiota and regulatory CD4 T cells (Tregs). However, the importance of IL-17A in the regulation of gut microbiota and Treg is unknown. Here we show that IL-17A can regulate Treg and disease phenotype by modulating gut microbiota and provide a novel mechanism by which immune-mediators such as IL-17A impact the gut microbiota to alter immune cell function and ultimately disease outcomes. Transfer of milder disease phenotype from IL-17A deficient mice to IL-17A sufficient mice on cohousing indicate a dominant role of gut microbiota in disease suppression. Thus, our study lays the foundation for future studies to unravel the interplay between immunological responses and the gut microbiota which will result in the development of microbiota-based therapeutics to treat autoimmune diseases.


title: Run-on sequencing reveals nascent transcriptomics of the human microbiome

abstract: Precise regulation of transcription initiation and elongation enables bacteria to control cellular responses to environmental stimuli. RNAseq is the most common tool for measuring the transcriptional output of bacteria, comprising predominantly mature transcripts. To gain further insight into transcriptional dynamics, it is necessary to discriminate actively transcribed loci from those represented in the total RNA pool. One solution is to capture RNA polymerase (RNAP) in the act of transcription, but current methods are restricted to culturable and genetically tractable organisms. Here, we apply precision run-on sequencing (PRO-seq) to profile nascent transcription, a method amenable to diverse species. We find that PRO-seq is well-suited to profile small, structured, or post-transcriptionally modified RNAs, which are often excluded from RNAseq libraries. When PRO-seq is applied to the human microbiome, we identify taxon-specific RNAP pause motifs. We also uncover concurrent transcription and cleavage of guide RNAs and tRNA fragments at active CRISPR and tRNA loci. We demonstrate the specific utility of PRO-seq as a tool for exploring transcriptional dynamics in diverse microbial communities.


title: Circular mRNA encoded PROTAC (RiboPROTAC) as a new platform for the degradation of intracellular therapeutic targets

abstract: Although proteolysis targeting chimera (PROTAC) technology that hijacking the ubiquitin-proteasome system (UPS) to artificially degrade protein is an emerging promising technology for many undruggable targets, it still faces several challenges, such as the difficulty to select high specificity molecule to protein of interest (POI), and only few of the E3-ligase are suitable for PROTAC mediated protein degradation. Protein-based PROTAC, termed BioPROTAC, owns the advantage of specificity but lacks membrane permeability. Here, we develop a new targeted protein degrading platform, which we termed RiboPROTAC, by encoding BioPROTAC protein degraders with circular mRNA (cmRNA) and delivering intracellularly. In this way, intracellular protein GFP and nuclear protein PCNA were successfully degraded. For PCNA targeting, not only the level of target protein is strongly decreased, but also the cell function related is strongly interfered, such as cell proliferation, apoptosis, as well as the cell cycle. What is more, for the first time, we observed that degrading PCNA with RiboPROTAC causes immunogenic cell death (ICD), although not strong, but was verified in vivo. Importantly, our in vivo results demonstrated that cmRNA encoded PCNA degrader exhibited significant tumor suppression effect, thus we provide the first proof of concept for the application of RiboPROTAC as potential mRNA therapeutic. We consider that RiboPROTAC is a new and superior PROTAC technology for targeting the undruggable targets.

category: molecular biology


title: Adenine base editing is an efficient approach to restore function in FA patient cells without double-stranded DNA breaks

abstract: Fanconi Anemia (FA) is a debilitating genetic disorder with a wide range of severe symptoms including bone marrow failure and predisposition to cancer. CRISPR-Cas genome editing manipulates genotypes by harnessing DNA repair and has been proposed as a potential cure for FA. But FA is caused deficiencies in DNA repair itself, preventing the use of editing strategies such as homology directed repair. Recently developed base editing (BE) systems do not rely on double stranded DNA breaks and might be used to target mutations in FA genes, but this remains to be tested. Here we develop a proof of concept therapeutic base editing strategy to address two of the most prevalent FANCA mutations in patient cells. We find that optimizing adenine base editor construct, vector type, guide RNA format, and delivery conditions lead to very effective genetic modification in multiple FA patient backgrounds. Optimized base editing restored FANCA expression, molecular function of the FA pathway, and phenotypic resistance to crosslinking agents. ABE8e mediated editing in primary hematopoietic stem and progenitor cells from an FA patient was both genotypically effective and restored FA pathway function, indicating the potential of base editing strategies for future clinical application in FA.


title: Quantifying the fraction of new mutations that are recessive lethal

abstract: The presence and impact of recessive lethal mutations has been widely documented in diploid outcrossing species. However, precise estimates in different species of the proportion of mutations that are recessive lethal remain limited. Here, we attempt to quantify the fraction of new mutations that are recessive lethal using Fit{partial}a{partial}i, a commonly-used method for inferring the distribution of fitness effects (DFE) using the site frequency spectrum. Using simulations, we demonstrate that Fit{partial}a{partial}i cannot accurately estimate the fraction of recessive lethal mutations, as expected given that Fit{partial}a{partial}i assumes that all mutations are additive by default. Consistent with the idea that mis-specification of the dominance model can explain this performance, we find that Fit{partial}a{partial}i can accurately infer the fraction of additive lethal mutations. Moreover, we demonstrate that in both additive and recessive cases, inference of the deleterious non-lethal portion of the DFE is minimally impacted by a small proportion (<10%) of lethal mutations. Finally, as an alternative approach to estimate the proportion of mutations that are recessive lethal, we employ models of mutation-selection-drift balance using existing genomic parameters and segregating recessive lethals estimates for humans and Drosophila melanogaster. In both species, we find that the segregating recessive lethal load can be explained by a very small fraction (<1%) of new nonsynonymous mutations being recessive lethal. Our results refute recent assertions of a much higher recessive lethal mutation fraction (4-5%), while highlighting the need for additional information on the joint distribution of selection and dominance coefficients.


title: Genetic dissection of the pluripotent proteome through multi-omics data integration

abstract: Genetic background is a major driver of phenotypic variability in pluripotent stem cells (PSCs). Most studies of variation in PSCs have relied on transcript abundance as the primary molecular readout of cell state. However, little is known about how proteins, the primary functional units in the cell, vary across genetically diverse PSCs, how protein abundance relates to variation in other cell characteristics, and how genetic background confers these effects. Here we present a comprehensive genetic study characterizing the pluripotent proteome of 190 unique mouse embryonic stem cell lines (mESCs) derived from genetically heterogeneous Diversity Outbred (DO) mice. The quantitative proteome is highly variable across DO mESCs, and we identified differentially activated pluripotency-associated pathways in the proteomics data that were not evident in transcriptome data from the same cell lines. Comparisons of protein abundance to transcript levels and chromatin accessibility show broad co-variation across molecular layers and variable correlation across samples, with some lines showing high and others low correlation between these multi-omics datasets. Integration of these three molecular data types using multi-omics factor analysis revealed shared and unique drivers of quantitative variation in pluripotency-associated pathways. QTL mapping localized the genetic drivers of this quantitative variation to a number of genomic hotspots, and demonstrated that multi-omics data integration consolidates the influence of genetic signals shared across molecular traits to increase QTL detection power and overcome the limitations inherent in mapping individual molecular features. This study reveals transcriptional and post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome, and in so doing provides a regulatory map for mouse ESCs that can provide a rational basis for future mechanistic studies, including studies of human PSCs.

category: genetics


title: The molecular consequences of androgen activity in the human breast

abstract: The mammary gland has been extensively studied for estrogen and progesterone reactivity, but the molecular effects of androgen in the breast remain largely unexplored. Transgender men are recorded female at birth but identify as male and may undergo gender-affirming androgen therapy to align their physical characteristics and gender identity. Here we perform single cell resolution transcriptome, chromatin, and spatial profiling of androgen treated breasts from transgender men. We find male-biased androgen receptor gene targets are upregulated in cells expressing androgen receptor, and that paracrine signaling drives sex-relevant changes in other cell types. We observe an altered epithelium, shifts in immune populations, and a reduction of capillary vasculature. Finally, we find evidence of the metabolic impact of androgen and identify a gene regulatory network driving androgen-directed fat loss. This work elucidates the molecular consequences of androgen in the human breast at single cell resolution.

category: genomics


title: A phased chromosome-level genome and full mitochondrial sequence for the dikaryotic myrtle rust pathogen, Austropuccinia psidii

abstract: The fungal plant pathogen Austropuccinia psidii is spreading globally and causing myrtle rust disease symptoms on plants in the family Myrtaceae. A. psidii is dikaryotic, with two nuclei that do not exchange genetic material during the dominant phase of its life-cycle. Phased and scaffolded genome resources for rust fungi are important for understanding heterozygosity, mechanisms of pathogenicity, pathogen population structure and for determining the likelihood of disease spread. We have assembled a chromosome-level phased genome for the pandemic biotype of A. psidii and, for the first time, show that each nucleus contains 18 chromosomes, in line with other distantly related rust fungi. We show synteny between the two haplo-phased genomes and provide a new tool, ChromSyn, that enables efficient comparisons between chromosomes based on conserved genes. Our genome resource includes a fully assembled and circularised mitochondrial sequence for the pandemic biotype.


title: Peroxisomal ATPase ATAD1 acts in quality control of the protein import machinery

abstract: ATAD1 is an AAA-ATPase which shows a dual localization at mitochondria and peroxisomes. While its peroxisomal function is not known, in mitochondria ATAD1 is part of a quality control mechanism extracting mislocalised tail-anchored and accumulated precursor proteins from the outer membrane. Here, we studied the peroxisomal interactome of ATAD1 and could show that human ATAD1 interacts with PEX5, a cytosolic receptor for peroxisomal matrix proteins which transiently inserts into peroxisomal membranes. Upon cargo-release, mono-ubiquitinated PEX5 is recycled into the cytosol by the AAA-peroxins PEX1 and PEX6. The accumulation of ubiquitinated PEX5 is known to trigger degradation of whole organelles called pexophagy. Here, we used ATAD1-, PEX1- and ATAD1/PEX1-CRISPR-Knockout cell lines to investigate the physiological role of an ATAD1-PEX5 interaction. We could show an influence of ATAD1 on the stability of accumulated PEX5 and hypothesize a role in a peroxisomal quality control mechanism enabling clearance of ubiquitinated receptor from the membrane.


title: Simple within-stride changes in treadmill speed can drive selective changes in human gait symmetry

abstract:
BackgroundMillions of people worldwide are affected by clinical conditions that result in gait asymmetry (e.g., stroke, cerebral palsy, lower limb amputation). There is a need for customizable rehabilitation approaches that can flexibly target different aspects of gait asymmetry with minimal need for specialized equipment. Here, we studied how simple within-stride changes in treadmill speed could drive selective, predictable changes in human gait symmetry.

MethodsIn Experiment 1, ten healthy young adults walked on an instrumented treadmill with and without a closed-loop controller engaged. The controller changed the treadmill speed to 1.50 m/s or 0.75 m/s depending on whether the right or left leg generated propulsive (i.e., forward-directed) ground reaction forces, respectively. In Experiment 2, a separate group of ten healthy young adults walked on the treadmill with and without an open-loop controller engaged. This controller changed the treadmill speed to 1.50 m/s or 0.75 at a prescribed time interval. We used a metronome to guide the participants to step at a series of different time points relative to the controller-driven speed change. We collected kinematic and kinetic data in Experiments 1 and 2.

ResultsIn Experiment 1, participants walked with asymmetric kinematics and ground reaction forces when the closed-loop controller was engaged. The leg that accelerated during propulsion (right leg) showed a smaller leading limb angle and a larger trailing limb angle than the leg that decelerated during propulsion (left leg). The right leg also generated smaller propulsive forces than the left leg. In Experiment 2, the patterns of asymmetry in spatiotemporal gait parameters, kinematics, and ground reaction forces depended on the timing of the speed change within the gait cycle. Step times, leading limb angles, and peak propulsion became asymmetric when the treadmill speed changed early in stance. When the treadmill speed changed later in stance, step lengths, step times, and propulsion impulses became asymmetric.

ConclusionsSimple manipulations of treadmill speed can drive predictable, selective changes in human gait symmetry. Future work will explore this customizable technique as a potential approach for restoring gait symmetry in clinical populations.

category: bioengineering


title: Detection and discrimination of single nucleotide polymorphisms by quantification of CRISPR-Cas catalytic efficiency

abstract: The specificity of CRISPR-Cas12 assays is attractive for the detection of single nucleotide polymorphisms (SNPs) implicated in, e.g., SARS-CoV-2 variants. Such assays often employ endpoint measurements of SNP or wild type (WT) activated Cas12 trans-cleavage activity; however, the fundamental kinetic effects of SNP versus WT activation remain unknown. We here show that endpoint-based assays are limited by arbitrary experimental choices (like used reporter concentration and assay duration) and work best for known target concentrations. More importantly, we show that SNP (versus WT) activation results in measurable shifts in the Cas12 trans-cleavage substrate affinity (KM) and apparent catalytic efficiency [Formula]. To address endpoint-based assay limitations, we then develop an assay based on the quantification of Michalis-Menten parameters and apply this assay to a 20-base pair WT target of the SARS-CoV-2 E gene. We find that the [Formula] measured for WT is 130-fold greater than the lowest [Formula] among all 60 measured SNPs (compared to a 4.8-fold for endpoint fluorescence of the same SNP). KM also offers strong ability to distinguish SNPs, varies 27-fold over all the cases, and is insensitive to target concentration. Lastly, we point out trends among kinetic rates and SNP base and location within the CRISPR-Cas12 targeted region.


title: Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites

abstract:
MotivationProtein phosphorylation is a key post-translational modification that plays a central role in many cellular processes. With recent advances in biotechnology, thousands of phosphorylated sites can be identified and quantified in a given sample, enabling proteome-wide screening of cellular signaling. However, the kinase(s) that phosphorylate most (> 90%) of the identified phosphorylation sites are unknown. Knowledge of kinase-substrate associations is also mostly limited to a small number of well-studied kinases, with 20% of known kinases accounting for the phosphorylation of 87% of currently annotated sites. The scarcity of available annotations calls for the development of computational algorithms for more comprehensive and reliable prediction of kinase-substrate associations.

ResultsTo broadly utilize available structural, functional, evolutionary, and contextual information in predicting kinase-substrate associations, we develop a network-based machine learning framework. Our framework integrates a multitude of data sources to characterize the landscape of functional relationships and associations among phosphosites and kinases. To construct a phosphosite-phosphosite association network, we use sequence similarity, shared biological pathways, co-evolution, co-occurrence, and co-phosphorylation of phosphosites across different biological states. To construct a kinase-kinase association network, we integrate protein-protein interactions, shared biological pathways, and membership in common kinase families. We use node embeddings computed from these heterogeneous networks to train machine learning models for predicting kinase-substrate associations. Our systematic computational experiments using the PhosphositePLUS database shows that the resulting algorithm, NetKSA, outperforms state-of-the-art algorithms and resources, including KinomeXplorer and LinkPhinder, in reliably predicting KSAs. By stratifying the ranking of kinases, NetKSA also enables annotation of phosphosites that are targeted by relatively less-studied kinases. Finally, we observe that the performance of NetKSA is robust to the choice of network embedding algorithms, while each type of network contributes valuable information that is complementary to the information provided by other networks.

ConclusionRepresentation of available functional information on kinases and phosphorylation sites, along with integrative machine learning algorithms, has the potential to significantly enhance our knowledge on kinase-substrate associations.

AvailabilityThe code and data are available at compbio.case.edu/NetKSA.


title: Multiple modes of substrate hydrolysis-induced covalent modification of strigolactone receptors

abstract: The strigolactone signaling pathway in plants is unconventional among plant hormone signaling pathways in that the receptor also acts as an enzyme that hydrolyzes the strigolactone substrate. While the canonical view of strigolactone hydrolysis is that it occurs via a nucleophilic attack on the butenolide ring of strigolactone, an alternative Michael addition mechanism in which hydrolysis occurs via a nucleophilic attack on the enol-ether bridge has been proposed. Furthermore, while it is known that a hydrolysis-induced covalent modification to the receptor promotes strigolactone receptor activation, the nature of this covalent modification has been disputed. Here, we employ QM/MM string method simulations to determine the favored pathway of strigolactone hydrolysis and the nature of the covalent modification that acts as a promoter of strigolactone receptor activation. Our simulations show that strigolactone hydrolysis occurs via an acyl substitution pathway beginning with nucleophilic attack on the butenolide ring, which is well corroborated by previous experimental literature. Additionally, we show that multiple possible modes of covalent modifications to the catalytic residues by the butenolide ring are able to form and interconvert, reconciling several seemingly conflicting views on the hydrolysis-induced covalent modification to strigolactone receptors.


title: cMYC protein interactions and chromatin association in NUT carcinoma

abstract:
The oncogene cMYC (HGNC:7553) is a critical genomic target of the BRD4-NUT (B4N) protein that defines many of the NUTM1-rearrangement cancer subtypes in NUT carcinoma (NC). B4N interacts with the EP300 lysine acetyltransferase (KAT3B) to create hyperacetylated "megadomains" that activate downstream genes such as cMYC. However, it is less well understood how mis-regulation of cMYC in turn affects its protein interactions and target genes. The goals of this study are to define the protein and genomic interactions of cMYC in NC, and to test whether those change in response to B4N inactivation. We used CRISPR-Cas9 mediated knock-in of a BioTAP affinity tag to analyze cMYC protein expressed from its normal chromosomal context. This allowed us to adapt a crosslinking purification method termed BioTAP-XL to preserve cMYC integrity and chromatin association for genomic and mass spectrometry-based proteomic analyses. We found that cMYC interacts primarily with the NuA4 KAT5 lysine acetyltransferase complex and that the interactions were maintained despite a decrease in cMYC levels after JQ1 treatment. We conclude that a cascade of aberrant acetyltransferase activities, first via EP300 recruitment and then by KAT5 interaction with MYC, drive NC cell proliferation and blockade to differentiation.

Simple SummaryA longstanding goal in biology is to understand how protein interactions influence and reflect cellular disease states. MYC is a critical regulator of cellular proliferation that is mis-regulated in many cancers, including those with NUTM1-rearrangements featured in this issue. NUT carcinoma cells are dependent on MYC expression, which blocks differentiation. Using a small molecule inhibitor to induce differentiation of a NUTM1-rearranged patient cell line, we sought to understand how MYC protein interactions are affected by cellular status. When cells differentiate, we found MYC levels were globally diminished, yet the identities of its protein partners and genomic binding sites remained constant. During both growth and differentiation, MYC protein interacted with subunits of the NuA4 lysine acetyltransferase complex, similar to its associations in non-NUTM1 cell lines. Taken together, our results suggest that lysine acetyltransferase activities participate in multiple oncogenic steps in NUT carcinoma.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=134 HEIGHT=200 SRC="FIGDIR/small/489219v1_ufig1.gif" ALT="Figure 1">
View larger version (23K):
org.highwire.dtl.DTLVardef@1272fb8org.highwire.dtl.DTLVardef@1ae1311org.highwire.dtl.DTLVardef@165e3cdorg.highwire.dtl.DTLVardef@4ed595_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Engineered extracellular matrices reveal stiffness-mediated chemoresistance in patient-derived pancreatic cancer organoids

abstract: Pancreatic ductal adenocarcinoma (PDAC) is characterized by its fibrotic and stiff extracellular matrix (ECM); however, the role that altered cell-ECM signaling may play in driving PDAC phenotype has historically been difficult to dissect. Here, we design an engineered matrix that recapitulates key hallmarks of the tumor ECM and show that patient-derived PDAC organoids develop gemcitabine chemoresistance when cultured within high stiffness matrices mechanically matched to in vivo tumors. Using genetic barcoding, we find that while matrix-specific clonal selection occurs, cellular heterogeneity is not the main driver of chemoresistance. Instead, stiffness-induced chemoresistance occurs due to the development of a plastic cancer stem cell phenotype - mediated by hyaluronan mechanosignaling - with increased expression of drug efflux transporters. Moreover, PDAC chemoresistance is reversible following transfer from high to low stiffness matrices, suggesting that mechanotherapeutics targeting the fibrotic ECM may sensitize chemoresistant tumors. Overall, we demonstrate the power of engineered matrices and patient-derived organoids to elucidate how ECM properties influence human disease pathophysiology.


title: Polarly localized WPR proteins interact with PAN receptors and the actin cytoskeleton during maize stomatal development

abstract: Polarization of cells prior to asymmetric cell division is crucial for correctly orienting the cell division plane, and for subsequent cell fate and overall tissue patterning. In maize stomatal development, polarization of subsidiary mother cells prior to asymmetric division is controlled by the BRK-PAN-ROP pathway. Two catalytically inactive receptor-like kinases, PANGLOSS2 (PAN2) and PAN1, are polarized in subsidiary mother cells prior to division and required for correct division planes. Each of the proteins in the BRK-PAN-ROP pathway are polarized in subsidiary mother cells, with the polarization of each protein dependent on the previous one. Most of these proteins do not physically interact with one another, indicating there are likely unknown molecules in the pathway. We identified WEB1-PMI2 RELATED (WPR) proteins as new players during subsidiary mother cell polarization. WPRs physically interact with PAN2 and PAN1, and polarly accumulate in subsidiary mother cells at sites of guard mother cell contact. The polarized localization of WPR proteins depends on PAN2 but not PAN1. CRISPR-Cas9-induced mutations result in division plane defects in subsidiary mother cells, and mild overexpression of fluorescent protein tagged lines result in stomatal defects and alterations to the actin cytoskeleton. We further show that a subgroup of the WPR proteins directly interact with F-actin through their N-terminal domain. Our data implicate WPR proteins as potentially regulating actin filaments, which provides insight into their molecular function. Together, these results demonstrate WPR proteins as important for cell polarization and grass stomatal development.


title: The effect of sleep continuity disruption on multimodal emotion processing and regulation: a laboratory-based, randomized, controlled experiment in good sleepers

abstract: Previous research shows that experimental sleep deprivation alters emotion processing, suggesting a potential mechanism linking sleep disruption to mental ill-health. Extending previous work, we experimentally disrupted sleep continuity in good sleepers and assessed next-day emotion processing and regulation using tasks with established sensitivity to depression. In a laboratory-based study, 51 good sleepers (37 female; mean age = 24 years, SD= 3.63) were randomized to one night (23:00-07:00) of uninterrupted sleep (n=24) or sleep continuity disruption (n=27). We assessed emotion perception, attention, and memory the following day. Participants also completed an emotion regulation task and measures of self-reported affect, anxiety, sleepiness, overnight declarative memory consolidation, and psychomotor vigilance. Confirming the effects of the manipulation, sleep continuity disruption led to a marked decrease in polysomnography-defined total sleep time (229.98 mins vs 434.57 mins), increased wake-time after sleep onset (260.66 mins vs 23.84 mins) and increased sleepiness (d=0.81). Sleep continuity disruption led to increased anxiety (d=0.68), decreased positive affect (d=-0.62), reduced overnight declarative memory consolidation (d=-1.08) and reduced psychomotor vigilance [longer reaction times (d=0.64) and more lapses (d=0.74)], relative to control. However, contrary to our hypotheses, experimental sleep disruption had no effect on perception of, or bias for, emotional facial expressions, emotional memory for words, or emotion regulation following worry induction. In conclusion, one night of sleep continuity disruption had no appreciable effect on objective measures of emotion processing or emotion regulation in response to worry induction, despite clear effects on memory consolidation, vigilance, and self-reported affect and anxiety.


title: Ventral Hippocampal Infusions of C20:0 Ceramide Stimulate Microglia and Induce Anhedonia-like Behavior in Female and Male Rats

abstract: Increased long-chain C20:0 ceramides have been found in the serum of patients with depression. Moreover, ceramides are linked with increased microglia reactivity and inflammatory cytokine production, which are associated with depression. Since ceramides can readily cross the blood brain barrier, peripheral C20:0 ceramides could enter the brain, activate microglia, and induce depressive-like behavior. In this study, we determined whether localized infusion of C20:0 ceramides into the ventral hippocampus (VH) of rats is sufficient to activate microglia and induce depressive-like behaviors. Adult male and female rats received infusions of C20:0 ceramides or vehicle solution every other day for 2 weeks. After the third infusion, C20:0-infused animals showed reduced sucrose preference suggesting anhedonia-like behavior. However, 4-6 days after the last infusion, animals infused with C20:0 ceramides did not show anhedonia-like or despair-like behavior suggesting the behavioral effect was reversible. After the final behavioral test, C20:0-infused animals had more Iba-1+ microglia in the VH. Despite the increased number of VH microglia, the expression of inflammatory genes was not increased. In conclusion, our data suggest that localized increases in C20:0 ceramides in the VH are sufficient to induce microglia activation and reversible anhedonia-like behavior.


title: Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice.

abstract:
BACKGROUNDCocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. HPTMs act combinatorically, yet few studies examine multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In the current study, we defined regulation of K4&K27 bivalency at Nr4a1 following cocaine treatment in male and female mice. The inclusion of female mice can shed light on the epidemiological relevance of sex to cocaine use disorder.

METHODSMale and female mice were injected with saline or cocaine (i.p. 20mg/kg). We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). Pearsons correlation matrices quantified relationships within each brain region across treatment conditions for each sex.

RESULTSWe defined K4&K27 bivalency at the Nr4a1 promoter in all three brain regions, in both sexes. In female STR, cocaine increased Nr4a1 mRNA, coupled to maintenance of Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and failed to increase Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC.

CONCLUSIONThis study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice. Cocaine treatment in female mice increased Nr4a1 mRNA in STR, but there was no change in Nr4a1 H3K27me3 or K4&K27 promoter bivalency. Following cocaine treatment in male mice, Nr4a1 mRNA did not change in STR, HPC, or PFC, and Nr4a1 H3K27me3 and K4&K27 promoter bivalency increased in the STR.


title: Individual prediction tendencies facilitate cortical speech tracking

abstract: Listening can be conceptualized as a process of active inference, in which the brain forms internal models to predict and integrate auditory information in a complex interaction of bottom-up and top-down processes. Whether inter-individual "prediction tendencies" shape listening experiences of real-world stimuli such as speech is, however, unknown. In the current study, we used a passive paradigm presenting tone sequences of varying entropy level, to independently quantify auditory prediction tendency (as the tendency to anticipate low-level acoustic features according to their contextual probability) for each individual. This measure was then used to predict the magnitude of cortical speech (envelope) tracking in a multi speaker listening task, where participants listened to audiobooks narrated by a target speaker in isolation or interfered by 1 or 2 distractors. Furthermore, rare semantic violations were introduced into the story, enabling us to also examine effects of word surprisal during continuous speech processing. Our results show that individual prediction tendency facilitates cortical speech tracking. Furthermore, we find interactions between individual prediction tendency and background noise as well as word surprisal in disparate brain regions. In sum, our findings suggest that individual prediction tendencies are generalizable across different listening situations and may serve as a valuable element to explain interindividual differences in natural listening experience.


title: Neural connectivity molecules best identify the heterogeneous clock and dopaminergic cell types in the Drosophila adult brain

abstract: Our recent single cell sequencing of most adult Drosophila circadian neurons indicated striking gene expression heterogeneity, about 2-3 cells per clock neuron group. To extend this characterization to other adult fly brain neurons, we used the identical plate-based methods to generate single cell data from a similar subset of dopaminergic neurons. To minimize batch effects and to apply an additional sequencing strategy, we also assayed these two populations together with 10X Chromium. An unsupervised clustering algorithm indicates that dopaminergic neurons are comparably heterogeneous, suggesting that the transcriptomic diversity of adult fly brain neurons parallels its EM connectome. The results here further indicate that connectivity molecules like cell surface molecules best characterize all neuron groups. We suggest that these surprising features are general and make major contributions to neuronal identity and connectivity of the adult central brain as well as underlie the complex behavioral repertoire of Drosophila.


title: Dual RNA-seq reveals a type 6 secretion system-dependent blockage of TNF-α signaling and BicA as a Burkholderia pseudomallei virulence factor important during gastrointestinal infection

abstract: Melioidosis is a disease caused by the Gram-negative bacillus Burkholderia pseudomallei (Bpm), commonly found in soil and water of endemic areas. Naturally acquired human melioidosis infections can result from either exposure through percutaneous inoculation, inhalation, or ingestion of soil-contaminated food or water. Our prior studies recognized Bpm as an effective enteric pathogen, capable of establishing acute or chronic gastrointestinal infections following oral inoculation. However, the specific mechanisms and virulence factors involved in the pathogenesis of Bpm during intestinal infection are unknown. In our current study, we standardized an in vitro intestinal infection model using primary intestinal epithelial cells (IECs) and demonstrated that Bpm requires a functional T6SS for full virulence. Further, we performed dual RNA-seq analysis on Bpm-infected IECs to evaluate differentially expressed host and bacterial genes in the presence or absence of a T6SS. Our results showed a dysregulation in the TNF- signaling via NF-{kappa}B pathway in the absence of the T6SS, with some of the genes involved in inflammatory processes and cell death also affected. Analysis of the bacterial transcriptome identified virulence factors and regulatory proteins playing a role during infection, with association to the T6SS. By using a Bpm transposon mutant library and isogenic mutants, we showed that deletion of the bicA gene, encoding a putative T3SS/T6SS regulator, ablated intracellular survival and plaque formation by Bpm and impacted survival and virulence when using murine models of acute and chronic gastrointestinal infection. Overall, these results highlight the importance of the type 6 secretion system in the gastrointestinal pathogenesis of Bpm.


title: Locomotion control during curb descent: Bilateral ground reaction variables covary consistently during the double support phase regardless of future foot placement constraints

abstract: During community ambulation, anticipatory adaptations in gait are key for navigating built, populated and natural environments. It has been argued that some instability in gait can be functionally beneficial in situations demanding high maneuverability, and while the mechanisms utilized to maintain locomotor balance are well understood, relatively less is known about how the control of gait stability changes to facilitate upcoming maneuvers in challenging environments. The double support phase may be important in this regard; since both feet can push off the ground simultaneously, there is greater control authority over the bodys movement during this phase. Our goal was to identify how this control authority is exploited to prepare for upcoming maneuvers in challenging environments. We used synergy indices to quantify the degree of coordination between the ground reaction forces and moments under the two feet for stabilizing the resultant force and moment on the body during the double support phase of curb descent. In contrast to our expectations, we observed that the kinetic synergy indices during curb descent were minimally influenced by expected foot targeting maneuvers for the subsequent step. Only the resultant moment in the frontal plane showed reduced stability when targeting was required, but the synergy index was still high, indicating that the resultant moment was stable. Furthermore, the synergy indices indicated that the main function of the ground reaction variables is to maintain stability of whole-body rotations during double support, and this prerogative was minimally influenced by the subsequent foot targeting tasks, likely because the cost of losing balance while descending a curb would be higher than the cost of mis-stepping on a visual target. Our work demonstrates the salience of stabilizing body rotations during curb negotiation and improves our understanding of locomotor control in challenging environments.


title: Implications for food safety of the size and location of fragments of lead shotgun pellets embedded in hunted carcasses of small game animals intended for human consumption

abstract: Carcasses of common pheasants (Phasianus colchicus) killed by hunters using shotguns are widely used or sold in the United Kingdom and elsewhere for human consumption. Almost all of the birds are shot using shotgun pellets composed principally of lead (Pb). Lead shotgun pellets often fragment on impact within the bodies of gamebirds, leaving small lead particles in the meat that are difficult for consumers to detect and remove and from which a greater proportion of lead is likely to be absorbed. Chronic exposure to even low levels of lead is associated with negative health effects in humans and especially in groups particularly vulnerable to the effects of lead, which include young children and pregnant women. Our study used a high-resolution computerised tomography X-ray scanner to locate, in three dimensions, metal fragments embedded within carcasses of eight pheasants sold for human consumption in the UK. Small radio-dense fragments (<2 mm diameter), assumed to be metallic lead, were present in all of the pheasant carcasses examined (mean number: 39 per carcass) and many were too small (<0.1 mm diameter) and too distant from the nearest large shotgun pellet for it to be practical for consumers to detect and remove them without discarding a large proportion of otherwise usable meat. Consumers of carcasses of pheasants killed using lead shotgun ammunition are likely to be exposed to elevated levels of dietary lead, even if careful food preparation is practiced to remove shotgun pellets and the most damaged tissue.

category: pharmacology and toxicology


title: Metabolic size scaling reflects growth performance effects on age-size relationships in mussels (Mytilus galloprovincialis).

abstract: Body-size scaling of metabolic rate in animals is typically allometric, with mass exponents that vary to reflect differences in the physiological status of organisms of both endogenous and environmental origin. Regarding the intraspecific analysis of this relationship in bivalve molluscs, one important source of metabolic variation comes from the large inter-individual differences in growth performance characteristic of this group. In the present study, we aimed to address the association of growth rate differences recorded among individual mussels (Mytilus galloprovincialis) with variable levels of the standard metabolic rate (SMR) resulting in growth-dependent shift in size scaling relationships. SMR was measured in mussels of different sizes and allometric functions fitting SMR vs. body-mass relationships were compared both inter- and intra-individually. The results revealed a metabolic component (the overhead of growth) attributable to the differential costs of maintenance of feeding and digestion structures between fast and slow growers; these costs were estimated to amount to a 3% increase in SMR per unit of increment in the weight specific growth rate. Scaling exponents computed for intraindividual SMR vs body-mass relationships had a common value b = 0.79 (~ [3/4]); however, when metabolic effects caused by differential growth were discounted, this value declined to 0.67 (= [2/3]), characteristic of surface dependent processes. This last value of the scaling exponent was also recorded for the interindividual relationships of both SMR and RMR after long-lasting maintenance of mussels under optimal uniform conditions in the laboratory. The above results were interpreted based on the metabolic level boundary (MLB) hypothesis.

category: physiology


title: Characterization of human immunodeficiency virus (HIV-1) envelope glycoprotein variants selected for resistance to a CD4-mimetic compound

abstract:
Binding to host cell receptors, CD4 and CCR5/CXCR4, triggers conformational changes in the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer that promote virus entry. CD4 binding allows the gp120 exterior Env to bind CCR5/CXCR4 and induces a pre-hairpin intermediate conformation in the gp41 transmembrane Env. Small-molecule CD4-mimetic compounds (CD4mcs) bind within the conserved Phe-43 cavity of gp120, near the binding site for CD4. CD4mcs inhibit HIV-1 infection by competing with CD4 and by prematurely activating Env, leading to irreversible inactivation. BNM-III-170 is a CD4mc that inhibits the infection of approximately 70% of HIV-1 strains at micromolar concentrations. We selected and analyzed variants of the primary HIV-1AD8 strain resistant to BNM-III-170. Two changes (S375N and I424T) in gp120 residues that flank the Phe-43 cavity each conferred [~]5-fold resistance to BNM- III-170 with minimal fitness cost. A third change (E64G) in Layer 1 of the gp120 inner domain resulted in [~]100-fold resistance to BNM-III-170, [~]2-3-fold resistance to soluble CD4-Ig, and a moderate decrease in viral fitness. The gp120 changes additively or synergistically contributed to BNM-III-170 resistance. The sensitivity of the Env variants to BNM-III-170 inhibition of virus entry correlated with their sensitivity to BNM-III-170- induced Env activation and shedding of gp120. The S375N and I424T changes, but not the E64G change, conferred resistance to BMS-806, a potent HIV-1 entry inhibitor that blocks Env conformational transitions. These studies identify pathways whereby HIV-1 can develop resistance to CD4mcs and BMS-806 conformational blockers, two classes of entry inhibitors that target the conserved gp120 Phe-43 cavity.

IMPORTANCECD4-mimetic compounds (CD4mcs) and BMS-806 are small-molecule inhibitors of human immunodeficiency virus (HIV-1) entry into host cells. Although CD4mcs and BMS-806 inhibit HIV-1 entry by different mechanisms, they both target a pocket on the viral envelope glycoprotein (Env) spike that is used for binding to the receptor, CD4, and is highly conserved among HIV-1 strains. Our study identifies changes near this pocket that can confer various levels of resistance to the antiviral effects of both a CD4mc and BMS-806. We relate the antiviral potency of a CD4mc against this panel of HIV-1 variants to the ability of the CD4mc to activate changes in Env conformation and to induce the shedding of the gp120 exterior Env from the spike. These findings will guide efforts to improve the potency and breadth of small-molecule HIV-1 entry inhibitors.


title: Isotopic reconstruction of the subsistence strategy for a Central Italian Bronze Age community (Pastena cave, 2nd millennium BCE).

abstract: The Pastena cave is located in central Italy and its best-preserved sector is Grotticella W2, which is dated radiometrically to the Early-Middle Bronze Age. The aim of this paper is to explore human diet, animal husbandry, and plant management analyzing the findings there discovered. Carbon and nitrogen stable isotope analysis have been carried out on 40 charred seeds, 6 faunal remains and 4 human specimens, investigating the whole bio-archaeological samples available. To the best of our knowledge, this is one of the first papers presenting stable isotope analysis on carpological remains dated to the Italian Early-Middle Bronze Age. The obtained results are consistent with a diet based on terrestrial protein, mainly on plants and secondly on meat and animal products. The data suggest that plants, especially broad beans, were partially subjected to human management, while livestock was managed through different husbandry strategies. The cooperation between archaeological studies and molecular analysis allows us to contribute to clarify the economic strategies for a Central Italian community in a scenario that is still poor in published data.


title: A natural variation-based screen in mouse cells reveals USF2 as a regulator of the DNA damage response and cellular senescence

abstract:
Cellular senescence is a program of cell cycle arrest, apoptosis resistance, and cytokine release induced by stress exposure in mammalian cells. Landmark studies in laboratory mice have characterized a number of master senescence regulators, including p16INK4a, p21, NF-kB, p53, and C/EBP{beta}. To discover other molecular players in senescence, we developed a screening approach to harness the evolutionary divergence between mouse species. We found that primary cells from the Mediterranean mouse Mus spretus, when treated with DNA damage to induce senescence, produced less cytokine and had less-active lysosomes than cells from laboratory M. musculus. We used allele-specific expression profiling to catalog senescence-dependent cis-regulatory variation between the species at thousands of genes. We then tested for correlation between these expression changes and interspecies sequence variants in the binding sites of transcription factors. Among the emergent candidate senescence regulators, we chose a little-studied cell cycle factor, USF2, for molecular validation. In acute irradiation experiments, cells lacking USF2 exhibited compromised DNA damage repair and response.

Longer-term senescent cultures without USF2 mounted an exaggerated senescence regulatory program--shutting down cell cycle and DNA repair pathways, and turning up cytokine expression, more avidly than wild-type. We interpret these findings under a model of pro-repair, anti-senescence regulatory function by USF2. Our study affords new insights into the mechanisms by which cells commit to senescence, and serves as a validated proof of concept for natural variation-based regulator screens.


title: A method to enrich polypeptidyl-tRNAs to capture snapshots of translation in the cell

abstract:
Life depends on proteins, which all exist in nascent states when the growing polypeptide chain is covalently attached to a tRNA within the ribosome. Although the nascent chains; i.e., polypeptidyl-tRNAs (pep-tRNAs), are considered as merely transient intermediates during protein synthesis, recent advances have revealed that they are directly involved in a variety of cell functions, such as gene expression control. An increasing appreciation for fine-tuning at translational levels demands a general method to handle the pep-tRNAs on a large scale. Here, we developed a method to enrich the pep-tRNAs by organic solvent extraction and silica column separation, and then identify their polypeptide moieties by mass spectrometry. As a proof-of-concept experiment using Escherichia coli, we identified [~]500 peptides derived from the pep-tRNAs, which were markedly biased towards the N-terminal regions, reflecting that the method captured the intermediate pep-tRNA population during translation. Furthermore, the method identified a subset of pep-tRNAs that were resistant to puromycin treatment, suggesting that these pep-tRNAs accumulated due to nascent-chain dependent translational pausing. Although the current specificity and comprehensiveness of the pep-tRNA enrichment have room for improvement, this new method will complement conventional methods for profiling nascent chains.

Significance StatementIn the central dogma of biology, RNA, an informational molecule, and protein, a functional molecule, are usually regarded as two completely independent molecular species. However, they are combined into a single species called peptidyl-tRNA (pep-tRNA) during the translation process in the ribosome. Despite the importance of pep-tRNAs as precursors of all proteins in the cell, a general method to analyze pep-tRNAs on a large scale was lacking. Taking advantage of the properties of pep-tRNAs as RNA and protein, we developed a method termed peptidyl-tRNA enrichment using organic extraction and silica adsorption (PETEOS). PETEOS not only provides a unique approach to examine the nascent state of proteins but also may be effective in exploring peptides that cause translational pauses.