title: Epigenetic Landscape of HIV Infection in Primary Human Macrophage

abstract:
HIV-infected macrophages are long-lived cells that sustain persistent virus expression, which is both a barrier to viral eradication and contributor to neurological complications in patients despite antiretroviral therapy (ART). To better understand the regulation of HIV in macrophages, we compared HIV infected primary human monocyte derived macrophages (MDM) to acutely infected primary CD4 T cells and Jurkat cells latently infected with HIV (JLAT 8.4). HIV genomes in MDM were actively transcribed despite enrichment with heterochromatin-associated H3K9me3 across the complete HIV genome in combination with elevated activation marks of H3K9ac and H3K27ac at the LTR. Macrophage patterns contrasted with JLAT cells, which showed conventional bivalent H3K4me3/H3K27me3, and acutely infected CD4 T cells, which showed an intermediate epigenotype. 5 -methylcytosine (5mC) was enriched across the HIV genome in latently infected JLAT cells, while 5 -hydroxymethylcytosine (5hmc) was enriched in CD4 and MDM. HIV infection induced multinucleation of MDMs along with DNA damage associate p53 phosphorylation, as well as loss of TET2 and the nuclear redistribution of 5-hydoxymethylation. Taken together, our findings suggest that HIV induces a unique macrophage nuclear and transcriptional profile, and viral genomes are maintained in a non-canonical bivalent epigenetic state.

ImportanceMacrophages serve as a reservoir for long-term persistence and chronic production of HIV. We found an atypical epigenetic control of HIV in macrophages marked by heterochromatic H3K9me3 despite active viral transcription. HIV infection induced changes in macrophage nuclear morphology and epigenetic regulatory factors. These findings may identify new mechanisms to control chronic HIV expression in infected macrophage.


title: Phenotypic and genotypic characterization of Listeria monocytogenes in clinical ruminant cases in Korea

abstract: Listeria monocytogenes is a foodborne human and veterinary pathogen. This study aimed to determine the phenotypic and genotypic characteristics of L. monocytogenes isolates from clinical cases of Korean ruminants. We collected 24 L. monocytogenes isolates from clinical cases with caprine neurological symptoms and bovine abortion. The most prevalent serotypes were 4b (IVb), 1/2a (IIa; IIc), and 1/2b (IIb). All isolates, including two found in humans, formed three genetically diverse pulsed-field gel electrophoresis clusters according to serotype, lineage, and sequence type. The most prevalent sequence type was ST1, followed by ST365 and ST91. L. monocytogenes isolates from ruminant listeriosis were resistant to oxacillin and ceftriaxone. These clinical ruminant isolates showed diverse lineage, serotype (serogroup), and sequence type characteristics. Considering that the atypical sequence types exhibited clinical manifestations and histopathological lesions, further study is needed to elucidate the pathogenicity of genetically diverse ruminant L. monocytogenes isolates. Furthermore, continuous monitoring of antimicrobial resistance is required to prevent the emergence of L. monocytogenes strains resistant to common antimicrobials.

category: microbiology


title: Dysregulation of stress-induced translational control by Porphyromonas gingivalis in host cells

abstract:
Periodontitis, a chronic inflammatory gum disease, is caused in part by the periodontopathogen Porphyromonas gingivalis. Infection triggers activation of host inflammatory responses which induce stresses such as oxidative stress. Under such conditions, cells can activate the Integrated Stress Response (ISR), a signalling cascade which functions to determine cellular fate, by either downregulating protein synthesis and initiating a stress-response gene expression program, or if stress cannot be overcome, initiating programmed cell death. Recent studies have implicated the ISR signalling in both host antimicrobial defences and within the pathomechanism of certain microbes.

In this study, we investigated how P. gingivalis infection alters translation attenuation during oxidative stress-induced activation of the ISR pathway in oral epithelial cells. P. gingivalis infection alone did not result in ISR activation. In contrast, infection coupled with stress led to differential stress granule formation and composition, along with dysregulation of the microtubule network. Infection also heightened stress-induced translational repression, a response which could not be rescued by ISRIB, a potent ISR inhibitor. Heightened translational repression during stress was observed with both P. gingivalis conditioned media and outer membrane vesicles, implicating the role of a secretory factor, probably proteases known as gingipains, in this exacerbated translational repression. The effects of gingipain inhibitors and gingipains-deficient P. gingivalis mutants further confirmed these pathogen-specific proteases as the effector.

Gingipains are known to degrade the mammalian target of rapamycin (mTOR) and these studies implicate the gingipain-mTOR axis as the effector of host translational dysregulation during stress.


title: Culture and genomic analysis of Arsenophonus apicola sp. nov. isolated from the honeybee 	Apis mellifera

abstract: The genus Arsenophonus has been traditionally considered to be comprised of heritable bacterial symbionts of arthropods. Recent work has reported a microbe related to the type species A. nasoniae as infecting the honey bee, Apis mellifera. The association was unusual for members of the genus in that the microbe-host interaction arose through environmental and social exposure rather than vertical transmission. In this study, we describe the in vitro culture of ArsBeeUS, a strain of this microbe isolated from A. mellifera in the USA. The 16S rRNA sequence of the isolated strain clearly indicates it falls within the genus Arsenophonus. Biolog analysis indicates the bacterium has a restricted range of nutrients that support growth. In vivo experiments demonstrate the strain proliferates rapidly on injection into A. mellifera hosts. We further report the closed genome sequence for the strain. The genome is 3.3 MB and 37.6% GC, which is smaller than A. nasoniae but larger than the genomes reported for non-culturable Arsenophonus symbionts. The genome is complex, with 6 plasmids and 11 predicted intact phage elements, but notably less complex than A. nasoniae. With 92% average nucleotide identity (ANI) to the type strain A. nasoniae, the ArsBeeUS strain isolated is clearly distinct from the type species, and we propose the name Arsenophonus apicola sp. nov. (CECT 30499; LMG 32504).


title: Wolbachia promotes its own uptake by host cells

abstract: Wolbachia pipientis is an incredibly widespread bacterial symbiont of insects, present in an estimated 25-52% of species worldwide. Wolbachia is faithfully maternally transmitted both in a laboratory setting and in the wild. In an established infection, Wolbachia is primarily intracellular, residing within host-derived vacuoles that are associated with the endoplasmic reticulum. However, Wolbachia also frequently transfer between host species, requiring an extracellular stage to their life cycle. Indeed, Wolbachia has been moved between insect species for the precise goal of controlling populations. The use of Wolbachia in this application requires we better understand how it initiates and establishes new infections. Here we designed a novel method for live-tracking Wolbachia during infection using a combination of stains and microscopy. We show that live Wolbachia are taken up by host cells at a much faster rate than dead Wolbachia cells, indicating that Wolbachia play a role in their own uptake and that Wolbachia colonization is not just a passive process. We also show that the host actin cytoskeleton must be intact for this to occur, and that drugs that disrupt the actin cytoskeleton effectively abrogate Wolbachia uptake. The development of this live infection assay will assist in future efforts to characterize Wolbachia factors used during host infection.


title: Biodistribution and Environmental Safety of a Live-attenuated YF17D-vectored SARS-CoV-2 Vaccine Candidate

abstract: New platforms are urgently needed for the design of novel prophylactic vaccines and advanced immune therapies. Live-attenuated yellow fever vaccine YF17D serves as vector for several licensed vaccines and platform for novel vaccine candidates. Based on YF17D, we developed YF-S0 as exceptionally potent COVID-19 vaccine candidate. However, use of such live RNA virus vaccines raises safety concerns, i.e., adverse events linked to original YF17D (yellow fever vaccine-associated neurotropic; YEL-AND, and viscerotropic disease; YEL-AVD). In this study, we investigated the biodistribution and shedding of YF-S0 in hamsters. Likewise, we introduced hamsters deficient in STAT2 signaling as new preclinical model of YEL-AND/AVD. Compared to parental YF17D, YF-S0 showed an improved safety with limited dissemination to brain and visceral tissues, absent or low viremia, and no shedding of infectious virus. Considering yellow fever virus is transmitted by Aedes mosquitoes, any inadvertent exposure to the live recombinant vector via mosquito bites is to be excluded. The transmission risk of YF-S0 was hence evaluated in comparison to readily transmitting YFV-Asibi strain and non-transmitting YF17D vaccine, with no evidence for productive infection of vector mosquitoes. The overall favorable safety profile of YF-S0 is expected to translate to other novel vaccines that are based on the same YF17D platform.


title: Despite the odds: formation of the SARS-CoV-2 methylation complex.

abstract: Coronaviruses protect their single-stranded RNA genome with a methylated cap during replication. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16 where nsp10 acts as a co-factor to both. Aditionally, nsp14 carries an exonuclease domain, which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins should be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex. This interaction is expected to encourage formation of mature capped viral mRNA, modulating the nsp14s exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.


title: Circuit-seq: Circular reconstruction of cut in vitro transposed plasmids using Nanopore sequencing

abstract: Recombinant DNA is a fundamental tool in biotechnology and medicine. Validation of the resulting plasmid sequence is a critical and time-consuming step, which has been dominated for the last 35 years by Sanger sequencing. As plasmid sequences grow more complex with new DNA synthesis and cloning techniques, we need new approaches that address the corresponding validation challenges at scale. Here we prototype a high-throughput plasmid sequencing approach using DNA transposition and Oxford Nanopore sequencing. Our method, Circuit-seq, creates robust, full-length, and accurate plasmid assemblies without prior knowledge of the underlying sequence for approximately $1.50 per plasmid. We demonstrate the power of Circuit-seq across a wide range of plasmid sizes and complexities, generating accurate and contiguous plasmid maps. We then leverage our long read-data to characterize epigenetic marks and estimate plasmid contamination levels. Circuit-seq scales to large numbers of samples at a lower cost than commercial Sanger sequencing, accelerating a key step in synthetic biology, with low startup costs make it practical for individual laboratories.

category: molecular biology


title: The SARS-CoV-2 protein NSP2 impairs the microRNA-induced silencing capacity of human cells

abstract: The coronavirus SARS-CoV-2 is the cause of the ongoing pandemic of COVID-19. Given the absence of effective treatments against SARS-CoV-2, there is an urgent need for a molecular understanding of how the virus influences the machineries of the host cell. The SARS-CoV-2 generates 16 Non-Structural Proteins (NSPs) through proteolytic cleavage of a large precursor protein. In the present study, we focused our attention on the SARS-CoV-2 protein NSP2, whose role in the viral pathogenicity is poorly understood. Recent proteomic studies shed light on the capacity of NSP2 to bind the 4EHP-GIGYF2 complex, a key factor involved in microRNA-mediated silencing of gene expression in human cells. In order to gain a better understanding of the function of NSP2, we attempted to identify the molecular basis of its interaction with 4EHP-GIGYF2. Our data demonstrate that NSP2 physically associates with the endogenous 4EHP-GIGYF2 complex in the cytoplasm. Using co-immunoprecipitation and in vitro interaction assays, we identified both 4EHP and a central segment in GIGYF2 as binding sites for NSP2. We also provide functional evidence that NSP2 impairs the function of GIGYF2 in mediating mRNA silencing using reporter-based assays, thus leading to a reduced activity of microRNAs. Altogether, these data reveal the profound impact of NSP2 on the post-transcriptional silencing of gene expression in human cells, pointing out 4EHP-GIGYF2 targeting as a possible strategy of SARS-CoV-2 to take over the silencing machinery and to suppress host defenses.

category: cell biology


title: Structural diversity of the SARS-CoV-2 Omicron spike

abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility.

category: biochemistry


title: SARS-CoV-2 Omicron Variant AI-based Primers

abstract: As the COVID-19 pandemic continues to affect the world, a new variant of concern, B.1.1.529 (Omicron), has been recently identified by the World Health Organization. At the time of writing, there are still no available primer sets specific to the Omicron variant, and its identification is only possible by using multiple targets, checking for specific failures, amplifying the suspect samples, and sequencing the results. This procedure is considerably time-consuming, in a situation where time might be of the essence. In this paper we use an Artificial Intelligence (AI) technique to identify a candidate primer set for the Omicron variant. The technique, based on Evolutionary Algorithms (EAs), has been already exploited in the recent past to develop primers for the B.1.1.7/Alpha variant, that have later been successfully tested in the lab. Starting from available virus samples, the technique explores the space of all possible subsequences of viral RNA, evaluating them as candidate primers. The criteria used to establish the suitability of a sequence as primer includes its frequency of appearance in samples labeled as Omicron, its absence from samples labeled as other variants, a specific range of melting temperature, and its CG content. The resulting primer set has been validated in silico and proves successful in preliminary laboratory tests. Thus, these results prove further that our technique could be established as a working template for a quick response to the appearance of new SARS-CoV-2 variants.

category: bioinformatics


title: A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex

abstract: CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.

category: biophysics


title: T cell transcription factor expression evolves as adaptive immunity matures in granulomas from Mycobacterium tuberculosis-infected cynomolgus macaques

abstract: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a global health concern, yearly resulting in 10 million new cases of active TB. Immunologic investigation of lung granulomas is essential for understanding host control of bacterial replication. We identified and compared the pathological, cellular, and functional differences in granulomas at 4, 12, and 20 weeks post-infection in Chinese cynomolgus macaques. Original granulomas differed in transcription factor expression within adaptive lymphocytes with those at 12 weeks showing higher frequencies of CD8+T-bet+ T cells, while increases in CD4+T-bet+ T cells were observed at 20 weeks post-infection. The appearance of T-bet+ adaptive T cells at 12 and 20 weeks was coincident with a reduction in bacterial burden, suggesting their critical role in Mtb control. This study highlights the evolution of T cell responses within lung granulomas, suggesting that vaccines promoting the development and migration of T-bet+ T cells would enhance mycobacterial control.

category: immunology


title: The Alternative Sigma Factor SigL Influences Clostridioides difficile Toxin Production, Sporulation, and Cell Surface Properties

abstract:
The alternative sigma factor SigL (Sigma-54) facilitates bacterial adaptation to the extracellular environment by modulating the expression of defined gene subsets. A homolog of the gene encoding SigL is conserved in the diarrheagenic pathogen Clostridioides difficile. To explore the contribution of SigL to C. difficile biology, we generated sigL-disruption mutants (sigL::erm) in strains belonging to two phylogenetically distinct lineages - the human-relevant Ribotype 027 (strain BI-1) and the veterinary-relevant Ribotype 078 (strain CDC1). Comparative proteomics analyses of mutants and isogenic parental strains revealed lineage-specific SigL regulons. Concomitantly, loss of SigL resulted in pleotropic and distinct phenotypic alterations in the two strains. Sporulation kinetics, biofilm formation, and cell surface-associated phenotypes were altered in CDC1 sigL::erm relative to the isogenic parent strain, but remained unchanged in BI-1 sigL::erm. In contrast, secreted toxin levels were significantly elevated only in the BI-1 sigL::erm mutant relative to its isogenic parent. We also engineered SigL overexpressing strains and observed enhanced biofilm formation in the CDC1 background, and reduced spore titers as well as dampened sporulation kinetics in both strains. Thus, we contend that SigL is a key, pleiotropic regulator that dynamically influences C. difficiles virulence factor landscape, and thereby, its interactions with host tissues and co-resident microbes.

Contribution to the FieldAlternative sigma factors modulate bacterial gene expression in response to environmental and metabolic cues. C. difficile encodes multiple alternative sigma factors which mediate critical cellular processes. A Sigma-54 ortholog, SigL, is conserved across all sequenced strains, yet its function remains to be elucidated. We demonstrate that SigL dynamically influences C. difficile biology in fundamental, but distinct, ways in two strains representing two clinically-relevant C. difficile phylogenetic lineages (ribotypes). Loss of SigL results in changes in sporulation kinetics, biofilm formation, alterations in cell surface properties, and secreted toxin levels in a strain-specific manner. SigL overexpression, however, uniformly impedes sporulation. Thus, SigL plays a fundamental role in regulating the expression of C. difficile virulence factors and likely profoundly impacts pathogenesis in a strain-specific manner.


title: SepN is essential for assembly and gating of septal junctions in Nostoc sp. PCC 7120

abstract: The multicellular life style of filamentous cyanobacteria like Nostoc sp. PCC7120 relies on a cell-cell communication system involving so called septal junctions. These are multiprotein complexes, which traverse the septal peptidoglycan through nanopores, connecting the neighboring cells and enabling molecule transfer along the filament. The intercellular communication is crucial when different cell types in the filament, vegetative cells and heterocysts, have to exchange metabolites and signaling molecules. Septal junctions of cyanobacteria can even control the molecule exchange by gating. The multiprotein complex consists of three modules: the septum spanning tube, the plug residing within the cytoplasmic membrane at both ends of the tube and a membrane associated cap module, covering the plug/tube modules on the cytoplasmic side of each neighboring cell. Until now, FraD was the only identified protein component of the septal junction protein complexes and localizes to the plug module. Here, we identified SepN as a new component via co-immunoprecipitation using FraD as bait and further demonstrated its essential role in septal junction assembly. Despite normal septal nanopore formation, a mutant in sepN exhibited a highly reduced rate of intercellular communication and was unable to gate the exchange of molecules. Cryo-electron tomography of cryo-focused ion beam thinned sepN-mutant filaments revealed septal junctions lacking the plug module and lateral cap openings. The combination of missing plug but present cap allowed to deduce the importance of the plug module in ensuring the correct cap architecture and, more importantly, in sealing the diffusion area in the closed septal junction state.


title: Deconstructing the role of iron and heme in the structure of healthy human gut microbial communities

abstract: The response of the human gut microbiome to disruptions is often difficult to discern without model systems that remove the complexity of the host environment. Fluctuations in iron availability provide a case in point: the responses of pathogenic bacteria to iron in vitro are much better understood than those of the indigenous human gut commensal microbiota. In a clinical study of iron supplementation in healthy humans, we identified gradual, participant-specific microbiota shifts correlated with bacterial iron internalization. To identify direct effects due to taxon-specific iron sensitivity, we used stool samples from these participants as inocula to derive in vitro communities. Iron supplementation of these communities caused small shifts in structure, similar to in vivo, whereas iron deprivation dramatically inhibited growth with irreversible and cumulative reduction in diversity and replacement of some dominant species. Sensitivity of individual species to iron deprivation during growth in axenic culture generally predicted iron dependency in a community context. Finally, exogenous heme acted as a source of inorganic iron to prevent depletion of some community members. Our results highlight the complementarity of in vivo and in vitro studies in deconstructing how environmental factors affect gut microbiome structure.


title: Yersinia pestis genomes reveal plague in Britain 4,000 years ago

abstract: Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Central Europe and Asia between 5,000 and 3,500 years before present (BP). One of these, the  LNBA lineage (Late Neolithic and Bronze Age), has been suggested to have spread into Central Europe with human groups expanding from the Eurasian steppes. Here, we show that LNBA plague was spread to Europes northwestern periphery by sequencing Yersinia pestis genomes from two individuals dating to ~4,000 cal BP from an unusual mass burial context in Somerset, England, UK. This represents the earliest evidence of plague in Britain documented to date. These British Yersinia pestis genomes belong to a sublineage previously observed in two Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Central Asia ~3,600 BP. While the severity of disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility.

category: evolutionary biology


title: A phenotype-based forward genetic screen identifies Dnajb6 as a sick sinus syndrome gene

abstract: Sick sinus syndrome (SSS) is a group of heart rhythm disorders caused by malfunction of the sinus node, the hearts primary pacemaker. Partially owing to its aging-associated phenotypic manifestation and low expressivity, molecular mechanisms of SSS remain difficult to decipher. Here, we aim to develop a phenotype-based forward genetic approach in the zebrafish (Danio rerio) animal model for discovering essential genes which dysfunction could result in SSS-like phenotypes. Previously we showed the generation of protein trap library by using a revertible gene-breaking transposon (GBT)-based insertional mutagenesis system. Here, we reported the generation of a collection of 35 zebrafish insertional cardiac lines derived from this protein trap library, which was screened using electrocardiographic measurements. As a result, three mutants with SSS-like phenotypes were identified. We then focused on one of these 3 GBT mutants called GBT411 in which dnajb6b gene was disrupted, and conducted expressional, genetic, transcriptome, and electrophysiological studies using both zebrafish and mouse models. These studies confirmed the identity of Dnajb6 as a novel SSS causative gene with a unique expression pattern within the specialized population of sinus node pacemaker cardiomyocytes that lack the expression of HCN4 channels. Together, this study demonstrates the feasibility of a genetic screening approach in an adult vertebrate animal model for discovering new genetic factors for a heart rhythm disorder such as SSS.

category: genetics


title: Investigation of oxidative processes and revealing the changes in purine nucleoside phosphorylase activity levels in model animals in the development of diabetes mellitus

abstract: Diabetes mellitus is a global and one of the most common healthcare problems. The immune system, having a certain autonomy in the recognition and removal of foreign cells, antigens and other compounds is also under strict homeostatic control, in which a lot of/ variety of biochemical reactions take part. And since the problem of treatment of diabetes mellitus is still not solved, it requires detailed research of different elements of pathogenesis at the molecular level. Taking into account the fact that the connection/ link between immune processes and enzymes of purine metabolism is doubtless, it is of interest to investigate the changes in purine metabolism. In previous studies a frequent combination and interrelation of purine and carbohydrate metabolism was shown. Aim of this study was the investigation of the enzymatic activity of PNP in serum, liver and in pancreas, and also determination of levels of lipid peroxidation indicators, NO content in blood plasma, glutathione peroxidase activity in the mitochondrial fraction of the pancreatic tissue of white rats with modeled alloxan diabetes. The obtained results have demonstrated statistically significant changes in the PNP activity level indicators in the investigated organs and stages of the disease. The indicators of oxidative processes MDA, NO and changes of the activity of GPx and PNP can be used as additional paraclinical indicators for early diagnostics and for detection and refinement of the level of activity of the pathologic process, its development and stage of the disease, which contributes to the appointment of individualized adequate therapy.


title: Dexamethasone, a direct modulator of AQP2 in Meniere s disease.

abstract:
Menieres disease is a chronic illness characterized by intermittent episodes of vertigo associated with fluctuating sensorineural hearing loss, tinnitus and aural pressure. This pathology strongly correlates with a dilatation of the fluid compartment of the endolymph, so-called hydrops. Dexamethasone is one of the therapeutic approaches recommended when conventional antivertigo treatments have failed. Several mechanisms of actions have been hypothesized for the mode of action of dexamethasone such as anti-inflammatory effect or as a regulator of the inner ear water homeostasis. However, none of them have been experimentally confirmed so far. Aquaporins (AQPs) are transmembrane water channels and are hence central in the regulation of trans-cellular water fluxes. In the present study we investigated the hypothesis that dexamethasone could impact water fluxes in the inner ear through direct interaction with AQP2. We addressed this question through molecular dynamics simulations approaches and managed to demonstrate a direct interaction between AQP2 and dexamethasone and its significant impact on the channel water permeability. We also describe the molecular mechanisms involved in dexamethasone binding and in its regulatory action upon AQP2 function.

HighlightsO_LIAQP2 water permeability is modulated by dexamethasone at physiological concentrations
C_LIO_LIThe interaction impacts water fluxes through a direct interaction with the extra-cellular surface of the aquaporin
C_LIO_LIKey interactions implicate conserved residues of the ar/R constriction
C_LIO_LINew insights on corticosteroids mode of actions in Menieres disease treatment
C_LI


title: Divergent binding mode for a protozoan BRC repeat to RAD51

abstract: Interaction of BRCA2 through ca. 30 amino acid residue motifs, BRC repeats, with RAD51 is a conserved feature of the double-strand DNA break repair process in eukaryotes. In humans the binding of the eight BRC repeats is relatively well understood, with structure of BRC4 repeat bound to human RAD51 showing how two sequence motifs, FxxA and LFDE, in the BRC repeat interact with distinct sites on RAD51. Little is known however of the interaction of BRC repeats in other species, especially in protozoans where variable number of BRC repeats are found in BRCA2 proteins. Here we have studied in detail the interactions of the two BRC repeats in Leishmania infantum BRCA2 with RAD51. We show that the LiBRC1 is a high affinity repeat with a KD of 0.29 M while LiBRC2 binds to RAD51 with a KD of 13.5 M. A crystal structure of LiBRC1 complexed with LiRAD51 revels an extended {beta}-hairpin compared to human BRC4 and shows that the equivalent of human LFDE motif is not interacting with LiRAD51. A truncation analysis of LiBRC1 confirms that a shorter repeat is sufficient for high affinity interaction and this minimal repeat is functional in inhibiting the formation of LiRAD51-ssDNA nucleofilament.


title: S-Acylation Regulates the Membrane Association and Activity of Calpain-5

abstract: Calpain-5 (CAPN5) is a member of the calpain family of calcium-activated neutral thiol proteases. CAPN5 is partly membrane associated, despite its lack of a transmembrane domain. Unlike classical calpains, CAPN5 contains a C-terminal C2 domain. C2 domains often have affinity to lipids, mediating membrane association. We recently reported that the C2 domain of CAPN5 was essential for its membrane association and the activation of its autolytic activity. However, despite the removal of the C2 domain by autolysis, the N-terminal fragment of CAPN5 remained membrane associated. S-acylation, also referred to as S-palmitoylation, is a reversible post-translational lipid modification of cysteine residues that promotes membrane association of soluble proteins. In the present study several S-acylated cysteine residues were identified in CAPN5 with the acyl-PEG exchange method. Data reported here demonstrate that CAPN5 is S-acylated on up to three cysteine residues including Cys-4 and Cys-512, and likely Cys-507. The D589N mutation in a potential calcium binding loop within the C2 domain interfered with the S-acylation of CAPN5, likely preventing initial membrane association. Mutating specific cysteine residues of CAPN5 interfered with both its membrane association and the activation of CAPN5 autolysis. Taken together, our results suggest that the S-acylation of CAPN5 is critical for its membrane localization which appears to favor its enzymatic activity.


title: ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA

abstract: One-dimensional (1D) target search is a well characterized phenomenon for many DNA binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome depleted region (NDR) at promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 m2/sec, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cells.


title: ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA


title: The Third Transmembrane Domain of Synaptophysin Regulates Initial Fusion Pore Dynamics during Ca2+ -Triggered Exocytosis in Chromaffin cells

abstract: Synaptophysin (syp) is a major secretory vesicle protein comprising four transmembrane domains (TMDs) and a large cytoplasmic C-terminus. The C-terminus of syp has been shown to regulate exocytosis, vesicle cycling, and synaptic plasticity, but the roles of its TMDs remain unclear. SNARE TMDs line initial fusion pores, and structural work along with sequence analysis suggest that TMD III of syp may play a similar role. To test this hypothesis, we expressed TMD III tryptophan mutants in chromaffin cells from mice lacking both syp and its homolog synaptogyrin, and used amperometry to evaluate fusion pores. In contrast to SNARE TMDs, tryptophan substitutions in syp TMD III had no effect on the flux through initial fusion pores. However, these mutants increased the fraction of kiss-and-run events and decreased the initial fusion pore lifetime. Thus, syp TMD III does not line the initial fusion pore, but interacts with it to influence its stability and choice of release mode.


title: Cognitive Deficits and Altered Cholinergic Innervation in Young Adult Mice Carrying a Parkinson's Disease LRRK2-G2019S Knockin Mutation

abstract:
Impaired executive function is a common and debilitating non-motor symptom of idiopathic and hereditary Parkinsons disease (PD), but there is little understanding of the underlying pathophysiological mechanisms and circuits. The G2019S mutation in the kinase domain of leucine-rich repeat kinase 2 (LRRK2) greatly increases risk for late-onset PD, and non-manifesting LRRK2-G2019S carriers also exhibit early and significant cognitive impairment. Here, we subjected young adult mice carrying a Lrrk2-G2019S knockin mutation to touchscreen-based operant tasks that measure attention, goal-directed learning and cognitive flexibility, all of which rely on prefrontal-striatal connectivity and are strongly modulated by cholinergic innervation. In a visuospatial attention task, mutant mice exhibited significantly more omissions and longer response latencies than controls that could not be attributed to deficits in motivation, visual sensory perception per se or locomotion, thereby suggesting impairment in divided attention and slower information processing speed. Pretreating mice with the acetylcholinesterase inhibitor donepezil normalized both higher omission rates and longer reward latencies in the mutants, but did not affect any performance metric in controls. Strikingly, cholinergic fiber density in mPFC and dorsomedial striatum was significantly sparser in mutants than in controls, while further behavioral interrogation of the mutants revealed significant impairments in action-outcome associations but preserved cognitive flexibility. These data suggest that the G2019S mutation impacts cholinergic innervation and impairs corticostriatal network function in young adulthood that may contribute to early PD-associated cognitive deficits.

STATEMENT OF SIGNIFICANCEThe LRRK2-G2019S mutation causes hereditary Parkinsons disease and is found in some idiopathic cases. Early cognitive impairment is a common symptom of hereditary and idiopathic PD, yet there is little mechanistic understanding of such impairment. Here, we tested young adult Lrrk2-G2019S knockin mice in a series of touchscreen-based visuospatial tasks. We found that mutants exhibited significant deficits in attention and goal-directed learning, and had significantly slower information processing speed. Treatment with an acetylcholinesterase inhibitor reversed some of these behavioral deficits, while anatomical analyses showed significantly sparser cholinergic innervation of brain structures important for executive function. These findings suggest the G2019S mutation alters cholinergic signaling in young adulthood, and thus may contribute to early PD-associated impairment in several cognitive domains.

category: neuroscience


title: Abnormal CCK/CB1R axon targeting in mouse models of dystroglycanopathy

abstract: Dystroglycan (Dag1) is a cell adhesion molecule that links the extracellular matrix to the actin cytoskeleton, and is critical for normal muscle and brain development. Mutations in Dag1 or the genes required for its functional glycosylation result in dystroglycanopathy, which is characterized by a wide range of phenotypes including muscle weakness, brain defects, and cognitive impairments. Whereas Dystroglycans role in muscle and early brain development are well defined, much less is known about its role at later stages of neural circuit development including synapse formation and refinement. Recent work has found that selective deletion of Dag1 from pyramidal neurons leads to a loss of presynaptic CCK+ inhibitory neurons (INs) early in development. In this study, we investigated how IN development is affected in multiple mouse models of dystroglycanopathy. Widespread forebrain deletion of Dag1 or Pomt2, which is required for Dystroglycan glycosylation, recapitulates brain phenotypes seen in severe forms of dystroglycanopathy. CCK+ INs were present in Dag1 and Pomt2 mutant mice, but their axons failed to properly target the somatodendritic compartment of pyramidal neurons in the hippocampus. In contrast, CCK+ IN axon targeting was largely normal in mouse models of mild dystroglycanopathy with partially reduced Dystroglycan glycosylation (B4gat1, Fkrp). Furthermore, the intracellular domain of Dystroglycan appears to be dispensable for CCK+ IN axon targeting. Collectively, these data show that synaptic defects are a hallmark of severe dystroglycanopathy.


title: Binocular visual experience and sleep promote visual cortex plasticity and restore binocular vision in a mouse model of amblyopia

abstract: Amblyopia arises from an altered balance of input from the two eyes to the binocular zone of primary visual cortex (bV1) during childhood, causing long-lasting visual impairment. Amblyopia is commonly treated by patching the dominant eye, however, the relative impacts of monocular vs. binocular visual experiences on restoration of bV1 function remains unclear. Moreover, while sleep has been implicated in V1 plasticity in response to vision loss, its role in recovery from amblyopia is unknown. We used monocular deprivation (MD) in juvenile mice to model amblyopia in bV1. We compared recovery of visual responses for the two eyes among bV1 regular spiking (RS, putative principal) neurons and fast-spiking (FS, putative parvalbumin-expressing [PV+]) interneurons after identical-duration, identical-quality binocular recovery (BR) or monocular, reverse occlusion (RO) experiences. We find that BR is quantitatively superior to RO with respect to renormalizing both bV1 populations visual responses. However, this recovery was seen only in freely-sleeping mice; post-BR sleep deprivation prevented functional recovery. Thus, both binocular visual experience and subsequent sleep are required to optimally renormalize bV1 responses in a mouse model of amblyopia.


title: Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

abstract: Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. By analogy to mercury, As methylation was proposed to be catalyzed by sulfate-reducing bacteria. However, to date, there are no anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harboring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.


title: Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells

abstract: The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.


title: Nutrient and salt depletion synergistically boosts glucose metabolism in individual bacteria


title: In vitro activity of ertapenem against Neisseria gonorrhoeae clinical isolates with decreased susceptibility or resistance to extended spectrum cephalosporins in Nanjing, China (2013-2019)

abstract:
ObjectiveNeisseria gonorrhoeae isolates collected in Nanjing, China, that possessed decreased susceptibility (or resistance) to extended spectrum cephalosporins (ESCs), were examined for susceptibility to ertapenem and their sequence types determined.

MethodsCeftriaxone and cefixime minimum inhibitory concentrations (MICs) [≥] 0.125 mg/L and [≥] 0.25 mg/L, respectively, were first determined in 259 strains isolated between 2013 and 2019 and then MICs of ertapenem were measured using the antimicrobial gradient epsilometer test (Etest). Genetic determinants of ESC resistance and multi-antigen sequence typing (NG-MAST) were also determined to analyze associations with ertapenem susceptibility.

ResultsAll isolates displayed ertapenem MICs between 0.006 mg/L-0.38 mg/L; the overall MIC50 and MIC90 were 0.032 mg/L and 0.125 mg/L. 44 (17.0%) isolates displayed ertapenem MICs of [≥] 0.125 mg/L; 10 (3.9%) had MICs [≥] 0.25 mg/L. The proportion of isolates with ertapenem MICs [≥] 0.125 mg/L increased from 4.0% in 2013, to 20.0% in 2019 ({chi}2= 24.144, P<0.001; Chi square test for linear trend). The penA mosaic allele was present in a significantly higher proportion of isolates with ertapenem MICs [≥] 0.125 mg/L compared to isolates with MICs [≤] 0.094 mg/L) (97.7% vs. 34.9%, respectively; {chi}2=58.158, P<0.001). ST5308 was the most prevalent NG-MAST type (8.5%); ST5308 was also significantly more common among isolates with ertapenem MICs [≥] 0.125 mg/L vs. isolates with MICs [≤] 0.094mg/L (22.7% and 5.6% respectively; {chi}2=13.815, P=0.001).

ConclusionsErtapenem may be effective therapy for gonococcal isolates with decreased susceptibility or resistance to ESCs and isolates with identifiable genetic resistance determinants.


title: Transient RNA structures cause aberrant influenza virus replication and innate immune activation

abstract: During infection, the influenza A virus RNA polymerase produces both full-length and aberrant RNA molecules, such as defective viral genomes (DVG) and mini viral RNAs (mvRNA). Subsequent innate immune activation involves the binding of host pathogen receptor retinoic acid-inducible gene I (RIG-I) to viral RNAs. However, not all influenza A virus RNAs are strong RIG-I agonists. Here we show that potent innate immune activation by mvRNAs is determined by transient RNA structures, called template loops (t-loop) that stall the viral RNA polymerase and trigger aberrant RNA synthesis. The effect of t-loops depends on the formation of an RNA duplex near the template entry and exit channels of the RNA polymerase, and their effect is enhanced by mutation of the template exit path from the RNA polymerase active site. Overall, these findings provide a mechanism that links aberrant viral replication to the activation of the innate immune response.


title: A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance.

abstract: Detailed knowledge on how bacteria evade antibiotics and eventually develop resistance could open avenues for novel therapeutics and diagnostics. It is thereby key to develop a comprehensive genome-wide understanding of how bacteria process antibiotic stress, and how modulation of the involved processes affects their ability to overcome said stress. Here we undertake a comprehensive genetic analysis of how the major human pathogen Streptococcus pneumoniae responds to 20 antibiotics. We built a genome-wide atlas of drug susceptibility determinants and generate a genetic interaction network that connects cellular processes and genes of unknown function, which we show can be used as therapeutic targets. Pathway analysis reveals a genome-wide "tolerome", defined by cellular processes that can make a bacterium less susceptible, and often tolerant, in an antibiotic specific manner. Importantly, modulation of these processes confers fitness benefits during active infections under antibiotic selection. Moreover, screening of sequenced clinical isolates demonstrates that mutations in tolerome genes readily evolve and are frequently associated with resistant strains, indicating such mutations may be an important harbinger for the emergence of antibiotic resistance.


title: An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit flesh color in Japanese plum

abstract: Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach, with at least three copies of PsMYB10.1. Polymorphisms in one of these copies correlate with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the flesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We explored LG3-PsMYB10 variability, including the analysis of long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red flesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We provide a molecular marker for the red flesh trait which, together with that for skin color, will serve for the early selection of fruit color in breeding programs.


title: Gut bacterial nutrient preferences quantified in vivo

abstract: Great progress has been made in understanding gut microbiomes products and their effects on health and disease. Less attention, however, has been given to the inputs that gut bacteria consume. Here we quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. The main input to microbial carbohydrate fermentation is dietary fiber, and to branched-chain fatty acids and aromatic metabolites is dietary protein. In addition, circulating host lactate, 3-hydroxybutyrate and urea (but not glucose or amino acids) feed the gut microbiome. To determine nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. We find systematic differences in nutrient use: Most genera in the phylum Firmicutes prefer dietary protein, Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, diet shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients.


title: Recommendations for tissue homogenisation and extraction in DNA metabarcoding of Malaise trap samples

abstract: With increased application of DNA metabarcoding in fast and high-resolution biodiversity assessment, various laboratory protocols have been optimised in recent years and their further evaluation is subject of current research. Homogenisation of bulk samples and subsequent DNA extraction from destructed tissue is one way of starting the metabarcoding process. This essential step in the protocol can either be conducted from wet sample material (e.g. bulk insect samples) soaked in fixative or from completely dried individuals. While the latter method appears to produce more consistent results, it is time consuming and more prone to cross-contamination. We tested both homogenisation approaches with regard to time efficiency and biodiversity assessment of complex arthropod bulk samples, in particular how the amount of processed tissue affects taxon recovery. Both approaches reveal similar taxa compositions and detect a similar total OTU diversity in a single extraction reaction. Increased amounts of tissue used in DNA extraction improved OTU diversity detection and recovered particularly specific low-biomass taxa, making this approach valuable for samples with high biomass and/or diversity. Due to less handling time and lower vulnerability for cross-contamination we recommend the processing of wet material when sample homogenisation is applied.


title: Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

abstract: With the continual evolution of new strains of SARS-CoV-2 that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs. SARS-CoV-2 main protease (Mpro) is a leading target for drug design due to its conserved and indispensable role in the viral life cycle. Drugs targeting Mpro appear promising but will elicit selection pressure for resistance. To understand resistance potential in Mpro, we performed a comprehensive mutational scan of the protease that analyzed the function of all possible single amino acid changes. We developed three separate high-throughput assays of Mpro function in yeast, based on either the ability of Mpro variants to cleave at a defined cut-site or on the toxicity of their expression to yeast. We used deep sequencing to quantify the functional effects of each variant in each screen. The protein fitness landscapes from all three screens were strongly correlated, indicating that they captured the biophysical properties critical to Mpro function. The fitness landscapes revealed a non-active site location on the surface that is extremely sensitive to mutation making it a favorable location to target with inhibitors. In addition, we found a network of critical amino acids that physically bridge the two active sites of the Mpro dimer. The clinical variants of Mpro were predominantly functional in our screens, indicating that Mpro is under strong selection pressure in the human population. Our results provide predictions of mutations that will be readily accessible to Mpro evolution and that are likely to contribute to drug resistance. This complete mutational guide of Mpro can be used in the design of inhibitors with reduced potential of evolving viral resistance.


title: Target-dependent siRNA suppression distinguishes self from non-self endogenous siRNAs in C. elegans germline

abstract: Despite their prominent role in transposon silencing, expression of endo-siRNAs is not limited to the "non-self" DNA elements. Transcripts of protein-coding genes ("self" DNA) in some cases also produce endo-siRNAs in yeast, plants, and animals [1]. How cells distinguish these two populations of siRNAs to prevent unwanted silencing of self-genes in animals is not well understood. To address this question, we examined the expression of ectopic siRNAs from an LTR retrotransposon in C. elegans germline. We found that the abundance of ectopic siRNAs was dependent on their homologous target genes: ectopic siRNAs against genes expressed only in somatic cells can be abundantly expressed. In contrast, ectopic siRNAs against germline-expressed genes are often suppressed. This phenomenon, which we termed "target-directed siRNA suppression", is dependent on the target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur to naturally produced endo-siRNAs. We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing.


title: Interaction of the Proline-Rich Domain of Fission Yeast WASp (Ws1p1) with Actin Filaments

abstract:
BackgroundThe Wiskott-Aldrich Syndrome protein (WASp) family of proteins plays a crucial role in the activation of the Arp2/3 (actin-related protein 2/3) complex to promote the branching of actin filaments. The proline-rich domain (PRD) of WASp is known to contribute to branching nucleation but was overlooked, until experiments showed that the PRD of budding yeast Las17 can bind actin filaments (1).

MethodsWe purified recombinant proline-rich domains from fission yeast S. pombe Wsp1 and budding yeast S. cerevisiae Las17 to test in biochemical assays of actin binding and polymerization.

ResultsThe PRD of the S. pombe Wsp1 binds actin filaments with micromolar affinity. The PRDs of both Wsp1 and Las17 slowed the rate of actin filament elongation by Mg-ATP-actin monomers by half and slowed the spontaneous polymerization of Mg-ATP-actin monomers modestly.

ConclusionThe affinity of PRDs of WASp-family proteins for actin filaments is high enough to contribute to the reported stimulation of actin filament branching by Arp2/3 complex.


title: Humans recognize affective cues in primate vocalizations: Acoustic and phylogenetic perspectives

abstract: Humans are adept in extracting affective information from the vocalisations of not only humans but also other animals. Current research has mainly focused on phylogenetic proximity to explain such cross-species emotion recognition abilities. However, because research protocols are inconsistent across studies, it remains unclear whether human recognition of vocal affective cues of other species is due to cross-taxa similarities between acoustic parameters, the phylogenetic distances between species, or a combination of both. To address this, we first analysed acoustic variation in 96 affective vocalizations, including agonistic and affiliative contexts, of humans and three other primate species - rhesus macaques, chimpanzees and bonobos - the latter two being equally phylogenetically distant from humans. Using Mahalanobis distances, we found that chimpanzee vocalizations were acoustically closer to those of humans than to those of bonobos, confirming a potential derived vocal evolution in the bonobo lineage. Second, we investigated whether 68 human participants recognized the affective basis of vocalisations through tasks by asking them to categorize ( A vs B) or discriminate ( A vs non-A) vocalisations based on their affective content. Results showed that participants could reliably categorize and discriminate most of the affective vocal cues expressed by other primates, except threat calls by bonobos and macaques. Overall, participants showed greatest accuracy in detecting chimpanzee vocalizations; but not bonobo vocalizations, which provides support for both the phylogenetic proximity and acoustic similarity hypotheses. Our results highlight for the first time the importance of both phylogenetic and acoustic parameter level explanations in cross-species affective perception, drawing a more complex picture to explain our natural understanding of animal signals.

category: animal behavior and cognition


title: Enhanced anticipatory biasing of visuospatial attention in deaf native-signing adults indexed by alpha-band (8-14 Hz) oscillatory neural activity

abstract:
Deaf people show increased visuospatial attention abilities, especially towards peripheral inputs, but the neural mechanisms of these heightened abilities are not yet understood. In hearing individuals, topographically-specific alpha-band oscillatory activity (8-14 Hz) over parieto-occipital regions has been associated with active suppression of irrelevant locations. Here, we asked whether increases in this spatially-specific anticipatory oscillatory mechanism might underpin enhanced visuospatial attention abilities in deaf individuals, on the premise that deaf people might be more adept at transiently engaging and disengaging attentional processes involved in processing peripheral inputs. An alternative hypothesis was that deaf individuals might not produce lateralized alpha-band activity, because of the need to continuously monitor the periphery due to the absence of an auxiliary auditory spatial alerting system. High-density electroencephalography was recorded from 20 deaf native signers and 20 hearing non-signers performing a cued covert visuospatial attention task. Deaf participants responded significantly more rapidly and accurately and showed highly typical alpha-band lateralization during the cue-target interval of the task. Topographic analysis showed a greater extent of alpha-band anticipatory activity over right parietal scalp, suggesting sequestration of extra-visual attentional circuits (i.e., unused auditory regions), and post-hoc analysis pointed to substantially earlier onset of this activity during the cue-target interval. The presence of cue-evoked anticipatory alpha lateralization in deaf participants suggests that they are rapidly engaging and disengaging attentional processes involved in orienting attention to the periphery. The earlier and more extensive engagement of these anticipatory oscillatory processes may contribute to the improved visuospatial performance observed in these individuals.

Significance StatementPrior to this study, it was not known whether deaf people demonstrate lateralization of alpha-band oscillatory electroencephalographic (EEG) activity over the posterior region of the brain, which plays a role in the suppression of uncued regions of space during cued visuospatial attention tasks. We found that this lateralized pattern was observable in deaf participants and was not significantly different from that seen in hearing participants, except that alpha activity onsets earlier in deaf participants. However, when cue directions were collapsed, the scalp topographies of deaf participants showed a greater distribution of alpha activity, suggesting that they recruited a brain region typically reserved for audiospatial attentional control during the visuospatial attention task. Additionally, deaf participants responded significantly more quickly and accurately compared to hearing participants, demonstrating increased visuospatial attention abilities.


title: The way of the light: how visual information reaches the auditory cortex in congenitally deaf adults

abstract: Human and animal studies on cross-modal plasticity under congenital deafness suggest that early auditory cortex plays a significant role in the processing of visual information when congenitally deprived from its typical (auditory) input. However, the pathway by which early auditory cortex is fed with visual information is still understudied. Here we focused on addressing how visual information reaches the auditory cortex under congenital deafness. We put forth a mechanistic model that proposes that different corticocortical and subcortical connections play a central role in rerouting visual information to the early auditory cortex of congenitally deaf individuals. Specifically, we show, using Representational Connectivity Analysis (RCA) and Dynamic Causal Modeling (DCM), that connections from the right superior colliculus to the right inferior colliculus, as well as connections from right early visual cortical regions to the right early auditory cortex play a role in rerouting visual information to early auditory cortex in congenitally deaf individuals. These findings shed light on how visual information reaches the early auditory cortex of deaf individuals - specifically, they suggest that neuroplasticity reshapes subcortical connections in order to re-route visual information to the auditory stream.


title: Reconstitution of muscle cell microtubule organization in vitro

abstract: Skeletal muscle differentiation occurs as muscle precursor cells (myoblasts) elongate and fuse to form multinucleated syncytial myotubes in which the highly-organized actomyosin sarcomeres of muscle fibers assemble. Although less well characterized, the microtubule cytoskeleton also undergoes dramatic rearrangement during myogenesis. The centrosome-nucleated microtubule array found in myoblasts is lost as the nuclear membrane acquires microtubule nucleating activity and microtubules emerge from multiple sites in the cell, eventually rearranging into a grid-like pattern in myotubes. In order to characterize perinuclear microtubule organization using a biochemically tractable system, we isolated nuclei from mouse C2C12 skeletal muscle cells during the course of differentiation and incubated them in cytoplasmic extracts prepared from eggs of the frog Xenopus laevis. Whereas centrosomes associated with myoblast nuclei gave rise to radial microtubule arrays in extracts, myotube nuclei produced a sun-like pattern with microtubules transiently nucleating from the entire nuclear envelope. Perinuclear microtubule growth was suppressed by inhibition of Aurora A kinase or by degradation of RNA, treatments that also inhibited microtubule growth from sperm centrosomes. Myotube nuclei displayed microtubule motor-based movements leading to their separation, as occurs in myotubes. This in vitro assay therefore recapitulates key features of microtubule organization and nuclear movement observed during muscle cell differentiation.


title: Data-driven modelling captures dynamics of the circadian clock ofNeurospora crassa

abstract: Eukaryotic circadian clocks are based on self-sustaining, cell-autonomous oscillatory feedback loops that can synchronize with the environment via recurrent stimuli (zeitgebers) such as light. The components of biological clocks and their network interactions are becoming increasingly known, calling for a quantitative understanding of their role for clock function. However, the development of data-driven mathematical clock models has remained limited by the lack of sufficiently accurate data. Here we present a comprehensive model of the circadian clock of Neurospora crassa that describe free-running oscillations in constant darkness and entrainment in light-dark cycles. To parameterize the model, we measured high-resolution time courses of luciferase reporters of morning and evening specific clock genes in WT and a mutant strain. Fitting the model to such comprehensive data allowed estimating parameters governing circadian phase, period length and amplitude, and the response of genes to light cues. Our model suggests that functional maturation of the core clock protein Frequency (FRQ) causes a delay in negative feedback that is critical for generating circadian rhythms.

category: systems biology


title: Entorhinal layer 6b subplate neurons govern spatial learning and memory

abstract: The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a "trisynaptic loop", processing input originating from the superficial layers of the entorhinal cortex (EC) in a linear fashion, and sending it back to its deeper layers. Here, we show that contrary to this canonical view, excitatory neurons in the deepest layer of the mouse EC, exhibiting the unique morphology and molecular profile of layer 6b cortical subplate neurons (SPNs), project to all sub-regions comprising the HF, with a preference towards CA3 pyramidal neurons, and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory post-synaptic currents (EPSCs), capable of driving plateau-like potentials in their target cells. Optogenetic inhibition of the EC-6b pathway markedly affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide the first evidence of a functional role for the cortical layer 6b neurons in the adult brain and elucidate a critical novel element determining cortico-hippocampal activity patterns.


title: The small GTPase Arf1 regulates ATP synthesis and mitochondria homeostasis by modulating fatty acid metabolism

abstract: Lipid mobilization through fatty acid {beta}-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where {beta}-oxidation products enter mitochondria and fuel the TCA cycle. Little is known about the physical and metabolic cooperation between these organelles. We found that expression of fatty acid transporters and of the rate-limiting enzyme involved in {beta}-oxidation are decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. As a consequence, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although {beta}-oxidation occurs mainly in mitochondria in mammals, Arf1s role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact-sites.


title: A timer gene network is spatially regulated by the terminal system in the Drosophila embryo

abstract: In insects, patterning of the anteroposterior axis relies on exquisite coordination of segmentation gene expression in space and time. And yet, there is also wide variation across species in the timing of segmentation and the geometry of the embryonic fate map. The majority of described species exhibit sequential segmentation during posterior growth. Other species, such as the fly Drosophila melanogaster, specify almost all of their segments simultaneously prior to gastrulation. The dynamics of both sequential segmentation and simultaneous segmentation correlate with the spatiotemporal expression of the "timer" genes caudal, Dichaete and odd-paired, which are expressed sequentially within segmenting tissues. These genes have critical roles in the development of many species; however, even in the extensively studied Drosophila embryo, the regulatory interactions responsible for shaping their expression remain poorly understood. In particular, it is not known whether the timer genes cross-regulate each other, nor why they are differentially expressed between the broad region of the blastoderm that gives rise to the gnathal, thoracic and abdominal segments and the small posterior region that gives rise to the embryonic terminalia. In this work, we investigate these questions using multiplexed fluorescent in situ hybridisation and high resolution confocal imaging of wild-type and mutant Drosophila embryos. First, we re-examine segmentation gene expression in the posterior of the embryo, and discover that two parasegment-like boundaries are generated sequentially from the terminal region during germband extension and posterior growth. Next, we find that caudal, Dichaete, and odd-paired dynamically cross-regulate each other, and also that they are differentially spatially regulated by the posterior terminal genes. Finally, we formalise the regulatory network we inferred from our data as a logical computational model. Our model qualitatively recapitulates both wild-type development and the mutant phenotypes we examined. Our findings resolve a decades-long ambiguity over the number of segments formed during Drosophila embryogenesis. In addition, they reveal how dynamic spatial inputs from an extrinsic signalling centre modulate the intrinsic dynamics of a gene regulatory network to generate an essential developmental pattern.

category: developmental biology


title: Smart sealants for prevention and monitoring of gastrointestinal anastomotic leaks using portable smartphone-controlled ultrasound transducers

abstract:
Millions of patients every year undergo gastrointestinal surgery. While often lifesaving, sutured and stapled reconnections leak in around 10% of the cases. Penetration of digestive fluids into the peritoneal cavity may lead to dreadful complications, including sepsis and premature death. Modern suture supports and tissue adhesives only insufficiently address the issue. Due to the scarcity of alternatives, surgeons rely on monitoring surrogate markers and clinical symptoms, which oftentimes lack sensitivity and specificity, hence only offering late-stage detection of already fully developed leaks.

Here, a first-of-its-kind, modular, intelligent suture support patch capable of sealing and monitoring leaks under harsh gastrointestinal conditions is presented. The smart adhesive layered hydrogel patch provides, in addition to unprecedented tissue sealing under most demanding conditions, unique leak-detection capabilities based on pH and/or enzyme-responsive sensing elements, which can be read out by non-invasive point-of-need ultrasound imaging. Reliable detection of the breaching of sutures in as little as 3 hours in intestinal leak and 15 minutes in gastric leak conditions, and before an actual leak develops, is demonstrated. This technology paves the way for next-generation suture support materials that offer disambiguation in cases of anastomotic leaks based on point-of-need monitoring, without reliance on complex electronics or bulky (bio)electronic implantables.

SummaryElectronic-free smart surgical hydrogel sealants leveraging tissue-penetrating polymer networks and trigger-responsive echogenic entities to enable point-of-need monitoring and early anastomotic leak detection using a hand-held ultrasound transducer and a smartphone.

category: bioengineering


title: Do water and host size interactively affect the impact of a native hemiparasite on a major invasive legume?

abstract: It is unknown how the combined effects of host size and water availability influence parasitic plant:host associations. This is a major gap considering that parasitic plants would frequently encounter hosts of different size growing in different water conditions in nature. In a glasshouse experiment, small or large Ulex europaeus (major invasive host) were provided high or low water supply and infected or not with the Australian native shoot hemiparasitic vine, Cassytha pubescens. Infection significantly decreased host total, shoot and root biomass, in both low water and high water conditions but more severely so in the latter. Infection also significantly decreased total biomass of both large and small plants and more severely so for the latter. Infection significantly decreased host foliar nitrogen and potassium concentrations in well-watered but not in low water conditions. Infection significantly suppressed host predawn and midday quantum yield, midday electron transport rates, foliar phosphorus concentration and nodule biomass, irrespective of water conditions or host size. Parasite biomass (including g-1 host total biomass) was significantly greater on hosts growing in well-watered than in low water conditions. Our results suggest that some native parasitic plants may effectively control major invasive hosts, particularly in wetter habitats and or when the host is small, leading to enhanced biodiversity protection in those settings.

category: plant biology


title: Impact of a native hemiparasitic plant on invasive and native hosts in the field.

abstract: There is increasing evidence that native parasitic plants are showing potential as biocontrols for plant invasions which are a major global threat to biodiversity. However, for this potential to be realised, the range of invasive hosts that can be controlled needs to be identified while also evaluating any potential off-target effects the parasite may pose. To address this, we investigated the impact of the Australian native shoot hemiparasitic plant, Cassytha pubescens on the major invasive species Rubus anglocandicans and two native shrubs, Acacia pycnantha and Bursaria spinosa in naturally occurring populations in southern Australia. We measured foliar predawn and midday quantum yield, electron transport rate (ETR), stomatal conductance (gs), carbon isotope composition and foliar nitrogen concentration [N] of uninfected and infected plants and, apart from gs, also for C. pubescens. Infection significantly decreased predawn and midday quantum yield, ETR and gs of invasive R. anglocandicans. In contrast, infection had no effect on predawn and midday quantum yield, ETR or carbon isotope composition of the native hosts. However, C. pubescens had a significant negative effect on native host gs, and a positive effect on host [N]. Parasite stem [N] was significantly higher when infecting A. pycnantha than B. spinosa. These results strengthen evidence for native parasitic plants having greater impact on invasive hosts while having mild off-target effects on native hosts and thus, show potential to mitigate plant invasions and help protect biodiversity.


title: BOLD cofluctuation 'events' are predicted from static functional connectivity

abstract:
Recent work identified single time points ("events") of high regional cofluctuation in functional Magnetic Resonance Imaging (fMRI) which contain more large-scale brain network information than other, low cofluctuation time points. This suggested that events might be a discrete, temporally sparse signal which drives functional connectivity (FC) over the timeseries. However, a different, not yet explored possibility is that network information differences between time points are driven by sampling variability on a constant, static, noisy signal. Using a combination of real and simulated data, we examined the relationship between cofluctuation and network structure and asked if this relationship was unique, or if it could arise from sampling variability alone. First, we show that events are not discrete - there is a gradually increasing relationship between network structure and cofluctuation; [~]50% of samples show very strong network structure. Second, using simulations we show that this relationship is predicted from sampling variability on static FC. Finally, we show that randomly selected points can capture network structure about as well as events, largely because of their temporal spacing. Together, these results suggest that, while events exhibit particularly strong representations of static FC, there is little evidence that events are unique timepoints that drive FC structure. Instead, a parsimonious explanation for the data is that events arise from a single static, but noisy, FC structure.

HIGHLIGHTSO_LIPast results suggested high cofluctuation BOLD "events" drive fMRI functional connectivity, FC
C_LIO_LIHere, events were examined in both real fMRI data and a stationary null model to test this model
C_LIO_LIIn real data, >50% of BOLD timepoints show high modularity and similarity to time-averaged FC
C_LIO_LIStationary null models identified events with similar behavior to real data
C_LIO_LIEvents may not be a transient driver of static FC, but rather an expected outcome of it.
C_LI


title: Computational modeling of macrophage iron sequestration during host defense against Aspergillus

abstract:
Iron is essential to the virulence of Aspergillus species, and restricting iron availability is a critical mechanism of antimicrobial host defense. Macrophages recruited to the site of infection are at the crux of this process, employing multiple intersecting mechanisms to orchestrate iron sequestration from pathogens. To gain an integrated understanding of how this is achieved in invasive aspergillosis, we generated a transcriptomic time-series of the response of human monocyte-derived macrophages to Aspergillus and used this and the available literature to construct a mechanistic computational model of iron handling of macrophages during this infection. We found an overwhelming macrophage response beginning 2-4 hours after exposure to the fungus, which included upregulated transcription of iron import proteins transferrin receptor-1, divalent metal transporter-1, and ZIP family transporters, and downregulated transcription of the iron exporter ferroportin. The computational model, based on a discrete dynamical systems framework, consisted of 21 3-state nodes, and was validated with additional experimental data that were not used in model generation. The model accurately captures the steady state and the trajectories of most of the quantitatively measured nodes. In the experimental data, we surprisingly found that transferrin receptor-1 upregulation preceded the induction of inflammatory cytokines, a feature that deviated from model predictions. Model simulations suggested that direct induction of TfR1 after fungal recognition, independent of the Iron Regulatory Protein - Labile Iron Pool system, explains this finding. We anticipate that this model will contribute to a quantitative understanding of iron regulation as a fundamental host defense mechanism during aspergillosis.

ImportanceInvasive pulmonary aspergillosis is a major cause of death among immunosuppressed individuals despite the best available therapy. Depriving the pathogen of iron is an essential component of host defense in this infection, but the mechanisms by which the host achieves this are complex. To understand how recruited macrophages mediate iron deprivation during the infection, we developed and validated a mechanistic computational model that integrates the available information in the field. The insights provided by this approach can help in designing iron modulation therapies as anti-fungal treatments.


title: Leveraging CD39 To Identify Tumor-Reactive CD8 T cells In Human Lung Cancer

abstract: CD39 has emerged as a marker of tumor-reactive CD8 T cells. Using single-cell CITE/RNA/TCRseq, we show that CD39+ CD8 T cells in human lung cancers demonstrate transcriptional and proteomic features of exhaustion, tumor reactivity, and clonal expansion. Flow cytometry of 440 lung cancer specimens revealed that CD39 level on CD8 T cells is only weakly correlated with tumoral features, such as histology, driver mutation, PD-L1 and tumor mutation burden. CD8 T cells reactive against EGFR driver mutations preferentially expressed CD39, suggesting that CD39 can be leveraged to identify neoantigen-reactive CD8 T cells. PD-1 axis blockade, but not cytotoxic chemotherapy, increased intratumoral CD39+ CD8 T cells. CD39 correlated with PD-1 expression on CD8 T cells and high pre-treatment/early-on-treatment levels were associated with improved clinical outcomes from immune checkpoint blockade. This extensive and comprehensive profiling of the clinical, pathological and molecular features highlights the utility of CD39 as a proxy for tumor-reactive CD8 T cells in human lung cancer.


title: The evolutionary history of mammoth wasps (Hymenoptera: Scoliidae)

abstract: Scoliid wasps comprise a clade of aculeate insects whose larvae are parasitoids of scarabaeid beetle grubs. While scoliids have been studied and used as biological control agents, research into the groups evolution, as well as the stability of scoliid taxonomy, has been limited by a lack of reliable phylogenies. We use ultraconserved element (UCE) data under concatenation and the multispecies coalescent to infer a phylogeny of the Scoliidae. In order to mitigate potential issues arising from model misspecification, we perform data filtering experiments using posterior predictive checks and matched-pairs tests of symmetry. Our analyses confirm the position of Proscolia as sister to all other extant scoliids. We also find strong support for a sister group relationship between the campsomerine genus Colpa and the Scoliini, rendering the Campsomerini non-monophyletic. Campsomerini excluding Colpa (hereafter Campsomerini sensu stricto) is inferred to be monophyletic, with the Australasian genus Trisciloa recovered as sister to the remaining members of the group. Many sampled genera, including Campsomeriella, Dielis, Megascolia, and Scolia are inferred to be non-monophyletic. Analyses incorporating fossil data indicate an Early Cretaceous origin of the crown Scoliidae, with the split between Scoliini + Colpa and Campsomerini s.s. most probably occurring in the Late Cretaceous. Posterior means of Scoliini + Colpa and Campsomerini s.s. crown ages are estimated to be in the Paleogene, though age 95% HPD intervals extend slightly back past the K-Pg boundary, and analyses including fossils of less certain placement result in more posterior mass on older ages. Our estimates of the stem ages of Nearctic scoliid clades are consistent with dispersal across Beringia during the Oligocene or later Eocene. Our study provides a foundation for future research into scoliid wasp evolution and biogeography by being the first to leverage genome-scale data and model-based methods. However, the precision of our dating analyses is constrained by the paucity of well-preserved fossils reliably attributable to the scoliid crown group. Despite concluding that the higher-level taxonomy of the Scoliidae is in dire need of revision, we recommend that taxonomic changes be predicated on datasets that extend the geographic and taxonomic sampling of the current study.


title: Bioinspired Stretchable Transducer for Wearable Continuous Monitoring of Respiratory Patterns in Humans and Animals

abstract: We report a bio-inspired continuous wearable respiration sensor modeled after the lateral line system of fish which is used by the fish for detecting mechanical disturbances in the water. Despite the clinical importance of monitoring respiratory activity in humans and animals, continuous measurements of breathing patterns and rates are rarely performed in or outside of clinics. This is largely due to conventional sensors being too inconvenient or expensive for wearable sensing for most individuals and animals. The bio-inspired air-silicone composite transducer is placed on the chest and measures respiratory activity by continuously measuring the force applied to an air channel embedded inside a silicone-based elastomeric material. The force applied on the surface of the transducer during breathing changes the air pressure inside the channel which is measured using a commercial pressure sensor and mixed-signal wireless electronics. We extensively characterized the transducer produced in this work and tested it with humans, dogs, and laboratory rats. The bio-inspired air-silicone composite transducer may enable the early detection of a range of disorders that result in altered patterns of respiration. The technology reported can also be combined with artificial intelligence and cloud computing to algorithmically detect illness in humans and animals remotely, reducing unnecessary visits to clinics.


title: Genomic analyses identify significant molecules and biological processes in colorectal cancer cells with DNA damage

abstract: Colorectal cancer is a major cause of cancer deaths in the US. DNA damage is considered to be a novel target for the treatment of colorectal cancer. However, the molecular mechanisms and functions are still unclear. In this study, we aim to identify the significant molecules and signaling by analyzing the RNA-seq data. The GSE189366 was created by the BGISEQ-500 (Homo sapiens). The KEGG and GO analyses indicated the p53 signaling pathway and Hippo signaling pathway are major affected processes in colorectal cancer by DNA damage. Furthermore, we identified ten key interactive molecules including CDK1, STAT3, MDM2, CCNB1, CCNA2, CDKN1A, PCNA, AURKA, PLK1, and CDC6. Our study may provide potential drug targets for colorectal cancer.


title: RecombineX: a generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis

abstract:
Meiotic recombination is an essential biological process that ensures faithful chromosome segregation and promotes parental allele shuffling. Tetrad analysis is a powerful approach to quantify the genetic makeups and recombination landscapes of meiotic products. Here we present RecombineX (https://github.com/yjx1217/RecombineX), a generalized computational framework that automates the full workflow of marker identification, gamete genotyping, and tetrad-based recombination profiling based on any organisms and genetic backgrounds with batch processing capability. Aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which enables analyzing meiotic recombination landscapes in their native genomic contexts. Additional features such as copy number variation profiling and missing genotype inference further enhance downstream analysis. RecombineX also includes a dedicate module for simulating the genomes and reads of recombinant tetrads, which enables fine-tuned simulation-based hypothesis testing. This simulation module revealed the power and accuracy of RecombineX even when analyzing tetrads with very low sequencing depths (e.g., 1-2X). Tetrad sequencing data from the budding yeast Saccharomyces cerevisiae and green alga Chlamydomonas reinhardtii were further used to demonstrate the accuracy and robustness of RecombineX for organisms with both small and large genomes, manifesting RecombineX as an all-around one stop solution for future tetrad analysis.

Author SummaryMeiosis is a fundamental cellular process that ensures faithful chromosome segregation and promotes allele shuffling. Tetrad analysis, which isolates and genotypes all four meiotic products (i.e., tetrad) derived from a single meiosis, remains the most straightforward and powerful way of studying meiotic recombination and its modulators at fine scales. The wide application of tetrad analysis in yeasts, filamentous fungi, green algae, and land plants have substantially expand our understanding of meiotic recombination in terms of both genome-wide landscapes and molecular mechanisms. Here we described the first generalized computational framework named RecombineX that automates the full workflow of tetrad analysis based on any organisms and genetic backgrounds. In addition, aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which enables analyzing meiotic recombination landscapes in their native genomic contexts. Using both simulated and real tetradsequencing data, we further demonstrated RecombineXs trustable performance, versatile usage, and batch-processing capability, manifesting RecombineX as an all-around one stop solution for tetrad analysis. Especially considering that meiotic gamete genome sequencing from different natural and mutant backgrounds can now be acquired, we expect RecombineX to become a popular tool that empowers future tetrad analysis across different genetic backgrounds and species.


title: Deconstructing replicative senescence heterogeneity of human mesenchymal stem cells at single cell resolution reveals therapeutically targetable senescent cell sub-populations

abstract: Cellular senescence is characterised by a state of permanent cell cycle arrest. It is accompanied by often variable release of the so-called senescence-associated secretory phenotype (SASP) factors, and occurs in response to a variety of triggers such as persistent DNA damage, telomere dysfunction, or oncogene activation. While cellular senescence is a recognised driver of organismal ageing, the extent of heterogeneity within and between different senescent cell populations remains largely unclear. Elucidating the drivers and extent of variability in cellular senescence states is important for discovering novel targeted seno-therapeutics and for overcoming cell expansion constraints in the cell therapy industry. Here we combine cell biological and single cell RNA-sequencing approaches to investigate heterogeneity of replicative senescence in human ESC-derived mesenchymal stem cells (esMSCs) as MSCs are the cell type of choice for the majority of current stem cell therapies and senescence of MSC is a recognized driver of organismal ageing. Our data identify three senescent subpopulations in the senescing esMSC population that differ in SASP, oncogene expression, and escape from senescence. Uncovering and defining this heterogeneity of senescence states in cultured human esMSCs allowed us to identify potential drug targets that may delay the emergence of senescent MSCs in vitro and perhaps in vivo in the future.


title: A real-time cellular thermal shift assay (RT-CETSA) to monitor target engagement

abstract:
Determining a molecules mechanism of action is paramount during chemical probe development and drug discovery. The cellular thermal shift assay (CETSA) is a valuable tool to confirm target engagement in cells for a small molecule that demonstrates a pharmacological effect. CETSA directly detects biophysical interactions between ligands and protein targets, which can alter a proteins unfolding and aggregation properties in response to thermal challenge. In traditional CETSA experiments, each temperature requires an individual sample, which restricts throughput and requires substantial optimization. To capture the full aggregation profile of a protein from a single sample, we developed a prototype real-time CETSA (RT-CETSA) platform by coupling a real-time PCR instrument with a CCD camera to detect luminescence. A thermally stable Nanoluciferase variant (ThermLuc) was bioengineered that withstood unfolding at temperatures greater than 90 degrees Celsius and was compatible with monitoring target engagement events when fused to diverse targets. Utilizing well-characterized inhibitors of lactate dehydrogenase alpha, RT-CETSA showed significant correlation with enzymatic, biophysical, and other cell-based assays. A data analysis pipeline was developed to enhance the sensitivity of RT-CETSA to detect on-target binding. The RT-CETSA technology advances capabilities of the CETSA method and facilitates the identification of ligand-target engagement in cells, a critical step in assessing the mechanism of action of a small molecule.

SignificanceValidating target engagement is a critical step when characterizing a small molecule modulator. The cellular thermal shift assay (CETSA) is a common approach to examine target engagement, as alterations in the thermal stability of a protein can be conferred by ligand binding. An advantage of CETSA is that it does not require modification of the protein target or small molecule. Major limitations are the throughput and ease-of-use, as the traditional detection method uses western blots, which limits the number of samples that can be processed. Higher-throughput CETSA methods have been developed but are performed at a single temperature and require target-specific optimization. We developed a high-throughput real-time CETSA to circumvent these challenges, providing a rapid and cost-effective strategy to assess on-target activity of a small molecule in living cells.

category: pharmacology and toxicology


title: Hijacking Methyl Reader proteins for Nuclear-Specific Protein Degradation

abstract: Targeted protein degradation (TPD) by PROTACs is a promising strategy to control disease-causing protein levels within the cell. While TPD is emerging as an innovative drug discovery paradigm, there are currently only a limited number of E3 ligase: ligand pairs that are employed to induce protein degradation. Herein, we report a novel approach to induce protein degradation by hijacking a methyl reader: E3 ligase complex. L3MBTL3 is a methyl lysine reader protein that binds to the Cul4DCAF5 E3 ligase complex and targets methylated proteins for proteasomal degradation. By co-opting this natural mechanism, we report the design and biological evaluation of L3MBTL3-recruiting PROTACs and demonstrate nuclear-specific degradation of FKBP12 and BRD2. We envision this as a generalizable approach to utilize other reader protein-associated E3 ligase complexes in PROTAC design to expand the E3 ligase toolbox and explore the full potential of TPD.


title: Dopamine D1-like receptor blockade and stimulation decreases operant responding for nicotine and food in male and female rats

abstract: Dopamine has been implicated in smoking, but there remains a need for a better understanding of the effects of dopamine D1-like receptor agonists on nicotine intake and the role of sex in the effects of dopaminergic drugs on nicotine intake. This work studied the effects of D1-like receptor stimulation and blockade on operant responding for nicotine and food and locomotor activity in male and female rats. The effects of the D1-like receptor antagonist SCH 23390 (0.003, 0.01, 0.03 mg/kg) and the D1-like receptor agonist A77636 (0.1, 0.3, 1 mg/kg) on responding for nicotine and food, and locomotor activity were investigated. The effects of SCH 23390 were investigated 15 min and 24 h after treatment, and the effects of the long-acting drug A77636 were investigated 15 min, 24 h, and 48 h later. Operant responding for nicotine and food was decreased 15 min, but not 24 h, after treatment with SCH 23390. Operant responding for nicotine was decreased 15 min, 24 h, and 48 h after treatment with A77636, and food responding was decreased 15 min and 24 h later. Locomotor activity was decreased 15 min, but not 24 h, after treatment with SCH 23390. A77636 only decreased locomotor activity 48 h after treatment. There were no sex differences in the effects of SCH 23390 or A77636. In conclusions, the D1-like receptor antagonist SCH 23390 reduces nicotine intake and causes sedation in rats. Stimulation of D1-like receptors with A77636 decreases nicotine intake at time points that the drug is not sedative.