title: SARS-CoV-2 T cell responses are expected to remain robust against Omicron

abstract: Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its effect on T cell responses remains to be determined. Here, we assess the effect of Omicron mutations on known T cell epitopes and report data suggesting T cell responses to remain broadly robust against this new variant.


title: Potential cross-protection against SARS-CoV-2 from previous exposure to bovine coronavirus

abstract: Humans have long shared infectious agents with cattle, and the common cold OC-43 CoV is a not-so-distant example of cross-species viral spillover. Human exposure to BCoV is certainly common, as the virus is endemic in cattle-raising regions. This article shows an in silico investigation of shared viral epitopes between BCoV and SARS-CoV-2. HLA recognition and lymphocyte reactivity were assessed using freely-available resources. Several epitopes were shared between BCoV and SARS-CoV-2, both for B and T lymphocytes. These data demonstrate that possible cross-protection is being induced by human exposure to cattle.

category: immunology


title: Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion

abstract: Defense-associated sirtuins (DSR) comprise a family of proteins that defend bacteria from phage infection via an unknown mechanism. These proteins are common in bacteria and harbor an N-terminal sirtuin (SIR2) domain. In this study we report that DSR proteins degrade nicotinamide adenine dinucleotide (NAD+) during infection, depleting the cell of this essential molecule and aborting phage propagation. Our data show that one of these proteins, DSR2, directly identifies phage tail tube proteins and then becomes an active NADase in Bacillus subtilis. Using a phage mating methodology that promotes genetic exchange between pairs of DSR2-sensitive and DSR2-resistant phages, we further show that some phages express anti-DSR2 proteins that bind and repress DSR2. Finally, we demonstrate that the SIR2 domain serves as an effector NADase in a diverse set of phage defense systems outside the DSR family. Our results establish the general role of SIR2 domains in bacterial immunity against phages.

category: microbiology


title: Adaptive changes in the fungal cell wall mediate copper homeostasis

abstract:
Copper homeostasis mechanisms are essential for microbial adaption to changing copper levels within the host during infection. In the opportunistic fungal pathogen Cryptococcus neoformans (Cn), the Cn Cbi1/Bim1 protein is a newly identified copper binding and release protein that is highly induced during copper limitation. Recent studies demonstrated that Cbi1 functions in copper uptake through the Ctr1 copper transporter during copper limitation. However, the mechanism of Cbi1 action is unknown. The fungal cell wall is a dynamic structure primarily composed of carbohydrate polymers, such as chitin and chitosan, polymers known to strongly bind copper ions. We demonstrated that Cbi1 depletion affects cell wall integrity and architecture, connecting copper homeostasis with adaptive changes within the fungal cell wall. The cbi1{Delta} mutant strain possesses an aberrant cell wall gene transcriptional signature as well as defects in chitin and chitosan deposition. These changes are reflected in altered macrophage activation and changes in the expression of specific virulence-associated phenotypes. Furthermore, using Cn strains defective in chitosan biosynthesis, we demonstrated that cell wall chitosan modulates the ability of the fungal cell to withstand copper stress. In conclusion, our data suggest a dual role for the fungal cell wall, in particular the inner chitin / chitosan layer, in protection against toxic levels of copper and providing a source of metal ion availability during copper starvation. Given the previously described role for Cbi1 in copper uptake, we propose that this copper-binding protein is involved in shuttling copper from the cell wall to the copper transporter Ctr1 for regulated microbial copper uptake.

Author summaryMicroorganisms must be equipped to readily acquire essential micro-nutrients like copper from nutritionally poor environments while simultaneously shielding themselves from conditions of metal excess. We explored mechanisms of microbial copper homeostasis in the human opportunistic fungal pathogen Cryptococcus neoformans (Cn) by defining physiological roles of the newly described copper-binding and release protein Cn Cbi1/Bim1. Highly induced during copper limitation, Cbi1 has been shown to interact with the high-affinity copper transporter Ctr1. We defined Cbi1-regulated changes in the fungal cell wall, including controlling levels of the structural carbohydrates chitin and chitosan. These polysaccharides are embedded deeply in the cell wall and are known to avidly bind copper. We also defined the host immunological alterations in response to these cell wall changes. Our data suggest a model in which the fungal cell wall, especially the chito-oligomer layer, serves as a copper-binding structure to shield the cell from states of excess copper, while also serving as a copper storage site during conditions of extracellular copper depletion. Given its ability to bind and release copper, the Cbi1 protein likely shuttles copper from the cell wall to copper transporters for regulated copper acquisition.


title: Adaptive strategies under prolonged starvation and role of slow growth in bacterial fitness

abstract: 1.Adaptive evolution has the power to illuminate genetic mechanisms under a pre-defined set of selection factors in a controlled environment. Laboratory evolution of bacteria under long-term starvation has gained importance in recent years because of its ability to uncover adaptive strategies to overcome prolonged nutrient limitation- a condition thought to be encountered often by natural microbial isolates. In this evolutionary paradigm, bacteria are maintained in an energy-restricted environment in the growth phase called as long-term stationary phase or LTSP. This phase is characterized by a stable viable population size and highly dynamic genetic changes. Multiple independent iterations of LTSP evolution experiments have given rise to mutants that are slow-growing compared to the ancestor. Although the antagonistic regulation between rapid growth and stress response is fairly well-known in bacteria (especially Escherichia coli), the reason behind the growth deficit of many LTSP-adapted mutants has not been explored in detail. In this review, I revisit the trade-off between growth and stress response and delve into the regulatory mechanisms currently known to control growth under nutrient deficiency. Focusing on the theme of "sigma-factor competition" I try to search for the evolutionary reasoning of slow growth amongst mutants adapted to prolonged starvation. Additionally, I present novel experimental data indicating the dynamics of four such slow-growing variants that evolved during a 30-day long LTSP evolution experiment with Escherichia coli.


title: In silico evidence of superantigenic features in ORF8 protein from COVID-19

abstract: Very early on COVID-19 pandemic outbreak, it was noted that the some of the virus-induced clinical conditions resembled features of toxaemia caused by the toxic shock syndrome toxin type 1, which is a soluble superantigen produced by Staphylococcus aureus. Among all SARS proteins, the ORF8 protein from SARS-2 virus is significantly different from other known SARS-like coronaviruses, and therefore could exhibit unique pathogenic properties. We assess if ORF8 protein bears super antigenic features using in silico tools. We show that ORF8 has properties of an extracellular soluble protein and shares a significant degree of amino acid sequence identity with toxic shock syndrome toxin. Besides, docking and binding affinity analyses between monomeric and homodimeric ORF-8 with V{beta} 2.1 and TRBV11-2 reveal strong interaction and high binding affinity. ORF8-TRBV11-2 strong interaction can contribute to the observed clonal expansion of that chain during COVID-19-associated multisystem inflammatory syndrome. Taken together, the evidence presented here supports the hypothesis that ORF8 protein from SARS-2 bears super antigenic properties.


title: Simulated colonic fluid replicates the in vivo growth capabilities of Citrobacter rodentium mutants and highlights a critical role for the Cpx envelope stress response in mediating stressors encountered in the gastrointestinal tract

abstract: Citrobacter rodentium is an attaching and effacing (A/E) pathogen used as a model for enteropathogenic and enterohemorrhagic Escherichia coli infections in mice. While in the host, C. rodentium must adapt to stresses in the gastrointestinal tract such as antimicrobial peptides, pH changes, and bile salts. The Cpx envelope stress response (ESR) is a two-component system used by some bacteria to remediate stress by modulating gene expression and is necessary for C. rodentium pathogenesis in mice. To investigate genes in the Cpx regulon that may contribute to C. rodentium pathogenesis, RNA-Seq, SILAC, and microarray data from previous research was mined and the genes yebE, ygiB, bssR, and htpX were confirmed to be strongly upregulated by the presence of CpxRA using lux reporter constructs. To determine the function of these genes in vivo, knockout mutants were tested in C57Bl/6J and C3H/HeJ mice. Although none of the mutants exhibited marked virulence phenotypes, the {Delta}cpxRA mutant had reduced colonization and attenuated virulence, as previously determined. We also found that the absence of the Cpx ESR resulted in higher expression of the LEE master regulator, ler. In addition, we determined that the {Delta}cpxRA mutant had a growth defect in medium simulating the colon, as did several of the mutants bearing deletions in Cpx-upregulated genes. Overall, these results indicate that the {Delta}cpxRA virulence defect is not due to any single Cpx regulon gene examined. Instead, attenuation may be the result of defective growth in the colonic environment resulting from the collective impact of multiple Cpx-regulated genes.


title: Multi-virulence and phenotypic spread of Campylobacter jejuni carried by chicken meat in Brazil

abstract:
Campylobacter jejuni is the most incriminated pathogen in bacterial gastroenteritis, and therefore, characteristics of its epidemiology must be continuously investigated to support possible mitigating measures. This is particularly important when evaluating representative strains of the worlds leading chicken meat exporter, Brazil. We evaluated a panel of 14 virulence genes in 359 strains of C. jejuni isolated from chilled broiler carcasses of Brazil. The genes were classified into five virulence categories (B: biofilm/motility; SS: secretion/cytotoxicity system; CI: invasion/colonization; GB: Guillain-Barre and AE: adaptation to stress). The percentage of strains with stress adaptation genes (86.07%) indicates the potential to adapt to unfavorable environmental conditions and hcp gene in 97.77%, indicates the ability to cause serious infections in humans. Genes related to GBS in 77.44% of strains are an additional concern, which must be monitored. The gene panel showed the presence of 124 virulence profiles. Individual analyzes by carcass, slaughter establishment, and municipalities where they were located showed high I.Var., of 0.82, 0.87 and 0.78, respectively. Georeferencing indicated state A as a hotspot for virulent strains. Higher levels of isolation and multi-virulence were identified in the summer, which in Brazil is hot and humid. Proteomics was able to discriminate the strains, but due to the high heterogeneity between them, it did not allow to explain their dissemination. Together, our results showed that the studied strains are a potential danger to public health and that there is an urgent need for their surveillance and the adoption of control measures, especially in state A.

AUTHOR SUMMARYCampylobacter jejuni is a bacterium considered one of the main causes of foodborne illnesses and the consumption of undercooked chicken meat is one of the main sources of human infection. In Brazil, epidemiological studies of this pathogen are still scarce, when compared to countries with structured surveillance, as well as, its analysis is not required by public health agencies in any group of foods intended for human consumption. Here we investigate the epidemiology of C. jejuni strains isolated from chilled chicken carcasses in Brazil, determining virulent and multivirulent strains, by the origin of the sample and its phenotypic patterns. The strains showed a high potential for adaptation to the environment, being classified as virulent and multivirulent, with a seasonal pattern in the hottest and humid periods of the year. In state A, the strains with the highest evolutionary level were isolated, when compared to the other states in the region. We hope that this study will help to better understand the potential risks that C. jejuni poses to the population and support surveillance agencies in tracking and adopting measures to minimize the dangers that this pathogen poses to public health.


title: A salvaging strategy enables stable metabolite provisioning among free-living bacteria

abstract: All organisms rely on complex metabolites such as amino acids, nucleotides, and cofactors for essential metabolic processes. Some microbes synthesize these fundamental ingredients of life de novo, while others rely on uptake to fulfill their metabolic needs. Although certain metabolic processes are inherently  leaky, the mechanisms enabling stable metabolite provisioning among microbes in the absence of a host remain largely unclear. In particular, how can metabolite provisioning among free-living bacteria be maintained under the evolutionary pressure to economize resources? Salvaging, the process of  recycling and reusing, can be a metabolically efficient route to obtain access to required resources. Here, we show experimentally how precursor salvaging in engineered Escherichia coli populations can lead to stable, long-term metabolite provisioning. We find that salvaged cobamides (vitamin B12 and related enzyme cofactors) are readily made available to non-productive population members, yet salvagers are strongly protected from overexploitation due to partial metabolite privatization. We also describe a previously unnoted benefit of precursor salvaging, namely the removal of the non-functional, proliferation-inhibiting precursor. As long as compatible precursors are present, any microbe possessing the terminal steps of a biosynthetic process can, in principle, forgo de novo biosynthesis in favor of salvaging. Consequently, precursor salvaging likely represents a potent, yet overlooked, alternative to de novo biosynthesis for the acquisition and provisioning of metabolites in free-living bacterial populations.


title: Sir2-domain associated short prokaryotic Argonautes provide defence against invading mobile genetic elements through NAD+ depletion

abstract: Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID, and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). Intriguingly, the majority ([~]60%) of prokaryotic Agos (pAgos) identified bioinformatically are shorter (comprised of only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here, we show that short pAgos from Geobacter sulfurreducens, Caballeronia cordobensis and Paraburkholderia graminis, together with the NAD+-bound Sir2-proteins form a stable heterodimeric Sir2/Ago complex that recognizes invading plasmid or phage DNA through the pAgos subunit and activates Sir2 subunit triggering the endogenous NAD+ depletion and cell death thus preventing the propagation of invading DNA. This is the first demonstration that short Sir2-associated pAgos provide defence against phages and plasmids and underscores the diversity of mechanisms of prokaryotic Agos.

category: molecular biology


title: Key features of inhibitor binding to the human mitochondrial pyruvate carrier hetero-dimer

abstract: The mitochondrial pyruvate carrier (MPC) has emerged as a promising drug target for metabolic disorders, including non-alcoholic steatohepatitis and diabetes, metabolically dependent cancers and neurodegenerative diseases. Human MPC is a protein complex, but the composition of its active form is debated and the mechanisms of transport and inhibition are not resolved. We have recombinantly expressed and purified the human hetero-complex MPC1L/MPC2 and demonstrate that it is a functional hetero-dimer, like the yeast MPC hetero-dimers. Unlike the latter, human MPC1L/MPC2 binds the known inhibitors with high potencies. We identify the essential chemical features shared between these structurally diverse inhibitors and demonstrate that high affinity binding is not attributed to covalent bond formation with MPC cysteines, as previously thought. We also identify 14 new inhibitors of MPC, one outperforming the most potent compound UK5099 by tenfold. Two of them are the commonly prescribed drugs entacapone and nitrofurantoin, suggesting possible off-target mechanisms associated with their adverse effects. This work advances our understanding of MPC inhibition and will accelerate the development of clinically relevant MPC modulators.


title: Islet primary cilia motility controls insulin secretion

abstract: Primary cilia are specialized cell-surface organelles that mediate sensory perception and, in contrast to motile cilia and flagella, are thought to lack motility function. Here we show that primary cilia in pancreatic beta cells exhibit movement that is required for glucose-dependent insulin secretion. Beta cell cilia contain motor proteins conserved from those found in classic motile cilia, and their 3D motion is dynein-driven and dependent on ATP and glucose metabolism. Inhibition of cilia motion blocks beta cell calcium influx and insulin secretion. Beta cells from humans with type 2 diabetes have altered expression of cilia motility genes. Our findings redefine primary cilia as dynamic structures possessing both sensory and motile function and establish that pancreatic beta cell cilia movement plays a critical role in controlling insulin secretion.

category: cell biology


title: Nanoscale details of mitochondrial fission revealed by cryo-electron tomography

abstract: Mitochondrial fission is required for proper segregation during cell division, quality control, and cellular homeostasis (metabolism and energy production). Despite its importance, models of the process remain speculative. Here we apply cryogenic electron tomography to image the nanoscale architecture of mitochondrial fission in mammalian cells. We find that constriction of the inner and outer membranes is coordinated, suggesting that force on both membranes is applied externally. While we observe ER at constriction sites, it did not encircle constrictions. Instead, we find long bundles of both unbranched actin and septin filaments enriched at constrictions. Actin bundles align with the central region of division bridges and septin bundles with the necks on either side. Septin bundles appear to guide microtubules to constriction sites, suggesting, along with autolysosomes observed in the vicinity, a pathway for mitophagy. Together, our results rule out several existing models for mitochondrial fission and provide empirical parameters to inform the development of realistic coarse-grained models in the future.


title: Cdc42 GTPase activating proteins Rga4 and Rga6 coordinate septum synthesis and membrane trafficking at the division plane during cytokinesis

abstract:
Fission yeast cytokinesis is driven by simultaneous septum synthesis, membrane furrowing and actomyosin ring constriction. The septum consists of a primary septum flanked by secondary septa. First, delivery of the glucan synthase Bgs1 and membrane vesicles initiate primary septum synthesis and furrowing. Next, Bgs4 is delivered for secondary septum formation. It is unclear how septum synthesis is coordinated with membrane furrowing. Cdc42 promotes delivery of Bgs1 but not Bgs4. We find that after primary septum initiation, Cdc42 inactivators Rga4 and Rga6 localize to the division site. In rga4{Delta}rga6{Delta} mutants Cdc42 activity is enhanced during late cytokinesis and cells take longer to separate. Electron micrographs of the division site in these mutants exhibit malformed septum with irregular membrane structures. These mutants have a larger division plane with enhanced Bgs1 delivery but fail to enhance accumulation of Bgs4 and several exocytic proteins. Additionally, these mutants show endocytic defects at the division site. This suggests that Cdc42 regulates only specific membrane trafficking events. Our data indicate that while active Cdc42 promotes primary septum synthesis, as cytokinesis progresses Rga4 and Rga6 localize to the division site to decrease Cdc42 activity. This couples specific membrane trafficking events with septum formation to allow proper septum morphology.

Abstract Figure

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/472679v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@ef042aorg.highwire.dtl.DTLVardef@1fa81adorg.highwire.dtl.DTLVardef@157a4a5org.highwire.dtl.DTLVardef@fa516d_HPS_FORMAT_FIGEXP  M_FIG C_FIG SynopsisThe GTPase Cdc42 regulates cytokinesis in cell-walled fission yeast. Active Cdc42 promotes the initiation of septum (new cell wall) synthesis to physically divide daughter cells. Here we show that Cdc42 activity must be decreased at the later stages of cytokinesis to enable proper septum formation. Mutants lacking Cdc42 inactivators, Rga4 and Rga6, lead to membrane trafficking defects and malformed septa consequently delaying cell separation.


title: Elevation drives activity of soil bacteria, but not of bacterial viruses

abstract: Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyze a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and altitudinal gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages co-decline across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at 5 sites across 400 elevational meters in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient. Bacteriophage activity pattern, however, is divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, to understand the magnitude of viral contributions to mobilize bacterial cell carbon when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.

category: ecology


title: An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome

abstract: Hormones coordinate long-range cell-cell communication in multicellular organisms and play vital roles in normal physiology, metabolism, and health. Using the newly-completed organism-wide single cell transcriptional atlas of a non-human primate, the mouse lemur (Microcebus murinus), we have systematically identified hormone-producing and -target cells for 87 classes of hormones, and have created a browsable atlas for hormone signaling that reveals previously unreported sites of hormone regulation and species-specific rewiring. Hormone ligands and receptors exhibited cell-type-dependent, stereotypical expression patterns, and their transcriptional profiles faithfully classified the discrete cell types defined by the full transcriptome, despite their comprising less than 1% of the transcriptome. Although individual cell types generally exhibited the same characteristic patterns of hormonal gene expression, a number of examples of similar or seemingly-identical cell types (e.g., endothelial cells of the lung versus of other organs) displayed different hormonal gene expression patterns. By linking ligand-expressing cells to the cells expressing the corresponding receptor, we constructed an organism-wide map of the hormonal cell-cell communication network. The hormonal cell-cell network was remarkably densely and robustly connected, and included classical hierarchical circuits (e.g. pituitary [->] peripheral endocrine gland [->] diverse cell types) as well as examples of highly distributed control. The network also included both well-known examples of feedback loops and a long list of potential novel feedback circuits. This primate hormone atlas provides a powerful resource to facilitate discovery of regulation on an organism-wide scale and at single-cell resolution, complementing the single-site-focused strategy of classical endocrine studies. The network nature of hormone regulation and the principles discovered here further emphasize the importance of a systems approach to understanding hormone regulation.

category: genomics


title: 2.7 A cryo-EM structure of ex vivo RML prion fibrils

abstract: Mammalian prions are lethal infectious agents that propagate as distinct strains and are composed of multichain assemblies of misfolded host-encoded prion protein (PrP), often referred to as prion rods. The structural features that define infectious prion rods and the molecular determinants of prion strain diversity are poorly understood. Here, we present a near-atomic resolution cryo-EM structure of PrP fibrils present in highly infectious prion rod preparations isolated from the brains of RML prion-infected mice. We found that prion rods comprise single-protofilament helical amyloid fibrils that coexist with twisted pairs of the same protofilaments. Each rung of the protofilament is formed by a single PrP monomer with the ordered core comprising PrP residues 94-225, which folds to create two asymmetric lobes with the N-linked glycans and the glycosylphosphatidylinositol anchor projecting from the C-terminal lobe. The overall architecture is comparable to that of recently reported PrP fibrils isolated from the brain of hamsters infected with the 263K prion strain. However, there are marked conformational variations that could result from differences in PrP primary sequence and/or represent distinguishing features of the distinct prion strains. These conformational changes impact the overall geometry of the fibrils and may also impact fibril pairing, one or both of which may critically influence PrP glycoform selection that occurs during strain-specific prion propagation.

category: biochemistry


title: ADAPs intrinsically disordered region is an actin sponge regulating T cell motility

abstract: Intrinsically disordered proteins (IDPs) play a vital role in biological processes that rely on transient molecular compartmentation1. In T cells, the dynamic switching between migration and adhesion mandates a high degree of plasticity in the interplay of adhesion and signaling molecules with the actin cytoskeleton2,3. Here, we show that the N-terminal intrinsically disordered region (IDR) of adhesion- and degranulation-promoting adapter protein (ADAP) acts as a multipronged scaffold for G- and F-actin, thereby promoting actin polymerization and bundling. Positively charged motifs, along a sequence of at least 200 amino acids, interact with both longitudinal sides of G-actin in a promiscuous manner. These polymorphic interactions with ADAP become constrained to one side once F-actin is formed. Actin polymerization by ADAP acts in synergy with a capping protein but competes with cofilin. In T cells, ablation of ADAP impairs adhesion and migration with a time-dependent reduction of the F-actin content in response to chemokine or T cell receptor (TCR) engagement. Our data suggest that IDR-assisted molecular crowding of actin above the critical concentration defines a new mechanism to regulate cytoskeletal dynamics. The principle of IDRs serving as molecular sponges to facilitate regulated self-assembly of filament-forming proteins might be a general phenomenon.


title: Validated Determination of NRG1 Ig-like Domain Structure by Mass Spectrometry Coupled with Computational Modeling

abstract: High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally-informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure leaving questions of unintentional bias and applicability to unknown structures unresolved. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 [A]. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure.

category: biophysics


title: Myricetin allosterically inhibits Dengue NS2B-NS3 protease as studied by NMR and MD simulations

abstract:
Dengue NS2B-NS3 protease existing in equilibrium between the active and inactive forms is essential for virus replication, thus representing a key drug target. Here Myricetin, a plant flavonoid, was characterized to non-competitively inhibit Dengue protease. Further NMR study identified the protease residues perturbed by binding to Myricetin, which were utilized to construct the Myricetin-protease complexes. Strikingly, in the active form Myricetin binds a new allosteric site (AS2) far away from the active site pocket and allosteric site (AS1) for binding Curcumin, while in the inactive form it binds both AS1 and AS2. To decipher the mechanism for the allosteric inhibition by Myricetin, we conducted molecular dynamics (MD) simulations on different forms of Dengue NS2B-NS3 protease. Unexpectedly, the binding of Myricetin to AS2 is sufficient to disrupt the active conformation by displacing the characteristic NS2B C-terminal {beta}- hairpin from the active site pocket. By contrast, the binding of Myricetin to AS1 and AS2 results in locking the inactive conformation. Therefore Myricetin represents the first small molecule which allosterically inhibits Dengue protease by both disrupting the active conformation and locking the inactive conformation. The results enforce the notion that a global allosteric network exists in Dengue NS2B-NS3 protease, which is susceptible to allosteric inhibition by small molecules such as Myricetin and Curcumin. As Myricetin has been extensively used as a food additive, it might be directly utilized to fight the Dengue infections and as a promising starting for further design of potent allosteric inhibitors.

Graphic Abstract

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title: Physical model of electrical synapses in a neural network

abstract: A theoretical model of electrical synapses is proposed, in which connexons play the role of "nails" that hold unmyelinated areas of neurons at a distance of about 3.5 nm, and the electrical connection between them is provided by charging the membrane of an inactive neuron with currents generated in the intercellular electrolyte (saline) by the action potential in the active neuron. This mechanism is similar to the salutatory conduction of the action potential between the nodes of Ranvier in myelinated axons and the ephaptic coupling of sufficiently close spaced neurons.


title: Structural dissection of the first events following membrane binding of the islet amyloid polypeptide

abstract: Amyloid forming proteins are involved in many pathologies and often belong to the class of intrinsically disordered proteins. One of these proteins is the islet amyloid polypeptide (IAPP), which is the main constituent of the amyloid fibrils found in the pancreas of type 2 diabetes patients. The molecular mechanism of IAPP-induced cell death is not yet understood, however it is known that cell membrane plays a dual role, being a catalyst of IAPP aggregation and the target of IAPP toxicity. Using FTIR spectroscopy, transmission electron microscopy, and molecular dynamics simulations we investigate the very first molecular steps following IAPP binding to a lipid membrane. In particular, we assess the combined effects of the charge state of amino-acid residue 18 and the IAPP-membrane interactions on the structures of monomeric and aggregated IAPP. Both our experiments and simulations reveal distinct IAPP-membrane interaction modes for the various IAPP variants. Membrane binding causes IAPP to fold into an amphipathic helix, which in the case of H18K- and H18R-IAPP can easily insert into the membrane. For all IAPP variants but H18E-IAPP, the membrane-bound -helical structure is an intermediate on the way to IAPP amyloid aggregation, while H18E-IAPP remains in a stable helical conformation. The fibrillar aggregates of wild-type IAPP and H18K-IAPP are dominated by an antiparallel {beta}-sheet conformation, while H18R- and H18A-IAPP exhibit both antiparallel and parallel {beta}-sheets as well as amorphous aggregates. In summary, our results emphasize the importance of residue 18 for the structure and membrane interaction of IAPP. This residue is thus a good target for destabilizing amyloid fibrils of IAPP and inhibit its toxic actions by possible therapeutic molecules.


title: Introduction of loxP sites by electroporation in the mouse genome; a simple approach for conditional allele generation in complex targeting loci.

abstract:
BackgroundThe discovery of the CRISPR-Cas9 system and its applicability in mammalian embryos has revolutionized the way we generate genetically engineered animal models. To date, models harbouring conditional alleles (i.e.: two loxP sites flanking an exon or a critical DNA sequence of interest) remain the most challenging to generate as they require simultaneous cleavage of the genome using two guides in order to properly integrate the repair template. In the current manuscript, we describe a modification of the sequential electroporation procedure described by Horii et al (2017). We demonstrate production of conditional allele mouse models for eight different genes via one of two alternative strategies: either by consecutive sequential electroporation (strategy A) or non-consecutive sequential electroporation (strategy B).

ResultsBy using strategy A, we demonstrated successful generation of conditional allele models for three different genes (Icam1, Lox, and Sar1b), with targeting efficiencies varying between 5 to 13%. By using strategy B, we generated five conditional allele models (Loxl1, Pard6a, Pard6g, Clcf1, and Mapkapk5), with targeting efficiencies varying between 3 to 25%.

ConclusionOur modified electroporation-based approach, involving one of the two alternative strategies, allowed the production of conditional allele models for eight different genes via two different possible paths. This reproducible method will serve as another reliable approach in addition to other well-established methodologies in the literature for conditional allele mouse model generation.


title: Structure-guided optimization of light-activated chimeric G-protein coupled receptors

abstract: G-protein coupled receptors (GPCRs) are the largest human receptor family and involved in virtually every physiological process. One hallmark of GPCR function is the specific coupling of activated receptors to selected downstream signaling pathways. The ability to tune this coupling would permit the development of receptors with new capabilities. GPCRs and G-proteins have been recently resolved structurally at high resolution, but this information was in only very few cases harnessed for a rational engineering of these protein complexes. Here, we demonstrate the structure-guided optimization of coupling in chimeric light-activated GPCRs (OptoXRs). Our hypothesis was that the incorporation of structural GPCR-G contacts will lead to improved receptor activity. We first evaluated structure-based alignments as complements to existing sequence-based methods for generation of chimeric receptors. We then show in a prototypical light-activated {beta}2AR that inclusion of -helical residues forming structural contacts to G resulted in receptors with 7- to 20-fold increased function compared to other design strategies. In turn, elimination of GPCR-G contacts diminished function. Finally, the efficient receptor design served as a platform for the optimization of a further light-activated receptor and spectral tuning of the photoreceptor core domain. Our work exemplifies how increased OptoXR potency and new functionalities can be achieved through structure-based design towards targeted inputs into cells and cellular networks.


title: A Multiscale computational model of YAP signaling in epithelial fingering behaviour

abstract:
In epithelial-mesenchymal transition (EMT), cells organized into sheets break away and become motile mesenchymal cells. EMT plays a crucial role in wound healing, embryonic development, and cancer metastasis. Intracellular signaling in response to mechanical, topographic, or chemical stimuli can promote EMT. We present a multiscale model for EMT downstream of the protein YAP, which suppresses the cell-cell adhesion protein E-cadherin and activates the GTPase Rac1 that enhances cell migration. We first propose an ODE model for YAP/Rac1/E-cadherin interactions. The model dynamics are bistable, accounting for motile loose cells as for adherent slower cells. We implement this model in a cellular Potts model simulation of 2D wound-healing using the open source platform Morpheus. We show that, under suitable stimuli (depicting topographic cues) the sheet exhibits finger-like projections and EMT. Morphological, as well as quantitative differences in YAP levels as well as cell speed across the sheet are consistent with preexisting experimental observations of epithelial sheets grown on topographic features in vitro. The simulation is also consistent with experiments that knockdown or over-express YAP, inhibit Rac1, or block E-cadherin.

SIGNIFICANCEIn normal wound-healing, cell in an epithelium divide, grow, and migrate so as to seal a gap. In some pathological states, epithelial-mesenchymal transition (EMT) can lead to abnormal morphology, including fingering, breakage of single cells or multicellular clusters from the sheet edge. The mechanochemical control of this behaviour by cell signaling circuits (YAP, Rac1, and E-cadherin) reveals how the competition between cell adhesion and cell migration contributes to the process. We use the open-source computational platform Morpheus to investigate a multiscale model for the interactions of the proteins inside cells and the resulting morphology of the cell sheet. Results are consistent with experimental results in the literature.


title: pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo

abstract:
Patterning of the anterior-posterior axis is fundamental to animal development. The Wnt pathway plays a major role in this process by activating the expression of posterior genes in animals from worms to humans. This observation raises the question of whether the Wnt pathway or other regulators control the expression of the many anterior-expressed genes. We found that the expression of five anterior-specific genes in Caenorhabditis elegans embryos depends on the Wnt pathway effectors pop-1/TCF and sys-1/{beta}-catenin. We focused further on one of these anterior genes, ref-2/ZIC, a conserved transcription factor expressed in multiple anterior lineages. Live imaging of ref-2 mutant embryos identified defects in cell division timing and position in anterior lineages. Cis-regulatory dissection identified three ref-2 transcriptional enhancers, one of which is necessary and sufficient for anterior-specific expression. This enhancer is activated by the T-box transcription factors TBX-37 and TBX-38, and surprisingly, concatemerized TBX-37/38 binding sites are sufficient to drive anterior-biased expression alone, despite the broad expression of TBX-37 and TBX-38. Taken together, our results highlight the diverse mechanisms used to regulate anterior expression patterns in the embryo.

Graphical Abstract

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category: genetics


title: A unified model for the biogenesis of mitochondrial outer membrane multi-span proteins

abstract:
The mitochondrial outer membrane (MOM) harbors proteins that traverse the membrane via several helical segments, so-called multi-span proteins. Two contradicting mechanisms were suggested to describe their integration into the MOM. The first proposes that the mitochondrial import (MIM) complex facilitates this process and functions as an insertase, whereas the second suggests that such proteins can integrate into the lipid phase without the assistance of import factors in a process that is enhanced by phosphatidic acid. To resolve this discrepancy and obtain new insights on the biogenesis of these proteins, we addressed this issue using yeast mitochondria and the multi-span protein Om14. Testing different truncation variants, we show that only the full-length protein contains all the required information that assure targeting specificity. Employing a specific insertion assay and several single and double deletion strains, we show that neither the import receptor Tom70 nor any other protein with a cytosolically exposed domain have a crucial contribution to the biogenesis process. We further demonstrate that Mim1 and Porin are required for optimal membrane integration of Om14 but none of them is absolutely required. Unfolding of the newly synthesized protein, its optimal hydrophobicity, as well as higher fluidity of the membrane dramatically enhanced the import capacity of Om14. Collectively, our findings suggest that MOM multi-span proteins can follow different biogenesis pathways in which proteinaceous elements and membrane behavior contribute to a variable extent to the combined efficiency.

SummaryZhou et al. provide new insights to the biogenesis of mitochondrial outer membrane proteins. They demonstrate that such proteins can follow various routes where both proteinaceous elements and membrane behavior regulate the efficiency and specificity of this process.


title: tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction

abstract: tRNA fragments (tRFs) are small RNAs comparable to the size and function of miRNAs. tRFs are generally Dicer independent, are found associated with Ago, and can repress expression of genes post-transcriptionally. Given that this expands the repertoire of small RNAs capable of post-transcriptional gene expression, it is important to predict tRF targets with confidence. Some attempts have been made to predict tRF targets, but are limited in the scope of tRF classes used in prediction or limited in feature selection. We hypothesized that established miRNA target prediction features applied to tRFs through a random forest machine learning algorithm will immensely improve tRF target prediction. Using this approach, we show significant improvements in tRF target prediction for all classes of tRFs and validate our predictions in two independent cell lines. Finally, Gene Ontology analysis suggests that among the tRFs conserved between mice and humans, the predicted targets are enriched significantly in neuronal function, and we show this specifically for tRF-3009a. These improvements to tRF target prediction further our understanding of tRF function broadly across species and provide avenues for testing novel roles for tRFs in biology. We have created a publicly available website for the targets of tRFs predicted by tRForest.

category: bioinformatics


title: Novel inhibitors designing against the potential drug target of Plasmodium falciparum M17 Leucyl Aminopeptidase - PfM17LAP

abstract: Malaria is one of the major disease of concern worldwide especially in the African regions. According to the recent WHO reports, African regions share 95% of the total deaths worldwide that occurs due to malaria. Plasmodium falciparum M17 Leucyl Aminopeptidase (PfM17LAP) plays an important role in the regulation of amino acids release and for the survival of the parasite. We performed molecular docking and simulation studies to find the potential inhibitors against PfM17LAP using ChEMBL antimalarial library. Molecular docking studies and post-docking analysis revealed that molecules CHEMBL369831 and CHEMBL176888 showed better binding than the reference molecule BESTATIN. LibDock and X-SCORES of molecules BES, CHEMBL369831 and CHEMBL176888 are 130.071, 230.38, 223.56 and -8.75 Kcal/mol, -10.90 Kcal/mol, -11.05 Kcal/mol respectively. ADMET profiling of the top ten ranked molecules was done by using the Discovery Studio. Molecular dynamic studies revealed that the complex PfM17LAP-CHEMBL369831 is stable throughout the simulation. Finally, we have reported novel inhibitors which possess more binding affinity towards PfM17LAP.


title: Sequence based prediction of protein phase separation into disordered condensates using machine learning

abstract:
Several proteins which are responsible for neuro-degenrerative disorders (Alzheimers, Parkinsons etc) are shown to undergo a mechanism known as liquid liquid phase separation (LLPS). We in this research build a predictor which would answer whether a protein molecule would undergo LLPS or not. For this we used some protein sequences for which we already knew the answer. The ones who undergo LLPS were considered as the positive set and the ones who do not, were taken as the negative set. Depending on the knowledge of amino-acid sequences we identified some relevant variables in the context of LLPS e.g. number of amino acids, length of the best pairings, average register shifts. Using these variables we built a number of scoring functions which were basically analytic functions involving these variables and we also combined some scores already existing in the literature. We considered a total of 43636 protein sequences, among them only 121 were positive. We applied logistic regression and performed cross validation, where 25% of the data were used as the training set and the performance of the obtained results were tested on the remaining 75% of the data. In the training process, we used Simplex algorithm to maximize area under the curve (AUC) in receiver operator characteristics (ROC) space for each of the scores we defined. The optimised parameters were then used to evaluate AUC on the test set to check the accuracy. The best performing score was identified as the predicting model to answer the question whether a protein chain would undergo phase separating behavior or not.

Author summaryLiquid-liquid phase separation (LLPS) is a classic subject in polymer physics. The essen- tial physics is aptly captured within the Flory-Huggins (FH) approach, a simple lattice mean-field theory. Evidence has been mounting in the last decade that protein LLPS underlies the formation of membrane-less organelles (MLOs) in living cells, explaining why proteins and other bio-molecules can remain in a dense liquid condensate without diffusing away. Intrinsically disordered regions (IDRs), with a sequence-intrinsic prefer- ence for conformational heterogeneity or disorder under native conditions, are enriched in proteins that have the ability of switching on LLPS. The detailed understanding of the biological function of disordered bio-molecular condensates, whose formation is driven by LLPS, is currently the focus of a major effort in cell biology. Several key proteins in neuro-degenerative disorders are components of MLOs, and a further liquid-to-solid transition to unsoluble amyloid aggregates may be triggered by pathogenic mutants. Non-equilibrium active processes are also known to drive non trivial spatio-temporal organization patterns in MLOs. In this research we aim to predict which proteins can undergo LLPS in physiological conditions in living cells, and the corresponding phase behavior, based on theoretical tools and on the knowledge of the amino-acid sequence alone. We derive specific knowledge-based potentials for the different kind of short-range interactions that are believed to drive protein LLPS and use them to build a simple yes/no predictor of phase separation in physiological conditions.


title: The loader complex Scc2/4 forms co-condensates with DNA as loading sites for cohesin

abstract: The genome is organized by diverse packaging mechanisms like nucleosome formation, loop extrusion and phase separation, which all compact DNA in a dynamic manner. Phase separation additionally drives protein recruitment to condensed DNA sites and thus regulates gene transcription. The cohesin complex is a key player in chromosomal organization that extrudes loops to connect distant regions of the genome and ensures sister chromatid cohesion after S-phase. For stable loading onto the DNA and for activation, cohesin requires the loading complex Scc2/4. As the precise loading mechanism remains unclear, we investigated whether phase separation might be the initializer of the cohesin recruitment process. We found that, in absence of cohesin, budding yeast Scc2/4 forms phase separated co-condensates with DNA, which comprise liquid-like properties shown by droplet shape, fusion ability and reversibility. We reveal in DNA curtain and optical tweezer experiments that these condensates are built by DNA bridging and bending through Scc2/4. Importantly, Scc2/4-mediated condensates recruit cohesin efficiently and increase the stability of the cohesin complex. We conclude that phase separation properties of Scc2/4 enhance cohesin loading by molecular crowding, which might then provide a starting point for the recruitment of additional factors and proteins.


title: RNA binding protein RBM3 augments kissing loop formation with lncRNAs to enhance translational control

abstract: It is becoming apparent that translational regulation involves the coordinated actions of RNA binding proteins (RBPs) and non-coding RNAs. For efficient translation, mRNA needs to be circularized, which is catalyzed by RNA binding proteins and translation factors. However, the role of lncRNAs in the process is not yet defined. We first performed RNA-seq and RNA- immunoprecipitation coupled-Seq and identified LSAMP-3 and Flii-1. Moreover, modeling studies suggest enhanced kissing loop interactions including of transcripts that encode angiogenesis and epithelial mesenchymal transition. While intestinal epithelial cell specific RBM3 transgenic mice showed increased LSAMP-3 and Flii-1, this was reduced in knockout mice. Also, RBM3 overexpression increased tumor xenograft growth, this was suppressed by knockdown of the lncRNAs. Also, knockdown of endogenous RBM3 reduced lncRNA levels and tumor xenograft growth. In addition, it reduced colitis-associated cancers. We propose that RBPs such as RBM3 mediate their function through regulatory lncRNAs that enable circularization to control translation.

category: cancer biology


title: A calibrated cell-based functional assay to aide classification of MLH1 DNA mismatch repair gene variants

abstract:
PURPOSEFunctional assays provide important evidence for classifying the disease significance of germline variants in the DNA mismatch repair genes. We sought to develop a cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene.

METHODSUsing CRISPR gene editing, we knocked-in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact at the RNA and protein level, including their ability to maintain stability of microsatellite sequences and instigate a DNA damage response. We calibrated these assays by testing well-established pathogenic and benign control variants.

RESULTSFive VUS resulted in functionally abnormal protein, 15 VUS resulted in functionally normal protein, and one VUS showed mixed results. Furthermore, we converted the functional outputs into a single odds in favor of pathogenicity score for each VUS.

CONCLUSIONOur CRISPR-based functional assay successfully models phenotypes observed in patients in a cellular context. Using this approach, we generated evidence for or against pathogenicity for utilization by variant classification expert panels. Ultimately, this information will assist in proper diagnosis and disease management for suspected Lynch syndrome patients.


title: 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives

abstract: 5-carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and baseexcision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ~10-20 kJ mol-1 at 37 {degrees}C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the s time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caCs subtle sensitivity to acidic pH contribute to the long standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.


title: Season-long infection of diverse hosts by the entomopathogenic fungus Batkoa major

abstract: Populations of the entomopathogenic fungus Batkoa major were analyzed using sequences of four genomic regions and evaluated in relation to their genetic diversity, insect hosts and collection site. This entomophthoralean pathogen killed numerous insect species from 23 families and five orders in two remote locations during 2019. The host list of this biotrophic pathogen contains flies, true bugs, butterflies and moths, beetles, and barkflies. Among the infected bugs (Order Hemiptera), the spotted lanternfly (Lycorma delicatula) is a new invasive planthopper pest of various woody plants that was introduced to the USA from Eastern Asia. A high degree of clonality occurred in the studied populations and high gene flow was revealed using four molecular loci for the analysis of population structure. We did not detect any segregation in the population regarding host affiliation (by family or order), or collection site. This is the first description of population structure of a biotrophic fungus-generalist in the entomopathogenic Order Entomophthorales. This analysis aimed to better understand the potential populations of entomopathogen-generalists infecting emerging invasive hosts in new ecosystems.


title: Prevalence and Characteristics of Cannabis-induced Toxicoses in Pets: Results from a Survey of Veterinarians in North America

abstract: Cannabis legalization in North America has coincided with an increase in reports of cannabis-induced toxicosis in pets, but the magnitude of this problem, as well as outcomes of these incidents remain unknown. Therefore, we examined the frequency, diagnostic criteria, clinical signs, and prognoses of cannabis toxicoses in pets in North America. We conducted an online survey between January, 2021 and April, 2021 targeting veterinarians practicing in Canada and the United States (US). Out of the 251 study participants, 191 practiced in Canada. Cannabis toxicosis was most commonly reported in dogs (n=226 veterinarians), and the number of toxicosis cases increased significantly in Canada (p<0.0001) and the US (p=0.002) after October, 2018. Frequently reported clinical signs of cannabis toxicosis included: urinary incontinence (n=195), disorientation (n=182), ataxia (n=178), lethargy (n=150), hyperesthesia (n=134), and bradycardia (n=112). Edibles were most commonly suspected to be the cause of toxicosis (n=116). The most common route of exposure was ingestion (n=135), while the most cited reason was ingestion while unattended (n=135). Cannabis toxicosis was mostly diagnosed using supportive clinical signs (n=229), the most common treatment was outpatient monitoring (n=182), and pets were most often treated as out-patients (n=103). The legalization of cannabis use in Canada and the US is likely an important factor associated with the increased cannabis toxicosis cases in pets; however, the legal status may also increase reporting. The medicinal use of cannabis by pet-owners for pets may also contribute to a portion of the reported toxicoses. Most pets that experienced cannabis toxicosis recovered completely, suggesting that most cannabis toxicoses do not result in long-term ill effects. Even though some deaths (n=16) were reported in association with cannabis toxicosis, the presence of confounders such as toxins, and underlying conditions cannot be ruled out, emphasizing the need for rigorous controlled laboratory studies to investigate this important issue.

category: pharmacology and toxicology


title: Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species

abstract: Harnessing the plant microbiome has the potential to improve agricultural yields and protect plants against pathogens and/or abiotic stresses, while also relieving economic and environmental costs of crop production. While previous studies have gained valuable insights into the underlying genetics facilitating plant-fungal interactions, these have largely been skewed towards certain fungal clades (e.g. arbuscular mycorrhizal fungi). Several different phyla of fungi have been shown to positively impact plant growth rates, including Mortierellaceae fungi. However, the extent of the plant growth promotion (PGP) phenotype(s), their underlying mechanism(s), and the impact of bacterial endosymbionts on fungal-plant interactions remain poorly understood for Mortierellaceae. In this study, we focused on the symbiosis between soil fungus Linnemannia elongata (Mortierellaceae) and Arabidopsis thaliana (Brassicaceae), as both organisms have high-quality reference genomes and transcriptomes available, and their lifestyles and growth requirements are conducive to research conditions. Further, L. elongata can host bacterial endosymbionts related to Mollicutes and Burkholderia. The role of these endobacteria on facilitating fungal-plant associations, including potentially further promoting plant growth, remains completely unexplored. We measured Arabidopsis aerial growth at early and late life stages, seed production, and used mRNA sequencing to characterize differentially expressed plant genes in response to fungal inoculation with and without bacterial endosymbionts. We found that L. elongata improved aerial plant growth, seed mass and altered the plant transcriptome, including the upregulation of genes involved in plant hormones and "response to oxidative stress", "defense response to bacterium", and "defense response to fungus". Furthermore, the expression of genes in certain phytohormone biosynthetic pathways were found to be modified in plants treated with L. elongata. Notably, the presence of Mollicutes- or Burkholderia-related endosymbionts in Linnemannia did not impact the expression of genes in Arabidopsis or overall growth rates.

category: plant biology


title: Impact of contamination on biology, biochemical, and histology of Eobania vermiculata and Monacha obstructa during different seasons in Ismailia, Egypt

abstract: Land snails are found to be an appropriate sentinel organism, and the biomarkers chosen are effective for terrestrial heavy metal biomonitoring. The study aimed to compare the biological, biochemistry, and histology of two land snails in the Ismailia governorate, Egypt during different seasons. Random snails were collected from January 2015 to December 2015 from two sites in the Ismailia Governorate, on wet days during each seasons middle month. Soft tissues were taken from the dissected snails. It was noticed that most of the morphometric parameters measured shell height (ShH), last whorl width (LWW), maximum diameter (MaxD), aperture height (AH), and aperture width (AW) were higher in Eobania vermiculata (Sp. 1) than those measured in Monacha obstructa (Sp. 2), except for shell height measurement, which was the same in both species. The growth rate of Sp. 1 and Sp. 2 changed seasonally. In the more polluted areas with heavy metals, lipid peroxidation (LPO) was higher in snails and total protein content than in the snails collected from the less polluted areas for all seasons. However, the snails displayed lower levels of glutathione (GSH) as compared to snails at a less polluted site. GSH and LPO levels, on the other hand, have a negative relationship between them. Histopathological alterations in the digestive gland were more obvious in the general architecture of the digestive gland that had lost its tubular appearance. The excretory cells showed an increase in their excretory granules number and size while calcium cells decreased. Also, gonad follicles have lost their normal architecture with the degeneration of some stages of spermatogenesis and oogenesis. In conclusion, There was a strong correlation between GSH levels and total protein content in the same soft tissues. GSH and LPO levels, on the other hand, have a negative relationship. The overall results display the usefulness of E. vermiculata and M. obstructa land snails as bioindicator organisms and support the application of this ecotoxicological approach for evaluating the biologic impact of toxins. E. vermiculata is more abundant than M. obstructa. The density, morphometric, biochemical, and histology of E. vermiculata and M. obstructa were different at different seasons.

category: zoology


title: The effects of social environment and the metapleural gland on disease resistance in acorn ants

abstract: Eusocial species differ in living conditions when compared to solitary species primarily due to the dense living conditions of genetically related individuals. Consequently, these crowded conditions can induce a high rate of pathogen transmission and pathogen susceptibility. To resist an epidemic, individuals rely on sets of behaviors, known as social immunity, to decrease pathogen transmission among nestmates. Alongside social immunity, ants have a pair of secretory metapleural glands (MG), thought to secrete antimicrobial compounds important for antisepsis, that are believed to be transferred among nestmates by social immune behaviors such as grooming. To investigate the effects of social immunity on pathogen resistance, we performed a series of experiments by inoculating acorn ants Temnothorax curvispinosus with a lethal spore concentration of the entomopathogenic fungus Metarhizium brunneum. After inoculation ant survival was monitored in two environments: solitary and in groups. Additionally, the MG role in pathogen resistance was evaluated for both solitary and grouped living ants, by sealing the MG prior to inoculations. Individuals within a group environment had a higher survival compared to those in a solitary environment, and individuals with sealed glands had significantly decreased survival than ants with non-sealed-MG in both solitary and social environments. We observed the lowest survival for solitary-sealed-MG individuals. Although sealing the MG reduced survival probability, sealing the MG did not remove the benefits of grouped living. We show here that social living plays a crucial role in pathogen resistance and that the MG has an important role in pathogen resistance of individual T. curvispinosus ants. Although important for an individuals pathogen resistance, our data show that the MG does not play a strong role in social immunity as previously believed. Overall, this study provides insights into mechanisms of social immunity and the role of MG in disease resistance.


title: Population genomic analysis of the speckled dace species complex (Rhinichthys osculus) identifies three species-level lineages in California

abstract: The speckled dace (Rhinichthys osculus) is small cyprinid fish that is widespread in the Western USA. Currently treated as a single species, speckled dace consists of multiple evolutionary lineages that can be recognized as species and subspecies throughout its range. Recognition of taxonomic distinctiveness of speckled dace populations is important for developing conservation strategies. In this study, we collected samples of speckled dace from 38 locations in the American West, with a focus on California. We used RAD sequencing to extract thousands of SNPs across the genome from samples to identify genetic differences among seven California populations informally recognized as speckled dace subspecies: Amargosa, Owens, Long Valley, Lahontan, Klamath, Sacramento, and Santa Ana speckled dace. We performed principal component analysis, admixture analysis, estimated pairwise Fst, and constructed a phylogeny to explore taxonomic relationships among these groups and test if these subspecies warrant formal recognition. Our analyses show that the seven subspecies fit into three major lineages equivalent to species: western (Sacramento-Klamath), Santa Ana, and Lahontan speckled dace. Death Valley speckled dace were determined to be two lineages (Amargosa and Long Valley) within Lahontan speckled dace. Western and Lahontan speckled dace lineages had branches that can be designated as subspecies. These designations fit well with the geologic history of the region which has promoted long isolation of populations. This study highlights the importance of genetic analysis for conservation and management of freshwater fishes.


title: Control of G2 phase duration by CDC25B modulates the switch from direct to indirect neurogenesis in the neocortex

abstract: During development, cortical neurons are produced in a temporally regulated sequence from apical progenitors, directly, or indirectly through the production of intermediate basal progenitors. The balance between these major progenitors types is determinant for the production of the proper number and types of neurons and it is thus important to decipher the cellular and molecular cues controlling this equilibrium. Here we address the role of a cell cycle regulator, the CDC25B phosphatase, in this process. We show that deleting CDC25B in apical progenitors leads to a transient increase of the production of TBR1+ neurons at the expense of TBR2+ basal progenitors in mouse neocortex. This phenotype is associated with lengthening of the G2 phase of the cell cycle, the total cell cycle length being unaffected. Using in utero electroporation and cortical slice cultures, we demonstrate that the defect in TBR2+ basal progenitor production requires interaction with CDK1 and is due to the G2 phase lengthening in CDC25B mutants. Altogether, this study identifies a new role for CDC25B and the length of the G2 phase in direct versus indirect neurogenesis at early stages of the cortical development.

category: developmental biology


title: Preterm birth alters the maturation of the GABAergic system in the human prefrontal cortex

abstract: Developmental changes in GABAergic and glutamatergic systems during frontal lobe development have been hypothesized to play a key role in neurodevelopmental disorders seen in children born very preterm or low birth weight, but the associated cellular changes have not yet been identified. Here we studied the molecular development of the GABAergic system specifically in the dorsolateral prefrontal cortex, a region that that has been implicated in neurodevelopmental and psychiatric disorders. The maturation state of the GABAergic system in this region was assessed in human post-mortem brain samples, from term infants ranging in age from 0 to 8 months (n=17 male, 9 female). Gene expression was measured for 47 GABAergic genes and used to calculate a maturation index. This maturation index was significantly more dynamic in male than female infants. To evaluate the impact of premature birth on the GABAergic system development, samples from one-month-old term (n=9 male, 4 female) and one-month corrected-age (n=8 male, 6 female) very preterm infants, were compared using the same gene list and methodology. The maturation index for the GABAergic system was significantly lower (-50% p<0.05) in male preterm infants, with major alterations in genes linked to GABAergic function in astrocytes, suggesting astrocytic GABAergic developmental changes as a new cellular mechanism underlying preterm brain injury.

category: neuroscience


title: learnMET: an R package to apply machine learning methods for genomic prediction using multi-environment trial data

abstract: We introduce the R-package learnMET, developed as a flexible framework to enable a collection of analyses on multi-environment trial (MET) breeding data with machine learning-based models. learnMET allows the combination of genomic information with environmental data such as climate and/or soil characteristics. Notably, the package offers the possibility of incorporating weather data from field weather stations, or can retrieve global meteorological datasets from a NASA database. Daily weather data can be aggregated over specific periods of time based on naive (for instance, non-overlapping 10-day windows) or phenological approaches. Different machine learning methods for genomic prediction are implemented, including gradient boosted trees, random forests, stacked ensemble models, and multi-layer perceptrons. These prediction models can be evaluated via a collection of cross-validation schemes that mimic typical scenarios encountered by plant breeders working with MET experimental data in a user-friendly way. The package is fully open source and accessible on GitHub.


title: Improvement in peripherical visual attentional performance in professional soccer players following a single neurofeedback training.

abstract: The effectiveness of EEG-neurofeedback (EEG-NFB) in modulating cognition has been the subject of much research for several years, particularly in relation to attentional functions in healthy subjects and those with attentional deficits. However, its effectiveness on sports performance remains poorly studied and its use is not widely practised among athletes, notably because of its accessibility and questionable effectiveness. The aim of this study is to show that this technology can be accessible, and that Alpha EEG-NFB is immediately effective. Fifteen professional soccer players took part in this study. Using a novel EEG headset that can be installed in less than one minute, and new processing software, the players performed two peripherical attentional tasks before and after, immediately and one month, a single Alpha EEG-NFB training session. The results showed a significant effect on both tasks immediately after EEG-NFB training, with a benefit of more than 30% and this performance continued after one month (20%). This study, the first to use this headset and software, shows that the improvement in sports performance can be related to cognitive performance, especially peripherical visual attentional functions. Furthermore, it demonstrates that the use of the EEG-NFB is accessible and effective for high-level athletes.


title: The Geometry of Representational Drift in Natural and Artificial Neural Networks

abstract: Neurons in sensory areas encode/represent stimuli. Surprisingly, recent studies have suggested that, even during persistent performance, these representations are not stable and change over the course of days and weeks. We examine stimulus representations from fluorescence recordings across hundreds of neurons in the visual cortex using in vivo two-photon calcium imaging and we corroborate previous studies finding that such representations change as experimental trials are repeated across days. This phenomenon has been termed "representational drift". In this study we geometrically characterize the properties of representational drift in the primary visual cortex of mice in two open datasets from the Allen Institute and propose a potential mechanism behind such drift. We observe representational drift both for passively presented stimuli, as well as for stimuli which are behaviorally relevant. Across experiments, the drift most often occurs along directions that have the most variance, leading to a significant turnover in the neurons used for a given representation. Interestingly, despite this significant change due to drift, linear classifiers trained to distinguish neuronal representations show little to no degradation in performance across days. The features we observe in the neural data are similar to properties of artificial neural networks where representations are updated by continual learning in the presence of dropout, i.e. a random masking of nodes/weights, but not other types of noise. Therefore, we conclude that a potential reason for the representational drift in biological networks is driven by an underlying dropout-like noise while continuously learning and that such a mechanism may be computational advantageous for the brain in the same way it is for artificial neural networks, e.g. preventing overfitting.


title: Trends in Pacific Canadian groundfish stock status

abstract: We assembled estimated biomass (B) time series from stock assessments for 24 Pacific Canadian groundfish stocks and modelled average and stock status through 2020 based on biomass relative to each stocks (1) Limit Reference Point (B/LRP), (2) Upper Stock Reference (B/USR), and (3) biomass at maximum sustainable yield (B/BMSY). The overall mean B/LRP in 2020 was 3.2 (95% credible interval [CI]: 2.6-3.9). The overall mean B/USR and B/BMSY in 2020 was 1.5 (95% CI: 1.3-1.9) and 1.4 (95% CI: 1.1-1.7), respectively. Average stock status declined from 1950 to around 2000 and has remained relatively stable since then. The change around 2000 followed the implementation of ITQs (individual transferable quotas) for the trawl fleet and the commencement of the synoptic trawl surveys. As of their last assessment, four stocks (Strait of Georgia Lingcod [Area 4B], coastwide Bocaccio, and inside and outside Quillback Rockfish) had a greater than 5% probability of being below their LRP (i.e., in the " critical zone"); Pacific Cod in Area 3CD had a 4.6% probability. Roughly one-third of stocks had a greater than 1 in 4 chance of being below their USR (i.e., in the " cautious zone"). Conversely, two-thirds of assessed groundfish stocks had a high (>75%) probability of being above the USR (i.e., in the " healthy zone").


title: Variability in mosquito community composition associated with estuarine wetlands in Northern NSW, Australia

abstract: The Northern Rivers region of NSW, Australia, is well documented as being impacted by nuisance-biting mosquitoes and mosquito-borne disease. Mosquitoes of greatest concern are those associated with estuarine and brackish water habitats associated with coastal wetlands and understanding the spatial variability in abundance and diversity will assist the assessment of risk and inform surveillance and control programs. Adult mosquito populations were sampled, using carbon dioxide baited traps, at four locations within the Richmond River estuary at Ballina, NSW, Australia, during January and February 2021. Concomitant sampling of habitats for immature mosquitoes was also undertaken. A total of 16,467 mosquitoes was collected at all sites across two sampling periods with the most abundant mosquitoes, Verrallina funerea, Aedes vigilax, and Culex sitiens, those typically associated with estuarine environments. Culex annulirostris, a mosquito associated with freshwater habitats, and Aedes notoscriptus, a mosquito associated with water-holding containers, were also commonly collected. The mosquito communities differed, in relative abundance and species richness, between the four locations. The result highlighted the need for authorities to understand the variability in productivity of potential mosquito habitats, beyond those determinants associated with vegetation communities alone, when assessing suitable locations of mosquito surveillance and integrated mosquito management.


title: BRG1 defines a genomic subset of inflammatory genes transcriptionally controlled by the glucocorticoid receptor

abstract:
Glucocorticoids (such as Dexamethasone) are commonly used immunomodulatory drugs with potent anti-inflammatory effects, whose mechanisms of action remain incompletely understood. They bind to the Glucocorticoid Receptor (GR), a nuclear hormone receptor that acts as a transcription factor to directly control the expression of inflammatory genes. To elucidate the complex molecular mechanisms employed by GR during the suppression of innate immune responses, we have performed proteomics, ChIP-seq, ATAC-seq, RNA-seq and bioinformatics together with genetic and pharmacological loss of function studies in primary mouse macrophages. We found that GR interacts with the ATP-dependent SWI/SNF chromatin remodeling complex to regulate a specific subset of target genes. Here we show that the central catalytic subunit BRG1 is required not only for the transcriptional activation of classical GR target genes such as Fkbp5 or Klf9, but also for the transcriptional repression of cytokines and chemokines such as Ccl2, Cxcl10 or Il1a. We demonstrate that loss of BRG1 activity leads to reduced histone deacetylase (HDAC) function, and consequently increased histone acetylation, at these repressive GR binding sites. Altogether, our findings suggest that GR interacts with BRG1 to assemble a functional co-repressor complex at a defined fraction of macrophage cis-regulatory elements. These results may indicate additional non-classical, remodeling-independent functions of the SWI/SNF complex and may have implications for the development of future immunomodulatory therapies.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/472398v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1d9d238org.highwire.dtl.DTLVardef@1788bb1org.highwire.dtl.DTLVardef@11b3d4dorg.highwire.dtl.DTLVardef@155b9fc_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO In macrophages (m{Phi}) responding to bacterial LPS and Dexamethasone, the Glucocorticoid Receptor (GR) activates target genes like Klf9 or Fkbp5 via interaction with the BRG1-containing SWI/SNF complex, chromatin remodeling and Mediator recruitment. At the same time, GR represses the expression of inflammatory cytokines and chemokines such as Ccl2, Cxcl10, Il1a etc. by assembling a BRG1-containing co-repressor complex and de-acetylating surrounding histone tails. Loss of BRG1 activity affects both the transcriptional activation and repression of a subset of myeloid GR target genes via distinct mechanisms. (iTF: inflammatory transcription factor; Ac: histone acetylation) (Created with BioRender.com.)

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title: Chemical-induced Gene Expression Ranking and its Application to Pancreatic Cancer Drug Repurposing

abstract: Chemical-induced gene expression profiles provide critical information on the mode of action, off-target effect, and cellar heterogeneity of chemical actions in a biological system, thus offer new opportunities for drug discovery, system pharmacology, and precision medicine. Despite their successful applications in drug repurposing, large-scale analysis that leverages these profiles is limited by sparseness and low throughput of the data. Several methods have been proposed to predict missing values in gene expression data. However, most of them focused on imputation and classification settings which have limited applications to real-world scenarios of drug discovery. Therefore, a new deep learning framework named chemical-induced gene expression ranking (CIGER) is proposed to target a more realistic but more challenging setting in which the model predicts the rankings of genes in the whole gene expression profiles induced by de novo chemicals. The experimental results show that CIGER significantly outperforms existing methods in both ranking and classification metrics for this prediction task. Furthermore, a new drug screening pipeline based on CIGER is proposed to select approved or investigational drugs for the potential treatments of pancreatic cancer. Our predictions have been validated by experiments, thereby showing the effectiveness of CIGER for phenotypic compound screening of precision drug discovery in practice.


title: Single-cell multi-omic velocity infers dynamic and decoupled gene regulation

abstract: Single-cell multi-omic datasets, in which multiple molecular modalities are profiled within the same cell, provide a unique opportunity to discover the relationships between cellular epigenomic and transcriptomic changes. To realize this potential, we developed MultiVelo, a mechanistic model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression from single-cell data, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes. Incorporating chromatin accessibility data significantly improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Fitting MultiVelo on single-cell multi-omic datasets from brain, skin, and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. Our model also identifies four types of cell states-two states in which epigenome and transcriptome are coupled and two distinct decoupled states. The parameters inferred by MultiVelo quantify the length of time for which genes occupy each of the four states, ranking genes by the degree of coupling between transcriptome and epigenome. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. We provide an open-source Python implementation of MultiVelo on PyPI and GitHub (https://github.com/welch-lab/MultiVelo).


title: Proximity-assisted photoactivation (PAPA): Detecting molecular interactions in live-cell single-molecule imaging

abstract: Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the "sender") can reactivate a second fluorophore (the "receiver") from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Forster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a sub-population of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.


title: Broad misappropriation of developmental splicing profile by cancer in multiple organs

abstract: Oncogenesis mimics key aspects of embryonic development. However, the underlying molecular determinants are not completely understood. Leveraging temporal transcriptomic data during development in multiple human organs, we demonstrate that the  embryonic positive (EP) alternative splicing events, specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. EP events are associated with key oncogenic processes and their reactivation predicts proliferation rates in cancer cell lines as well as patient survival. EP exons are significantly enriched for nitrosylation and transmembrane domains coordinately regulating splicing in multiple genes involved in intracellular transport and N-linked glycosylation respectively, known critical players in cancer. We infer critical splicing factors (CSF) potentially regulating these EP events and show that CSFs exhibit copy number amplifications in cancer and are upregulated specifically in malignant cells in the tumor microenvironment. Mutational inactivation of CSFs results in decreased EP splicing, further supporting their causal role. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of CSFs in brain and liver, which can be potentially targeted using FDA approved drugs. Our study provides the first comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest novel targets including splicing events, splicing factors, and transcription factors.


title: Determining Risk Factors for Triple Whammy Acute Kidney Injury

abstract: Concurrent use of a diuretic, a renin-angiotensin system (RAS) inhibitor, and a non-steroidal anti-inflammatory drug (NSAID) significantly increases the risk of acute kidney injury (AKI). This phenomenon is known as "triple whammy". Diuretics and RAS inhibitors, such as an angiotensin converting enzyme inhibitor or angiotensin receptor blocker, are often prescribed in tandem for the treatment of hypertension, whereas some NSAIDs, such as ibuprofen, are available over the counter. As such, concurrent treatment with all three drugs is common. The goals of this study are to better understand the mechanisms underlying the development of triple whammy AKI and to identify physiological factors that may increase an individuals susceptibility. To accomplish these goals, we utilize computational models of long-term blood pressure regulation. These models include variables describing the heart and circulation, kidney function, sodium and water reabsorption in the nephron and the RAS and are parameterized separately for men and women. Hypertension is modeled as overactive renal sympathetic nervous activity. Model simulations suggest that individual variations in water intake, the myogenic response, and drug sensitivity may predispose patients with hypertension to develop triple whammy-induced AKI.

category: physiology


title: Multimodal IVA fusion for detection of linked neuroimaging biomarkers

abstract: With the increasing availability of large-scale multimodal neuroimaging datasets, it is necessary to develop data fusion methods which can extract cross-modal features. A general framework, multidataset independent subspace analysis (MISA), has been developed to encompass multiple blind source separation approaches and identify linked cross-modal components in multiple datasets. In this work we utilized the multimodal independent vector analysis model in MISA to directly identify meaningful linked features across three neuroimaging modalities -- structural magnetic resonance imaging (MRI), resting state functional MRI and diffusion MRI -- in two large independent datasets, one comprising of healthy subjects and the other including patients with schizophrenia. Results show several linked subject profiles (the sources/components) that capture age-associated reductions, schizophrenia-related biomarkers, sex effects, and cognitive performance.


title: LRRFIP2 modulates the response to hypoxia during embryonic cardiogenesis

abstract:
Oxygen is crucial for appropriate embryonic and fetal development, including cardiogenesis. The heart is the first organ formed in the embryo and is required to provide oxygen and nutrients to all cells in the body. Embryonic cardiogenesis is a complex process finely regulated and prone to congenital malformations. It takes place in a hypoxic environment that activates the HIF-1 signaling pathway which mediates cellular and systemic adaptations to low oxygen levels. Since inhibition or overactivation of the HIF-1 signaling pathway in the myocardium lead to severe cardiac malformations and embryonic lethality, it is important that the cellular response to hypoxia be precisely regulated. While many gene regulatory networks involved in embryonic cardiogenesis have been characterized in detail, the modulation of the response of cardiomyocytes (CM) to hypoxia has remained less studied. We identified LRRFIP2 as a new negative cofactor of HIF-1. Indeed, we have shown that the absence of Lrrfip2 expression in a mouse KI model led to an enhance of many HIF-1 target genes including Igfbp3, Bnip3 and Ndufa4l2 in embryonic CM during development. As results, the absence of Lrrfip2 led to the inhibition of the PI3K/Akt survival pathway, growth defects, mitochondrial dysfunction and to a precocious maturation of the embryonic CMs. Altogether, these defects led to the formation of a smaller heart unable to provide sufficient oxygen to the embryo and finally to a severe hypoxia and a precocious lethality.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/472540v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1cb5836org.highwire.dtl.DTLVardef@10c7b97org.highwire.dtl.DTLVardef@86263aorg.highwire.dtl.DTLVardef@137da51_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LILRRFIP2 regulates negatively the HIF-1 activity
C_LIO_LILrrfip2 deletion leads to an embryonic lethality between E11.5 and E13.5
C_LIO_LILRRFIP2 controls ROS production and CM maturation
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title: Morphological variation and phylogeny of Karenia selliformis (Gymnodiniales, Dinophyceae) in an intensive cold-water algal bloom in eastern Hokkaido, Japan in September-November 2021

abstract:
Harmful algal blooms responsible for mass mortalities of marine organisms have so far been rare in Hokkaido, northern Japan, although fish killing blooms have been frequently reported from western Japanese coasts. In September-November 2021, a huge and prolonged cold-water bloom occurred along the Pacific coast of eastern Hokkaido, Japan, and was associated with intensive mortalities of sea urchin, fish, octopus, shellfish, etc. In this study, morphology and phylogeny of the dominant and co-occurred unarmored dinoflagellates of the Kareniaceae in the bloom were examined by using light microscopy, scanning electron microscopy and molecular phylogeny inferred from ITS and LSU rDNA (D1-D3) sequences. Morphological observation and molecular phylogeny showed that the dominant species was Karenia selliformis, with co-occurrences of other kareniacean dinoflagellates, Kr. longicanalis, Kr. mikimotoi, Karlodinium sp., Takayama cf. acrotrocha, Takayama tuberculata and Takayama sp. The typical cell forms of K. selliformis in the bloom were discoid, dorsoventrally flattened, and larger than the cell sizes in previous reports, 35.3-43.6 (39.4{+/-}2.1) m in length. Transparent cells of Kr. selliformis lacking or having several shrunken chloroplasts and oil droplets were also found. Cells of Kr. selliformis had morphological variation, but the species could be distinguished from other co-occurred Karenia species by its numerous (46-105) and small granular (2.9-4.6 m in diameter) chloroplasts and the nucleus positioned in the hypocone. Cell density of Kr. selliformis exceeding 100 cells/mL was recorded in the range of temperature 9.8-17.6{degrees}C. The rDNA sequences determined from Kr. selliformis in the blooms of Hokkaido, Japan in 2021 were identical to those from another bloom in Kamchatka, Russia in 2020.

HighlightsO_LIA marine fauna-destructive harmful algal bloom in the Pacific coast of eastern Hokkaido, Japan in September-November 2021 was dominated by Karenia selliformis.
C_LIO_LICells of Karenia selliformis typical in the bloom were discoid and possessing numerous small chloroplasts, approximately 70 in number.
C_LIO_LICells of Karenia selliformis showed morphological variation in size and shape, and transparent motile cells lacking or having degraded chloroplasts were also present.
C_LIO_LICo-occurred kareniaceans in the bloom were Karenia longicanalis, Karenia mikimotoi, Karlodinium sp. and Takayama spp.
C_LIO_LIrDNA sequences of Karenia selliformis in the blooms of Hokkaido in 2021 and Kamchatka in 2020 were identical, which belong to the group I of Kr. selliformis.
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title: A calibrated functional patch clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome

abstract:
PurposeModern sequencing technologies have revolutionised our detection of gene variants. In most genes, including KCNH2, the majority of missense variants are currently classified as variants of uncertain significance (VUS). The aim of this study is to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in the KCNH2 gene.

MethodsThe assay was designed according to recommendations of the ClinGen sequence variant interpretation framework. Thirty-one control variants of known clinical significance (17 pathogenic/likely pathogenic, 14 benign/likely benign) were heterozygously expressed in Flp-In HEK293 cells. Variants were analysed for effects on current density and channel gating. A panel of 44 VUS was then assessed for reclassification.

ResultsAll 17 pathogenic variant controls had reduced current density and 13/14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying moderate or supporting evidence strength for variant classification. Inclusion of KCNH2 functional assay evidence enabled us to reclassify 6 out of 44 VUS as likely pathogenic.

ConclusionThe high-throughput patch clamp assay can provide moderate strength evidence for clinical interpretation of clinical KCNH2 variants and demonstrates the value proposition for developing automated patch clamp assays for other ion channel genes.


title: The effect of constraining mediolateral ankle moments and foot placement on the use of the counter-rotation mechanism during walking

abstract: Stability during walking can be maintained by shifts of the Center of Pressure through modulation of foot placement and ankle moments (CoP-mechanism). An additional mechanism to stabilize gait, is the counter-rotation mechanism i.e. changing the angular momentum of segments around the Center of Mass (CoM) to change the direction of the ground reaction force. It is unknown if and how humans use the counter-rotation mechanism to control the CoM during walking and how this interacts with the CoP-mechanism. Thirteen healthy adults walked on a treadmill, while full-body kinematic and force plate data were obtained. The contributions of the CoP and the counter-rotation mechanisms to control the CoM were calculated during steady-state walking, walking on LesSchuh, i.e. constraining mediolateral CoP shifts underneath the stance foot and walking on LesSchuh at 50% of normal step width, constraining both foot placement and ankle mechanisms (LesSchuh50%). A decreased magnitude of within-stride control by the CoP-mechanism was compensated for by an increased magnitude of within-stride control by the counter-rotation mechanism during LesSchuh50% compared to steady-state walking. This suggests that the counter-rotation mechanism is used to stabilize gait when needed. However, the mean contribution of the counter-rotation mechanism over strides did not increase during LesSchuh50% compared to steady-state walking. The CoP-mechanism was the main contributor to the total CoM acceleration. The use of the counter-rotation mechanism may be limited because angular accelerations ultimately need to be reversed and because of interference with other task constraints, such as head stabilization and preventing interference with the gait pattern.

category: bioengineering