title: HSV Tegument Protein pUL51 Interacts with Host Dynactin for Viral Spread

abstract:
Dynein motors are microtubule associated protein complexes that mediate multiple essential cellular processes, such as long-distance cargo trafficking and stabilization of the microtubule organization center. Most of these functions and their regulations depend on the dynein motor subunit dynactin. By using an infection-inducible system, we disrupted dynein motor function after HSV entry by overexpressing a dominant-negative inhibitor of dynein, resulting in a 5-fold growth defect in Vero cells and 1000-fold growth defect in CAD neuronal cells. Also, we found that in infected CAD cells, the dynein complex was recruited to viral assembly sites regardless of microtubule polymerization. Based on these observations, we then identified a novel interaction between conserved HSV-1 tegument protein pUL51 and p150Glued. pUL51 is a palmitoylated Golgi membrane-associated protein that is required for efficient virus assembly and spread. Overexpression of pUL51 alone was sufficient to recruit p150Glued to Golgi membranes. Sequences that are important and sufficient for pUL51-p150Glued interaction were mapped to residues 90 to 124 in pUL51 and residues 548 to 911 in p150Glued. Deletion of a.a 90-124 in pUL51 resulted in a moderate viral growth defect, a profound spread defect, and failure to accumulate both dynactin and the viral spread factor glycoprotein E (gE) at cell-cell junctions. A synthetic peptide that contains pUL51 a.a 90-125 could also inhibit viral growth and spread in pUL51-dependent manner. Taken together, our results suggest that the proper function of pUL51 in efficient viral assembly and spread depends on its interaction with p150Glued.

Author SummaryDuring their life-long infections, herpesviruses can spread within the human body in spite of a powerful immune response that includes antibodies that inactivate the virus. The virus accomplishes this by targeting its newly made infectious particles to junctions where infected cells meet their uninfected neighbors. Junctional targeting of virus particles requires that the virus hijack normal cellular machinery used for moving large cargoes within the cell, a process that is only partially understood. In this study, we have discovered a critical interaction between a virus protein that is present in all herpesviruses and a host cell cargo-moving protein that is required for virus spread between cells and shown that this interaction is common to several medically important human herpesviruses. We have also identified a short piece of this virus protein that is responsible for the interaction and shown that this short piece can be used to interrupt the interaction and prevent spread of herpes simplex virus (HSV) in cultured cells. Our study provides prove-of-concept evidence that the spread pathway of HSV, and possibly other herpesviruses, can be targeted for therapeutic purposes.


title: Leveraging shared ancestral variation to detect local introgression

abstract: Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Pattersons D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.

category: evolutionary biology


title: Exon7 Targeted CRISPR-Prime Editing Approaches for SMN2 Gene Editing in Spinal Muscular Atrophy (SMA) Disease Can Increase In Vitro SMN Expression

abstract: Spinal Muscular Atrophy (SMA) is a fatal neuromuscular disease characterized by motor neuron loss and advanced muscle weakness, which occurs in functional SMN (Survival Motor Neuron) protein deficiency with SMN1 gene-induced deletions and mutations. The incidence of SMA, which is an autosomal recessive disease, is 1/10,000 in the world. The SMN protein acts as a molecular chaperone in the formation of the spliceosome complex, which catalyzes the splicing of pre-mRNA, enabling mRNAs and non-coding RNAs to mature. Since the current SMN1-encoding Adeno-associated virus (AAV) or SMN2 gene targeting antisense oligonucleotide-based strategies cannot provide long-term stable SMN expression in neuron cells, more effective methods need to be developed. CRISPR technology, which adds a new dimension to genetic engineering and gene therapies, makes it possible to treat many genetic diseases. In terms of SMA, some previous studies in the literature prove that it is possible to treat SMA with the CRISPR strategy. Homology Directed Repair (HDR)-based CRISPR technology, which results in a high rate of in-del (insertion-deletion) mutations rather than editing, was shown unsuitable for therapeutic applications. CRISPR-Prime editing (PE) technology is a new generation of gene editing approach that precisely provides various genomic modifications without the need for double-strand breakage or donor DNA sequences. CRISPR-Prime Editing method has also been used in rare diseases such as sickle cell anemia and Tay-Sachs, and their efficiency in editing various pathogenic mutations has been demonstrated. However, CRISPR Prime Editing-mediated gene editing for Spinal Muscular Atrophy (SMA) have not yet been investigated. The c.840 T-C transition and c.859 G-C transformations in the SMN2 gene and the correction of these point mutations with a single pegRNA at the same time were investigated for the first time in this study. Here, we showed that CRISPR-PE systems could increase SMN2 gene activity and SMN protein expression by ensuring exon 7 participation by editing c.840 T-C transition and c.859 G-C transformations. The fact that Prime Editing method showed the efficacy and stability of modifications in SMN2 genes that were investigated in SMN-low Jurkat cells as a proof-of-concept. This study enabled the next step with the CRISPR-Prime Editing approach to be tested ex vivo in primary cell lines from SMA patients and SMN-low neuronal cells.

category: genetics


title: Enabling automated and reproducible spatially resolved transcriptomics at scale

abstract: Tissue spatial information is an essential component to reach a holistic overview of gene expression mechanisms. The sequencing-based Spatial transcriptomics approach allows to spatially barcode the whole transcriptome of tissue sections using microarray glass slides. However, manual preparation of high-quality tissue sequencing libraries is time-consuming and subjected to technical variability. Here, we present an automated adaptation of the 10x Genomics Visium library construction on the widely used Agilent Bravo Liquid Handling Platform. Compared to the manual Visium library preparation, our automated approach reduces hands-on time by over 80% and provides higher throughput and robustness. Our automated Visium library preparation protocol provides a new strategy to standardize spatially resolved transcriptomics analysis of tissues at scale.


title: Identification of a Novel SARS-CoV-2 Delta-Omicron Recombinant Virus in the United States

abstract: Recombination between SARS-CoV-2 virus variants can result in different viral properties (e.g., infectiousness or pathogenicity). In this report, we describe viruses with recombinant genomes containing signature mutations from Delta and Omicron variants. These genomes are the first evidence for a Delta-Omicron hybrid Spike protein in the United States.

category: genomics


title: Deep topographic proteomics of a human brain tumour

abstract: Cellular protein expression profiles within tissues are key to understanding disease pathology, and their spatial organisation determines cellular function. To precisely define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping the expression of many hundreds to thousands of proteins within tissue structures. Here, we present a workflow for spatially resolved, quantitative proteomics of tissue that generates maps of protein expression across a tissue slice derived from a human atypical teratoid-rhabdoid tumour (AT/RT). We employ spatially-aware statistical methods that do not require prior knowledge of tissue structure to highlight proteins and pathways with varying spatial abundance patterns. We identify novel aspects of AT/RT biology that map onto the brain-tumour interface. Overall, this work informs on methods for spatially resolved deep proteo-phenotyping of tissue heterogeneity. Advanced spatially resolved tissue proteomics will push the boundaries of understanding tissue biology and pathology at the molecular level.

category: cancer biology


title: Humoral and cellular immune memory to four COVID-19 vaccines

abstract: Multiple COVID-19 vaccines, representing diverse vaccine platforms, successfully protect against symptomatic COVID-19 cases and deaths. Head-to-head comparisons of T cell, B cell, and antibody responses to diverse vaccines in humans are likely to be informative for understanding protective immunity against COVID-19, with particular interest in immune memory. Here, SARS-CoV-2-spike--specific immune responses to Moderna mRNA-1273, Pfizer/BioNTech BNT162b2, Janssen Ad26.COV2.S and Novavax NVX-CoV2373 were examined longitudinally for 6 months. 100% of individuals made memory CD4+ T cells, with cTfh and CD4-CTL highly represented after mRNA or NVX-CoV2373 vaccination. mRNA vaccines and Ad26.COV2.S induced comparable CD8+ T cell frequencies, though memory CD8+ T cells were only detectable in 60-67% of subjects at 6 months. Ad26.COV2.S was not the strongest immunogen by any measurement, though the Ad26.COV2.S T cell, B cell, and antibody responses were relatively stable over 6 months. A differentiating feature of Ad26.COV2.S immunization was a high frequency of CXCR3+ memory B cells. mRNA vaccinees had substantial declines in neutralizing antibodies, while memory T cells and B cells were comparatively stable over 6 months. These results of these detailed immunological evaluations may also be relevant for vaccine design insights against other pathogens.

category: immunology


title: Disruption of the MICOS complex leads to an aberrant cristae structure and an unexpected, pronounced lifespan extension in Podospora anserina

abstract: Mitochondria are dynamic eukaryotic organelles involved in a variety of essential cellular processes including the generation of adenosine triphosphate (ATP) and reactive oxygen species (ROS) as well as in the control of apoptosis and autophagy. Impairments of mitochondrial functions lead to aging and disease. Previous works with the ascomycete Podospora anserina demonstrated that mitochondrial morphotype as well as mitochondrial ultrastructure change during aging. The latter goes along with an age-dependent reorganization of the inner mitochondrial membrane leading to a change from lamellar cristae to vesicular structures. Especially from studies with yeast it is known that beside the F1Fo-ATP-synthase and the phospholipid cardiolipin also the  mitochondrial contact site and cristae organizing system (MICOS) complex, existing of the Mic60- and Mic10-subcomplex, is essential for proper cristae formation. In the present study, we aimed to understand the mechanistic basis of age-related changes of the mitochondrial ultrastructure. We observed that MICOS subunits are co-regulated at the posttranscriptional level. This regulation partially depends on the mitochondrial iAAA-protease PaIAP. Most surprisingly, we made the counterintuitive observation that, despite the loss of lamellar cristae and of mitochondrial impairments, the ablation of MICOS subunits (except of PaMIC12) leads to a pronounced lifespan extension. Moreover, simultaneous ablation of subunits of both MICOS subcomplexes synergistically increases lifespan, providing formal genetic evidence that both subcomplexes affect lifespan by different and at least partially independent pathways. At the molecular level we found that ablation of Mic10-subcomplex components leads to a mitohormesis-induced lifespan extension, while lifespan extension of Mic60-subcomplex mutants seems to be controlled by another pathway. Overall, our data demonstrate that both MICOS subcomplexes have different functions and play distinct roles in the aging process of P. anserina.

category: molecular biology


title: Paradoxical activation of SREBP1c and de novo lipogenesis by hepatocyte-selective ACLY depletion in obese mice.

abstract: Hepatic steatosis associated with high fat diets, obesity and type 2 diabetes is thought to be the major driver of severe liver inflammation, fibrosis, and cirrhosis. Cytosolic acetyl-coenzyme A (AcCoA), a central metabolite and substrate for de novo lipogenesis (DNL), is produced from citrate by ATP-citrate lyase (ACLY) and from acetate through AcCoA synthase short chain family member 2 (ACSS2). However, the relative contributions of these two enzymes to hepatic AcCoA pools and DNL rates in response to high fat feeding is unknown. We report here that hepatocyte-selective depletion of either ACSS2 or ACLY caused similar 50% decreases in liver AcCoA levels in obese mice, showing that both pathways contribute to generation of this DNL substrate. Unexpectedly however, the hepatocyte ACLY depletion in obese mice paradoxically increased total DNL flux measured by D2O incorporation into palmitate, while in contrast ACSS2 depletion had no effect. The increase in liver DNL upon ACLY depletion was associated with increased expression of nuclear sterol regulatory element-binding protein 1c (SREBP1c) and of its target DNL enzymes. This upregulated DNL enzyme expression explains the increased rate of palmitate synthesis in ACLY depleted livers. Furthermore, this increased flux through DNL may also contribute to the observed depletion of AcCoA levels due to its increased conversion to Malonyl CoA (MalCoA) and palmitate. Together, these data indicate that in HFD fed obese mice, hepatic DNL is not limited by its immediate substrates AcCoA or MalCoA, but rather by activities of DNL enzymes.


title: Triple Notch/Tgfβ/FoxO1 blockade converts multiple intestinal sub-lineages into β-like cells and lowers glycemia in diabetic animals

abstract: Insulin is the essential treatment of Type 1 (T1D) and is often used in Type 2 Diabetes. For nearly five decades, efforts have been focused on replenishing {beta}-cells in T1D patients as a more durable treatment. Gut endocrine cells can be converted into insulin-producing cells, but their numbers are limited. In this study we report that insulin-immunoreactive cells with Paneth/goblet cell features are present in human fetal intestine, in addition to enteroendocrine cells. Accordingly, lineage tracing experiments show that, besides enterochromaffin cells, the Paneth/goblet lineage can undergo conversion to the insulin lineage upon genetic or pharmacologic Foxo1 ablation in mice. We leveraged these data to design a screening platform in organoids to accurately quantitate {beta}-like cell reprogramming and fine-tune a combination treatment to increase the efficiency of the conversion process by expanding the intestinal secretory lineage. We identified a triple blockade of FoxO1, Notch, and Tgf{beta} that, when tested in insulin-deficient diabetic animals resulted in a near-normalization of glucose levels, associated with the appearance of gut insulin-producing cells. The findings illustrate a therapeutic approach to replace insulin treatment in diabetes.

category: cell biology


title: Genomic insights into metabolic flux in ruby-throated hummingbirds

abstract: Hummingbirds are very well adapted to sustain efficient and rapid metabolic shifts. They oxidize ingested nectar to directly fuel flight when foraging but have to switch to oxidizing stored lipids derived from ingested sugars during the night or long-distance migratory flights. Understanding how this organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation. To explore these questions, we generated a chromosome level de novo genome assembly of the ruby-throated hummingbird (A. colubris) using a combination of long and short read sequencing and scaffolding using other existing assemblies. We then used hybrid long and short-read RNA-sequencing for a comprehensive transcriptome assembly and annotation. Our genomic and transcriptomic data found positive selection of key metabolic genes in nectivorous avian species and a deletion of critical genes (GLUT4, GCK) involved in glucostasis in other vertebrates. We found expression of fructose-specific GLUT5 putatively in place of insulin-sensitive GLUT4, with predicted protein models suggesting affinity for both fructose and glucose. Alternative isoforms may even act to sequester fructose to preclude limitations from transport in metabolism. Finally, we identified differentially expressed genes from fasted and fed hummingbirds suggesting key pathways for the rapid metabolic switch hummingbirds undergo.


title: Irc3 of the thermotolerant yeast Ogataea polymorpha is a branched-DNA-specific mitochondrial helicase

abstract: The Saccharomyces cerevisiae Irc3 protein is a mitochondrial Superfamily II DNA helicase that, according to genomic data, is conserved in different yeast species. Here we characterize Irc3 helicase from the thermotolerant yeast Ogataea polymorpha (Irc3op) that throughout its helicase motor domain has approximately 82% similarity with the S. cerevisiae protein. Irc3op retains enzymatic activity at considerably higher temperatures than Irc3sc, displaying the fastest rate of ATP hydrolysis at 41 {degrees}C and a Tm of 45.3 {degrees}C for its secondary structure melting. We demonstrate that Irc3op is a structure-specific DNA helicase translocating on both single- and double-stranded DNA molecules. Like the homolog of S. cerevisiae, Irc3op can unwind only DNA molecules that contain branched structures. Different DNA molecules containing three- and four-way branches are utilized by Irc3op as unwinding substrates. Importantly, the preferred unwinding substrate of Irc3op is a DNA fork containing the nascent lagging strand, suggesting a possible role in replication restart following a block in leading strand polymerization. A lower unwinding efficiency of four-way branched DNA molecules could explain why Irc3op only partially complements the irc3{Delta} phenotype in S. cerevisiae.

category: biochemistry


title: Compact engineered human transactivation modules enable potent and versatile synthetic transcriptional control

abstract: Engineered transactivation domains (TADs) combined with programmable DNA binding platforms have revolutionized synthetic transcriptional control. Despite recent progress in programmable CRISPR/Cas-based transactivation (CRISPRa) technologies, the TADs used in these systems often contain components from viral pathogens and/or are prohibitively large for many applications. Here we defined and optimized minimal TADs built from human mechanosensitive transcription factors (MTFs). We used these components to construct potent and compact multipartite transactivation modules (MSN, NMS, and eN3x9) and to build the CRISPR-dCas9 recruited enhanced activation module (CRISPR-DREAM) platform. We found that CRISPR-DREAM was specific, robust across mammalian cell types, and efficiently stimulated transcription from diverse regulatory loci within the human genome. We also showed that MSN and NMS were portable across Type I, II, and V CRISPR systems, TALEs, and ZF proteins, and further that these TADs permitted superior multiplexed transactivation. Finally, as a proof of concept, we used dCas9-NMS to efficiently reprogram human fibroblasts into iPSCs. Altogether, the compact human TADs, design rules, and fusion proteins we have developed here could be valuable for applications where sophisticated synthetic transactivation is needed.

category: bioengineering


title: Solvent-induced allosteric transition of the Hepatitis C virus human cellular receptor CD81 large extracellular loop

abstract:
CD81 is a tetraspanin receptor that clusters into microdomains to mediate cell signalling processes. CD81 is also one of the four primary cellular receptors of the Hepatitis C virus (HCV). Previous structural studies on the -helical CD81 large-extracellular-loop domain (CD81LEL) have shown that it can adopt different conformations (from closed to open), likely depending on the environmental conditions. This conformational plasticity has been implicated in the endosomal fusion of HCV upon entry. However, the precise mechanism governing the CD81LEL plasticity has remained elusive so far.

Here, by combining molecular dynamics simulations and circular dichroism experiments on wt-CD81LEL and two mutants at different endosomal pH conditions, pH 5.5 and pH 4.6, we show that the modulation of the solvation shell governs the plasticity of CD81LEL. The primarily implicated residues are D139 and E188, respectively, located near a loop preceded by a helix. At acidic conditions, their interaction with water is reduced, causing a re-ordering of the water molecules, and thus triggering the dynamics of CD81LEL. However, mutations E188Q and D139N retain the solvation shell and restrict the conformational space that the head subdomain can explore.

We propose that residues E188 and D139 control the solvent-induced allosteric transition of the CD81LEL domain. This mechanism might play a role in other cellular receptors that function along the endosomal pathway.

Popular SummaryUnderstanding the cellular mechanisms that are exploited by viruses to infect their host is key for the development of therapeutics. Here, in the context of Hepatitis C Virus infection we report the mechanism that governs the plasticity of the extra-cellular domain of tetraspanin CD81, one of the major cellular receptors of this virus. The mechanism proposed here is a novel form of solvent-induced allosteric transition in proteins mediated by two antenna residues located in the head subdomain of CD81. We propose that it could serve as a pH sensing strategy to time the endosomal pathway and trigger a signal at the right time for HCV fusion.

category: biophysics


title: The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity

abstract: The cell autonomous balance of immune-inhibitory and -stimulatory signals is a critical yet poorly understood process in cancer immune evasion. Using patient-derived co-culture models and humanized mouse models, we show that an intact CD58:CD2 interaction is necessary for anti-tumor immunity. Defects in this axis lead to multi-faceted immune evasion through impaired CD2-dependent T cell polyfunctionality, T cell exclusion, impaired intra-tumoral proliferation, and concurrent protein stabilization of PD-L1. We performed genome-scale CRISPR-Cas9 and CD58 coimmunoprecipitation mass spectrometry screens identifying CMTM6 as a key stabilizer of CD58, and show that CMTM6 is required for concurrent upregulation of PD-L1 in CD58 loss. Single-cell RNA-seq analysis of patient melanoma samples demonstrates that most TILs lack expression of primary costimulatory signals required for response to PD-1 blockade (e.g. CD28), but maintain strong CD2 expression, thus providing an opportunity to mobilize a so far therapeutically untapped pool of TILs for anti-tumor immunity. We identify two potential therapeutic avenues, including rescued activation of human CD2-expressing TILs using recombinant CD58 protein, and targeted disruption of PD-L1/CMTM6 interactions. Our work identifies an underappreciated yet critical axis at the nexus of cancer immunity and evasion, uncovers a fundamental mechanism of co-inhibitory and -stimulatory signal balancing, and provides new approaches to improving cancer immunotherapies.


title: Multi-modal Imaging of Disease Progression in TH-MYCN Mouse Models of Neuroblastoma

abstract: MYCN is a major driver for neuroblastoma (NB) and the tyrosine hydroxylase (TH)-MYCN transgenic mouse model is extensively used for preclinical NB studies. However, spatio-temporal NB progression in the TH-MYCN model has not been studied, and questions remain about the value of implanted models as a surrogate for transgenic mice. In this work, we used magnetic resonance imaging (MRI) to study tumor progression and nanoparticle contrast-enhanced computed tomography (n-CECT) to assess tumor vascular architecture in TH-MYCN transgenic mice (2-7 weeks of age) and TH-MYCN+/+-derived orthotopic allograft and syngeneic mice (2-5 weeks post-tumor implantation). Tumors in TH-MYCN transgenic mice became evident in the abdominal paraspinal region at week 5. A delayed thoracic paraspinal mass became evident at week 6 and most mice succumbed by week 7. In allograft and syngeneic mice, single mass tumor growth was restricted to the peritoneal cavity. N-CECT revealed a predominantly microvascular network in TH-MYCN tumors while implanted tumors exhibited heterogeneous and tortuous vessels. N-CECT quantitative analysis demonstrated high vascularity (tumor fractional blood volume ~ 0.12) in all models. Multi-modal imaging of TH-MYCN transgenic and implanted models revealed differences in growth patterns and vascular architecture that should be considered in designing preclinical studies.


title: Splenic clearance of rigid erythrocytes as an inherited mechanism for splenomegaly and natural resistance to malaria

abstract:
In malaria-endemic areas, subjects from specific groups like Fulani have a peculiar protection against malaria, with high levels of IgM but also frequent anemia and splenomegaly. The mechanisms underlying this phenotype remain elusive. In Benin, West Africa, we measured the deformability of circulating erythrocytes in genetically distinct groups (including Fulani) living in sympatry, using ektacytometry and microsphiltration, a mimic of how the spleen clears rigid erythrocytes. Compared to non-Fulani, Fulani displayed a higher deformability of circulating erythrocytes, pointing to an enhanced clearance of rigid erythrocytes by the spleen. This phenotype was observed in individuals displaying markers of Plasmodium falciparum infection. The heritability of this new trait was high, with a strong multigenic component. Five of the top 10 genes selected by a population structure-adjusted GWAS, expressed in the spleen, are potentially involved in splenic clearance of erythrocytes (CHERP, MB, PALLD, SPARC, PDE10A), through control of vascular tone, collagen synthesis and macrophage activity. In specific ethnic groups, genetically-controlled processes likely enhance the innate retention of infected and uninfected erythrocytes in the spleen, explaining splenomegaly, anemia, cryptic intrasplenic parasite loads, hyper-IgM, and partial protection against malaria. Beyond malaria-related phenotypes, inherited splenic hyper-filtration of erythrocytes may impact the pathogenesis of other hematologic diseases.

Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThe genetic background of individuals influences their susceptibility to infectious diseases. Specific human groups, like the Fulani in Africa, react to malaria parasites (named Plasmodium) in a specific way. Upon infection, Fulani develop a grossly enlarged spleen, and high levels of anti-Plasmodium antibodies in their blood. They also carry smaller numbers of parasites in their blood, and thus are considered partially protected against malaria. The mechanisms underlying this natural protection, different from other natural protective mechanisms such as the sickle cell trait, are not well understood.

Malaria impairs the deformability of red blood cells and the spleen is a key organ to controlling red blood cell quality. We have recently demonstrated that red blood cells containing live malaria parasites accumulate intensely in the spleen of subjects with long term exposure to these parasites. Enhanced retention of infected and uninfected red blood cells in the spleen would explain why the spleen is larger and why lower numbers of parasites are left in circulation. We thus explored whether the retention of infected and uninfected red blood cells could explain why Fulani are partially protected against malaria. Because it is unethical to perform spleen puncture or biopsies for research purposes, our explorations were indirect by carefully analyzing the properties of circulating red blood cells in a large number of subjects and by assessing whether observations could be explained by their genetic make-up.

Added value of this studyIn more than 500 subjects, we confirmed the high frequency of large spleens in Fulani and, through 2 different methods, we demonstrated an enhanced deformability of their circulating red blood cells, that likely stems from the more efficient removal of the less deformable ones. This enhanced deformability was found to be inheritable based on carefully collected family links and refined analysis of genetic markers.

Implications of all the available evidenceOur findings indicate that genes potentially driving the filtration of red blood cells by the spleen likely influence how subjects in specific groups in Africa and elsewhere react to malaria. While most previous hypotheses pointed to conventional immunological mechanisms as the trigger, we propose that a simple physiological mechanism that controls the quality of red blood cells may drive natural protection from malaria even before the intervention of immunological cells. A better understanding of these processes is of great importance in the context of malaria elimination efforts.

These findings may also have an impact on the understanding of other red blood cell-related disorders, such as inherited red cell diseases, in which splenic filtration of abnormal red blood cells may precipitate splenic complications.

category: physiology


title: Polypyrimidine Tract-Binding Protein 1 (PTBP1) regulates CD4 T cell Activation independent of its role in proliferation

abstract: Our previous work found that the RNA binding protein polypyrimidine tract-binding protein (PTBP1) is critical for regulating multiple events in T cell activation including changes in proliferation, and expression of activation markers and cytokines. These changes corresponded to the regulation of the ERK1/2 and NF-{kappa}B pathways as well as through changes in steady-state RNA levels. Because proliferation is critical for driving T cell activation, it was unclear whether PTBP1 was required for optimal activation per se or whether changes were secondary to a requirement for initiating/sustaining proliferation. To address this question, the human T cell lymphoma cell line, Jurkat, which recapitulates many of the molecular events of TCR-induced activation, was used to understand how PTBP1 impacts early events in T cell activation with ongoing proliferation. Using two phenotypically distinct Jurkat subclones (D1.1 and B2.7), we first profiled global RNA expression patterns using RNAseq analysis and found marked differences between the two cell lines with the D1.1 line giving a more antigen-experienced phenotype. Reducing PTBP1 by shPTB expression, to 60% WT levels resulted in no significant decrease in proliferation in the two subclones. However, we observed that PTBP1 was required for both optimal expression of activation markers, CD25, CD38, CD69, and CD40L, and signaling through the ERK1/2, P38 and AKT pathways. Importantly, limiting PTBP1 had different effects on the activation signals for each cell line suggesting that the differentiation state of the cell is a critical factor in understanding the role of PTBP1 in T cell activation. This was further reinforced by our finding that PTBP1 regulated distinct groups of genes specific for each line. Together, our findings suggest that PTBP1 regulates specific T cell activation responses independent of its role in proliferation and that the initial phenotype of the T cell plays an essential role in the dependency of the cell on PTBP1 for driving these changes.


title: A neutrophil-B-cell axis governs disease tolerance during sepsis via Cxcr4

abstract:
Sepsis is a life-threatening condition characterized by uncontrolled systemic inflammation and coagulation, leading to multi-organ failure. Therapeutic options to prevent sepsis-associated immunopathology remain scarce.

Here, we established a model of long-lasting disease tolerance during severe sepsis, manifested by diminished immunothrombosis and organ damage in spite of a high pathogen burden. We found that, both neutrophils and B cells emerged as key regulators of tissue integrity. Enduring changes in the transcriptional profile of neutrophils, included upregulated Cxcr4 expression in protected, tolerant hosts. Neutrophil Cxcr4 upregulation required the presence of B cells, suggesting that B cells promoted tissue tolerance by suppressing tissue damaging properties of neutrophils. Finally, therapeutic administration of a Cxcr4 agonist successfully promoted tissue tolerance and prevented liver damage during sepsis. Our findings highlight the importance of a critical B-cell/neutrophil interaction during sepsis and establish neutrophil Cxcr4 activation as a potential means to promote disease tolerance during sepsis.

SummaryWe show that a B cell/neutrophil interaction in the bone marrow facilitates tissue tolerance during severe sepsis. By affecting neutrophil Cxcr4 expression, B cells can impact neutrophil effector functions. Finally, therapeutic activation of Cxcr4 successfully promoted tissue tolerance and prevented liver damage during sepsis.


title: Synergistic Regulation of Notch Signaling by Different O-Glycans Promotes Hematopoiesis

abstract:
Glycosylation of Notch receptors by O-fucose glycans regulates Notch ligand binding and Notch signaling during hematopoiesis. However, roles in hematopoiesis for other O-glycans that modify Notch receptors have not been determined. Here we show that the EGF domain specific GlcNAc transferase EOGT is required in mice for the optimal production of lymphoid and myeloid cells. The phenotype of Eogt null mice was largely cell-autonomous, and Notch target gene expression was reduced in T cell progenitors. Moreover, EOGT supported residual Notch signaling following conditional deletion of Pofut1 in hematopoietic stem cells (HSC). Eogt:Pofut1 double mutant HSC had more severe defects in bone marrow, and in T and B cell development in thymus and spleen, compared to deletion of Pofut1 alone. The combined results show that EOGT and O-GlcNAc glycans are required for optimal hematopoiesis and T and B cell development, and that they act synergistically with POFUT1 and O-fucose glycans to promote Notch signaling in lymphoid and myeloid differentiation.

One Sentence SummaryO-GlcNAc glycans and EOGT promote lymphopoiesis and myelopoiesis and support Notch signaling in the absence of POFUT1 and O-fucose glycans.


title: Downregulation of Stem-loop binding protein by nicotine via α7-nicotinic acetylcholine receptor and its role in nicotine-induced cell transformation

abstract: The use of electronic-cigarettes (e-cigs) has increased substantially in recent years, particularly among the younger generations. Liquid nicotine is the main component of e-cigs. Previous studies have shown that mice exposed to e-cig aerosols developed lung adenocarcinoma and bladder hyperplasia. These findings implicated a potential role for e-cig aerosols and nicotine in cancer development, although the underlying mechanisms are not fully understood. Here we report that exposure to liquid nicotine or nicotine aerosol generated from e-cig induces downregulation of Stem-loop binding protein (SLBP) and polyadenylation of canonical histone mRNAs in human bronchial epithelial cells and in mice lungs. Canonical histone mRNAs typically do not end in a poly(A) tail and the acquisition of such a tail via depletion of SLBP has been shown to causes chromosome instability. We show that nicotine-induced SLBP depletion is reversed by an inhibitor of 7-nAChR (nicotinic acetylcholine receptors) or siRNA specific for 7-nAChR, indicating a nAChR-dependent reduction of SLBP by nicotine. Moreover, not only CDK1 and CK2, two kinases well known for their function for SLBP phosphorylation and degradation, but also CDK2 and PI3K/AKT pathways are shown to be involved, 7-nAChR-dependently, in nicotine-induced SLBP depletion. Importantly, nicotine-induced anchorage-independent cell growth is attenuated by inhibition of 7-nAChR and is rescued by overexpression of SLBP. We propose that the SLBP depletion and polyadenylation of canonical histone mRNAs via activation of 7-nAChR and a series of downstream signal transduction pathways, are critical for nicotine-induced cell transformation and potential carcinogenesis.


title: Illumina-based Whole De Novo Transcriptome Profiling and Diosgenin Biosynthetic pathway of Tribulus terrestris: A Medicinal herb

abstract: Tribulus terrestris L. (Chota gokhuru), an annual herb of the Zygophyllaceae family accumulates steroidal-type triterpenoids of diosgenin in root, leaf, fruit, which have been used as a traditional medicine to cure steroidal hormonal diseases such as estrogen, progesterone, and cardiovascular and urogenital. However, to date, the diosgenin biosynthetic pathway of T. terrestris is unknown. In this research paper, identification of candidate genes involved in bioactive compounds (diosgenin) was conducted via whole transcriptome profiling of T. terrestris using the Illumina HiSeq sequencing platform, which generated 482 million reads. RNA-Seq reads were assembled and clustered into 148871 unigenes. NCBI non-redundant (NR) and Swiss-Prot databases search anchored 50% unigenes with the functional annotations based on similarities of sequence. Further, in Gene Ontology and KEGG-KAAS pathways, a total of 126 unigenes were highly expressed in the terpenoids backbone biosynthesis, in which diosgenin pathways (two genes of glycolytic, three genes of mevalonate, two genes of MEP/DOX, one gene of mono-terpenoids, and seven genes of steroidal pathways) were identified. In addition, 9 genes were randomly selected for confirmation through real-time PCR. T. terrestris showed the highest homology with the Citrus sinensis and Juglans regia. 27478 unigenes of transcription factors were assembled, in which top ten transcription factors were highly expressed. A total of 17623 SSR was assembled, amongst them unigenes of di-nucleotide were highly repeated. This research work will improve our understanding of the diosgenin pathway and lay the groundwork for future molecular research on metabolic engineering, as well as raise diosgenin content in T. terrestris.


title: The S. cerevisiae m6A-reader Pho92 impacts meiotic recombination by controlling key methylated transcripts

abstract: N6-methyladenosine (m6A), the most abundant internal modification of eukaryotic mRNAs, participates in the post-transcriptional control of gene expression. In Saccharomyces cerevisiae, m6A is only found during meiosis. Although the deletion of the m6A- methyltransferase Ime4 impairs this process, the molecular impact of m6A on gene expression remains ill defined. Here we investigated the function of the budding yeast m6A reader Pho92. We found that Pho92 is specifically expressed during meiosis and impacts meiotic progression. We used high-throughput RNA sequencing and mapping of Pho92-binding sites following UV-crosslinking to show that Pho92 is recruited to specific mRNAs in an m6A-dependent manner during the meiotic prophase, preceding their down-regulation. Strikingly, point mutations altering m6A sites in mRNAs targeted by Pho92 are sufficient to delay their down-regulation and, in one case, to impact meiotic progression. Altogether, our results indicate that Pho92 facilitate the meiotic progression by accelerating the down-regulation of timely-regulated mRNAs during meiotic recombination.


title: Prot2Prot: A Deep Learning Model for Rapid, Photorealistic Macromolecular Visualization

abstract:
MotivationMolecular visualization is a cornerstone of structural biology, providing insights into the form and function of biomolecules that are difficult to achieve any other way. Scientific analysis, publication, education, and outreach often benefit from photorealistic molecular depictions rendered using advanced computer-graphics programs such as Maya, 3ds Max, and Blender. However, setting up molecular scenes in these programs can be laborious even for expert users, and rendering often requires substantial time and computer resources.

ResultsWe have created a deep-learning model called Prot2Prot that quickly imitates photorealistic visualization styles, given a much simpler, easy-to-generate molecular representation. The resulting images are often indistinguishable from images rendered using industry-standard 3D graphics programs, but they can be created in a fraction of the time, even when running in a web browser. To the best of our knowledge, Prot2Prot is the first example of image-to-image translation applied to macromolecular visualization.

AvailabilityProt2Prot is available free of charge, released under the terms of the Apache License, Version 2.0. Users can access a Prot2Prot-powered web app without registration at http://durrantlab.com/prot2prot.


title: Metagenomics Study of Bacterial Communities from Yamuna River water of city of Taj, Agra

abstract: Yamuna river water of Agra city is heavily contaminated with toxic pollutants including heavy metal that causes severe damage to ecological and social aspects. At present, the direct use of river water for the purpose of drinking causes severe hazards due to anthropogenic activities causing environmental pollution in rivers. In present study, Yamuna River water was collected from three different sites of Agra city. Various physico-chemical parameters were estimated by following the standard methods of APHA and the concentration of heavy metals were measured using Atomic Absorption Spectrophotometer (AAS). In case of physico-chemical parameters characterization, the obtained values were extremely above the permissible limits. On account of the research work; the Yamuna river water samples contains heavy metal concentrations (Cadmium, Chromium, Copper, Lead and Nickel) above the desirable and admissible levels except for Zinc. During analysis of non-culturable bacteria a substantial bacterial diversity was observed in the Yamuna river water samples collected from different sites. The water samples were subjected to metagenomic analysis using Illumina platform which revealed that Proteobacteria (phylum), Betaproteobacteria (class), Burkholderiales (order), Comamonadaceae (family), Hydrogenophaga (genus) and Chloroflexi bacterium OLB 14 (species) were found as the most dominant bacterial taxonomic abundance in the river water samples. The presence of such bacterial communities in water indicates the availability of pollutants and suggests the futuristic use in the field of bioremediation.


title: Systematic analysis of YFP gene traps reveals common discordance between mRNA and protein across the nervous system

abstract:
While post-transcriptional control is thought to be required at the periphery of neurons and glia, its extent is unclear. Here, we investigate systematically the spatial distribution and expression of mRNA at single molecule sensitivity and their corresponding proteins of 200 YFP trap protein trap lines across the intact Drosophila nervous system. 98% of the genes studied showed discordance between the distribution of mRNA and the proteins they encode in at least one region of the nervous system. These data suggest that post-transcriptional regulation is very common, helping to explain the complexity of the nervous system. We also discovered that 68.5% of these genes have transcripts present at the periphery of neurons, with 9.5% at the glial periphery. Peripheral transcripts include many potential new regulators of neurons, glia and their interactions. Our approach is applicable to most genes and tissues and includes powerful novel data annotation and visualisation tools for post-transcriptional regulation.

Brief outlineA novel high resolution and sensitive approach to systematically co-visualise the distribution of mRNAs and proteins in the intact nervous system reveals that post-transcriptional regulation of gene expression is very common. The rich data landscape is provided as a browsable resource (link), using Zegami, a cloud-based data exploration platform (link). Our solution provides a paradigm for the characterisation of post-transcriptional regulation of most genes and model systems.

HighlightsO_LI196/200 (98%) Drosophila genes show discordant RNA and protein expression in at least one nervous system region
C_LIO_LI137/200 (68.5%) mRNAs are present in at least one synaptic compartment
C_LIO_LINovel localised mRNA and protein discovered in periphery of glial processes
C_LIO_LINew paradigm for analysis of post-transcriptional regulation and data exploration
C_LI


title: Cfdp1 is Essential for Cardiac Development and Function

abstract: Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide and account for the most common noncommunicable disease. CVDs describe a wide spectrum of disorders affecting the proper function, physiology and morphogenesis of the heart and blood vessels. The risk of developing cardiovascular diseases is modulated by a combination of environmental and genetic effectors. Thus, its highly important to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in coronary artery disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family and up to date, its function and mechanism of action in Cardiovascular Development is still unclear. In this study, we utilize zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology and the ease of experimentally manipulation. We showed that cfdp1 is expressed during development and at 120 hours post fertilization its expression is restricted to the region of the heart and the head. We then generated a cfdp1-null zebrafish line using CRISPR-Cas9 system which led to a lethal phenotype since knockout embryos do not reach adulthood. cfdp1-/- embryos develop arrhythmic hearts and defective cardiac performance exhibiting statistically significant differences in heart features including End Diastolic Volume, Cardiac Output, Ejection Fraction and Stroke Volume. Myocardial trabeculation is also impaired in cfdp1-/- embryonic hearts, implying its regulatory role also in this developmental process. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process.

category: developmental biology


title: Molecular drivers of insecticide resistance in the Sahelo-Sudanian populations of a major malaria vector

abstract: Information on common markers of metabolic resistance in malaria vectors from countries/regions sharing similar eco-climatic characteristics can facilitate coordination of malaria control. Here, we characterized populations of the major malaria vector Anopheles coluzzii from Sahelian transect/region, spanning four sub-Saharan African countries: Nigeria, Niger, Chad and Cameroon. Genome-wide transcriptional analysis identified major genes previously implicated in pyrethroid and/or cross resistance to other insecticides, overexpressed across the Sahel, including CYP450s, glutathione S-transferases, carboxylesterases, and cuticular proteins. Several, well-known variants/markers of insecticide resistance were found in high frequencies - including in the voltage-gated sodium channel (V402L, I940T, L995F, I1527T and N1570Y), the acetylcholinesterase-1 gene (G280S) and the CYP4J5-L43F, which is fixed. High frequencies of the phenotypically important chromosomal inversions, 2La, 2Rb and 2Rc were observed ([~]80% for 2La and 2Rb). The 2La alternative arrangement is fixed across the Sahel. Low frequencies of these inversions (<10%) were observed in the fully insecticide susceptible laboratory colony of An. coluzzii (Ngoussou). Several of the most commonly overexpressed metabolic resistance genes sit in these three inversions. Two commonly overexpressed genes, GSTe2 and CYP6Z2 were functionally validated. Transgenic Drosophila melanogaster expressing GSTe2 exhibited extremely high DDT and permethrin resistance (mortalities < 10% in 24h). Serial deletion of the 5 intergenic region, to identify putative nucleotide(s) associated with GSTe2 overexpression, revealed that simultaneous insertion of adenine nucleotide and a transition (T->C), between Fork-head box L1 and c-EST putative binding sites are responsible for the high overexpression of GSTe2 in the resistant mosquitoes, across the Sahel. Transgenic flies expressing CYP6Z2 exhibited marginal resistance towards 3-phenoxybenzylalcohol (a primary product of pyrethroid hydrolysis by carboxylesterases) and a type II pyrethroid, -cypermethrin. However, significantly higher mortalities were obtained in CYP6Z2 transgenic flies compared with controls, on exposure to the neonicotinoid, clothianidin. This suggests a possible bioactivation of clothianidin into a toxic intermediate, which if true make it an ideal insecticide against populations of An. coluzzii overexpressing this P450. These findings will facilitate regional collaborations within the Sahel region, and refine implementation strategies through re-focusing interventions, improving evidence-based, cross-border policy towards local and regional malaria pre-elimination.


title: Confrontation of AlphaFold2 models with cryo-EM and crystal structures enlightens alternate geometries of the CYP102A1 multidomain protein

abstract: Large range structural dynamics plays a critical role for the function of electron transfer proteins. This information is generally not available from crystallographic structures, while cryo-electron microscopy (cryo-EM) can provide some elements but frequently with a degraded spatial resolution. Recently, AlphaFold-based structural modelling was extended to the prediction of protein complexes. In this work, bacterial CYP102A1 from Priestia megaterium was used as a test case to evaluate the capability of AlphaFold2 to predict alternative structures critical for catalysis. CYP102A1 monooxygenase, a NADPH-supported fatty acid hydroxylase, works as a soluble homodimer, each monomer harboring two flavins (FAD and FMN) and one heme cofactors. Large conformational changes are required during catalytic cycle to allow successive electron transfers from FAD to FMN and finally heme iron. We used the recently released AlphaFold2_advanced notebook (AF2A), to predict the possible alternate conformations supporting electron transfers in CYP102A1 homodimer. Challenging AF2A-derived models with previously reported experimental data revealed an unforeseen domain connectivity of the diflavin reductase part of the enzyme. Intermolecular crossed complex constitutes a novel type of structural organization never previously described. The predicted formation within the dimer of a stable complex between the heme containing domains was challenged and found consistent with uninterpreted features of reported crystallographic structures and cryo-EM imaging. The particularly efficient CYP102A1 catalytic mechanism was revisited to the light of the new evidenced connectivity in which the FMN-binding domain of each monomer oscillates on themselves to alternatively receive and transfer electrons without needing large structural change in the dimer. Such model was found explanatory for previously contradictory reported biochemical data. Possibility to mimic CYP102A1 structural organization into bicomponent eukaryotic P450 systems was evaluated by designing and modeling in silico synthetic reductase domains built from composite sequence segments from P. megaterium and human origins. More generally, this work illustrates how the ability of AF2A to predict alternate complex structures can enlighten and explain conformational changes critical for bio-assemblies.


title: Deep learning models for RNA secondary structure prediction (probably) do not generalise across families

abstract:
AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSThe secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary structure prediction. Many of these papers report impressive results for intra-family predictions, but seldom address the much more difficult (and practical) inter-family problem.

ResultsWe demonstrate it is nearly trivial with convolutional neural networks to generate pseudo-free energy changes, modeled after structure mapping data, that improve the accuracy of structure prediction for intra-family cases. We propose a more rigorous method for inter-family cross-validation that can be used to assess the performance of learning-based models. Using this method, we further demonstrate that intra-family performance is insufficient proof of generalisation despite the widespread assumption in the literature, and provide strong evidence that many existing learning-based models have not generalised inter-family.

AvailabilitySource code and data is available at https://github.com/marcellszi/dl-rna.

category: bioinformatics


title: Three-dimensional structure of the single domain cupredoxin AcoP

abstract: Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper center coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in term of copper-binding ligands, copper center geometry, redox potential, as well as biological function. AcoP is a periplasmic protein belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features: highly resistant to acidic pH, it possesses a constrained green-type copper center of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structure of AcoP at 1.65 [A] resolution unveils a typical cupredoxin fold with extended loops, never observed in previously characterized cupredoxins, that might be involved in the interaction of AcoP with its physiological partners. Moreover, the structure shows that the green color of AcoP cannot be attributed to nonclassical copper ligands, its green-colored copper center raising from a long Cu-S (Cys) bond, determined by both X-ray diffraction and EXAFS. The crystal structures of two AcoP mutants confirm that the active center of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active center rigidity due to the presence of an extensive hydrogen bond network.


title: The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16

abstract: The TMEM16 family of transmembrane proteins includes Ca2+-activated phospholipid scramblases (PLS) that can also function as non-selective ion channels. Extensive structural and functional studies have established that a membrane-exposed hydrophilic groove in TMEM16 PLS can serve as a translocation pathway for lipids. However, it is still unclear how the TMEM16 PLS conduct ions. A "protein-delimited pore" model suggests that ions are translocated through a narrow opening of the groove region, which is not sufficiently wide to allow lipid movement, whereas a "proteolipid pore" model envisions ions and lipids translocating through an open conformation of the groove. We investigated the dynamic path of potassium ion (K+) translocation that occurs when an open groove state of nhTMEM16 is obtained from long atomistic molecular dynamics (MD) simulations and calculated the free energy profile of the ion movement through the groove with umbrella sampling methodology. The free energy profile identifies effects of specific interactions along the K+ permeation path. The same calculations were performed to investigate ion permeation through a groove closed to lipid permeation in the nhTMEM16 L302A mutant which exhibits a stable conformation of the groove that does not permit lipid scrambling. Our results identify structural and energy parameters that enable K+ permeation and suggest that the presence of lipids in the nhTMEM16 groove observed in the simulations during scrambling or in/out diffusion, affect the efficiency of K+ permeation to various extents.


title: Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli

abstract:
The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogen lyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H2 during fermentation, its reversibility, allowing H2-dependent CO2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown.

Here we report cryo-EM structures of FHL in its aerobically- and anaerobically-isolated forms at resolutions reaching 2.6 [A]. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in preventing reverse activity in vivo, and evaluate possible structural determinants of the bias toward hydrogen production over its oxidation.


title: HDAC6 inhibitor ACY-1083 shows lung epithelial protective features in COPD

abstract:
Airway epithelial damage is a common feature in respiratory diseases such as COPD and has been suggested to drive inflammation and progression of disease. These features manifest as remodeling and destruction of lung epithelial characteristics including loss of small airways which contributes to chronic airway inflammation. Histone deacetylase 6 (HDAC6) has been shown to play a role in epithelial function and dysregulation, such as in cilia disassembly, epithelial to mesenchymal transition (EMT) and oxidative stress responses, and has been implicated in several diseases. We thus used ACY-1083, an inhibitor with high selectivity for HDAC6, and characterized its effects on epithelial function including epithelial disruption, cytokine production, remodeling, mucociliary clearance and cell characteristics.

Primary lung epithelial air-liquid interface cultures from COPD patients were used and the impacts of TNF, TGF-{beta}, cigarette smoke and bacterial challenges on epithelial function in the presence and absence of ACY-1083 were tested. Each challenge increased the permeability of the epithelial barrier whilst ACY-1083 blocked this effect and even decreased permeability in the absence of challenge. TNF was also shown to increase production of cytokines and mucins, with ACY-1083 reducing the effect. We observed that COPD-relevant stimulations created damage to the epithelium as seen on immunohistochemistry sections and that treatment with ACY-1083 maintained an intact cell layer and preserved mucociliary function. Interestingly, there was no direct effect on ciliary beat frequency or tight junction proteins indicating other mechanisms for the protected epithelium.

In summary, ACY-1083 shows protection of the respiratory epithelium during COPD-relevant challenges which indicates a future potential to restore epithelial structure and function to halt disease progression in clinical practice.


title: CROSS-GENERATIONAL IMPACT OF EPIGENETIC MALE INFLUENCE ON PHYSICAL ACTIVITY IN RAT

abstract: The aim of this work was to study whether epigenetic events at conception influence the formation of behavioral features found in adult rats. First generational inheritance of activity level, anxiety, and learning ability was studied. To separate genetic and non-genetic inheritance, mating of males and females with average motor activity was carried out in the presence males with high or low activity. Our results show that offspring of parents who mated in the presence of males with a high motor activity were significantly more active than offspring of parents that were paired in the presence of males with low activity. Anxiety level and learning ability were not inherited in this way. It is possible that the phenomenon we discovered is important for maintaining a certain level of activity of specific populations of animals. It counteracts natural selection, which should lead to a constant increase in the activity of animals.

category: animal behavior and cognition


title: Floating Sphere Assay: A rapid qualitative method for microvolume analysis of gelation

abstract:
1A huge, unprecedented demand for gelatin coupled with its implications on global sustainability has resulted in the need to discover novel proteins with gelling attributes for applications in the food industry. Currently used gelation assays require large sample volumes and thus the screening for novel gelling proteins is a formidable technical challenge. In this paper, we report the  Floating Sphere Assay which is a simple, economical, and miniaturized assay to detect minimum gelling concentration with volumes as low as 50 l. Results from the Floating Sphere Assay are consistent with currently used methods for gelation tests and accurately estimate the Minimum Gelling Concentrations (MGCs) of gelatin, {kappa}-carrageenan and gellan gum. The assay was also able to differentiate the strengths of strong and weak gellan gum gels prepared at pH 3.5 and pH 7.0 respectively. The Floating Sphere Assay can be utilized in high-throughput screens for gelling proteins and can accelerate the discovery of gelatin substitutes.

2 HighlightsO_LIWe report the Floating Sphere Assay that can be used to assesses minimum gelling concentration of solutions with volumes as low as 50 l.
C_LIO_LIObserving whether a glass sphere placed on the surface of a test solution floats or sinks is diagnostic of gel formation
C_LIO_LIFloating Sphere Assay can distinguish a strong gel from a weak gel
C_LIO_LIFloating Sphere Assay is a rapid and cost-effective approach to screen for novel plant-based gelatin alternatives.
C_LI


title: Genomic insights into the evolutionary relationships and demographic history of kiwi

abstract: Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events among them. Here, we utilise single representative nuclear genomes of all extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic diversity, and deep-time (past million years) demographic analyses. We uncover low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post-divergence gene flow, concordant with recent reports of interspecific hybrids. The four species with available reference assemblies show relatively low levels of genetic diversity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we uncover similarities and differences in the demographic histories of the five kiwi species over the past million years, and suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the evolutionary history of the group.


title: Identification of a novel osteogenetic oligodeoxynucleotide (osteoDN) that promotes osteoblast differentiation in a TLR9-independent manner

abstract: Recent studies have revealed that oligodeoxynucleotides (ODNs) designed from genome sequences have the potential to regulate cell fate. Currently, ODNs that conduct cell differentiation are nanomolecular drug candidates for regenerative medicine. Herein, we demonstrate that iSN40, an 18-base ODN derived from the Lacticaseibacillus rhamnosus GG genome, promoted the differentiation and calcification of osteoblasts that play a central role during bone formation. In the murine osteoblast cell line MC3T3-E1, iSN40 enhanced alkaline phosphatase activity at the early stage of differentiation and facilitated calcium deposition at the late stage by inducing the expression of osteogenic genes such as Msx2, osterix, collagen type 1, osteopontin, and osteocalcin. Intriguingly, the CpG motif within iSN40 was not required for its osteogenetic activity, indicating that iSN40 functions in a TLR9-independent manner. These data suggest that iSN40, serving as an osteogenetic ODN (osteoDN), as a drug seed that target osteoblasts for bone regeneration.


title: Proteasomal subunit depletions differentially affect germline integrity in C. elegans

abstract: The 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist, but remain less well studied. We provide characterization of germline-specific functions of different 19S RP proteasome subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, potentially introducing C. elegans germ line as model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.


title: Cell-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil

abstract: When exposed to increased mechanical resistance from the soil, plant roots display non-linear growth responses that can not be solely explained by mechanical principles. Here, we aim to investigate how changes in tissue mechanical properties are biologically regulated in response to soil strength. A particle-based model was developed to solve root-soil mechanical interactions at the cellular scale, and a detailed numerical study explored factors that affect root responses to soil resistance. Results showed that growth through increasing soil strength is maintained through the softening of cell walls at the tip, a response likely linked to soil cavity expansion. The model also predicts the shortening and decreased anisotropy of the zone of cell elongation, which may improve the mechanical stability of the root against axial forces. The study demonstrates the potential of advanced modeling tools to help identify traits that confer plant resistance to abiotic stress.


title: Single-cell analyses of axolotl forebrain organization, neurogenesis, and regeneration

abstract: Salamanders are important tetrapod models to study brain organization and regeneration, however the identity and evolutionary conservation of brain cell types is largely unknown. Here, we delineate cell populations in the axolotl telencephalon during homeostasis and regeneration, representing the first single-cell genomic and spatial profiling of an anamniote tetrapod brain. We identify glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved GABAergic neuron classes. We infer transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific direct and indirect neurogenesis, and unravel conserved signatures. Following brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield key insights into the organization, evolution, and regeneration of a tetrapod nervous system.


title: Regionally distinct trophoblast regulate barrier function and invasion in the human placenta

abstract:
The human placenta contains two specialized regions: the villous chorion where gases and nutrients are exchanged between maternal and fetal blood, and the smooth chorion which surrounds more than 70% of the developing fetus but whose cellular composition and function is poorly understood. Here, we use single cell RNA sequencing to compare the cell types and molecular programs between these two regions in the second trimester human placenta. Each region consists of progenitor cytotrophoblasts (CTBs) and extra-villous trophoblasts (EVTs) with similar gene expression programs. While CTBs in the villous chorion differentiate into syncytiotrophoblasts, they take an alternative trajectory in the smooth chorion producing a previously unknown CTB population which we term smooth-chorion-specific CTBs (SC-CTBs). Marked by expression of region-specific cytokeratins, the SC-CTBs form a stratified epithelium above a basal layer of progenitor CTBs. They express epidermal and metabolic transcriptional programs consistent with a primary role in defense against physical stress and pathogens. Additionally, we show that SC-CTBs closely associate with EVTs and secrete factors that inhibit the migration of the EVTs. This restriction of EVT migration is in striking contrast to the villous region where EVTs migrate away from the chorion and invade deeply into the decidua. Together, these findings add an important new dimension to our understanding of CTB differentiation in these distinct regions of the human placenta. This knowledge has broad implications for studies of the development, functions, and diseases of the human placenta.

Impact StatementSingle cell RNA-sequencing of distinct regions of the human placenta identifies a smooth chorion-specific cytotrophoblast population responsible for unique functions of the smooth chorion, including acting as a barrier and restricting invasion.


title: Basal and stress-induced expression changes consistent with water loss reduction explain desiccation tolerance of natural Drosophila melanogaster populations

abstract:
BackgroundClimate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Integrating transcriptomics and physiology is key to advancing our knowledge on how species cope with desiccation stress, and these studies are still best accomplished in model organisms.

ResultsHere, we characterized the natural variation of European D. melanogaster populations across climate zones and found that strains from arid regions were similar or more tolerant to desiccation compared with strains from temperate regions. Tolerant and sensitive strains differed not only in their transcriptomic response to stress but also in their basal expression levels. We further showed that gene expression changes in tolerant strains correlated with their physiological response to desiccation stress and with their cuticular hydrocarbon composition. Transposable elements, which are known to influence stress response across organisms, were not found to be enriched nearby differentially expressed genes. Finally, we identified several tRNA-derived small RNA fragments that differentially targeted genes in response to desiccation stress.

ConclusionsOur results showed that by integrating transcriptomics with physiological trait analysis we can pinpoint the genetic basis of the differences in tolerance to desiccation stress found in natural D. melanogaster populations. Moreover, we showed that, beyond starvation and aging, tRNA-derived small RNA fragments (tRFs) appear to be relevant post-transcriptional gene regulators in response to desiccation stress.


title: Social information-mediated population dynamics in non-grouping prey

abstract:
Inadvertent social information (ISI) use, i.e., the exploitation of social cues including the presence and behaviour of others, has been predicted to mediate population-level processes even in the absence of cohesive grouping. However, we know little about how such effects may arise when the prey population lacks social structure beyond the spatiotemporal autocorrelation originating from the random movement of individuals. In this study, we built an individual-based model where predator avoidance behaviour could spread among randomly moving prey through the network of nearby observers. We qualitatively assessed how ISI use may affect prey population size when cue detection was associated with different probabilities and fitness costs, and characterised the structural properties of the emerging detection networks that would provide pathways for information spread in prey. We found that ISI use was among the most influential model parameters affecting prey abundance and increased equilibrium population sizes in most examined scenarios. Moreover, it could substantially contribute to population survival under high predation pressure, but this effect strongly depended on the level of predator detection ability. When prey exploited social cues in the presence of high predation risk, the observed detection networks consisted of a larger number of connected components with smaller sizes and smaller ego networks than corresponding randomized networks; this resulted in efficient information spread among connected individuals in the detection networks. Our study provides hypothetical mechanisms about how temporary local densities may allow information diffusion about predation threats among conspecifics and facilitate population stability and persistence in non-grouping animals.

Significance StatementThe exploitation of inadvertently produced social cues may not only modify individual behaviour but also fundamentally influence population dynamics and species interactions. Using an individual-based model, we investigated how the detection and spread of adaptive antipredator behaviour may cascade to changes in the demographic performance of randomly moving (i.e., non-grouping) prey. We found that social information use contributed to population stability and persistence by reducing predation-related per capita mortality and raising equilibrium population sizes when predator detection ability reached a sufficient level. We also showed that temporary detection networks had structural properties that allowed efficient information spread among prey under high predation pressure. Our work represents a general modelling approach that could be adapted to specific predator-prey systems and scrutinize how temporary local densities allow dynamic information diffusion about predation threats and facilitate population stability in non-grouping animals.


title: Personality variation is eroded by simple social behaviours in collective foragers

abstract: The movement of groups can be heavily influenced by  leader individuals who differ from the others in some way. A major source of differences between individuals is the repeatability and consistency of their behaviour, commonly considered as their  personality, which can influence both position within a group as well as the tendency to lead. However, links between personality and behaviour may also depend upon the immediate social environment of the individual; individuals who behave consistently in one way when alone may not express the same behaviour socially, when they may be conforming with the behaviour of others. Experimental evidence shows that personality differences can be eroded in social situations, but there is currently a lack of theory to identify the conditions where we would expect personality to be suppressed. Here, we develop a simple individualbased framework considering a small group of individuals with differing tendencies to perform risky behaviours when travelling away from a safe home site towards a foraging site, and compare the group behaviours when the individuals follow differing rules for aggregation behaviour determining how much attention they pay to the actions of their fellow group-members. We find that if individuals pay attention to the other members of the group, the group will tend to remain at the safe site for longer, but then travel faster towards the foraging site. This demonstrates that simple social behaviours can result in the repression of consistent inter-individual differences in behaviour, giving the first theoretical consideration of the social mechanisms behind personality suppression.


title: Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins

abstract:
Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.

AUTHOR SUMMARYAccurate prediction of the conformational ensemble dynamics sans bias is shown for intrinsically disordered proteins including the transactivation domain of p53.


title: Dynamic proteomic and phosphoproteomic atlas of corticostriatal axon neurodevelopment

abstract: Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.

category: neuroscience


title: Mechanisms underlying the reprogramming of mouse embryonic fibroblasts to thymic epithelial cells

abstract: Thymic epithelial cells (TECs) are a critical functional component of the thymuss ability to generate T cells for the adaptive immune system in vertebrates. However, no in vitro system for studying TEC function exists. Overexpression of the transcription factor FOXN1 initiates reprogramming of fibroblasts into TEC-like cells (iTECs) that support T cell differentiation in culture or after transplant. In this study, we characterized iTEC reprogramming at the cellular and molecular level to determine how reprogramming proceeds and identify mechanisms that can be targeted for improving this process. These data show that iTEC reprogramming consists of discrete gene expression changes that differ in early and late reprogramming, and that iTECs upregulate markers of both cortical and medullary TEC (cTEC and mTEC) lineages, although mTEC differentiation is blocked at a progenitor stage. We demonstrate that promoting proliferation enhances iTEC generation, and that Notch inhibition allows induction of mTEC differentiation. Finally, we show that a major difference between iTEC and fetal TEC is the expression of MHCII. This study supports future efforts to improve iTEC reprogramming for both research and translational uses.


title: Nr6a1 controls axially-restricted body elongation, segmentation, patterning and lineage allocation

abstract: The vertebrate main-body axis is laid down during embryonic stages in an anterior-to-posterior (head-to-tail) direction, driven and supplied by posteriorly located progenitors. For the vertebral column, the process of axial progenitor cell expansion that drives elongation, and the process of segmentation which allocates progenitor-descendants into repeating pre-vertebral units, occurs seemingly uninterrupted from the first to the last vertebra. Nonetheless, there is clear developmental and evolutionary support for two discrete modules controlling processes within different axial regions: a trunk and a tail module. Here, we identify Nuclear receptor subfamily 6 group A member 1 (Nr6a1) as a master regulator of elongation, segmentation, patterning and lineage allocation specifically within the trunk region of the mouse. Both gain- and loss-of-function in vivo analyses revealed that the precise level of Nr6a1 acts as a rheostat, expanding or contracting vertebral number of the trunk region autonomously from other axial regions. Moreover, Nr6a1 was found to be required for segmentation, but only for trunk-forming somites, with the timely clearance of Nr6a1 critical in supporting tail formation. In parallel with these morphological outcomes, we reveal Nr6a1 as a novel regulator of global Hox signatures within axial progenitors, preventing the precocious expression of multiple posterior Hox genes as the trunk is being laid down and thus reinforcing that patterning and elongation are coordinated. Finally, our data supports a crucial role for Nr6a1 in regulating gene regulatory networks that guide cell lineage choice of axial progenitors between neural and mesodermal fate. Collectively, these data reveal an axially-restricted role for Nr6a1 in all major cellular and tissue-level events required for vertebral column formation, supporting the view that modulation of Nr6a1 expression level or function is likely to underpin evolutionary changes in axial formulae that exclusively alter the trunk region.


title: Dissociable Cellular and Genetic Mechanisms of Cortical Thinning at Different Life Stages

abstract: Mechanisms underpinning age-related variations in cortical thickness in the human brain remain poorly understood. We investigated whether inter-regional age-related variations in cortical thinning (in a multicohort neuroimaging dataset from the ENIGMA Lifespan Working Group totalling 14,248 individuals, aged 4-89 years) depended on cell-specific marker gene expression levels. We found differences amidst early-life (<20 years), mid-life (20-60 years), and late-life (>60 years) in the patterns of association between inter-regional profiles of cortical thickness and expression profiles of marker genes for CA1 and S1 pyramidal cells, astrocytes, and microglia. Gene ontology and enrichment analyses indicated that each of the three life-stages was associated with different biological processes and cellular components: synaptic modeling in early life, neurotransmission in mid-life, and neurodegeneration in late-life. These findings provide mechanistic insights into age-related cortical thinning during typical development and aging.


title: Dual-Resolving of Lipid Positional and Geometric Isomers of C=C Bonds via Bifunctional Photocycloaddition-Photoisomerization Reaction System and Mass Spectrometry

abstract: The biological functions of lipids largely depend on their chemical structures. The position and configuration of C=C bonds are two of the essential attributes that determine the structures of unsaturated lipids. However, simultaneous identification of both attributes remains challenging. Here, we developed a bifunctional visible-light-activated photocycloaddition-photoisomerization reaction system, which enabled the dual-resolving of the positional and geometric isomerism of C=C bonds in lipids when combined with liquid chromatographic mass spectrometry. The dual-pathway reaction mechanism was demonstrated by experiments and density functional theory calculations. Based on this bifunctional reaction system, a workflow of deep structural lipidomics was established, and allowed the revealing of unique patterns of cis-trans-isomers in bacteria, as well as the tracking of C=C positional isomers changes in mouse brain ischemia. This study not only offers a powerful tool for deep lipid structural biology, but also provides a new paradigm for developing the multifunctional visible-light-induced reaction.


title: Spatial Patterns of Microbial Diversity, Composition and Community Structure in Fe-Mn Deposits and Associated Sediments in the Atlantic and Pacific Oceans

abstract:
Mining of deep-sea Fe-Mn deposits will remove crusts and nodules in large areas from the seafloor. The growth of a few millimeters of these minerals by Fe and Mn oxides precipitation takes millions of years, and yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea trophic webs, microbes have been identified to affect manganese oxide formation. Hence, polymetallic crusts and nodules may present unique habitats that deserve better understanding. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two oceanic elevations in the Atlantic Ocean, the Tropic Seamount in the northeast and the Rio Grande Rise (RGR) in the southwest. Sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform and statistical analyses using environmental data were performed in R. Additionally, we included public domain environmental DNA data of Fe-Mn crusts, nodules, and associated sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean to compare microbial diversity in Fe-Mn deposits from different ocean basins. Our results indicated that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to deposits from Pacific areas. Crusts and nodules from Atlantic seamounts revealed the presence of unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher relative abundance of sequences related to potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to crusts, nodules, and sediments geochemical composition. Furthermore, community structure analysis using principal coordinate analysis also showed that the microbial communities of all seamounts were significantly divided into ocean basins and sampling areas. Despite the time scale of million years for these deposits to grow, a combination of environmental settings (temperature, salinity, depth, substrate geochemistry, nutrient, and organic matter availability) played a significant role in shaping the crusts and nodules microbiome, which was distinct between the Atlantic and Pacific Fe-Mn deposits. Our results suggest that the microbial community inhabiting Fe-Mn deposits participate in biogeochemical reactions indispensable to deep-sea ecosystems, which implies that understanding the microbial community is of utmost importance for any baseline environmental study in areas of potential deep-sea mining.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/485154v1_ufig1.gif" ALT="Figure 1">
View larger version (49K):
org.highwire.dtl.DTLVardef@1214ccorg.highwire.dtl.DTLVardef@1139796org.highwire.dtl.DTLVardef@144f967org.highwire.dtl.DTLVardef@151f069_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIAtlantic deposits showed lower diversity and richness compared to Pacific deposits
C_LIO_LIFe-Mn crusts and nodules are a potential specific ecological niche
C_LIO_LIAtlantic Fe-Mn deposits harbor an unusual and unknown microbiome
C_LIO_LITemperature, salinity, depth, and substrate geochemistry at Atlantic Fe-Mn deposits may drive community composition
C_LI

category: microbiology


title: Physoxia influences global and gene-specific methylation in pluripotent stem cells

abstract:
Pluripotent stem cells (PSC) possess unlimited proliferation, self-renewal, and a differentiation capacity spanning all germ layers. Appropriate culture conditions are important for the maintenance of self-renewal, pluripotency, proliferation, differentiation, and epigenetic states. Oxygen concentrations vary across different human tissues depending on precise cell location and proximity to vascularisation. The bulk of PSC culture-based research is performed in a physiologically hyperoxic, air oxygen (21% O2) environment, with numerous reports now detailing the impact of physiologic normoxia (physoxia) low oxygen culture in the maintenance of stemness, survival, morphology, proliferation, differentiation potential, and epigenetic profiles. Epigenetic mechanisms affect multiple cellular characteristics including gene expression during development and cell fate determination in differentiated cells. We hypothesized that epigenetic marks are responsive to a reduced oxygen microenvironment in PSCs and their differentiation progeny.

Here, we evaluated the role of physoxia in PSC culture, the regulation of DNA methylation (5mC and 5hmC), and expression of regulatory enzymes DNMTs and TETs. Physoxia enhanced the functional profile of PSC including proliferation, metabolic activity, and stemness attributes. PSCs cultured in physoxia revealed significant downregulation of DNMT3B, DNMT3L, TET1, and TET3 vs. air oxygen, accompanied by significantly reduced 5mC and 5hmC levels. Downregulation of DNMT3B was associated with an increase in its promoter methylation. Coupled to above we also noted decreased HIF1A but increased HIF2A expression in physoxia cultured PSCs, versus air oxygen. In conclusion, PSCs display oxygen-sensitive methylation patterns that correlate with transcriptional and translational regulation of the de novo methylase DNMT3B.


title: Interacting active surfaces: a model for three-dimensional cell aggregates

abstract:
We introduce a modelling and simulation framework for cell aggregates in three dimensions based on interacting active surfaces. Cell mechanics is captured by a physical description of the acto-myosin cortex that includes cortical flows, viscous forces, active tensions, and bending moments. Cells interact with each other via short-range forces capturing the effect of adhesion molecules. We discretise the model constitutive equations using a finite element method, and provide a parallel implementation in C++. We discuss examples of application of this framework to simulations involving small and medium-sized aggregates: we consider the shape and dynamics of a cell doublet, a planar cell sheet, and a growing cell aggregate. This framework opens the door to the systematic exploration of the cell to tissue-scale mechanics of cell aggregates, which plays a key role in the morphogenesis of embryos and organoids.

Author summaryUnderstanding how tissue-scale morphogenesis arises from cell mechanics and cell-cell interactions is a fundamental question in developmental biology. Here we propose a mathematical and numerical framework to address this question. In this framework, each cell is described as an active surface representing the cell acto-myosin cortex, subjected to flows and shape changes according to active tensions, and to interaction with neighbouring cells in the tissue. Our method describes cellular processes such as cortical flows, cell adhesion, and cell shape changes in a deforming three-dimensional cellular aggregate. To solve the equations numerically, we employ a finite element discretisation, which allows us to solve for flows and cell shape changes with arbitrary resolution. We discuss applications of our framework to describe cell-cell adhesion in doublets, three-dimensional cell shape in a simple epithelium, and three-dimensional growth of a cell aggregate.


title: Humans Adapt Multi-Objective Control of Stepping To Perform Lateral Maneuvers While Walking

abstract:
To successfully traverse their environment, humans must often perform maneuvers to achieve desired task goals while simultaneously maintaining balance. Humans accomplish these tasks primarily by modulating their foot placements. As humans are more unstable laterally, we must better understand how humans modulate lateral foot placement. We previously developed a theoretical framework and corresponding computational models to describe how humans regulate lateral stepping during straight-ahead continuous walking. This framework yields goal functions for step width and lateral body position that define the walking task and determine the set of all possible task solutions as Goal Equivalent Manifolds (GEMs). Here, we used this framework to determine if humans can regulate lateral stepping during non-steady-state lateral maneuvers by minimizing errors in accordance with these goal functions. Twenty young healthy adults each performed four lateral lane-change maneuvers in a virtual reality environment. Within our general lateral stepping regulation framework, we first re-examined the requirements of such transient walking tasks. Doing so yielded new theoretical predictions regarding how steps during any such maneuver should be regulated to minimize error costs, consistent with the goals required at each step and with how these costs are adapted at each step during the maneuver. Humans performed the experimental lateral maneuvers in a manner consistent with our theoretical predictions. Furthermore, their stepping behavior was well modeled by merely adapting the parameters of our previous lateral stepping models from step to step. To our knowledge, our results are the first to demonstrate humans can use evolving cost landscapes in real time to perform such an adaptive motor task and, furthermore, that such adaptation can occur quickly - over only one step. Thus, the predictive capabilities of our general stepping regulation framework extend to a much greater range of walking tasks beyond just normal, straight-ahead walking.

AUTHOR SUMMARYWhen we walk in the real world, we rarely walk continuously in a straight line. Indeed, we regularly have to perform other tasks like stepping aside to avoid an obstacle in our path (either fixed or moving, like another person coming towards us). While we have to be highly maneuverable to accomplish such tasks, we must also remain stable to avoid falling while doing so. This is challenging because walking humans are inherently more unstable side-to-side. Sideways falls are particularly dangerous for older adults as they can lead to hip fractures. Here, we establish a theoretical basis for how people can accomplish such maneuvers. We show that humans execute a simple lateral lane-change maneuver consistent with our theoretical predictions. Importantly, we show that they can do so using simple adaptations of the same step-to-step regulation strategies they use to walk in a straight line. Moreover, these same control processes also explain how humans trade-off side-to-side stability to gain the maneuverability they need to perform such lateral maneuvers.