title: Enhanced microvasculature formation and patterning in iPSC-derived kidney organoids cultured in physiological hypoxia

abstract:
Functional kidney organoids have the potential to be used in implantable kidney grafts for patients with end-stage kidney disease, because they have been shown to self-organize from induced pluripotent stem cells into most important renal structures. To date, however, long-term kidney organoid culture has not succeeded, as nephrons lose their phenotype after approximately 25 days. Furthermore, the renal structures remain immature with diminishing endothelial networks with low connectivity and limited organoid invasion. We hypothesized that introducing long-term culture at physiological hypoxia, rather than the normally applied non-physiological, hyperoxic 21% O2, could initiate angiogenesis, lead to enhanced growth factor expression and improve the endothelial patterning. We therefore cultured the kidney organoids at 7% O2 instead of 21% O2 for up to 25 days and evaluated nephrogenesis, VEGF-A expression and vascularization. Whole mount imaging revealed a homogenous morphology of the endothelial network with enhanced sprouting and interconnectivity when the kidney organoids were cultured in hypoxia. Three-dimensional quantification confirmed that the hypoxic culture led to an increased average vessel length, likely due to the observed upregulation of proangiogenic VEGF-A189 mRNA and downregulation of the antiangiogenic protein VEGF-A165b measured in hypoxia. This research indicates the importance of optimization of oxygen availability in organoid systems and the potential of hypoxic culture conditions in improving the vascularization of organoids.

Significance statementCulturing kidney organoids in a hypoxic environment improved patterning of the endothelial network and improved vascularization. These findings may help improve the quality of kidney organoids, and could eventually improve the kidney graft for transplantation in patients with end-stage kidney disease. Furthermore, the organoids will be more suitable for drug testing and in developmental biology. The findings might also be translatable to other organoid models containing endothelial cells.

Graphical abstract

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title: Conjunctival epithelial cells resist productive SARS-CoV-2 infection

abstract: Although tropism of SARS-CoV-2 for respiratory tract epithelial cells is well established, an open question is whether the conjunctival epithelium is also a target for SARS-CoV-2. Conjunctival epithelial cells, which express viral entry receptors ACE2 and TMPRSS2, constitute the largest exposed epithelium of the ocular surface tissue, and may represent a relevant viral entry route. To address this question, we generated an organotypic air-liquid-interface model of conjunctival epithelium, composed of progenitor, basal and superficial epithelial cells and fibroblasts, which could be maintained successfully up to day 75 of differentiation. Using single-cell RNA Seq, with complementary imaging and virological assays, we observed that while all conjunctival cell types were permissive to SARS-CoV-2 genome expression, a productive infection did not ensue. The early innate immune response to SARS-CoV-2 infection in conjunctival cells was characterised by a robust autocrine and paracrine NF-K{beta} activity, without activation of antiviral interferon signalling. Collectively, these data enrich our understanding of SARS-CoV-2 infection at the human ocular surface, with potential implications for the design of preventive strategies and conjunctival transplants.

category: cell biology


title: Molecular and morphological analyses support recognition of Prostanthera volucris (Lamiaceae), a new species from the Central Tablelands of New South Wales

abstract: Research into the systematics of Prostanthera has recently revealed a close evolutionary relationship among P. phylicifolia s. str., the critically endangered P. gilesii, and a population of uncertain identity from the Central Tablelands of New South Wales, Australia. Previous analyses were unable to establish whether genetic boundaries separated these taxa. This study aimed to assess the species boundaries among these three taxa using a combination of single-nucleotide polymorphisms (SNP) sampled at the population-scale and multivariate analysis of morphological characters. Non-parametric and parametric statistics, neighbour-network analysis, phylogenetic analysis, and ancestry coefficient estimates all provided support for discrete genetic differences between the three taxa. Morphological phenetic analysis identified a suite of characters that distinguished each of these taxa. This corroboration of evidence supports the presence of three independently evolving lineages. Prostanthera gilesii and P. phylicifolia s. str. are distinct species independent from the third taxon which is described here as P. volucris R.P.ODonnell. A detailed description, diagnostic line drawings and photographs are provided. We evaluate P. volucris as satisfying criteria to be considered Critically Endangered.

category: evolutionary biology


title: The human RNA polymerase I structure reveals an HMG-like transcription factor docking domain specific to metazoans

abstract: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP-fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This  dock II domain resembles a truncated HMG-box incapable of DNA-binding which may serve as a downstream-transcription factor binding platform in metazoans. Biochemical analysis and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG-box domain containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.

category: biochemistry


title: Myopathy mutations in DNAJB6 slow conformer specific substrate processing that is rescued by NEF modulation

abstract: Molecular chaperones, or heat shock proteins (HSPs), protect against the toxic misfolding and aggregation of proteins. As such, mutations or deficiencies within the chaperone network can lead to disease. In fact, dominant mutations in DNAJB6 (Hsp40/Sis1), an Hsp70 co-chaperone, leads to a protein aggregate myopathy termed Limb-Girdle Muscular Dystrophy Type D1 (LGMDD1). DNAJB6 client proteins and co-chaperone interactions in skeletal muscle are not known. Here, we used the yeast prion model client in conjunction with in vitro chaperone activity assays to gain mechanistic insights, and found that LGMDD1 mutants affect Hsp40 functions. Strikingly, the mutants changed the structure of client protein aggregates, as determined by altered distribution of prion strains. They also impair the Hsp70 ATPase cycle, dimerization, and substrate processing and consequently poison the function of wild-type protein. These results define the mechanisms by which LGMDD1 mutations alter chaperone activity and provide avenues for therapeutic intervention.


title: Glycan engineering using synthetic ManNAc analogues enhances sialyl-Lewis-X expression and adhesion of leukocytes

abstract: Cell surface glycans, depending on their structures and dynamic modifications, act as the first point of contact and regulate cell-cell, cell-matrix, and cell-pathogen interactions. Particularly, the sialyl-Lewis-X (sLeX, CD15s) tetrasaccharide epitope, expressed on both gangliosides and glycoproteins, participates in leukocyte extravasation via interactions with selectins expressed on endothelial cells, lymphocytes, and platelets (CD62-E/L/P). Neutrophils carrying sLeX epitopes are thought to be responsible for chronic inflammatory diseases resulting in plaque formation and atherosclerosis. Intense efforts have been devoted to the development of sLeX mimetics for inhibition of cell adhesion. On the other hand, dysregulated expression of sLeX and poor extravasation are the major underlying causes of leukocyte adhesion deficiency-II (LAD-II) disorders that result in frequent infections and poor immune response. We hypothesized that metabolic processing of peracetyl N-(cycloalkyl)acyl-D-mannosamine derivatives, through the sialic acid pathway, might result in the expression of sialoglycans with altered hydrophobicity which in-turn could modulate their binding to endogenous lectins, including selectins. Herein, we show that treatment of HL-60 (human acute myeloid leukemia) cells with peracetyl N-cyclobutanoyl-D-mannosamine (Ac4ManNCb), at 50 microM for 48 h, resulted in a robust three to four fold increase in the binding of anti-sLeX (CSLEX1) antibody and enhanced cell adhesion to E-selectin coated surfaces; while the corresponding straight-chain analogue, peracetyl N-pentanoyl-D-mannosamine (Ac4ManNPent), and peracetyl N-cyclopropanoyl-D-mannosamine (Ac4ManNCp) both resulted in [~]2.5-fold increase compared to controls. The ability to enhance sLeX expression using small molecules has the potential to provide novel opportunities to address challenges in the treatment of immune deficiency disorders.


title: Correlated STORM-homoFRET Imaging: Applications to the Study of Membrane Receptor Self-Association and Clustering

abstract: Mapping the self-organization and spatial distribution of membrane proteins is key to understanding their function. We report here on a correlated STORM/homoFRET imaging approach for resolving the nanoscale distribution and oligomeric state of membrane proteins. Live cell homoFRET imaging of CEACAM1, a cell-surface receptor known to exist in a complex equilibrium between monomer and dimer/oligomer states, revealed highly heterogenous diffraction-limited structures on the surface of HeLa cells. Correlated super-resolved STORM imaging revealed that these structures comprised a complex mixture and spatial distribution of self-associated CEACAM1 molecules. This correlated approach provides a compelling strategy for addressing challenging questions about the interplay between membrane protein concentration, distribution, interaction, clustering, and function.

category: biophysics


title: ATP:Mg2+ shapes condensate properties of rRNA-NPM1 in vitro nucleolus model and its partitioning of ribosomes

abstract:
Nucleoli have viscoelastic gel-like condensate dynamics that are not well represented in vitro. Nucleoli models, such as those formed by nucleophosmin 1 (NPM1) and ribosomal RNA (rRNA), exhibit condensate dynamics orders of magnitude faster than in vivo nucleoli. Here we show that an interplay between magnesium ions (Mg2+) and ATP governs rRNA dynamics, and this ultimately shapes the physical state of these condensates. Using quantitative fluorescence microscopy, we demonstrate that increased RNA compaction occurs in the condensates at high Mg2+ concentrations, contributing to the slowed RNA dynamics. At Mg2+ concentrations above 7 mM, rRNA is fully arrested and the condensates are gels. Below the critical gel point, NPM1-rRNA droplets age in a temperature-dependent manner, suggesting that condensates are viscoelastic materials, undergoing maturation driven by weak multivalent interactions. ATP addition reverses the dynamic arrest of rRNA, resulting in liquefaction of these gel-like structures. Surprisingly, ATP and Mg2+ both act to increase partitioning of NPM1-proteins as well as rRNA, which influences the partitioning of small client molecules. By contrast, larger ribosomes form a halo around NPM1-rRNA coacervates when Mg2+ concentrations are higher than ATP concentrations. Within cells, ATP levels fluctuate due to biomolecular reactions, and we demonstrate that a dissipative enzymatic reaction can control the biophysical properties of in vitro condensates through depletion of ATP. This enzymatic ATP depletion also reverses the formation of the ribosome halos. Our results illustrate how cells, by changing local ATP concentrations, may regulate the state and client partitioning of RNA-containing condensates such as the nucleolus.

Significance StatementO_LIThere is a significant discrepancy between the dynamics of in vitro nucleolus models and in vivo nucleoli - with the latter more gel-like.
C_LIO_LIThe interplay between Mg2+ ions, ATP and the nucleolus components - specifically RNA - governs the dynamics, and ultimately the physical state, of nucleolus-like condensates.
C_LIO_LIWe show that the nucleolus are dynamically adapting condensates, responding to local ATP concentrations through Mg2+-induced compaction of the RNA, and reversible relaxation when ATP binds Mg2+ again. Other condensates containing RNA probably respond in similar ways to Mg2+ and ATP.
C_LI


title: A DNA-based optical force sensor for live-cell applications

abstract: Mechanical forces are relevant for many biological processes, from wound healing or tumour formation to cell migration and differentiation. Cytoskeletal actin is largely responsible for responding to forces and transmitting them in cells, while also maintaining cell shape and integrity. Here, we describe a novel approach to employ a FRET-based DNA force sensor in vitro and in cellulo for non-invasive optical monitoring of intracellular mechanical forces. We use fluorescence lifetime imaging to determine the FRET efficiency of the sensor, which makes the measurement robust against intensity variations. We demonstrate the applicability of the sensor by monitoring cross-linking activity in in vitro actin networks by bulk rheology and confocal microscopy. We further demonstrate that the sensor readily attaches to stress fibers in living cells which opens up the possibility of live-cell force measurements.


title: Hydrogen properties and charges in a sub-1.2 A resolution cryo-EM structure revealed by a cold field emission beam

abstract: The cold field emission (CFE) beam produces the less-attenuated contrast transfer function of electron microscopy, thereby enhancing high-resolution signals and this particularly benefits higher-resolution single particle cryogenic electron microscopy. Here, we present a sub-1.2 [A] resolution structure of a standard protein sample, apoferritin. Image data were collected with the CFE beam in a high-throughput scheme while minimizing beam tilt deviations from the coma-free axis. A difference map reveals positive densities for most hydrogen atoms in the core region of the protein complex including those in water molecules, while negative densities around acidic amino-acid side chains likely represent negative charges. The position of the hydrogen densities depends on parent bonded-atom type, which is validated by an estimated level of coordinate errors.


title: SerpinB3 drives cancer stem cell survival in glioblastoma

abstract:
Despite therapeutic interventions for glioblastoma (GBM), cancer stem cells (CSCs) drive recurrence. The precise mechanisms underlying CSC therapeutic resistance, namely inhibition of cell death, are unclear. We built on previous observations that the high cell surface expression of junctional adhesion molecule-A drives CSC maintenance and identified downstream signaling networks, including the cysteine protease inhibitor SerpinB3. Using genetic depletion approaches, we found that SerpinB3 is necessary for CSC maintenance, survival, and tumor growth, as well as CSC pathway activation. The knockdown of SerpinB3 also increased apoptosis and susceptibility to radiation therapy. Mechanistically, SerpinB3 was essential to buffer cathepsin L-mediated cell death, which was enhanced with radiation. Finally, we found that SerpinB3 knockdown dramatically increased the efficacy of radiation in pre-clinical models. Taken together, our findings identify a novel GBM CSC-specific survival mechanism involving a previously uninvestigated cysteine protease inhibitor, SerpinB3, and provide a potential target to improve the efficacy of standard-of-care GBM therapies against therapeutically resistant CSCs.

SummaryLauko et al. demonstrate a functional role for SerpinB3, which is elevated in glioblastoma cancer stem cells and protects against lysosomal-mediated cell death. SerpinB3 can be targeted to increase the efficacy of radiation in glioblastoma pre-clinical models.

category: cancer biology


title: BRPF3 knockdown or inhibition moderately reverses olaparib resistance in high grade serous ovarian carcinoma, but depletion of H3K14 acetylation has no effect

abstract:
BackgroundPARP inhibitors (PARPi) kill cancer cells by stalling DNA replication and preventing DNA repair, resulting in a critical accumulation of DNA damage. Resistance to PARPi is a growing clinical problem in the treatment of high grade serous ovarian carcinoma (HGSOC). Acetylation of histone H3 lysine 14 (H3K14ac) and associated histone acetyltransferases (HATs) have known functions in DNA repair and replication, but their expression and activities have not been examined in the context of PARPi-resistant HGSOC.

ResultsUsing mass spectrometry profiling of histone modifications, we observed altered H3K14ac enrichment in PARPi-resistant HGSOC cells relative to isogenic PARPi-sensitive lines. By RT-qPCR and RNA-Seq, we also observed altered expression of numerous HATs in PARPi-resistant HGSOC cells and a PARPi-resistant PDX model. Knockdown of HATs only modestly altered PARPi response, although knockdown and inhibition of PCAF significantly increased resistance. Pharmacologic inhibition of HBO1 severely depleted H3K14ac but did not affect PARPi response. However, knockdown and inhibition of BRPF3, which is known to interact in a complex with HBO1, did reduce PARPi resistance.

ConclusionsThis study demonstrates that severe depletion of H3K14ac does not affect PARPi response in HGSOC. Our data suggest that bromodomain functions of HAT proteins such as PCAF, or accessory proteins such as BRPF3, may play a greater role in PARPi response than acetyltransferase functions.


title: BRPF3 knockdown or inhibition moderately reverses olaparib resistance in high grade serous ovarian carcinoma


title: A dual-purpose real-time indicator and transcriptional integrator for calcium detection in living cells

abstract: Calcium is a ubiquitous second messenger in eukaryotes, correlated with neuronal activity and T-cell activation among other processes. Real-time calcium indicators such as GCaMP have recently been complemented by newer calcium integrators that convert transient calcium activity into stable gene expression. Here we introduce LuCID, a dual-purpose real-time calcium indicator and transcriptional calcium integrator that combines the benefits of both calcium detection technologies. We show that the calcium-dependent split luciferase component of LuCID provides real-time bioluminescence readout of calcium dynamics in cells, while the GI/FKF1 split GAL4 component of LuCID converts calcium-generated bioluminescence into stable gene expression. We also show that LuCIDs modular design enables it to also read out other cellular events such as protein-protein interactions. LuCID adds to the arsenal of tools for studying cells and cell populations that utilize calcium for signaling.

category: synthetic biology


title: Biofilm matrix proteome of clinical strain of P. aeruginosa

abstract: Extracellular matrix plays a pivotal role in biofilm biology. Despite the importance of matrix proteins as potential targets for the development of antibacterial therapeutics little is known about matrix proteomes. As matrix responsible for some extracellular functions, it is expected that protein composition should be different compared to embedded in biofilm cells. This difference reflects possible active processes in the matrix. While P. aeruginosa is one of the most important pathogens with emerging antibiotic resistance only a few studies are devoted to matrix proteomes and there are no studies describing matrix proteome for any clinical isolates. Here we report the first matrix proteome in comparison with embedded cells for the clinical isolate of P. aeruginosa. We have identified the largest number of proteins in the matrix among all published studies devoted to P. aeruginosa biofilms. Functional classification of enriched in matrix proteins resulted in several bioprocess groups. Bioprocess groups with the largest number of overrepresented in matrix proteins were oxidation-reduction processes, proteolysis, and transmembrane transport. The top three represented in matrix bioprocesses concerning the size of the GO annotated database were: cell redox homeostasis, nucleoside metabolism, and fatty acid synthesis. Finally, we discuss obtained data in a prism of possible directions for antibiofilm therapeutics development.

category: microbiology


title: Soil collected in the Great Smoky Mountains National Park yielded a novel Listeria species, L. swaminathanii, effectively expanding the sensu stricto clade to ten species

abstract:
Soil samples collected in the Great Smoky Mountains National Park yielded a Listeria isolate that could not be classified to the species level. Whole-genome sequence-based average nucleotide identity BLAST and in silico DNA-DNA Hybridization analyses confirmed this isolate to be a novel Listeria sensu stricto species with the highest similarity to L. marthii (ANI=93.9%, isDDH=55.9%). Additional whole-genome-based analysis using the Genome Taxonomy Database Toolkit, an automated program for classifying bacterial genomes, further supported delineation as a novel Listeria sensu stricto species, as this tool failed to assign a species identification but identified L. marthii as the closest match. Phenotypic and genotypic characterization results indicate that this species is nonpathogenic. Specifically, the novel Listeria species described here is phenotypically (i) non-hemolytic and (ii) negative for phosphatidylinositol-specific phospholipase C activity; the draft genome lacks all virulence genes found in the Listeria pathogenicity island 1 (LIPI-1), as well as the internalin genes inlA and inlB. While the type strain for the new species is phenotypically catalase-negative (an unusual characteristic for Listeria sensu stricto species), its genome contained an apparently intact catalase gene (kat); hence assessment of this phenotype with future isolates will be important. Rapid species identification systems (Listeria API, VITEK 2, VITEK MS) misidentified this novel species as either L. monocytogenes, L. innocua, or L. marthii. We propose the name L. swaminathanii, and the type strain is FSL L7-0020T (=ATCC TSD-239T).

IMPORTANCEL. swaminathanii is a novel sensu stricto species that originated from a US National Park, and its place of origin is ultimately preventing this species from achieving valid status. The US National Park Service restricts strain accessibility and open access is currently a prerequisite for species validation. Essentially the only criteria that was not met for L. swaminathanii validation is accessibility of the type strain, therefore nomenclature status should not negate the significance of this discovery. As a novel sensu stricto species, L. swaminathanii expands the group of species whose presence is associated with an increased risk of an L. monocytogenes contamination, and therefore could play an important role in public health. While developers of Listeria spp. detection methods historically only included validly publish species in their validation studies, L. swaminathanii is unequivocally a sensu stricto species and should be included as well.


title: Exploratory growth in Streptomyces venezuelae involves a unique transcriptional program, enhanced oxidative stress response, and profound acceleration in response to glycerol

abstract: Exploration is a recently discovered mode of growth and behaviour exhibited by some Streptomyces species that is distinct from their classical sporulating life cycle. While much has been uncovered regarding initiating environmental conditions and the phenotypic outcomes of exploratory growth, how this process is coordinated at a genetic level remains unclear. We used RNA-sequencing to survey global changes in the transcriptional profile of exploring cultures over time in the model organism Streptomyces venezuelae. Transcriptomic analyses revealed widespread changes in gene expression impacting diverse cellular functions. Investigations into differentially expressed regulatory elements revealed specific groups of regulatory factors to be impacted, including the expression of several extracytoplasmic function (ECF) sigma factors, second messenger signalling pathways, and members of the whiB-like (wbl) family of transcription factors. Dramatic changes were observed among primary metabolic pathways, especially among respiration-associated genes and the oxidative stress response; enzyme assays confirmed that exploring cultures exhibit an enhanced oxidative stress response compared with classically growing cultures. Changes in expression of the glycerol catabolic genes in S. venezuelae led to the discovery that glycerol supplementation of the growth medium promotes a dramatic acceleration of exploration. This effect appears to be unique to glycerol as an alternative carbon source and this response is broadly conserved across other exploration-competent species.


title: Multi-Pathway DNA Double-Strand Break Repair Reporters Reveal Extensive Cross-Talk Between End-Joining, Single Strand Annealing, and Homologous Recombination

abstract: DNA double-strand breaks (DSB) are repaired by multiple distinct pathways, with outcomes ranging from error-free repair to extensive mutagenesis and genomic loss. Repair pathway cross-talk and compensation within the DSB-repair network is incompletely understood, despite its importance for genomic stability, oncogenesis, and the outcome of genome editing by CRISPR/Cas9. To address this, we constructed and validated three fluorescent Cas9-based reporters, named DSB-Spectrum, that simultaneously quantify the contribution of multiple distinct pathways to repair of a DSB. These reporters distinguish between DSB-repair by error-free canonical non-homologous end-joining (c-NHEJ) versus homologous recombination (HR; reporter 1), mutagenic repair versus HR (reporter 2), and mutagenic end-joining versus single strand annealing (SSA) versus HR (reporter 3). Using these reporters, we show that inhibition of the essential c-NHEJ factor DNA-PKcs not only increases repair by HR, but also results in a substantial increase in mutagenic repair by SSA. We show that SSA-mediated repair of Cas9-generated DSBs can occur between Alu elements at endogenous genomic loci, and is enhanced by inhibition of DNA-PKcs. Finally, we demonstrate that the short-range end-resection factors CtIP and Mre11 promote both SSA and HR, whereas the long-range end-resection factors DNA2 and Exo1 promote SSA, but reduce HR, when both pathways compete for the same substrate. These new Cas9-based DSB-Spectrum reporters facilitate the rapid and comprehensive analysis of repair pathway crosstalk and DSB-repair outcome.

category: molecular biology


title: Molecular liver fingerprint reflects the seasonal physiology of the grey mouse lemur (Microcebus murinus) during winter

abstract: Grey mouse lemurs (Microcebus murinus) are a primate species exhibiting strong physiological seasonality in response to environmental energetic constraint. They notably store large amounts of lipids during early winter (EW), which are thereafter mobilized during late winter (LW), when food availability is low. In addition, they develop glucose intolerance in LW only. To decipher how the hepatic mechanisms may support such metabolic flexibility, we analyzed the liver proteome of adult captive male mouse lemurs, which seasonal regulations of metabolism and reproduction are comparable to their wild counterparts, during the phases of either constitution or use of fat reserves. We highlight profound changes that reflect fat accretion in EW at the whole-body level, however, without triggering an ectopic storage of fat in the liver. Moreover, molecular regulations would be in line with the lowering of liver glucose utilization in LW, and thus with reduced tolerance to glucose. However, no major regulation was seen in insulin signaling/resistance pathways, which suggests that glucose intolerance does not reach a pathological stage. Finally, fat mobilization in LW appeared possibly linked to reactivation of the reproductive system and enhanced liver detoxification may reflect an anticipation to return to summer levels of food intake. Altogether, these results show that the physiology of mouse lemurs during winter relies on solid molecular foundations in liver processes to adapt fuel partitioning while avoiding reaching a pathological state despite large lipid fluxes. This work emphasizes how the mouse lemur is of primary interest for identifying molecular mechanisms relevant to biomedical field.


title: A Single-copy Knock In Translating Ribosome ImmunoPrecipitation (SKI TRIP) tool kit for tissue specific profiling of actively translated mRNAs in C. elegans.

abstract: Translating Ribosome Affinity Purification (TRAP) methods have emerged as a powerful approach to profile actively translated transcripts in specific cell and tissue types. Epitope tagged ribosomal subunits are expressed in defined cell populations and used to pull down ribosomes and their associated mRNAs, providing a snapshot of cell type-specific translation occurring in that space and time. Current TRAP toolkits available to the C. elegans community have been built using multi-copy arrays, randomly integrated in the genome. Here we introduce a Single-copy Knock In Translating Ribosome ImmunoPrecipitation (SKI TRIP) tool kit, a collection of C. elegans strains engineered by CRISPR in which tissue specific expression of FLAG tagged ribosomal subunit protein RPL-22 is driven by cassettes present in single copy from defined sites in the genome. In depth characterization of the SKI TRIP strains and methodology shows that 3xFLAG tagged RPL-22 expressed from its endogenous locus or within defined cell types incorporates into actively translating ribosomes and can be used to efficiently and cleanly pull-down cell type specific transcripts without impacting overall mRNA translation or fitness of the animal. We propose SKI TRIP use for the study of processes that are acutely sensitive to changes in translation, such as aging.

category: genetics


title: Epi-MEIF, a flexible and efficient method for detection of high order epistatic interactions from complex phenotypic traits

abstract: Understanding the relationship between genetic variations and variations in complex and quantitative phenotypes remains an ongoing challenge. While Genome-wide association studies (GWAS) have become a vital tool for identifying single-locus associations, we lack methods for identifying epistatic interactions. In this article, we propose a novel method for high-order epistasis detection using mixed effect conditional inference forest (epiMEIF). The epiMEIF model is fitted on a group of potential causal SNPs and the tree structure in the forest facilitates the identification of n-way interactions between the SNPs. Additional testing strategies further improve the robustness of the method. We demonstrate its ability to detect true n-way interactions via extensive simulations in both cross-sectional and longitudinal synthetic datasets. This is further illustrated in an application to reveal epistatic interactions from natural variations of cardiac traits in flies (Drosophila). Overall, the method provides a generalized way to identify high order interactions from any GWAS data, thereby greatly improving the detection of the genetic architecture of complex phenotypes.


title: Preserving protein homeostasis prevents motor impairment in DNA Damage Response-compromised C. elegans

abstract: To maintain genome integrity, cells rely on a complex system of DNA repair pathways and cell cycle checkpoints, together referred to as the DNA damage response (DDR). Impairments in DDR pathways are linked to cancer, but also to a wide range of degenerative processes, frequently including progressive neuropathy and accelerated aging. How defects in mechanistically distinct DDR pathways can drive similar degenerative phenotypes is not understood. Here we show that defects in various DDR components are linked to a loss of protein homeostasis in Caenorhabditis elegans. Prolonged silencing of atm-1, brc-1 or ung-1, central components in respectively checkpoint signaling, double strand break repair and base excision repair enhances the global aggregation of proteins occurring in adult animals, and accelerates polyglutamine protein aggregation in a model for neurodegenerative diseases. Overexpression of the molecular chaperone HSP-16.2 prevents enhanced protein aggregation in atm-1, brc-1 or ung-1-compromised animals. Strikingly, rebalancing protein homeostasis with HSP-16.2 almost completely rescues age-associated impaired motor function in these animals as well. This reveals that the consequences of a loss of atm-1, brc-1 or ung-1 converge on an impaired protein homeostasis to cause degeneration. These findings indicate that a loss of protein homeostasis is a crucial downstream consequence of DNA repair defects, and thereby provide an attractive novel framework for understanding the broad link between DDR defects and degenerative processes.


title: The Geometry of ATG-Walks of the Omicron SARS CoV-2 Virus RNAs

abstract: In this message, the complete RNA sequences (GISAID) of Omicron (BA.1 and BA.2) SARS CoV-2 viruses are studied using the genomic ATG-walks. These walks are compared visually and numerically with a reference RNA (Wuhan, China, 2020), and the deviation levels are estimated. Statistical characteristics of these distributions are compared, including the fractal dimension values of coding-word length distributions. Most of the 17 RNA ATG walks studied here show relatively small deviations of their characteristics and resistance to forming a new virus family.

category: genomics


title: Structure of anchorless RML prion reveals motif variation between strains

abstract:
Little is known about the structural basis of prion strains. Here we provide a high (3.0 [A]) resolution cryo-electron microscopy-based structure of brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register {beta}-sheet-based core. However, detailed comparisons reveal that variations in shared structural motifs provide a basis for prion strain determination.

One-sentence summaryCryo-electron microscopy reveals a near-atomic structure of an infectious, brain-derived murine prion fibril and strain differences.


title: Using antibody synergy to engineer a high potency biologic cocktail against C. difficile

abstract: We applied a mathematical framework originally used to model the effects of multiple inhibitors on enzyme activity to guide the development a therapeutic antibody cocktail, LMN-201, to prevent and treat C. difficile infection (CDI). CDI causes hundreds of thousands of cases of severe, often recurrent diarrhea and colitis in the United States annually and is associated with significant morbidity and mortality worldwide. Current therapies for preventing recurrent CDI are only partially successful, and there are no options available to prevent initial bouts of CDI in at-risk populations. Almost all antibody therapies have been developed and administered as monotherapies. Antibody cocktails are relatively rare even though they have the potential to greatly increase efficacy. One reason for this is our limited understanding of how antibody interactions can enhance potency, which makes it difficult to identify and develop antibodies that can be assembled into optimally effective cocktails. In contrast to the view that antibody synergies depend on unusual instances of cooperativity or allostery, we show that synergistic efficacy requires nothing more than that the antibodies bind independently to distinct epitopes on a common target. Therefore, synergy may be achieved much more readily than is generally appreciated. Due to synergy the LMN-201 antibody cocktail, which targets the C. difficile exotoxin B (TcdB), is 300- to 3000-fold more potent at neutralizing the most clinically prevalent TcdB toxin types than bezlotoxumab, the only monoclonal antibody currently approved for treatment or prevention of CDI. The efficacy of LMN-201 is further enhanced by inclusion of a phage-derived endolysin that destroys the C. difficile bacterium, and which therefore has a complementary mechanism of action to the antibody cocktail. These observations may serve as a paradigm for the development of high potency biologic cocktails against targets that have proven challenging for single-agent therapies.

category: bioengineering


title: PAR recognition by multiple reader domains of PARP1 allosterically regulates the DNA-dependent activities and independently stimulates the catalytic activity of PARP1

abstract: Poly(ADP-ribosyl)ation is a post translational modification, predominantly catalyzed by Poly(ADP-ribose) polymerase 1 (PARP1) in response to DNA damage, mediating the DNA repair process to maintain genomic integrity. Single strand (SSB) and double strand (DSB) DNA breaks are bonafide stimulators of PARP1 activity. We identified that, in addition, single strand (ss) DNA also binds and stimulates the PARP1 activity. Poly(ADP-ribose) (PAR) is chemically similar to ssDNA. However, PAR mediated PARP1 regulation remains unexplored. Here, we report ZnF3, BRCT and WGR, hitherto uncharacterized, as PAR-specific reader domains of PARP1. Surprisingly, these domains recognize PARylated protein with a higher affinity compared to PAR, but do not bind to DNA. Conversely, N-terminal domains, ZnF1 and ZnF2, of PARP1 recognize DNA but not PAR. Further competition binding studies suggest that PAR binding, allosterically releases DNA from PARP1. Unexpectedly, PAR showed catalytic stimulation of PARP1 but hampers the DNA dependent stimulation. Altogether, our work discovers dedicated PAR and DNA reader domains of the PARP1, and uncovers a novel mechanism of allosteric stimulation of the catalytic activity of PARP1 but retardation of DNA-dependent activities of PARP1 by its catalytic product PAR.


title: ANTAGONISM OF SAXITOXIN AND TETRODOTOXIN BLOCK BY INTERNAL MONOVALENT CATIONS IN SQUID AXON

abstract: The block of voltage-dependent sodium channels by saxitoxin (STX) and tetrodotoxin (TTX) was investigated in voltage-clamped squid giant axons internally perfused with a variety of permeant monovalent cations. Substitution of internal Na+ by either NH4+ or N2H5+ resulted in a reduction of outward current through sodium channels under control conditions. In contrast, anomalous increases in both inward and outward currents were seen for the same ions if some of the channels were blocked by STX or TTX, suggesting a relief of block by these internal cations. External NH4+ was without effect on the apparent magnitude of toxin block. Likewise, internal inorganic monovalent cations were without effect, suggesting that proton donation by NH4+ might be involved in reducing toxin block. Consistent with this hypothesis, decreases in internal pH mimicked internal perfusion with NH4+ in reducing toxin block. The interaction between internally applied protons and externally applied toxin molecules appears to be competitive, as transient increases in sodium channel current were observed during step increases in intracellular pH in the presence of a fixed STX concentration. In addition to these effects on toxin block, low internal pH produced a voltage-dependent block of sodium channels and enhanced steady-state inactivation. Elevation of external buffer capacity only marginally diminished the modulation of STX block by internal NH4+, suggesting that alkalinization of the periaxonal space and a resultant decrease in the cationic STX concentration during NH4+ perfusion may play only a minor role in the effect. These observations indicate that internal monovalent cations can exert trans-channel influences on external toxin binding sites on sodium channels.


title: A lung targeted miR-29 Mimic as a Therapy for Pulmonary Fibrosis

abstract:
microRNAs are non-coding RNAs that negatively regulate gene networks. Previously, we reported a systemically delivered miR-29 mimic MRG-201 that reduced fibrosis in animal models, but at doses prohibiting clinical translation. Here, we generated MRG-229, a next-gen miR-29 mimic with improved chemical stability, conjugated with the internalization moiety BiPPB (PDGFbetaR-specific bicyclic peptide). In TGF-b-treated human lung fibroblasts and precision cut lung slices, MRG-229 decreased COL1A1 and ACTA2 gene expression and reduced collagen production. In bleomycin-treated mice, intravenous or subcutaneous delivery of MRG-229 downregulated profibrotic gene programs at doses more than ten-fold lower than the original compound. In rats and non-human primates, and at clinically relevant doses, MRG-229 was well tolerated, with no adverse findings observed. In human peripheral blood decreased mir-29 concentrations were associated with increased mortality in two cohorts potentially identified as a target population for treatment. Collectively, our results provide support for the development of MRG-229 as a potential therapy in humans with IPF.

One Sentence SummaryOne Sentence Summary: A stabilized, next-generation miR-29 mimic has been developed that demonstrates efficacy at commercially viable doses with a robust safety margin in non-human primates.


title: Sex, amitosis, and evolvability in the ciliate Tetrahymena thermophila

abstract: Understanding the mechanisms that generate genetic variation, and thus contribute to the process of adaptation, is a major goal of evolutionary biology. Mutation and genetic exchange have been well studied as mechanisms to generate genetic variation. However, there are additional processes that may also generate substantial genetic variation in some populations and the extent to which these variation generating mechanisms are themselves shaped by natural selection is still an open question. Tetrahymena thermophila is a ciliate with an unusual mechanism of nuclear division, called amitosis, which can generate genetic variation among the asexual descendants of a newly produced sexual progeny. We hypothesize that amitosis thus increases the evolvability of newly produced sexual progeny relative to species that undergo mitosis. To test this hypothesis, we used experimental evolution and simulations to compare the rate of adaptation in T. thermophila populations founded by a single sexual progeny to parental populations that had not had sex in many generations. The populations founded by a sexual progeny adapted more quickly than parental populations in both laboratory populations and simulated populations. This suggests that the additional genetic variation generated by amitosis of a heterozygote can increase the rate of adaptation following sex and may help explain the evolutionary success of the unusual genetic architecture of Tetrahymena and ciliates more generally.


title: Intrinsic apoptosis is evolutionary divergent among metazoans

abstract: Apoptosis is characterised by an analogous set of morphological features1 that depend on a proteolytic multigenic family, the caspases2,3. Each apoptotic signalling pathway involves a specific initiator caspase, upstream of the pathway regulation, which finally converges to common executioner caspases. Intrinsic apoptosis, previously known as the mitochondrial apoptotic pathway, is often considered as ancestral and evolutionary conserved among animals2,4-8. First identified in the nematode Caenorhabditis elegans, intrinsic apoptosis was next characterised in fruit fly Drosophila melanogaster and mammals. Intrinsic apoptosis depends on the key initiator caspase-9 (named Ced-3 and Dronc in Caenorhabditis and Drosophila, respectively), the activator Apaf-1 and the Bcl-2 multigenic family2,6,9. Many functional studies have led to a deep characterisation of intrinsic apoptosis based on those classical models. Nevertheless, the biochemical role of mitochondria, the pivotal function of cytochrome c and the modality of caspases activation remain highly heterogeneous and hide profound molecular divergences among apoptotic pathways in animals8,10. Independent of functional approaches, the phylogenetic history of the signal transduction actors, mostly the caspase family, is the Rosetta Stone to shed light on intrinsic apoptosis evolution. Here, after exhaustive research on CARD-caspases, we demonstrate by phylogenetic analysis that the caspase-9, the fundamental key of intrinsic apoptosis, is deuterostomes-specific, while it is the caspase-2 which is ancestral and common to bilaterians. Our analysis of Bcl-2 family and Apaf-1 confirm the high heterogeneity in apoptotic pathways elaboration in animals. Taken together, our results support convergent emergence of distinct intrinsic apoptotic pathways during metazoan evolution.


title: Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

abstract:
Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens has the potential to identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here we present SalmoNet2, a major update to SalmoNet, the first multi-layered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory and enzyme enzyme interactions. The new version extends the number of Salmonella genomes from 11 to 20, including strains such as S. Typhimurium D23580, an epidemic multidrug-resistant strain leading to invasive non-typhoidal Salmonella Disease (iNTS), and a strain from Salmonella bongori, another species in the Salmonella genus. The database now uses strain specific metabolic models instead of a generalised model to highlight differences between strains. This has increased the coverage of high-quality protein-protein interactions, and enhances interoperability with other computational resources by adopting standardised formats. The resource website has been updated with tutorials to help researchers analyse their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/.

ImportanceMulti-layered network databases collate information from multiple sources, and are powerful both as a knowledge base and platform for analysis. Here we present SalmoNet2, an integrated network resource of 20 Salmonella strains, containing protein-protein, transcriptional regulatory, and metabolic interactions. Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyse their data using SalmoNet2.

category: systems biology


title: THEMIS is a priming substrate of non-receptor tyrosine phosphatase PTPN6/SHP1 and plays dual roles during T cell development

abstract: THEMIS plays an indispensable role in T cells, but its mechanism of action is highly controversial. Using the systematic proximity labeling methodology PEPSI, we identified THEMIS as an uncharacterized substrate for the phosphatase SHP1. Saturated mutagenesis analysis revealed that THEMIS phosphorylation at the evolutionally conserved Tyr34 residue was oppositely regulated by SHP1 and the kinase LCK. Like THEMIS-/- mice, THEMISY34F/Y34F knock-in mice showed a significant decrease in CD4 thymocytes and mature CD4 T cells, but a normal thymic development and peripheral homeostasis of CD8 T cells. Mechanistically, phosphorylated THEMIS induced by TCR activation acts as a "priming substrate" to bind SHP1 and convert its phosphatase activity from basal level to nearly fully activated level, ensuring an appropriate negative regulation of TCR signaling. However, cytokine signaling in CD8 T cells failed to elicit THEMIS Y34 phosphorylation, revealing both phosphorylation-dependent and -independent roles of THEMIS in controlling T cell maturation and expansion.


title: Glycolytic flux-signaling controls mouse embryo mesoderm development

abstract: How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic Pfkfb3 (cytoPfkfb3). Overexpression of cytoPfkfb3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPfkfb3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.

category: developmental biology


title: A novel method for improving the accuracy of MR-derived patient-specific vascular models using X-ray angiography

abstract: MR imaging is a noninvasive imaging modality that is commonly used during clinical follow up and has been widely utilized to reconstruct realistic 3D vascular models for patient-specific analysis. In a recent work, we utilized patient-specific hemodynamic analysis of the circle of Willis to noninvasively assess stroke risk in pediatric Moyamoya disease (MMD)--a progressive steno-occlusive cerebrovascular disease that leads to recurrent stroke. The objective was to identify vascular regions with critically high wall shear rate (WSR), signifying elevated stroke risk. However, sources of error including insufficient resolution of MR images can negatively impact vascular model accuracy, especially in areas of severe pathological narrowing, and thus diminish clinical relevance of simulation results, as local hemodynamics are sensitive to vessel geometry. We have developed a novel method to improve the accuracy of MR-derived 3D vascular models utilizing 2D X-ray angiography (XA), which is considered the gold standard for clinically assessing vessel caliber. In this workflow, "virtual angiographies" (VA) of 3D MR-derived vascular models are conducted, producing 2D projections that are compared to corresponding XA images guiding the local adjustment of modeled vessels. This VA-comparison-adjustment loop is iterated until the two agree, as confirmed by an expert neuroradiologist. Using this method, we generated models of the circle of Willis of two patients with a history of unilateral stroke. Blood flow simulations were performed using a Navier-Stokes solver within an isogeoemtric analysis framework and WSR distributions were quantified. Results for one patient show as much as 45% underestimation of local WSR in the stenotic left anterior cerebral artery (LACA) and up to a 60% underestimation in the right anterior cerebral artery when using the initial MR-derived model compared to the XA-adjusted model, emphasizing the need for verifying improved accuracy of the adjusted model. To that end, vessel cross-sectional areas of the pre- and post-adjustment models were compared to those seen in 3D CTA images of the same patient. CTA has superior resolution and signal to noise ratio compared to MR imaging but is not commonly used in clinic due to radiation exposure concerns, especially in pediatric patients. While the vessels in the initial model had normalized root mean squared deviations (NRMSDs) ranging from 26% to 182% and 31% to 69% in two patients with respect to CTA, the adjusted vessel NRMSDs were comparatively smaller (32% to 53% and 11% to 42%). In the mildly stenotic LACA of patient 1, the NRMSDs for the pre- and post-adjusted models were 49% and 32%, respectively. These findings suggest that our XA-based adjustment method can considerably improve the accuracy of vascular models, and thus, stroke-risk prediction. An accurate individualized assessment of stroke risk would be of substantial clinical benefit because it would help guide the timing of preventative surgical interventions in pediatric MMD patients.


title: Biophysical and pharmacokinetic characterization of a small-molecule inhibitor of RUNX1/ETO tetramerization with anti-leukemic effects

abstract: Acute myeloid leukemia (AML) is a malignant disease of immature myeloid cells and the most prevalent acute leukemia among adults. The oncogenic homo-tetrameric fusion protein RUNX1/ETO results from the chromosomal translocation t(8;21) and is found in AML patients. The nervy homology region 2 (NHR2) domain of ETO mediates tetramerization; this oligomerization is essential for oncogenic activity. Previously, we identified the first-in-class small-molecule inhibitor of NHR2 tetramer formation, 7.44, which was shown to specifically interfere with NHR2, restore gene expression down-regulated by RUNX1/ETO, inhibit the proliferation of RUNX1/ETO-depending SKNO-1 cells, and reduce the RUNX1/ETO-related tumor growth in a mouse model. However, no biophysical and structural characterization of 7.44 binding to the NHR2 domain has been reported. Likewise, the compound has not been characterized as to physicochemical, pharmacokinetic, and toxicological properties. Here, we characterize the interaction between the NHR2 domain of RUNX1/ETO and 7.44 by biophysical assays and show that 7.44 interferes with NHR2 tetramer stability and leads to an increase in the dimer population of NHR2. The affinity of 7.44 with respect to binding to NHR2 is Klig = 3.95 {+/-} 1.28 M. By NMR spectroscopy combined with molecular dynamics simulations, we show that 7.44 binds with both heteroaromatic moieties to NHR2 and interacts with or leads to conformational changes in the N-termini of the NHR2 tetramer. Finally, we demonstrate that 7.44 has favorable physicochemical, pharmacokinetic, and toxicological properties. Together with biochemical, cellular, and in vivo assessments, the results reveal 7.44 as a lead for further optimization towards targeted therapy of t(8;21) AML.


title: L-type calcium channel blocker increases VEGF concentrations in retinal cells and human serum

abstract:
ObjectiveVascular endothelial growth factor (VEGF) plays a key role in diabetic retinopathy (DR). L-type calcium channel blockers (LTCCBs) have been widely used as antihypertensive medication (AHM), but their association with VEGF and DR is still unclear. Therefore, we explored the effect of LTCCBs compared to other AHMs on VEGF concentrations in retinal cells and human serum. Furthermore, we evaluated the association between the use of LTCCBs and the risk of severe diabetic eye disease (SDED).

Research design and methodsMuller cells (MIO-M1) were cultured as per recommended protocol and treated with LTCCBs and other AHMs. VEGF secreted from cells were collected at 24 hours intervals. In an interventional study, 39 individuals received LTCCBs or other AHM for four weeks with a four-week wash-out placebo period between treatments. VEGF was measured during the medication and placebo periods. Finally, we evaluated the risk of SDED associated with LTCCB usage in 192 individuals from the FinnDiane Study in an oberservational setting.

ResultsIn the cell cultures, medium VEGF concentration increased time-dependently after amlodipine (p<0.01) treatment, but not after losartan (p>0.01), or lisinopril (p>0.01). Amlodipine, but no other AHM, increased serum VEGF concentration (p<0.05) during the interventional clinical study. The usage of LTCCB was not associated with the risk of SDED in the observational study.

ConclusionsLTCCB increases VEGF concentrations in retinal cells and human serum. However, the usage of LTCCBs does not appear to be associated with SDED in adults with type 1 diabetes.

category: pharmacology and toxicology


title: Understanding Harmonic Structures Through Instantaneous Frequency

abstract: The analysis of harmonics and non-sinusoidal waveform shape in neurophysiological data is growing in importance. However, a precise definition of what constitutes a harmonic is lacking. In this paper, we propose a rigorous definition of when to consider signals to be in a harmonic relationship based on an integer frequency ratio, constant phase, and a well-defined joint instantaneous frequency. We show this definition is linked to extrema counting and Empirical Mode Decomposition (EMD). We explore the mathematics of our definition and link it to results from analytic number theory. This naturally leads to us to define two classes of harmonic structures, termed strong and weak, with different extrema behaviour. We validate our framework using both simulations and real data. Specifically, we look at the harmonics structure in the FitzHugh-Nagumo model and the non-sinusoidal hippocampal theta oscillation in rat local field potential data. We further discuss how our definition helps to address mode splitting in EMD. A clear understanding of when harmonics are present in signals will enable a deeper understanding of the functional and clinical roles of non-sinusoidal neural oscillations.

category: neuroscience


title: Visual, delay and oculomotor timing and tuning in macaque dorsal pulvinar during instructed and free choice memory saccades

abstract: Causal perturbation studies suggest that the primate dorsal pulvinar (dPul) plays a crucial role in target selection and saccade planning, but many of its basic visuomotor neuronal properties are unclear. While some functional aspects of dPul and interconnected frontoparietal areas - such as ipsilesional choice bias after inactivation - are similar, it is not known if dPul neurons share oculomotor response properties of cortical circuitry. In particular, the delay period and choice-related activity have not been explored. Here we investigated visuomotor timing and tuning in macaque dPul during instructed and free choice memory saccades using electrophysiological recordings. Most units (80%) showed significant visual (16%), visuomotor (29%) or motor-related (35%) responses. Visual cue responses were mainly contralaterally-tuned; motor responses showed weak contralateral bias. Saccade-related responses (enhancement and suppression) were more common (64%) than cue-driven responses (45%). Pre-saccadic enhancement was less frequent (9-15% depending on the definition), and only few units exhibited classical visuomotor patterns such as a combination of cue and continuous delay period activity up to the saccade onset, or pre-saccadic ramping. Instead, activity was often suppressed during movement planning (30%) and execution phases (19%). Interestingly, most spatially-selective neurons did not encode the upcoming decision during the delay in free choice trials. Thus, in absence of a visible goal, the dorsal pulvinar has only a limited role in the prospective motor planning, with response patterns partially complementary to its frontoparietal cortical partners. Conversely, prevalent cue and post-saccadic responses imply that the dorsal pulvinar participates in integrating spatial goals with processing across saccades.


title: Sequential propagation and routing of activity in a cortical network

abstract: Single spikes can trigger repeatable sequences of spikes in cortical networks. The mechanisms that support reliable propagation from such small events and their functional consequences for network computations remain unclear. We investigated the conditions in which single spikes trigger reliable and temporally precise sequences in a network model constrained by experimental measurements from turtle cortex. We examined the roles of connectivity, synaptic strength, and spontaneous activity in the generation of sequences. Sparse but strong connections support sequence propagation, while dense but weak connections modulate propagation reliability. Unsupervised clustering reveals that sequences can be decomposed into sub-sequences corresponding to divergent branches of strongly connected neurons. The sparse backbone of strong connections defines few failure points where activity can be selectively gated, enabling the controlled routing of activity. These results reveal how repeatable sequences of activity can be triggered, sustained, and controlled, with significant implications for cortical computations.


title: DNA fluctuations reveal the size and dynamics of topological domains

abstract:
DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real-time and at the single molecule level. Our approach is based on quantifying the extension fluctuations - in addition to the mean extension - of supercoiled DNA in magnetic tweezers. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our approach to enable quantification of the dynamics and reaction pathways of DNA processing enzymes and motor proteins, in the context of physiologically relevant forces and supercoiling densities.

SignificanceIn the cell, long DNA molecules carry the genetic information and must be stored and maintained, yet remain accessible for read out and processing. DNA supercoiling facilitates compaction of DNA, modulates its accessibility, and spatially juxtaposes DNA sites distant in linear DNA sequence. By binding to two sites in supercoiled DNA, DNA bridging proteins can pinch off topological domains and alter DNA plectoneme dynamics. Here we show how DNA bridging and topological domain dynamics can be detected from changes in the extension fluctuations of supercoiled DNA molecules tethered in magnetic tweezers. Our work highlights how considering DNA extension fluctuations, in addition to the mean extension, provides additional information and enables the investigation of protein-DNA interactions that are otherwise invisible.


title: Long-term non-invasive drug treatments for adult zebrafish

abstract:
Zebrafish embryos are widely used for drug-discovery however administering drugs to adult zebrafish is limited by current protocols that can cause stress. Here, we develop a drug formulation and administration method for adult zebrafish by producing food-based drug pellets which are consumed voluntarily. We apply this to zebrafish with BRAF-mutant melanoma, a model that has significantly advanced our understanding of melanoma progression, but not of drug resistance due to the limitations of current treatment methods. Short-term, precise, and daily dosing with drug-pellets made with the BRAFV600E inhibitor, vemurafenib, led to tumour regression. On-target drug efficacy was determined by phospho-ERK staining. Continued drug treatment led to the emergence, for the first time in zebrafish, of acquired drug resistance and melanoma relapse, modelling the responses seen in melanoma patients. This method presents a controlled, non-invasive approach that permits long-term drug studies, and can be widely applied to any adult zebrafish model.

SUMMARY STATEMENTThis drug-pellet approach is a precise dosing method to administer short or long-term drug treatments to adult zebrafish, that is stress-free for the fish and requires minimal animal handling. We use this method to develop new drug-resistant models of melanoma in zebrafish, opening new doors for modelling and screening drug treatments in adult zebrafish.


title: Alcohol availability during withdrawal gates the impact of alcohol vapor exposure on responses to alcohol cues

abstract:
BackgroundChronic intermittent ethanol (CIE) vapor inhalation is a widely used model of alcohol dependence, but the impact of CIE on cue-elicited alcohol seeking is not well understood. Here, we assessed the effects of CIE on alcohol-seeking elicited by previously learned cues, and on acquisition of new cue-alcohol associations.

MethodsIn Experiment 1, male and female Long Evans rats were first trained in a discriminative stimulus (DS) task, in which one auditory cue (the DS) predicts the availability of 15% ethanol and a control cue (the NS) predicts nothing. Rats then underwent CIE or served as controls. Subsets of each group received access to oral ethanol twice a week during acute withdrawal. After CIE, rats were presented with the DS and NS cues under extinction and retraining conditions to determine whether they would alter their responses to these cues. In Experiment 2, rats underwent CIE prior to training in the DS task. We also assessed alcohol consumption, aversion-resistant drinking, somatic withdrawal symptoms, and behavior in an open field.

ResultsWe found that CIE enhanced behavioral responses to previously learned alcohol cues, but only in rats that received access to alcohol during acute withdrawal. CIE disrupted cue responses in rats that did not. When CIE occurred before cue learning, male rats were slower to develop cue responses and less likely to enter the alcohol port, even though they had received alcohol during acute withdrawal. We also found that CIE increased alcohol consumption and aversion-resistant drinking in male but not female rats.

ConclusionsThese results suggest that CIE alone does not potentiate the motivational value of alcohol cues, but that an increase in cue responses requires the potentiation of the value of alcohol during acute withdrawal. Further, under some conditions CIE may disrupt responses to previously learned and subsequently acquired alcohol cues.


title: Evaluation of Commercially Available Glucagon Receptor Antibodies and Glucagon Receptor Expression

abstract: Glucagon is a key regulator of numerous metabolic functions including glucose, protein and lipid metabolism, and glucagon-based therapies are explored for diabetes, fatty liver disease and obesity. Insight into tissue and cell specific expression of the glucagon receptor (GCGR) is important to understand the biology of glucagon as well as to differentiate between direct and indirect actions of glucagon. However, it has been challenging to accurately localize the GCGR in tissue due to low expression levels and lack of specific methodologies. Immunohistochemistry has frequently been used for GCGR localization, but G-protein-coupled receptors (GPCRs) targeting antibodies are notoriously unreliable. In this study, we systematically evaluated all commercially available GCGR antibodies. Initially, twelve GCGR antibodies were evaluated using HEK293 cells transfected with mouse or human GCGR cDNA. Of the twelve antibodies tested, eleven showed positive staining of GCGR protein from both species. Human liver tissue was investigated using the same GCGR antibodies. Five antibodies failed to stain human liver biopsies (despite explicit claims to the contrary from the vendors). Immunohistochemical (IHC) staining demonstrated positive staining of liver tissue from glucagon receptor knockout (Gcgr-/-) mice and their wild-type littermates (Gcgr+/+) with only one out of the twelve available GCGR antibodies. Three antibodies were selected for further evaluation by western blotting and bands corresponding to the predicted size of the GCGR (62 kDa) were identified using two of these. Finally, a single antibody (no. 11) was selected for specific GCGR localization studies in various tissues. In mouse tissue the most intense immunostainings were found in lever, kidney, ileum, heart, and pancreas. Western blotting, performed on liver tissue from Gcgr+/+ and Gcgr-/- mice, confirmed the specificity of antibody no. 11, detecting a band at high intensity in material from Gcgr+/+and no bands in liver tissue from Gcgr-/-mice. Staining of human kidney tissue, with antibody no. 11, showed GCGR localization to the distal tubules. Autoradiography was used as an antibody-independent approach to support the antibody-based findings, revealing specific binding in liver, pancreas, and kidney. As a final approach, RNA-sequencing and single-cell RNA (scRNA)-sequencing were implemented. RNA-sequencing confirmed GCGR presence within liver and kidney tissue. The GCGR was specifically found to be expressed in hepatocytes by scRNA-sequencing and potentially also in collecting and distal tubule cells in the kidney. Our results clearly indicate the liver and the kidneys as the primary targets of glucagon action.

category: physiology


title: Depriving mice of sleep also deprives of food

abstract: Both sleep-wake behavior and circadian rhythms are tightly coupled to energy metabolism and food intake. Altered feeding times in mice are known to entrain clock-gene rhythms in brain and liver and sleep-deprived humans tend to eat more and gain weight. Previous observations in mice showing that sleep deprivation (SD) changes clock-gene expression might thus relate to altered food intake and not to the loss of sleep per se. Whether SD affects food intake in the mouse and how this might affect clock-gene expression is, however, unknown. We therefore quantified i) the cortical expression of the clock genes Per1, Per2, Dbp, and Cry1 in mice that had access to food or not during a 6h SD, and ii) food intake during baseline, SD, and recovery sleep. We found that food deprivation did not modify the SD-incurred clock-gene changes in the cortex. Moreover, we discovered that although food intake during SD did not differ from baseline, mice lost weight and increased food intake during subsequent recovery. We conclude that SD is associated with food deprivation and that the resulting energy deficit might contribute to the effects of SD that are commonly interpreted as a response to sleep loss.


title: Harmonizing labeling and analytical strategies to obtain protein turnover rates in intact adult animals.

abstract: Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [13C6]lysine or [2H2]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.


title: Scars of hope and forewarn of a bleak future: Post-mortem findings of dugongs (Dugong dugon) belonging to a relict population in the Gulf of Kachchh, India

abstract: A relict dugong population resides in the Gulf of Kachchh in Gujarat state of India. Very little is known on this population stemming from lack of focused studies and inadequate examinations of previous strandings. In this study, crucial ecological information is gathered through a systematic necropsy on stranded dugongs in the gulf. As indicated through dorsal tusk-rake scars on both the carcasses, this study presents first records of derivative physical evidence to the presence of a socially interacting population. Progressive healing and differences in width of the scars indicated more than two individuals had participated in a sexual agnostic or courtship event. Conversely, our findings report that both the animals suffered relative effects of asphyxiation after fishing net entanglement. An implication of a prior pathological condition(s) in the form of dermal cysts, swollen mesenteric lymph nodes, and endoparasites are also reported. Stomach content was examined for a qualitative dietary characterization. Other potential threats along with fishing net microfilaments found in the stomach contents of both dugongs are discussed in brief.

category: zoology


title: Histopathological Changes In The Intestine Of Infected Pigeons (Columba Livia Domestica) Caused By Helminthes Infection From Al-Qassim, Saudi Arabia

abstract: Helminthes infection causes extensive harm to the pigeon host. The purpose of this study was to observe histopathological changes caused by helminths infection. Thirty-five pigeons (C.L. domestica) were purchased weekly from a birds market from Al-Qassim region, Saudi Arabia. Out of the 35 pigeons examined, 9 pigeons (25.71%) were found infected with helminth parasites, which were identified as one cestode (Raillietina sp.), and one nematode (Ascaridia columbae). The infected pigeons suffered from growth retardation, emaciation, weakness, droopiness, and diarrhea. A lot of histopathological changes were seen in the intestine of infected pigeons including atrophy and distortion of villi, infiltration of inflammatory lymphocytic cells, erosion, and loss of the typical structure of the intestine, necrosis in villi, and blood vessels congestion. This study concludes, for the first time in AL-Qassim region-Saudi Arabia, that the infection with helminth parasites caused significant histopathological changes in the intestines of the infected pigeons, and this could lead to increased mortality to the infected pigeons. Further work is necessary in Saudi Arabia to determine the prevalence and biological factors that have a significant impact on the helminth parasites community.


title: CNTF enhances aerobic glycolysis and anabolic activities in degenerating retinas

abstract: Ciliary neurotrophic factor (CNTF) has potent neuroprotective activity in retinal degeneration animal models, yet the cellular mechanisms underlying its broad neuronal survival effects remain unclear. Here, we investigated the impact of CNTF on retinal metabolism in a mouse model of human retinitis pigmentosa. CNTF treatment resulted in improved mitochondrial morphology in mutant rod photoreceptors, but also led to reduced oxygen consumption and suppression of respiratory chain complex activities. Metabolomics analyses detected significantly higher levels of ATP and the energy currency phospho-creatine post CNTF exposure. In addition, CNTF-treated retinas contained elevated glycolytic metabolites and showed increased expression of genes and active enzymes of the glycolytic pathway. Metabolomics analyses also revealed increased TCA cycle products, lipid biosynthetic pathway intermediates, nucleotides, and amino acids, indicating an overall CNTF-dependent augmentation of anabolic activities. Moreover, CNTF treatment restored the key antioxidant glutathione to the wild type level in the degenerating retina. Taken together, these results demonstrate that CNTF profoundly impacts the metabolic status of degenerating retinas by promoting aerobics glycolysis and anabolism, enhancing energy supply, and restoring redox homeostasis. Our study thus reveals important cellular mechanisms underlying CNTF-mediated neuroprotection and provides novel insight for the on-going CNTF clinical trials treating blinding diseases.


title: Young APPKI NL-G-F/NL-G-F mice display high-fat diet-induced metabolic disturbances and specific disorders associated with brain energy homeostasis.

abstract:
AimType 2 diabetes mellitus (T2DM) is an increased risk factor for Alzheimers disease (AD); however, the relationship between the two conditions is controversial. High-fat diet (HFD) causes cognitive impairment with/without A{beta} accumulation in middle-aged or aged transgenic (Tg) and knock-in (KI) AD mouse models, except for metabolic disorders, which commonly occur in all mice types. Alternatively, whether HFD in early life impacts energy metabolism and neurological phenotypes in young AD mouse models remains unknown. In the present study, we examined the effects of HFD on young APPKI NL-G-F/NL-G-F mice, one of the novel knock-in (KI)-AD mouse models.

MethodsThe mice were categorized by diet into two experimental groups, normal diet (ND) and HFD. Four-week-old WT and APPKI NL-G-F/NL-G-F mice were fed ND or HFD for nine weeks. Both types of mice on ND and HFD were examined during young adulthood.

ResultsHFD causes T2DM-related metabolic disturbances in young WT and APPKI NL-G-F/NL-G-F mice and specific impairment of brain energy homeostasis only in young APPKI NL-G-F/NL-G-F mice. However, HFD-induced metabolic dysfunctions had no impact on behaviors, A{beta} levels, and specific IRS1 modifications in both young APPKI NL-G-F/NL- G-F mice and young WT mice.

ConclusionHFD in early life is effective in causing metabolic disturbances in young WT and APPKI NL-G-F/NL-G-F mice but is ineffective in inducing neurological disorders in young mice, which suggests that the aging effects along with long-term HFD cause neurological alterations.


title: Application of a simple device for "attracting" and "trapping" glioma cells in situ

abstract: Glioblastoma multiforme (GBM) is the most malignant adult brain tumor. The current adjuvant therapies for GBM are disappointing, which are based on cytotoxicity strategy. Thus, other ways should be explored to improve the curative effect. According to the strong invasive ability of GBM cells, we assume a new treatment strategy for GBM by developing a new cell trap device (CTD) with some kind of "attractive" medium loaded in it to attract and capture the tumor cells. The in vitro experiment showed that Hepatocyte Growth Factor (HGF) presented stronger chemotaxis on C6 and U87 cell line than the Epidermal Growth Factor (EGF) and Fibroblast Growth Factor (FGF). A simple in vitro CTD loaded with HGF was made and in vivo experiments results showed that HGF successfully attracted tumor cells from tumor bed in situ into the CTD. This study proposes the new strategy for GBM treatment of "attract and trap" tumor cells is proved to be feasible.


title: Quantifying defensive behavior and threat response through integrated headstage accelerometry

abstract:
BackgroundDefensive and threat-related behaviors are common targets of investigation, because they model aspects of human mental illness. These behaviors are typically quantified by video recording and post hoc analysis. Those quantifications can be laborious and/or computationally intensive.

Depending on the analysis method, the resulting measurements can be noisy or inaccurate. Other defensive behaviors, such as suppression of operant reward seeking, require extensive animal pre-training.

New MethodWe demonstrate a method for quantifying defensive behavior (immobility or freezing) by 3-axis accelerometry integrated with an electrophysiology headstage. We tested multiple pre-processing and smoothing methods, and correlated them against two common methods for quantification: freezing as derived from standard video analysis, and suppression of operantly shaped bar pressing. We assessed these three methods ability to track defensive behavior during a standard threat conditioning and extinction paradigm.

ResultsThe best approach to tracking defensive behavior from accelerometry was Gaussian filter smoothing of the first derivative (change score or jerk). Behavior scores from this method reproduced canonical conditioning and extinction curves at the group level. At the individual level, timepoint-to-timepoint correlations between accelerometry, video, and bar press metrics were statistically significant but modest (largest r=0.53, between accelerometry and bar press).

Comparison with existing methodsThe integration with standard electrophysiology systems and relatively lightweight signal processing may make accelerometry particularly well suited to detect behavior in resource-constrained or real-time applications. At the same time, there were modest cross-correlations between all three methods for quantifying defensive behavior.

ConclusionsAccelerometry analysis allows researchers already using electrophysiology to assess defensive behaviors without the need for additional behavioral measures or video. The similarities in behavioral tracking and modest correlations between each metric suggest that each measures a distinct aspect of defensive behavior. Accelerometry is a viable alternative to current defensive measurements, and its non-overlap with other metrics may allow a more sophisticated dissection of threat responses in future experiments.

HighlightsO_LIA novel method to assess defensive behavior and immobility based on headstage accelerometry
C_LIO_LICompatible with readily available, open-source neurophysiology systems
C_LIO_LIProvides behavioral insights without the need for video analysis software and with relatively minimal processing, suitable for rapid closed-loop experiments
C_LI


title: Induction of flight via midbrain projections to thecuneiform nucleus

abstract: The dorsal periaqueductal gray is a midbrain structure implicated in the control of defensive behaviors and the processing of painful stimuli. Electrical stimulation or optogenetic activation of excitatory neurons in dorsal periaqueductal gray results in freezing or flight behavior at low or high intensity, respectively. However, the output structures that mediate these defensive behaviors remain unconfirmed. Here we carried out a targeted classification of neuron types in dorsal periaqueductal gray using multiplex in situ sequencing and then applied cell-type and projection-specific optogenetic stimulation to identify projections from dorsal periaqueductal grey to the cuneiform nucleus that promoted goal-directed flight behavior. These data confirmed that descending outputs from dorsal periaqueductal gray serve as a trigger for directed escape behavior.


title: A network model of the modulation of gamma oscillations by NMDA receptors in cerebral cortex

abstract: Psychotic drugs such as ketamine induce symptoms close to schizophrenia, and stimulates the production of gamma oscillations, as also seen in patients, but the underlying mechanisms are still unclear. Here, we have used computational models of cortical networks generating gamma oscillations, and have integrated the action of drugs such as ketamine to partially block n-methyl-d-Aspartate (NMDA) receptors. The model can reproduce the modulation of gamma oscillations by NMDA-receptor antagonists, assuming that antagonists affect NMDA receptors predominantly on inhibitory interneurons. We next used the model to compare the responsiveness of the network to external stimuli, and found that when NMDA channnels are blocked an increase of Gamma power is observed altogether with an increase of network responsiveness. However, this responsiveness increase applies not only to gamma states, but also to asynchronous states with no apparent gamma. We conclude that NMDA antagonists induce increased excitability state, which may or may not produce gamma oscillations, but the response to external inputs is exacerbated, which may explain phenomena such as altered perception or hallucinations.


title: Local activation of focal adhesion kinase orchestrates the positioning of presynaptic scaffold proteins and Ca2+ channel function to control glucose dependent insulin secretion.

abstract: A developing understanding suggests that spatial compartmentalisation of components the glucose stimulus-secretion pathway in pancreatic {beta} cells are critical in controlling insulin secretion. To investigate the mechanisms, we have developed live-cell sub-cellular imaging methods using the organotypic pancreatic slice. We demonstrate that the organotypic pancreatic slice, when compared with isolated islets, preserves intact {beta} cell structure, and enhances glucose dependent Ca2+ responses and insulin secretion. Using the slice technique, we have discovered the essential role of local activation of integrins and the downstream component, focal adhesion kinase, in regulating {beta} cells. Integrins and focal adhesion kinase are exclusively activated at the {beta} cell capillary interface and using in situ and in vitro models we show their activation both positions presynaptic scaffold proteins, like ELKS and liprin, and regulates glucose dependent Ca2+ responses and insulin secretion. We conclude that focal adhesion kinase orchestrates the final steps of glucose dependent insulin secretion within the restricted domain where {beta} cells contact the islet capillaries.

category: cell biology


title: A vascularized 3D model of the human pancreatic islet for ex vivo study of immune cell-islet interaction

abstract: Insulin is an essential regulator of blood glucose homeostasis that is produced exclusively by {beta} cells within the pancreatic islets of healthy individuals. In those affected by diabetes, immune inflammation, damage, and destruction of islet {beta} cells leads to insulin deficiency and hyperglycemia. Current efforts to understand the mechanisms underlying {beta} cell damage in diabetes rely on in vitro-cultured cadaveric islets. However, isolation of these islets involves removal of crucial matrix and vasculature that supports islets in the intact pancreas. Unsurprisingly, these islets demonstrate reduced functionality over time in standard culture conditions, thereby limiting their value for understanding native islet biology. Leveraging a novel, vascularized micro-organ (VMO) approach, we have recapitulated elements of the native pancreas by incorporating isolated human islets within a three-dimensional matrix nourished by living, perfusable blood vessels. Importantly, these islets show long-term viability and maintain robust glucose-stimulated insulin responses. Furthermore, vessel-mediated delivery of immune cells to these tissues provides a model to assess islet-immune cell interactions and subsequent islet killing -- key steps in type 1 diabetes pathogenesis. Together, these results establish the islet-VMO as a novel, ex vivo platform for studying human islet biology in both health and disease.


title: Myofibroblast Senescence Promotes Arrhythmogenic Remodeling in the Aged Infarcted Rabbit Heart

abstract: Progressive tissue remodeling after myocardial infarction (MI) promotes cardiac arrhythmias. This process is well studied in young animals, but little is known about pro-arrhythmic changes in aged animals. Senescent cells accumulate with age and accelerate age-associated diseases. Senescent cells interfere with cardiac function and outcome post-MI with age, but studies have not been performed in large animals, and the mechanisms are unknown. Here, we investigated the role of senescence in regulating inflammation, fibrosis, and arrhythmogenesis in young and aged infarcted rabbits. Aged rabbits exhibited increased peri-procedural mortality and arrhythmogenic electrophysiological remodeling at the infarct border zone (IBZ) compared to young rabbits. Studies of the aged infarct zone revealed persistent myofibroblast senescence and increased inflammatory signaling over a twelve-week timecourse. Senescent IBZ myofibroblasts in aged rabbits appear to be coupled to myocytes, and our computational modeling showed that senescent myofibroblast- cardiomyocyte coupling prolongs action potential duration (APD) and facilitates conduction block permissive of arrhythmias. Aged infarcted human ventricles show levels of senescence consistent with aged rabbits, and senescent myofibroblasts also couple to IBZ myocytes. Our findings suggest that senolytic drugs may mitigate arrhythmias post-MI.


title: The origins of placental mesenchymal stromal cells: Full spectrum flow cytometry reveals mesenchymal heterogeneity in first trimester placentae, and phenotypic convergence in culture

abstract: Single-cell technologies (RNA-sequencing, flow cytometry) are critical tools to reveal how cell heterogeneity impacts developmental pathways. The placenta is a fetal exchange organ, containing a heterogeneous mix of mesenchymal cells (fibroblasts, myofibroblasts, perivascular, and progenitor cells). Placental mesenchymal stromal cells (pMSC) are also routinely isolated, for therapeutic and research purposes. However, our understanding of the diverse phenotypes of placental mesenchymal lineages, and their relationships remain unclear. We designed a 23-colour flow cytometry panel to assess mesenchymal heterogeneity in first-trimester human placentae.. Four distinct mesenchymal subsets were identified; CD73+CD90+ mesenchymal cells, CD146+CD271+ perivascular cells, podoplanin+CD36+ stromal cells, and CD26+CD90+ myofibroblasts. CD73+CD90+ and podoplanin+CD36+ cells expressed markers consistent with cultured pMSCs, and were explored further. Despite their distinct ex-vivo phenotype, in culture CD73+CD90+ cells and podoplanin+CD36+ cells underwent phenotypic convergence, losing CD271 or CD36 expression respectively, and homogenously exhibiting a basic MSC phenotype (CD73+CD90+CD31-CD144-CD45-). However, some markers (CD26, CD146) were not impacted, or differentially impacted by culture in different populations. Comparisons of cultured phenotypes to pMSCs further suggested cultured pMSCs originate from podoplanin+CD36+ cells. This highlights the importance of detailed cell phenotyping to optimise therapeutic capacity, and ensure use of relevant cells in functional assays.


title: Hemicentin mediated type IV collagen assembly strengthens juxtaposed basement membrane linkage

abstract:
Basement membrane (BM) matrices surround and separate most tissues. However, through poorly understood mechanisms, BMs of adjacent tissues can also stably link to support organ structure and function. Using endogenous knock-in fluorescent proteins, conditional RNAi, optogenetics, and quantitative live imaging, we identified matrix proteins mediating a BM linkage (B-LINK) between the uterine utse and epidermal seam cell BMs in Caenorhabditis elegans that supports the uterus during egg-laying. We found that hemicentin is secreted by the utse and promotes fibulin-1 assembly to jointly initiate the B-LINK. During egg-laying, however, both proteins decline in levels and are not required for B-LINK maintenance. Instead, we discovered that hemicentin also promotes type IV collagen assembly, which accumulates to high levels during egg-laying and sustains the B-LINK during the mechanically active egg-laying period. This work reveals mechanisms underlying BM-BM connection maturation and identifies a crucial function for hemicentin and fibulin-1 in initiating attachment and type IV collagen in strengthening this specialized form of tissue linkage.

SummaryTissue attachment through linking juxtaposed basement membranes (BMs) is crucial for the structure and function of many organs. Gianakas et al. identify a key role for hemicentin and fibulin-1 in initiating BM-BM attachment and type IV collagen in stabilizing this linkage and allowing it to resist high mechanical loads.


title: Alignment of genetic differentiation across trophic levels in a fig community

abstract:
Ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Co-occurrence is likely to be particularly intense when species exhibit obligate comigration, in which they not only overlap in spatial distributions but also travel together from patch to patch. In theory, this pattern of ecological co-occurrence should leave a distinct signature in the pattern of genetic differentiation within and among species. Perhaps the most famous mutual co-isolation partners are fig trees and their co-evolved wasp pollinators. Here, we add another tropic level to this system by examining patterns of genomic diversity in the nematode Caenorhabditis inopinata, a close relative of the C. elegans model system that thrives in figs and obligately disperses on fig wasps. We performed RADseq on individual worms isolated from the field across three Okinawan island populations. The male/female C. inopinata is about five times more diverse than the hermaphroditic C. elegans, and polymorphism is enriched on chromosome arms relative to chromosome centers. FST is low among island population pairs, and clear population structure could not be easily detected among figs, trees, and islands, suggesting frequent migration of wasps between islands. Moreover, inbreeding coefficients are elevated in C. inopinata, consistent with field observations suggesting small C. inopinata founding populations in individual figs. These genetic patterns in C. inopinata overlap with those previously reported in its specific fig wasp vector and are consistent with C. inopinata population dynamics being driven by wasp dispersal. Thus, interspecific interactions can align patterns of genetic diversity across species separated by hundreds of millions of years of evolutionary divergence.

HighlightsO_LIThe fig-dwelling female/male nematode Caenorhabditis inopinata is five times more diverse than its closest relative, the self-fertilizing nematode C. elegans.
C_LIO_LIC. inopinata migrates frequently among three Okinawan islands despite high levels of inbreeding within individual figs.
C_LIO_LIC. inopinata has patterns of genetic diversity that mirror its fig wasp vector.
C_LIO_LIEcological specialization aligns patterns of genetic differentiation in closely interacting species.
C_LI

category: evolutionary biology


title: Draft Genome of Cochliopodium minus (Amoebozoa): Insights into Its Complex Sexual Behavior, Across Domain Gene Acquisitions and Metazoan Type Signaling

abstract: To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodiums sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.