title: Water column stability as an important factor controlling nitrite-dependent anaerobic methane oxidation in stratified lake basins

abstract: Anaerobic oxidation of methane (AOM) with nitrate/nitrite as the terminal electron acceptor may play an important role in mitigating methane emissions from lacustrine environments to the atmosphere. We investigated AOM in the water column of two connected but hydrodynamically contrasting basins of a south-alpine lake in Switzerland (Lake Lugano). The North Basin is permanently stratified with year-round anoxic conditions below 120 m water depth, while the South Basin undergoes seasonal stratification with the development of bottom water anoxia during summer. We show that below the redoxcline of the North Basin a substantial fraction of methane was oxidized coupled to nitrite reduction by Candidatus Methylomirabilis. Incubation experiments with 14CH4 and concentrated biomass from showed at least 43-52%-enhanced AOM rates with added nitrate/nitrite as electron acceptor. Multiannual time series data on the population dynamics of Candidatus Methylomirabilis in the North Basin following an exceptional mixing event in 2005/2006 revealed their requirement for lasting stable low redox-conditions to establish. In the South Basin, on the other hand, we did not find molecular evidence for nitrite-dependent methane oxidizing bacteria. Our data suggest that here the dynamic mixing regime with fluctuating redox conditions is not conducive to the development of a stable population of relatively slow-growing Candidatus Methylomirabilis, despite a hydrochemical framework that seems more favorable for nitrite-dependent AOM than in the North Basin. We predict that the importance of N-dependent AOM in freshwater lakes will likely increase in future because of longer thermal stratification periods and reduced mixing caused by global warming.


title: Mitochondria transplantation between living cells

abstract: Mitochondria and the complex endomembrane system are hallmarks of eukaryotic cells. To date, it has been difficult to manipulate organelle structures within single live cells. We developed a FluidFM-based approach to extract, inject and transplant organelles from and into living cells with subcellular spatial resolution. The approach enabled the transfer of controlled quantities of mitochondria into cells while maintaining their viability and monitoring their fate in new host cells. Transplantation of healthy and drug-impaired mitochondria into primary keratinocytes allowed real-time tracking of mitochondrial subpopulation rescue. Fusion with the mitochondrial network of recipient cells occurred 20 min after transplantation and continued for over 16 hours. After transfer of mitochondria and cell propagation over generations, we show that donor mtDNA was replicated in recipient cells without the need for selection pressure. The approach opens new prospects for the study of organelle physiology and homeostasis, but also for mechanobiology, synthetic biology, and therapy.

category: cell biology


title: Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

abstract: Crops genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bt toxins can improve resistance monitoring, resistance management, and design of new insecticides. Here, we investigated the genetic basis of resistance to Bt toxin Cry1Ac in the lepidopteran Helicoverpa zea, one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species, which has 31 chromosomes containing 375 Mb and 15,482 predicted proteins. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250-kb quantitative trait locus (QTL) on chromosome 13 that was strongly associated with resistance in a strain of H. zea that had been selected for resistance in the field and lab. The mutation in this QTL contributed to but was not sufficient for resistance, which implies alleles in more than one gene contributed to resistance. This QTL contains no genes with a previously reported role in resistance or susceptibility to Bt toxins. However, in resistant insects, this QTL has a premature stop codon in a kinesin gene which is a primary candidate as a mutation contributing to resistance. We found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance.

category: genetics


title: Large-scale identification of RBP-RNA interactions by RAPseq refines essentials of post-transcriptional gene regulation

abstract:
Over the past decade, thousands of putative human RNA binding proteins (RBPs) have been identified and increased the demand for specifying RNA binding capacities. Here, we developed RNA affinity purification followed by sequencing (RAPseq) that enables in vitro large-scale profiling of RBP binding to native RNAs. First, by employing RAPseq, we found that vertebrate HURs recognize a conserved RNA binding motif and bind predominantly to introns in zebrafish compared to 3UTRs in human RNAs. Second, our dual RBP assays (co-RAPseq) uncovered cooperative RNA binding of HUR and PTBP1 within an optimal distance of 27 nucleotides. Third, we developed T7-RAPseq to discern m6A-dependent and - independent RNA binding sites of YTHDF1. Fourth, RAPseq of 26 novel non-canonical RBPs revealed specialized moonlighting interactions. Last, five pathological IGF2BP family variants exhibited different RNA binding patterns. Overall, our simple, scalable and versatile method enables to fast-forward RBP-related questions.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/467743v1_ufig1.gif" ALT="Figure 1">
View larger version (106K):
org.highwire.dtl.DTLVardef@1f77ce0org.highwire.dtl.DTLVardef@12778fcorg.highwire.dtl.DTLVardef@77ff8corg.highwire.dtl.DTLVardef@2a7f24_HPS_FORMAT_FIGEXP  M_FIG C_FIG HIGHLIGHTSO_LIRAPseq reveals in vitro-derived RBP-RNA interactomes
C_LIO_LIthe vertebrate-conserved HUR binding motif adapted to species-unique RNA features
C_LIO_LIco-RAPseq and T7-RAPseq uncover binding cooperativity and modification dependencies
C_LIO_LInon-canonical RBPs have specialized RNA interactomes
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category: genomics


title: Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells

abstract:
Variation in the human genome contributes to abundant diversity in human traits and vulnerabilities, but the underlying molecular and cellular mechanisms are not yet known, and will need scalable approaches to accelerate their recognition. Here, we advanced and applied an experimental platform that analyzes genetic, molecular, and phenotypic heterogeneity across cells from very many human donors cultured in a single, shared in vitro environment, with algorithms (Dropulation and Census-seq) for assigning phenotypes to individual donors. We used natural genetic variation and synthetic (CRISPR-Cas9) genetic perturbations to analyze the vulnerability of neural progenitor cells to infection with Zika virus. These analyses identified a common variant in the antiviral IFITM3 gene that regulated IFITM3 expression and explained most inter-individual variation in NPCs susceptibility to Zika virus infectivity. These and other approaches could provide scalable ways to recognize the impact of genes and genetic variation on cellular phenotypes.

HIGHLIGHTSO_LIMeasuring cellular phenotypes in iPSCs and hPSC-derived NPCs from many donors
C_LIO_LIEffects of donor sex, cell source, genetic and other variables on hPSC RNA expression
C_LIO_LINatural genetic variation and synthetic perturbation screens both identify IFITM3 in NPC susceptibility to Zika virus
C_LIO_LIA common genetic variant in IFITM3 explains most inter-individual variation in NPC susceptibility to Zika virus
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title: Pentameric assembly of the Kv2.1 tetramerization domain.

abstract: The Kv family of voltage-gated potassium channels regulate neuronal excitability. The biophysical characteristic of Kv channels can be matched to the needs of different neurons by forming homotetrameric or heterotetrameric channels within one of four subfamilies. The cytoplasmic tetramerization (T1) domain plays a major role in dictating the compatibility of different Kv subunits. The only Kv subfamily missing a representative structure of the T1 domain is the Kv2 family. We used X-ray crystallography to solve the structure of the human Kv2.1 T1 domain. The structure is similar to other T1 domains but surprisingly formed a pentamer instead of a tetramer. In solution the Kv2.1 T1 domain also formed a pentamer as determined with in-line SEC-MALS-SAXS and negative stain EM. The Kv2.1 T1-T1 interface involves electrostatic interactions including a salt bridge formed by the negative charges in a previously described CDD motif, and inter-subunit coordination of zinc. We show that zinc binding is important for stability. In conclusion, the Kv2.1 T1 domain behaves differently from the other Kv T1 domains which may reflect the versatility of Kv2.1, the only Kv subfamily that can assemble with the regulatory KvS subunits and scaffold ER-plasma membrane contacts.

category: biochemistry


title: Coordinated conformational changes in the V1 complex during V-ATPase reversible dissociation

abstract: Vacuolar-type ATPases (V-ATPases) are rotary enzymes that acidify intracellular compartments in eukaryotic cells. These multi-subunit complexes consist of a cytoplasmic V1 region that hydrolyzes ATP and a membrane-embedded VO region that transports protons. V-ATPase activity is regulated by reversible dissociation of the two regions, with the isolated V1 and VO complexes becoming autoinhibited upon disassembly and subunit C subsequently detaching from V1. In yeast, assembly of the V1 and VO regions is mediated by the RAVE complex through an unknown mechanism. We used cryoEM of yeast V-ATPase to determine structures of the intact enzyme, the dissociated but complete V1 complex, and the V1 complex lacking subunit C. Upon separation, V1 undergoes a dramatic conformational rearrangement, with its rotational state becoming incompatible for reassembly with VO. Loss of subunit C allows V1 to match the rotational state of VO, suggesting how RAVE could reassemble V1 and VO by recruiting subunit C.


title: Assessing and enhancing foldability in designed proteins

abstract: Recent advances in protein-design methodology have led to a dramatic increase in reliability and scale. With these advances, dozens and even thousands of designed proteins are automatically generated and screened. Nevertheless, the success rate, particularly in design of functional proteins, is low and fundamental goals such as reliable de novo design of efficient enzymes remain beyond reach. Experimental analyses have consistently indicated that a major reason for design failure is inaccuracy and misfolding relative to the design model. To address this challenge, we describe complementary methods to diagnose and ameliorate suboptimal regions in designed proteins: first, we develop a Rosetta atomistic computational mutation scanning approach to detect energetically suboptimal positions in designs (available on a web server https://pSUFER.weizmann.ac.il); second, we demonstrate that AlphaFold2 ab initio structure prediction flags regions that may misfold in designed enzymes and binders; and third, we focus FuncLib design calculations on suboptimal positions in a previously designed low-efficiency enzyme improving its catalytic efficiency by 330 fold. Furthermore, applied to a de novo designed protein that exhibited limited stability, the same approach markedly improved stability and expressibility. Thus, foldability analysis and enhancement may dramatically increase the success rate in design of functional proteins.


title: Data independent acquisition enables deep and fast label-free dynamic organellar mapping

abstract: The membrane compartments of eukaryotic cells organize the proteome into dynamic reaction spaces that control protein activity. This  spatial proteome and its changes can be captured systematically by our previously established Dynamic Organellar Maps (DOMs) approach, which combines cell fractionation and shotgun-proteomics into a profiling analysis of subcellular localization. Our original method relied on data dependent acquisition (DDA), which is inherently stochastic, and thus offers limited depth of analysis across replicates. Here we adapt DOMs to data independent acquisition (DIA), in a label-free format, and establish an automated data quality control tool to benchmark performance. Matched for mass spectrometry (MS) runtime, DIA-DOMs provide double the depth relative to DDA-DOMs, with substantially improved precision and localization prediction performance. Matched for depth, DIA-DOMs provide organellar maps in a third of the runtime. To test the DIA-DOMs performance for comparative applications, we mapped subcellular localization changes in response to starvation/disruption of lysosomal pH in HeLa cells, revealing a subset of Golgi proteins that cycle through endosomes. DIA-DOMs offer a superior workflow for label-free spatial proteomics, with a broad application spectrum in cell and biomedical research.


title: Glomerular function and urinary biomarker changes between vancomycin and vancomycin plus piperacillin-tazobactam in a translational rat model.

abstract: Clinical studies have reported additive nephrotoxicity associated with the combination of vancomycin (VAN) and piperacillin-tazobactam (TZP). This study assessed differences in glomerular filtration rate (GFR) and urinary biomarkers between rats receiving VAN and those receiving VAN+TZP. Male Sprague-Dawley rats (n=26) were randomized to receive 96 hours of intravenous VAN at 150mg/kg/day, intraperitoneal TZP at 1400 mg/kg/day, or VAN+TZP. Kidney function was evaluated using fluorescein-isothiocyanate sinistrin and a transdermal sensor to estimate real-time glomerular filtration rate (GFR). Kidney injury was evaluated via urinary biomarkers including kidney injury molecule-1 (KIM-1), clusterin, and osteopontin. Compared to a saline control, only rats in the VAN group showed significant declines in GFR by day 4 (-0.39 mL/min/100 g body weight, 95% CI: -0.68 to -0.10, p=0.008). When the VAN+TZP and VAN alone treatment groups were compared, significantly higher urinary KIM-1 was observed in the VAN alone group on day 1 (18.4 ng, 95% CI: 1.4 to 35.3, p=0.03), day 2 (27.4 ng, 95% CI: 10.4 to 44.3, p=0.002), day 3 (18.8 ng, 95% CI: 1.9 to 35.8, p=0.03), and day 4 (23.2 ng, 95% CI: 6.3 to 40.2, p=0.007). KIM-1 was the urinary biomarker that most correlated with decreasing GFR on day 3 (Spearmans rho: -0.45, p = 0.022) and day 4 (Spearmans rho: - 0.41, p = 0.036). Kidney function decline and increased KIM-1 were observed among rats that received VAN only, but not TZP or VAN+TZP. Addition of TZP to VAN does not worsen kidney function or injury in a validated translational rat model.

category: pharmacology and toxicology


title: Improvement of muscle strength in a mouse model for congenital myopathy treated with HDAC and DNA methyltransferase inhibitors

abstract: To date there are no therapies for patients with congenital myopathies, muscle disorders causing poor quality of life of affected individuals. In approximately 30% of the cases, patients with congenital myopathies carry either dominant or recessive mutations in the RYR1 gene; recessive RYR1 mutations are accompanied by reduction of RyR1 expression and content in skeletal muscles and are associated with fiber hypotrophy and muscle weakness. Importantly, muscles of patients with recessive RYR1 mutations exhibit increased content of class II histone de-acetylases and of DNA genomic methylation. We recently created a mouse model knocked-in for the p.Q1970fsX16+p.A4329D RyR1 mutations, which are isogenic to those carried by a severely affected child suffering from a recessive form of RyR1-related multi-mini core disease. The phenotype of the RyR1 mutant mice recapitulates many aspects of the clinical picture of patients carrying recessive RYR1 mutations. We treated the compound heterozygous mice with a combination of two drugs targeting DNA methylases and class II histone de-acetylases. Here we show that treatment of the mutant mice with drugs targeting epigenetic enzymes improves muscle strength, RyR1 protein content and muscle ultrastructure. This study provides proof of concept for the pharmacological treatment of patients with congenital myopathies linked to recessive RYR1 mutations.

category: physiology


title: ICOR: Improving codon optimization with recurrent neural networks

abstract: In protein sequences--as there are 61 sense codons but only 20 standard amino acids--most amino acids are encoded by more than one codon. Although such synonymous codons do not alter the encoded amino acid sequence, their selection can dramatically affect the expression of the resulting protein. Codon optimization of synthetic DNA sequences is important for heterologous expression. However, existing solutions are primarily based on choosing high-frequency codons only, neglecting the important effects of rare codons. In this paper, we propose a novel recurrent-neural-network based codon optimization tool, ICOR, that aims to learn codon usage bias on a genomic dataset of Escherichia coli. We compile a dataset of over 7,000 non-redundant, high-expression, robust genes which are used for deep learning. The model uses a bidirectional long short-term memory-based architecture, allowing for the sequential context of codon usage in genes to be learned. Our tool can predict synonymous codons for synthetic genes toward optimal expression in Escherichia coli. We demonstrate that sequential context achieved via RNN may yield codon selection that is more similar to the host genome, therefore improving protein expression more than frequency-based approaches. ICOR is evaluated on 1,481 Escherichia coli genes as well as a benchmark set of 40 select DNA sequences whose heterologous expression has been previously characterized. ICORs performance across five metrics is compared to that of five different codon optimization techniques. The codon adaptation index -- a metric indicative of high real-world expression -- was utilized as the primary benchmark in this study. ICOR is shown to improve the codon adaptation index by 41.69% and 17.25% compared to the original and Genscripts GenSmart-optimized sequences, respectively. Our tool is provided as an open-source software package that includes the benchmark set of sequences used in this study.

category: synthetic biology


title: PccGEO: prior constraints conditioned genetic elements optimization

abstract:
Functional genetic elements are one of the most essential units for synthetic biology. However, both knowledge-driven and data-driven methodology can hardly accomplish the complicated task of genetic elements design efficiently due to the lack of explicit regulatory logics and training samples. Here, we proposed a knowledge-constraint deep learning model named PccGEO to automatically design functional genetic elements with high success rate and efficiency. PccGEO utilized a novel "fill-in-the-flank" strategy with a conditional generative adversarial network structure to optimize the flanking regions of known functional sequences derived from the biological prior knowledge, which can efficiently capture the implicit patterns with a reduced searching space. We applied PccGEO in the design of Escherichia coli promoters, and found that the implicit patterns in flanking regions matter to the properties of promoters such as the expression level. The PccGEO-designed constitutive and inducible promoters showed more than 91.6% chance of success by in vivo validation. We further utilized PccGEO by setting a limited frequency of nucleotide modifications and surprisingly found that the expression level of E. coli sigma 70 promoters could show up to a 159.3-fold increase with only 10-bp nucleotide modifications. The results supported that the implicit patterns are important in the design of functional gene elements and validated the strong capacity of our method in the efficient design of functional genetic elements.

Availabilityhttps://github.com/WangLabTHU/PccGEO


title: Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43

abstract: Generation of oligodendrocytes in the adult brain enables both adaptive changes in neural circuits and regeneration of myelin sheaths destroyed by injury, disease, and normal aging. This transformation of oligodendrocyte precursor cells (OPCs) into myelinating oligodendrocytes requires processing of distinct mRNAs at different stages of cell maturation. Although mislocalization and aggregation of the RNA binding protein TDP-43 occur in both neurons and glia in neurodegenerative diseases, the consequences of TDP-43 loss within different stages of the oligodendrocyte lineage are not well understood. By performing stage-specific genetic inactivation of Tardbp in vivo, we show that oligodendrocyte lineage cells are differentially sensitive to loss of TDP-43. While OPCs depend on TDP-43 for survival, with conditional deletion resulting in cascading cell loss followed by rapid regeneration to restore their density, oligodendrocytes become less sensitive to TDP-43 depletion as they mature. Deletion of TDP-43 early in the maturation process led to eventual oligodendrocyte degeneration, seizures and premature lethality, while oligodendrocytes that experienced late deletion survived and mice exhibited a normal lifespan. At both stages, TDP-43 deficient oligodendrocytes formed fewer and thinner myelin sheaths and extended new processes that inappropriately wrapped neuronal somata and blood vessels. Transcriptional analysis revealed that in the absence of TDP-43, key proteins involved in oligodendrocyte maturation and myelination were misspliced leading to aberrant incorporation of cryptic exons. Inducible deletion of TDP-43 from oligodendrocytes in the adult CNS induced the same progressive morphological changes and mice acquired profound hindlimb weakness, suggesting that loss of TDP-43 function in oligodendrocytes may contribute to neuronal dysfunction in neurodegenerative disease.

category: neuroscience


title: Nuclear receptor subfamily 4A signaling as a key disease pathway of CD1c+ dendritic cell dysregulation in systemic sclerosis

abstract:
ObjectivesTo identify key disease pathways driving conventional dendritic cell (cDC) alterations in Systemic Sclerosis (SSc).

MethodsTranscriptomic profiling was performed on peripheral blood CD1c+ cDCs (cDC2s) isolated from 12 healthy donors and 48 SSc patients with all major disease subtypes. Differential expression analysis comparing the different SSc subtypes and healthy donors was performed to uncover genes dysregulated in SSc. To identify biologically relevant pathways, a gene co-expression network was built using Weighted Gene Correlation Network Analysis. We validated the role of key transcriptional regulators using ChIP-sequencing and in vitro functional assays.

ResultsWe identified 17 modules of co-expressed genes in cDC2s that correlated with SSc subtypes and key clinical traits including auto-antibodies, skin score, and occurrence of interstitial lung disease. A module of immune regulatory genes was markedly down regulated in patients with the diffuse SSc subtype characterized by severe fibrosis. Transcriptional regulatory network analysis performed on this module predicted NR4A (nuclear receptor 4A) subfamily (NR4A1, NR4A2, NR4A3) genes as the key transcriptional mediators of inflammation. Indeed, ChIP-sequencing analysis supported that these NR4A members target numerous differentially expressed genes in SSc cDC2s. Inclusion of NR4A receptor agonists in culture-based experiments provided functional proof that dysregulation of NR4As affects cytokine production by cDC2s and modulates downstream T-cell activation.

ConclusionsNR4A1, NR4A2 and NR4A3 are important regulators of immunosuppressive and fibrosis-associated pathways in SSc cDC2s. Thus, the NR4A family represent novel potential targets to restore cDC homeostasis in SSc.

KEY MESSAGESO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LICD1c+ conventional dendritic cells (cDC2s) are implicated as key players in Systemic Sclerosis (SSc), but key molecular mechanisms underlying their dysregulation were unknown.
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What does this study add?O_LITranscriptomic analysis and network analysis identified modules of coexpressed genes in cDC2s that correlated with SSc subtypes and key clinical traits.
C_LIO_LIThe NR4A (nuclear receptor 4A) subfamily (NR4A1, NR4A2, NR4A3) genes act as master regulators of key immune regulatory genes dysregulated in SSc cDC2s, as shown by multi-omics integration analysis using transcriptomics and targeted ChIP-sequencing.
C_LIO_LIPharmacological activation of NR4As inhibits pro-inflammatory cytokine production and CD4+ T-cell activation by cDC2s.
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How might this impact on clinical practice or future developments?O_LINR4As are attractive candidates for novel treatment options to attenuate pro-inflammatory and pro-fibrotic responses in SSc patients.
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category: immunology


title: Host-associated phages disperse across the extraterrestrial analogue Antarctica

abstract:
Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating or prophages) across the Antarctic continent can be tracked via their genetic signatures aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria including Ralstonia spp. We reconstructed the complete genome of a temperate phage with near-complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula in distance of 5538 km to the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for Astrobiology.

ImportanceHost-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to presence of these bacteria carrying genome-integrated prophages on space-related equipment, and the here demonstrated potential for dispersal of host-associated phages, our work has implications for Planetary Protection, a discipline in Astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.

category: microbiology


title: NorA, HmpX, and NorB cooperate to reduce NO toxicity during denitrification and plant pathogenesis in Ralstonia solanacearum

abstract:
Ralstonia solanacearum, which causes bacterial wilt disease of many crops, needs denitrifying respiration to succeed inside its plant host. In the hypoxic environment of plant xylem vessels this pathogen confronts toxic oxidative radicals like nitric oxide (NO), which is generated by both bacterial denitrification and host defenses. R. solanacearum has multiple distinct mechanisms that could mitigate this stress, including Repair of Iron Cluster (RIC) homolog NorA, nitric oxide reductase NorB, and flavohaemoglobin HmpX. During denitrification and tomato pathogenesis and in response to exogenous NO, R. solanacearum upregulated norA, norB, and hmpX. Single mutants lacking{Delta} norB, {Delta}norA, or{Delta} hmpX increased expression of many iron and sulfur metabolism genes, suggesting that losing even one NO detoxification system demands metabolic compensation. Single mutants suffered only moderate fitness reductions in host plants, possibly because they upregulated their remaining detoxification genes. However,{Delta} norA/norB, {Delta}norB/hmpX, and{Delta} norA/hmpX double mutants grew poorly in denitrifying culture and in planta. Loss of norA, norB, and hmpX may be lethal, since the methods used to construct the double mutants did not generate a triple mutant. Aconitase activity assays showed that NorA, HmpX and especially NorB are important for maintaining iron-sulfur cluster proteins. Additionally, plant defense genes were upregulated in tomatoes infected with the NO-overproducing{Delta} norB mutant, suggesting that bacterial detoxification of NO reduces pathogen visibility. Thus, R. solanacearums three NO detoxification systems each contribute to and are collectively essential for overcoming metabolic oxidative stress during denitrification, for virulence and growth in tomato, and for evading host plant defenses.

ImportanceThe soilborne plant pathogen Ralstonia solanacearum (Rs) causes bacterial wilt, a serious and widespread threat to global food security. Rs is metabolically adapted to low oxygen conditions, using denitrifying respiration to survive in the host and cause disease. However, bacterial denitrification and host defenses generate nitric oxide (NO), which is toxic and also alters signaling pathways in both plants and the pathogen. Rs mitigates NO with a trio of mechanistically distinct proteins: NO-reductase NorB, Repair of Iron Centers NorA, and oxidoreductase HmpX. This redundancy, together with analysis of mutants and in-planta dual transcriptomes, indicates that maintaining low NO levels is integral to Rs fitness in tomatoes (because NO damages iron-cluster proteins) and to evading host recognition (because bacterially produced NO can trigger plant defenses).


title: Spatial relationships of intra-lesion heterogeneity in Mycobacterium tuberculosis microenvironment, replication status, and drug efficacy

abstract: A hallmark of Mycobacterium tuberculosis (Mtb) infection with critical impact on disease development and outcome is the marked heterogeneity that exists, spanning differences in lesion types to changes in microenvironment as the infection progresses1-7. A mechanistic understanding of how this heterogeneity affects Mtb growth and treatment efficacy necessitates single bacterium-level studies in the context of intact host tissue architecture; however, such an evaluation has been technically challenging. Here, we exploit fluorescent reporter Mtb strains and the C3HeB/FeJ murine model in an integrated imaging approach to study microenvironment heterogeneity within a single lesion in situ, and analyze how these differences relate to non-uniformity in Mtb replication state, activity, and drug efficacy. We show that the pH and chloride environments differ spatially in a caseous necrotic lesion, with increased acidity and chloride levels in the lesion cuff versus the necrotic core. Conversely, a higher percentage of Mtb in the necrotic core versus the lesion cuff were in an actively replicating state, and correspondingly active in transcription and translation. Finally, examination of three first-line anti-tubercular drugs showed that efficacy of isoniazid was strikingly poor against bacteria in the lesion cuff. Our study reveals spatial relationships of intra-lesion heterogeneity, sheds light on important considerations in the development of anti-tubercular treatment strategies, and establishes a foundational framework for Mtb infection heterogeneity analysis at the single cell level in situ.


title: Sequestration of LINE-1 in novel cytosolic bodies by MOV10 restricts retrotransposition

abstract: LINE-1 (L1) are autonomous retroelements that have retained their ability to mobilize. Mechanisms regulating L1 mobility include DNA methylation in somatic cells and the Piwi-interacting RNA pathway in the germline. During pre-implantation stages of mouse embryonic development, however, both pathways are inactivated leading to a critical window necessitating alternate means of L1 regulation. We previously reported an increase in L1 levels in Dicer_KO mouse embryonic stem cells (mESCs). Intriguingly this was accompanied by only a marginal increase in retrotransposition, suggestive of additional mechanisms suppressing L1 mobility. Here, we demonstrate that L1 Ribonucleoprotein complexes (L1 RNP) accumulate as aggregates in Dicer_KO cytoplasm along with the RNA helicase MOV10. The combined overexpression of L1 RNAs and MOV10 is sufficient to create L1 RNP aggregates in stem cells. In Dicer_KO mESCs, MOV10 is upregulated due to the loss of its direct regulation by miRNAs. The newly discovered post-transcriptional regulation of Mov10 expression, and its role in preventing L1 retrotransposition by driving novel cytosolic aggregation affords alternate routes to explore for therapy and disease progression.


title: The evolutionary dynamics of genetic mutational load throughout tomato domestication history

abstract:
Understanding the evolution of deleterious mutations through domestication has fascinated evolutionary biologists and breeders alike. Some domesticated organisms have been reported to accumulate deleterious mutations, i.e. radical amino acid changes, through their domestication history ("cost of domestication"). However, more recent evidence paints a more complex picture of this phenomenon in different domesticated organisms. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. Specifically, we used phylogeny-based methods to identify deleterious mutations in the cultivated tomato as well as its closely related semi-wild and wild populations. We also explored a potential correlation between deleterious mutations and SVs. To create a functional link between deleterious alleles and phenotypes of interest for tomato breeding, we also conducted Genome-wide Association Studies (GWAS) on several fruit volatiles.

Our results implicate a downward trend, throughout tomato domestication history, in diversity of most alleles, regardless of their functional impact. This suggests that demographic factors, such as bottleneck events and inbreeding, have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. We also detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador, although the final stage of tomato domestication in Mexico did not seem to involve such an increase. However, deleterious alleles in cultivated tomato seem to be more frequent than expected by neutral theory of molecular evolution. Additionally, for all tomato populations, we found a higher proportion of deleterious mutations in genomic regions impacted by SVs.

Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavor regulation. Also, through genome-wide association studies (GWAS), we discovered deleterious alleles associated with two volatiles: isobutyl acetate, which is important for tomato fruit flavor, and methyl salicylate, involved in disease resistance and regulating flowering time. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 deleterious alleles identified in this study (https://github.com/hrazif/TomDel-0.1)


title: Structure-Activity Relationships in the Design of Mitochondria-Targeted Peptide Therapeutics

abstract: Mitochondria play a central role in metabolic homeostasis; hence, dysfunction of this organelle underpins the etiology of many heritable and aging-related diseases. Mitochondria-targeted tetrapeptides with alternating cationic and aromatic residues, such as SS-31 (Elamipretide), show promise as therapeutic compounds. In this study, we conducted a quantitative structure-activity analysis of three alternative tetrapeptide analogs that differed with respect to aromatic side chain composition and sequence register, benchmarked against SS-31. Using NMR and molecular dynamics approaches, we obtained the first structural models for this class of compounds, showing that all analogs except for SS-31 form compact reverse turn conformations in the membrane-bound state. All peptide analogs bound cardiolipin-containing membranes, yet they had significant differences in equilibrium binding behavior and membrane interactions. Notably, the analogs had markedly different effects on membrane surface charge, supporting a mechanism in which modulation of membrane electrostatics is a key feature of their mechanism of action. All peptide analogs preserved survival and energy metabolism more effectively than SS-31 in cell stress models. Within our peptide set, the analog containing tryptophan side chains, SPN10, had the strongest impact on most membrane properties and showed greatest efficacy in cell culture studies. Taken together, these results show that side chain composition and register strongly influence the activity of these mitochondria-targeted peptides. Furthermore, this work helps provide a framework for the rational design of next-generation therapeutics with enhanced potency.


title: Platelets are dispensable for the ability of CD8+ T cells to accumulate, patrol, kill and reside in the liver

abstract: Effector and memory CD8+ T cells accumulate in large numbers in the liver where they play key roles in the control of liver pathogens including Plasmodium. It has also been proposed that liver may act as the main place for elimination of effector CD8+ T cells at the resolution of immune responses. Platelets and the integrin LFA-1 have been proposed to be critical for the accumulation of protective CD8+ T cells in the liver; conversely, asialo-glycoprotein (ASGP) expression on the surface of CD8+ T cells has been proposed to assist in elimination of effector T cells in the liver. Here we investigated the contributions of these interactions in the accumulation of CD8+ T cells activated in vitro or in vivo by immunization with Plasmodium parasites. Using Mpl-/- mice with constitutive thrombocytopaenia and antibody-mediated platelet depletion models we found that severe reduction in platelet concentration in circulation did not strongly influence the accumulation and protective function of CD8+ T cells in the liver in these models. Surprisingly, inhibition of ASGP receptors did not inhibit the accumulation of effector cells in the liver, but instead prevented these cells from accumulating in the spleen. We further found that enforced expression of ASGP on effector CD8+ T cells using ST3GalI knockout cells lead to their loss from the spleen. These data suggest that platelets play a marginal role in CD8+ T cell function in the liver. Furthermore, ASGP-expressing effector CD8+ T cells are retained in the liver but are lost from the spleen.


title: Salmonella Outer Membrane Vesicles contain tRNA Fragments (tRFs) that Inhibit Bacteriophage P22 infection

abstract: Salmonella Outer Membrane Vesicles (OMVs) were recently shown to inhibit P22 bacteriophage infection. Furthermore, despite there being several published reports now independently describing (1) the marked prevalence of tRFs within secreted vesicle transcriptomes and (2) roles for specific tRFs in facilitating/inhibiting viral replication, there have been no examinations of the effects of vesicle-secreted tRFs on viral infection reported to date. Notably, while specific tRFs have been reported in a number of bacteria, the tRFs expressed by salmonellae have not been previously characterized. As such, we recently screened small RNA-seq datasets for the presence of recurrent, specifically excised tRFs and identified 31 recurrent, relatively abundant tRFs expressed by Salmonella enterica serovar Typhimurium (SL1344). Whats more, we find S. Typhimurium OMVs contain significant levels of tRFs highly complementary to known Salmonella enterica-infecting bacteriophage with 17 of 31 tRFs bearing marked complementarity to at least one known Salmonella enterica-infecting phage (averaging 97.4% complementarity over 22.9 nt). Most notably, tRNA-Thr-CGT-1-1, 44-73, bears 100% sequence complementary over its entire 30 nt length to 29 distinct, annotated Salmonella enterica-infecting bacteriophage including P22. Importantly, we find inhibiting this tRF in secreted OMVs improves P22 infectivity in a dose dependent manner whereas raising OMV tRF levels conversely inhibits P22 infectivity. Furthermore, we find P22 phage pre-incubation with OMVs isolated from naive, control SL1344 S. Typhimurium, successfully rescues the ability of S. Typhimurium transformed with a specific tRNA-Thr-CGT-1-1, 44-73 tRF inhibitor to defend against P22. Collectively, these experiments confirm tRFs secreted in S. Typhimurium OMVs are directly involved with and required for the ability of OMVs to defend against bacteriophage predation. As we find the majority of OMV tRFs are highly complementary to an array of known Salmonella enterica-infecting bacteriophage, we suggest OMV tRFs may primarily function as a broadly acting, previously uncharacterized innate antiviral defense.


title: A new prognostic model for pancreatic cancer based on pyroptosis-related genes

abstract:
Pancreatic cancer is one of the most common malignant tumors of the digestive tract. It is known as the "king of cancer" in the field of cancer, and is one of the worst prognosis malignant tumors. Pyroptosis is a kind of programmed cell death, which can promote the inflammatory response of cells. Studies have shown that the effect of pyroptosis-related genes in cancer is significant. However, the role of pyroptosis in pancreatic cancer is not clear. The aim of this study is to establish a prognostic model based on pyroptosis. The gene expression and clinical data of pancreatic cancer patients were obtained from TCGA and verified in GEO. The differential expression of 33 pyroptosis-related genes in pancreatic cancer and normal tissues was analyzed, of which 6 genes were up-regulated and 12 genes were down regulated. Then, it was analyzed that pyroptosis-related genes were mainly enriched in the defense against bacteria and pyroptosis pathways. A concise and reliable model is established by lasso-cox regression analysis. Km curve shows that there are differences between high-risk group and low-risk group. And the nomogram has reliable prediction ability. In conclusion, pyroptosis an important role in pancreatic cancer, which can be used for the prediction of pancreatic cancer and provide a new perspective for the treatment of pancreatic cancer.

AUTHOR APPROVALSThe authors have seen and approved the manuscript, and that it hasnt been accepted or published elsewhere.

COMPETING INTERESTSThe authors declare no competing interests.

category: molecular biology


title: Evidence for a long-r ange RNA-RNA interaction between ORF8 and the downstream region of the Spike polybasic insertion of SARS-CoV-2

abstract: SARS-CoV-2 has affected people all over the world as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV responsible for the 2002-2003 SARS outbreak in Asia. Intense research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Similar to other betacoronaviruses, long-range RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into different viral proteins. An important difference between both viruses is a polybasic insertion in the Spike region of SARS-CoV-2, absent in SARS-CoV. Here we show that a 26-base-pair long-range RNA-RNA interaction occurs between the genomic region downstream of the Spike insertion and ORF8 in SARS-CoV-2. Predictions suggest that the corresponding ORF8 region forms the most energetically favorable interaction with that of Spike region from amongst all possible candidate regions within SARS-CoV-2 genomic RNA. We also found signs of sequence covariation in the predicted interaction using a large dataset with 27,592 full-length SARS-CoV-2 genomes. In particular, a synonymous mutation in ORF8 accommodated for base pairing with Spike [G23675 C28045U], and a non-synonymous mutation in Spike accommodated for base pairing with ORF8 [C23679U G28042] both of which were in close proximity of one another. The predicted interactions can potentially be related to regulation of sub-genomic RNA production rates.

category: bioinformatics


title: Closely-related tree species with overlapping ranges exhibit divergent adaptation to climate

abstract: With global climate change shifting and altering temperature and precipitation regimes, the ability of natural forest stands to persist in their local environments are being challenged. For many taxa, particularly among long lived tree species, the potential to respond is underpinned by genetic and trait diversity and may be limited. We sampled 326 and 366 individuals of two widely distributed and closely-related red gum Eucalyptus species (E. blakelyi and E. tereticornis) from across their entire Australian range. We identified putatively adaptive variants associated within genes of key biological processes for both species. We mapped the change of allele frequencies of two hierarchical gene ontology groups shared by both species across geography and climate and predict genomically vulnerable regions under a projected 2070 climate scenario. Regions of potential vulnerability to decline under future climate differed between species and may be applied to guide conservation and restoration strategies. Our study indicated that some populations may contain the adaptive genomic variation necessary for these species to persist through climate change, while others may benefit from the adaptive variation of those populations to enhance resilience.

category: evolutionary biology


title: Pre- and post-mating reproductive isolation evolve independently during rapid adaptation to high temperature

abstract: Ambient temperature is one major ecological factor driving adaptation in natural populations, but its impact on the emergence of new species is not yet clear. Here, we explored the evolution of reproductive isolation during temperature adaptation by exposing 10 replicate Drosophila simulans populations to a hot temperature regime. Within less than 200 generations, both pre- and post-mating reproductive isolation evolved. The altered lipid metabolism of evolved flies also affected the cuticular hydrocarbon (CHCs) profiles. Different CHC profiles could explain the emerged assortative mating between ancestral and evolved populations. Hence, we identified the hallmark of ecological speciation driven by temperature adaptation. While this pre-mating isolation occurred only between ancestral and evolved replicate populations, post-mating reproductive isolation was observed among evolved replicate populations. We propose that epistatic interactions of reproduction-related genes between males and females resulted in adaptive co-evolution. Incompatibilities between different gene combinations favored in each replicate could explain the observed post-mating reproductive isolation. We anticipate that this "mutation-order-like speciation" from standing genetic variation, a new speciation process, is widespread in nature when highly polygenic traits are involved in adaptation.


title: TreeSearch: morphological phylogenetic analysis in R

abstract:
TreeSearch is an R package for phylogenetic analysis, optimized for morphological datasets. Tree search may be conducted using equal or implied step weights with an explicit (albeit inexact) allowance for inapplicable character entries, avoiding some of the pitfalls inherent in standard parsimony methods. Profile parsimony and user-specified optimality criteria are supported.

A graphical interface, which requires no familiarity with R, is designed to help a user to improve the quality of datasets through critical review of underpinning character codings; and to obtain additional information from results by identifying and summarizing clusters of similar trees, mapping the distribution of trees, and removing  rogue taxa that obscure underlying relationships.

Taken together, the package aims to support methodological rigour at each step of data collection, analysis, and the exploration of phylogenetic results.


title: Transcriptome analysis of SARS-CoV-2 naive and recovered individuals vaccinated with inactivated vaccine

abstract: The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naive individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the hosts molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.


title: The beryllium fluoride form of the Na+,K+-ATPase and the intermediates of the functional cycle

abstract: The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane. Here, we describe a 4.0 [A] resolution crystal structure of the pig kidney Na+,K+-ATPase stabilized by beryllium fluoride (denoted E2-BeFx). The structure shows high resemblance to the E2P phosphoenzyme obtained by phosphorylation from inorganic phosphate (Pi) and stabilised by cardiotonic steroids, and reveals a Mg2+ bound near the ion binding site II. Anomalous Fourier analysis of the crystals soaked in Rb+ (K+ congener) followed by a low resolution rigid-body refinement (6.9-7.5 [A]) revealed pre-occlusion transitions leading to activation of the desphosphorylation reaction. Mg2+ location indicates a site of an initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Despite the overall structural resemblance to the Pi-induced E2P phosphoform, BeFx inhibited enzyme is able to bind both ADP/ATP and ions - features that relate E2-BeFx complex to an intermediate of the functional cycle of the Na+,K+-ATPase prior E2P.


title: Large-scale conformational changes of FhaC provide insights into the two-partner secretion mechanism

abstract: The Two-Partner secretion pathway mediates protein transport across the outer membrane of Gram-negative bacteria. TpsB transporters belong to the Omp85 superfamily, whose members catalyze protein insertion into, or translocation across membranes without external energy sources. They are composed of a transmembrane {beta} barrel preceded by two periplasmic POTRA domains that bind the incoming protein substrate. Here we used an integrative approach combining in vivo assays, mass spectrometry, nuclear magnetic resonance and electron paramagnetic resonance techniques suitable to detect minor states in heterogeneous populations, to explore transient conformers of the TpsB transporter FhaC. This revealed substantial, spontaneous conformational changes with a portion of the POTRA2 domain coming close to the lipid bilayer and surface loops. Specifically, the amphipathic {beta} hairpin immediately preceding the first barrel strand can insert into the {beta} barrel. We propose that these motions enlarge the channel and hoist the substrate into it for secretion. An anchor region at the interface of the {beta} barrel and the POTRA2 domain stabilizes the transporter in the course of secretion. Our data propose a solution to the conundrum how these transporters mediate protein secretion without the need for cofactors, by utilizing intrinsic protein dynamics.

category: biophysics


title: RB1 loss overrides PARP inhibitor sensitivity driven by RNASEH2B loss in prostate cancer

abstract: Current targeted cancer therapies are largely guided by mutations of a single gene, which overlooks concurrent genomic alterations. Here, we show that RNASEH2B, RB1, and BRCA2, three closely located genes on chromosome 13q, are frequently deleted in prostate cancer individually or jointly. Loss of RNASEH2B confers cancer cells sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition due to impaired ribonucleotide excision repair and PARP trapping. When co-deleted with RB1, however, cells lose their sensitivity, in part, through E2F1-induced BRCA2 expression, thereby enhancing homologous recombination repair capacity. Nevertheless, loss of BRCA2 re-sensitizes RNASEH2B/RB1 co-deleted cells to PARP inhibition. Our results may explain some of the disparate clinical results from PARP inhibition due to interaction between multiple genomic alterations and support a comprehensive genomic testing to determine who may benefit from PARP inhibition. Finally, we show that ATR inhibition can disrupt E2F1-induced BRCA2 expression and overcome PARP inhibitor resistance caused by RB1 loss.

category: cancer biology


title: TIR domains of plant immune receptors are 2',3'-cAMP/cGMP synthetases mediating cell death

abstract: 2',3'-cAMP is a positional isomer of the well-established second messenger 3',5'-cAMP, but little is known on the biology of this noncanonical cyclic nucleotide monophosphate (cNMP). Toll/interleukin-1 receptor (TIR) domains of nucleotide-binding leucine-rich repeat (NLR) immune receptors have NADase function necessary but insufficient to activate plant immune responses. Here we show that plant TIR proteins, besides being NADases, act as 2',3'-cAMP/cGMP synthetases by hydrolyzing RNA/DNA. Structural data shows that a TIR domain adopts distinct oligomers with dual and exclusive enzymatic activity. Mutations specifically disrupting the synthetase activity abrogate TIR-mediated cell death in Nicotiana benthamiana, supporting an important role for these cNMPs in TIR signaling. Furthermore, the Arabidopsis negative regulator of TIR-NLR signaling, NUDT7 displays 2',3'-cAMP/cGMP but not 3',5'-cAMP/cGMP phosphodiesterase activity and suppresses cell death activity of TIRs in N. benthamiana. Our study identifies a novel family of 2',3'-cAMP/cGMP synthetase and establishes a role for the noncanonical cNMPs in plant immune responses.

category: plant biology


title: Delineation of dynorphin and kappa opioid receptor circuit elements in alcohol consumption

abstract: Alcohol use disorder is complex and multi-faceted, involving the engagement of multiple signaling systems across numerous brain regions to drive pathological behavior. Previous work has indicated that both the insular cortex and dynorphin (DYN)/Kappa opioid receptor (KOR) systems contribute to excessive alcohol use. More recently, we identified a microcircuit in the medial aspect of the insular cortex that signals through DYN/KOR. Here, we explored the role of insula DYN/KOR circuit elements on alcohol intake in a long-term intermittent access (IA) procedure. Using a combination of conditional knockout strategies and site-directed pharmacology, we discovered distinct and sex-specific roles for insula DYN and KOR systems in alcohol drinking and related behavior. Our findings show that insula DYN deletion blocked escalated consumption and decreased overall intake of and preference for alcohol in male and female mice. This effect was specific to alcohol in male mice, as DYN deletion did not impact their sucrose intake. In male mice, insula KOR antagonism reduced alcohol intake and preference during the early phase of IA only. Alcohol consumption as not affected by insula KOR knockout. In addition, we found that long-term IA decreased the intrinsic excitability of DYN and deep layer pyramidal neurons (DLPN) in the insula of male mice. Excitatory synaptic transmission was also impacted by IA, as it drove an increase in excitatory synaptic drive in both DYN neurons and DLPN. Combined, our findings suggest that there is a dynamic interplay between excessive alcohol consumption and insula DYN/KOR circuit elements.


title: Delineation of insula dynorphin and kappa opioid receptor circuit elements in alcohol consumption


title: Local and collective transitions in sparsely-interacting ecological communities

abstract: Interactions in natural communities can be highly heterogeneous, with any given species interacting appreciably with only some of the others, a situation commonly represented by sparse interaction networks. We study the consequences of sparse competitive interactions, in a theoretical model of a community assembled from a species pool. We find that communities can be in a number of different regimes, depending on the interaction strength. When interactions are strong, the network of coexisting species breaks up into small subgraphs, while for weaker interactions these graphs are larger and more complex, eventually encompassing all species. This process is driven by emergence of new allowed subgraphs as interaction strength decreases, leading to sharp changes in diversity and other community properties, and at weaker interactions to two distinct collective transitions: a percolation transition, and a transition between having a unique equilibrium and having multiple alternative equilibria. Understanding community structure is thus made up of two parts: first, finding which subgraphs are allowed at a given interaction strength, and secondly, a discrete problem of matching these structures over the entire community. In a shift from the focus of many previous theories, these different regimes can be traversed by modifying the interaction strength alone, without need for heterogeneity in either interaction strengths or the number of competitors per species.

category: ecology


title: Ecological validity of masking release with speech-like stimuli

abstract: Comodulated masking noise and binaural cues can facilitate grouping frequency components into the target sound and noise. This results in a decrease in detection thresholds, quantified as comodulation masking release (CMR) and binaural masking level difference (BMLD), respectively. However, their relevance to speech perception is unclear as most studies have used artificial stimuli different from speech. Here, we investigated the ecological validity of masking release by using stimuli with speech-like spectro-temporal dynamics. We designed stimuli reflecting formant changes in speech. Each stimulus consists of three masker bands centered at formant frequencies F1, F2, and F3 based on CV combination: /gu/, /fu/, and /pu/. Maskers were either uncorrelated or comodulated to estimate CMR. In addition, target tone was centered at F2 trajectories and presented either with no IPD or IPD of {pi} to induce BMLD. We found that the CMR was small (< 3 dB) while BMLD was comparable to previous findings (~ 9 dB). To conclude, we suggest that features other than comodulation play a dominant role in grouping frequency components, such as the spectral proximity, the number of masker bands, and and formant trajectories.

category: animal behavior and cognition


title: Multifunctional phosphate based nanoparticles as a platform for imaging, targeting and doxorubicin delivery to human breast cancer CD44+ cells.

abstract: Functionalized nanostructured systems can be used for imaging and drug delivery for anti-tumor therapy, including breast tumors. This is a more efficient approach that offers reduced systemic side effects compared to conventional diagnostic and chemotherapy methods. Multifunctional nanoparticles are potential tools in the diagnosis, location tracing and kill tumor cells through a less invasive manner. Functionalized phosphate-based nanoparticles are capable of encapsulating, or may be associated, with fluorescent probes. In this study, we synthesize a nanoparticle phosphate-based composite (NPC) and functionalize it with poly-ethylene glycol (PEG), hyaluronic acid (HA), the fluorescent probe rhodamin 6G (R6G) and the antimitotic doxorubicin (DOX). We focused on targeting human breast cancer cells reporting the biological effects of functionalized NPC on them. NPC and NPC formulations containing PEG, HA, and R6G did not cause cell viability reduction on MCF-7 and MDA-MB-231 cell lines. The cellular internalization of NPC was quantified by real-time in vitro observation, and confirmed by electron microscopy techniques. Intracellular NPC distribution is detected in the cytoplasm and nucleus of tumor cells by confocal fluorescent images. The percent association of doxorubicin to NPC matrix was approximately 18% and NPC formulations associated with doxorubicin led to a significant reduction in cell viability in MDA-MB-231 and MCF-7 cells. This data suggest the potential use of NPC as a non-cytotoxic platform for association with functional ligands to selective targeting breast cancer cells. NPC use can be also explored in drug delivery to cancer cells.

category: bioengineering


title: Morphological aspects of opossum (Didelphis aurita) pancreas during intramarsupial development

category: developmental biology


title: The Open Perimetry Initiative: a framework for cross-platform development for the new generation of portable perimeters

abstract: The Open Perimetry Initiative is fully open source and consists of the Open Perimetry Interface (OPI) and an accompanying package (visualFields) with analytical tools. The OPI package contains an ever-growing number of drivers for commercially available perimeters, head-mounted devices, and virtual reality headsets. The visualFields package contains tools for the analysis and visualization of visual field data, including methods to compute deviation values and probability maps. The use of the OPI and visualFields is shown through a custom static automated perimetry test for the full visual field (up to 50{degrees} nasally and 80{degrees} temporally) developed with the OPI driver for the Octopus 900 and using visualFields for statistical analysis. Its potential for the development of cross-platform apps for driving and testing portable devices is demonstrated with an OPI driver for an Android-based headset. With more than 55 citations in clinical and translational science as listed in Scopus, this initiative has contributed significantly to expanding the knowledge base in perimetry and clinical vision research at large, and with clinical translation. The continued support of researchers, clinicians, industry, and public institutions are key in transforming perimetry research from closed to open science. The Open Perimetry Initiative provides framework to achieve this.


title: Microtubule Lattice Spacing Governs Cohesive Envelope Formation of Tau Family Proteins

abstract: Tau is an intrinsically-disordered microtubule-associated protein (MAP) implicated in neurodegenerative disease. On microtubules, tau molecules segregate into two kinetically distinct phases, consisting of either independently diffusing molecules or interacting molecules that form cohesive "envelopes" around microtubules. Envelopes differentially regulate lattice accessibility for other MAPs, but the mechanism of envelope formation remains unclear. Here, we find that tau envelopes form cooperatively, locally altering the spacing of tubulin dimers within the microtubule lattice. Envelope formation compacted the underlying lattice, whereas lattice extension induced tau-envelope disassembly. Investigating other members of the tau-MAP family, we find MAP2 similarly forms envelopes governed by lattice-spacing, whereas MAP4 cannot. Envelopes differentially biased motor protein movement, suggesting that tau family members could spatially divide the microtubule surface into functionally distinct segments. We conclude that the interdependent allostery between lattice-spacing and cooperative envelope formation provides the molecular basis for spatial regulation of microtubule-based processes by tau and MAP2.


title: Distinct replay signatures for planning and memory maintenance

abstract: Theories of neural replay propose that it supports a range of functions, most prominently planning and memory maintenance. Here, we test the hypothesis that distinct signatures of replay in the same task are related to planning and memory maintenance. We designed a reward learning task wherein participants utilized structure knowledge for  model-based evaluation, while at the same time maintaining knowledge of two independent and randomly alternating task environments. Using magnetoencephalography (MEG) and multivariate analysis, we first identified temporally compressed sequential reactivation, or replay, both during planning and following reward feedback. Prospective replay strength was enhanced for the current task{-}relevant environment when the benefits of a model-based planning strategy were higher. Following reward receipt, replay for the alternative,  distal task environment was enhanced as a function of decreasing recency of experience with that environment. Consistent with a memory maintenance role, stronger maintenance-related replay related to subsequent choices. Critically, these planning and memory maintenance relationships were selective to pre-choice and post-feedback periods. Our results provide new support for key theoretical proposals for the role of replay and demonstrate that the relative strength of planning and memory-related signals are modulated by on{-}going computational and task demands.


title: Gray Matter Differentiation Between Two Subordinate Personality Traits of Extraversion: Enthusiasm and Assertiveness

abstract: Enthusiasm and assertiveness are two subordinate personality traits of extraversion. These traits reflect different aspects of extroversion and have distinct implications on mental health. Whereas enthusiasm predicts satisfaction in life and positive relationships, assertiveness predicts psychological distress and reduced social support. The neural basis of these subordinate traits is not well understood. To investigate brain regions where enthusiasm and assertiveness have diverging relationship with morphology, enthusiasm and assertiveness were regressed to gray matter volume (GMV) across the whole brain in a sample of 301 healthy individuals. A significant interaction was found between enthusiasm and assertiveness in the left angular gyrus (t(296) = 4.18, family wise error corrected, FWE p = .001 (cluster-level); Cluster size = 880 voxels). Larger GMV in this area was associated with more enthusiasm and less assertiveness. Our study emphasizes the value of separating extraversion into its subordinate traits when investigating associations to neuroanatomy.


title: Posterior integration and thalamo-frontotemporal broadcasting are impaired in disorders of consciousness

abstract: The study of the brains dynamical activity is opening a valuable source of assistance for the clinical diagnosis of patients with disorders of consciousness (DOC). For example, dysfunctional spread of naturalistic and synthetic stimuli has proven useful to characterize hampered consciousness. However, understanding of the mechanisms behind loss of consciousness following brain injury is still missing. Here, we study the propagation of endogenous and in-silico exogenous perturbations in patients with DOC, based upon directed and causal interactions estimated from resting-state fMRI. We found that patients with DOC suffer decreased capacity for neural propagation and responsiveness to events. Particularly, that loss of consciousness is related to the malfunctioning of two neural circuits: the posterior cortical regions failing to convey information, in conjunction with reduced broadcasting of information from subcortical, temporal, parietal and frontal regions. These results seed light on the mechanisms behind DOC, thus opening new possibilities for clinical applications.


title: Sources of variation in the spectral slope of the sleep EEG

abstract: Building on previous work linking changes in the electroencephalogram (EEG) spectral slope to arousal level, Lendner et al. (2021) reported that wake, non rapid eye movement (NREM) sleep and rapid eye movement (REM) sleep exhibit progressively steeper 30-45 Hz slopes, interpreted in terms of increasing cortical inhibition. Here we sought to replicate Lendner et al.s scalp EEG findings (based on 20 individuals) in a larger sample of 11,630 individuals from multiple cohorts in the National Sleep Research Resource (NSRR). In a final analytic sample of N = 10,255 distinct recordings, there was unambiguous statistical support for the hypothesis that, within individuals, the mean spectral slope grows steeper going from wake to NREM to REM sleep. We found that the choice of mastoid referencing scheme modulated the extent to which electromyogenic or electrocardiographic artifacts were likely to bias 30-45 Hz slope estimates, as well as other sources of technical, device-specific bias. Nonetheless, within individuals, slope estimates were relatively stable over time. Both cross-sectionally and longitudinal, slopes tended to become shallower with increasing age, particularly for REM sleep; males tended to show flatter slopes than females across all states. Although conceptually distinct, spectral slope did not predict sleep state substantially better than other summaries of the high frequency EEG power spectrum (>20 Hz, in this context) including beta band power, however. Finally, to more fully describe sources of variation in the spectral slope and its relationship to other sleep parameters, we quantified state-dependent differences in the variances (both within and between individuals) of spectral slope, power and interhemispheric coherence, as well as their covariances. In contrast to the common conception of the REM EEG as relatively wake-like (i.e.  paradoxical sleep), REM and wake were the most divergent states for multiple metrics, with NREM exhibiting intermediate profiles. Under a simplified modelling framework, changes in spectral slope could not, by themselves, fully account for the observed differences between states, if assuming a strict power law model. Although the spectral slope is an appealing, theoretically inspired parameterization of the sleep EEG, here we underscore some practical considerations that should be borne in mind when applying it in diverse datasets. Future work will be needed to fully characterize state-dependent changes in the aperiodic portions of the EEG power spectra, which appear to be consistent with, albeit not fully explained by, changes in the spectral slope.


title: Multi-parametric characterization of brain-wide hemodynamic and calcium responses to sensory stimulation in mice

abstract: Modern optical neuroimaging approaches are expanding our ability to elucidate complex brain function. Diverse imaging contrasts enable direct observation of neural activity with functional sensors along with the induced hemodynamic responses. To date, decoupling the complex interplay of neurovascular coupling and dynamical physiological states has remained challenging when employing single-modality functional neuroimaging tools. We devised a hybrid fluorescence optoacoustic tomography (FLOT) platform combined with a custom data processing pipeline based on statistical parametric mapping, accomplishing the first simultaneous noninvasive observation of both direct and indirect brain-wide activation patterns with optical contrast. Correlated changes in the oxy- and deoxygenated hemoglobin, total hemoglobin, oxygen saturation and rapid GCaMP6f fluorescence signals were observed in response to peripheral sensory stimulation. While the concurrent epifluorescence served to corroborate and complement the functional optoacoustic observations, the latter further aided in decoupling the rapid calcium responses from the slowly varying background in the fluorescence recordings mediated by hemodynamic changes. The hybrid imaging platform expands the capabilities of conventional neuroimaging methods to provide more comprehensive functional readings for studying neurovascular and neurometabolic coupling mechanisms and related diseases.


title: State-dependent modulation of activity in distinct layer 6 corticothalamic neurons in barrel cortex of awake mice

abstract: Layer 6 corticothalamic (L6 CT) neurons are in a strategic position to control sensory input to the neocortex, yet we understand very little about their functions. Apart from studying their anatomical, physiological and synaptic properties, most recent efforts have focused on the activity-dependent influences CT cells can exert on thalamic and cortical neurons through causal optogenetic manipulations. However, few studies have attempted to study them during behavior. In an attempt to address this gap, we performed juxtacellular recordings from optogenetically identified CT neurons in whisker-related primary somatosensory cortex (wS1) of awake, head-fixed mice (of either sex) free to rest quietly or self-initiate bouts of whisking and locomotion. We found a rich diversity of response profiles exhibited by CT cells. Broadly, their spiking patterns were either modulated by whisker-related behavior (~28%) or not (~72%). Whisker-related neurons exhibited both increases as well as decreases in firing rates. We also encountered cells with preceding modulations in firing rate before whisking onset. Overall, whisking better explained these changes in rates than overall changes in arousal. The CT cells that showed no whisker-related activity had low spontaneous firing rates (<0.5 Hz), with many all but silent. Remarkably, this relatively silent population preferentially spiked at the state transition point when pupil diameter constricted and the mouse entered quiet wakefulness. Thus, our results demonstrate that L6 CT neurons in wS1 show diverse spiking patterns, perhaps subserving distinct functional roles related to precisely timed responses during complex behaviors and transitions between discrete waking states.


title: Intra-individual Physiomic Landscape of Pyramidal Neurons in the Human Neocortex

abstract: Computation within cortical microcircuits is determined by functional properties of the neurons and their synaptic interactions. While heterogeneity of inhibitory interneurons is well established, the anatomical, physiological, and molecular differentiation of excitatory pyramidal neurons is not fully resolved. To identify functional subtypes within the pyramidal neuron population, we focused on human layer 2-3 cortex which greatly expanded during evolution. We performed multi-neuron patch-clamp recordings in brain slices from the temporal cortex of 22 epilepsy patients. We characterized the electrophysiological properties of up to 80 pyramidal neurons per patient, enabling us to assess inter- and intra-individual functional variability. Hierarchical clustering of the high-dimensional parameter space yielded functionally distinct clusters of pyramidal neurons which were present across individuals. This may represent a generic organizational principle converging with previously described transcriptomic heterogeneity. We further observed substantial heterogeneity in physiological parameters with intra-individual variability being severalfold larger than inter-individual variability. The phenotypic variability within and across pyramidal neuron subtypes has important implications for the computational capacity of the cortical microcircuit.


title: Boundary extension is constrained by naturalistic image properties

abstract:
Boundary extension (BE) is a classical memory illusion in which observers remember more of a scene than was presented. According to predictive accounts, BE reflects the integration of visual input and expectations of what is beyond a scenes boundaries. Alternatively, according to normalization accounts, BE reflects one end of a normalization process towards a scenes typically-experienced viewing distance, such that BE and boundary contraction (BC) are equally common. Here, we show that BE and BC depend on depth-of-field (DOF), as determined by the aperture settings on a camera. Photographs with naturalistic DOF led to the strongest BE across a large stimulus set, while BC was primarily observed for unnaturalistic DOF. The relationship between DOF and BE was confirmed in three controlled experiments that isolated DOF from co-varying factors. In line with predictive accounts, we propose that BE is strongest for scene images that resemble day-to-day visual experience.

Statement of RelevanceIn daily life, we experience a rich and continuous visual world in spite of the capacity limits of the visual system. Boundary extension (BE) is a memory illusion that sheds light on how observers compensate for such limits - that is, by filling-in the visual input with anticipatory representations of upcoming views, based on memory. However, not all images equally lead to BE. In this set of studies, we show that BE is strongest for images showing naturalistic depth-of-field, resembling human visual experience. Based on these findings, we propose that BE reflects a mechanism with adaptive value that is conditional to a scene being perceived as naturalistic. More generally, the strong reliance of a cognitive effect, such as BE, on naturalistic image properties indicates that it is imperative to use image sets that are ecologically-representative when studying the cognitive, computational, and neural mechanisms of natural vision.


title: Temporally robust spatial structure in ecosystems explained by local biodiversity regulation

abstract: The distribution of species site occupancy--the occupancy frequency distribution (OFD)--is a fundamental pattern in spatial ecology. Despite decades of research, the mechanisms responsible for the shape of the distribution remain incompletely understood. Here, we simultaneously examine both spatial and temporal patterns of site occupancy in communities of macroinverterbrates, macrophytes and diatoms. We find that the shape of the OFD at the catchment scale is typically time invariant despite substantial turnover in composition and species proportional occupancy over the 30 year time series. This can been seen as evidence in favour of an ecological mechanism for the shape of the OFD driven by local regulation of species richness and other biodiversity properties. We show that a simple, locally saturated patch occupancy model explains both the shape of the OFD and the temporal turnover rate in English rivers. This model is mathematically analogous to Hubbells neutral theory however concerns patches occupied by a given species rather its population size. Our analysis supports the view that metacommunities exist in a dynamic steady state arising from local ecological constraints and that this intrinsic regulation can drives the emergence of a wide variety of macroecological patterns. We also show that interspecific differences are unlikely to play a dominant role in driving large scale ecosystem structure.


title: Temporally robust occupancy frequency distributions in riverine ecosystems explained by local biodiversity regulation


title: Competitive asymmetry confers polyploid advantage under environmental stress

abstract:
O_LICompetitive asymmetry across heterogeneous environments is crucial for the success of polyploid plants, however, little is known about it. As the major force in plant evolution, polyploids are predicted to maintain the competitive dominance relative to diploids under increased stress conditions.
C_LIO_LITo evaluate the hypothesis of competitive asymmetry, we competed tetraploid and diploid plants of perennial herbaceous Chrysanthemum indicum L. (Asteraceae) at different relative frequencies under low and high water stress. We quantified the interaction intensity between competing plants of the same (intraploidy) and different ploidy levels (interploidy), and measured functional traits related to gas exchange and plant water use to understand the underlying mechanisms.
C_LIO_LIStronger competitive effects of the tetraploid on diploid provided evidence for the competitive asymmetry between polyploid and diploid plants in C. indicum. Such competitive asymmetry was not only maintained under drought (increased water stress), but also translated into higher fitness of the tetraploid consistently across water stress conditions. Functional traits associated with fast growth and efficient water use likely explained the competitive dominance of the tetraploid.
C_LIO_LIThese results will advance our understanding of species interactions between polyploid and diploid plants, and provide insights into population dynamics and species distribution under environmental change.
C_LI


title: Cohort Profile: Genetic data in the German Socio-Economic Panel Innovation Sample (Gene-SOEP)

abstract: The German Socio-Economic Panel (SOEP) serves a global research community by providing representative annual longitudinal data of private households in Germany. The sample provides a detailed life course perspective based on a rich collection of information about living conditions, socio-economic status, family relationships, personality, values, preferences, and health. We collected genetic data from 2,598 individuals in the SOEP Innovation Sample, yielding the first genotyped sample that is representative of the entire German population (Gene-SOEP). The Gene-SOEP sample is a longitudinal study that includes 107 full-sibling pairs, 501 parent-offspring pairs, and 152 parent-offspring trios that are overlapping with the parent-offspring pairs. We constructed a repository of 66 polygenic indices in the Gene-SOEP sample based on results from well-powered genome-wide association studies. The Gene-SOEP data provides a valuable resource to study individual differences, inequalities, life-course development, health, and interactions between genetic predispositions and environment.

category: genetics


title: Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese Subpopulations

abstract: Genetic findings suggested that ethnolinguistically diverse populations in China harbor differentiated genetic structure and complex evolutionary admixture history, which provide the genetic basis and theoretical foundation for forensic biogeographical ancestry inference (BGAI). Forensic assays for BGAI among intracontinental eastern Eurasians were previously conducted mainly based on the SNPs or InDels. Microhaplotypes, as a set of closely linked SNPs within 200 base pairs, possess the advantages of both STR and SNP and have great potential in forensic ancestry inference. However, the developed forensic assay based on the ancestry informative microhaplotypes in the BGAI remained to be comprehensively explored, especially in China with enriching genetic diversity. Here, we described a new BGAI panel based on 21 novel identified ancestry informative microhaplotypes that focused on dissected finer-scale ancestry composition of Chinese populations. We initially screened all possible microhaplotypes with high Fst values among five East Asian populations and finally employed 21 candidate microhaplotypes in two multiplex SNaPshot assays. Forensic amplification efficiency and statistically/physically phased haplotypes of the 21 microhaplotypes were validated using both SNaPshot and massively parallel sequencing (MPS) platforms. Followingly, we validated the efficiency of these microhaplotypes for BGAI in 764 individuals from ten Chinese populations. Fine-scale ancestry source and ancestry proportion estimated by the principal component analysis (PCA), multidimensional scaling (MDS), phylogenetic tree and model-based STRUCTURE among worldwide populations and East Asians showed that our customized panel could provide a higher discrimination resolution in both continental population stratification and East Asian regional substructure. East Asian populations could be further classified into linguistically/geographically different intracontinental subpopulations (Tibeto-Burman, Tai-Kadai and others). Finally, we obtained a higher estimated accuracy using training and tested datasets in the microhaplotype-based panel than traditional SNP-based panels. Generally, the above results demonstrated that this microhaplotype panel was robust and suitable for forensic BGAI in Chinese populations, which not only provided a high discriminatory power for continental populations but also discriminated East Asians into linguistically restricted subpopulations.


title: Detection of live breast cancer cells in brightfield microscopy images containing white blood cells by image analysis and deep learning

abstract:
SignificanceCirculating tumor cells (CTCs) are important biomarkers for cancer management. Isolated CTCs from blood are stained to detect and enumerate CTCs. However, the staining process is laborious and moreover makes CTCs unsuitable for drug testing and molecular characterization.

AimThe goal is to develop and test deep learning (DL) approaches to detect unstained breast cancer cells in bright field microscopy images that contain white blood cells (WBCs).

ApproachWe tested two convolutional neural network (CNN) approaches. The first approach allows investigation of the prominent features extracted by CNN to discriminate cancer cells from WBCs. The second approach is based on Faster Region-based Convolutional Neural Network (Faster R-CNN).

ResultsBoth approaches detected cancer cells with high sensitivity and specificity with the Faster R-CNN being more efficient and suitable for deployment. The distinctive feature used by the CNN used to discriminate is cell size, however in the absence of size difference, the CNN was found to be capable of learning other features. The Faster R-CNN was found to be robust with respect to intensity and contrast image transformations.

ConclusionsCNN-based deep learning approaches could be potentially applied to detect patient-derived CTCs from images of blood samples.


title: scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets

abstract:
AO_SCPLOWBSTRACTC_SCPLOWA common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. Here we present scGate, an algorithm that automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. scGate purifies a cell population of interest using a set of markers organized in a hierarchical structure, akin to gating strategies employed in flow cytometry. In our benchmark for blood-derived and tumor-infiltrating immune cells, scGate outperforms SingleR, a state-of-the-art classifier for single-cell data. scGate is implemented as an R package and integrated with the Seurat framework, providing an intuitive tool to isolate cell populations of interest from complex scRNA-seq datasets.

AvailabilityR package source code and reproducible tutorials are available at https://github.com/carmonalab/scGate


title: WATLAS: high resolution and real-time tracking of many small birds in the Dutch Wadden Sea

abstract: Movement is a fundamental aspect of life and tracking wild animals under natural conditions has become central to animal behaviour, ecology, and conservation science. Data from tracked animals have provided novel scientific insights on extreme migratory journeys, mechanisms of navigation, space use, and early warning signals of environmental change. Studying movement is therefore important, particularly in systems that may be vulnerable to anthropogenic effects. Technological advancements, and chiefly the development of GPS tags, have enabled animal tracking at high spatiotemporal resolution, yet trade-offs between cost, sampling frequency, tag weight and data retrieval limit the use of GPS tags to relatively few individuals and large species. A new  reverse-GPS wildlife tracking system, ATLAS, employs an array of receiver stations that detect and localise small ([~]0.6 g without battery), low-cost ([~]25 euro) tags by calculating differences in the arrival time of tag signal at minimally three stations. In this study, we introduce the Wadden Sea ATLAS system (WATLAS), implemented in the Dutch Wadden Sea, the Netherlands only natural UNESCO World Heritage Site, yet affected by a suite of anthropogenic activities, such as commercial fishing, mining, shipping, as well as sea level rise. From July 2017 to July 2021, we tracked 821 red knots, 182 sanderlings, 33 bar-tailed godwits, and 6 common terns. With four examples, we illustrate how WATLAS opens-up possibilities for studying space-use, among-individual variation in movement, and intra-specific interactions, and inter-specific (community) space use in the wild. We additionally argue that WATLAS could provide a tool for impact assessment, and thus aid nature conservation and management of the globally important Wadden Sea ecosystem.


title: Standardised empirical dispersal kernels emphasise the pervasiveness of long-distance dispersal in European birds

abstract:
O_LIDispersal is a key life-history trait for most species and essential to ensure connectivity and gene flow between populations and facilitate population viability in variable environments. Despite the increasing importance of range shifts due to global change, dispersal has proved difficult to quantify, limiting empirical understanding of this phenotypic trait and wider synthesis.
C_LIO_LIHere we aim to estimate and compare empirical dispersal kernels for European breeding birds considering average dispersal, natal (before first breeding) and breeding dispersal (between subsequent breeding attempts), and test whether different dispersal properties are phylogenetically conserved.
C_LIO_LIWe standardised and analysed data from an extensive volunteer-based bird ring-recoveries database in Europe (EURING) by accounting for biases related to different censoring thresholds in reporting between countries and to migratory movements. Then, we fitted four widely used probability density functions in a Bayesian framework to compare and provide the best statistical descriptions of the average, the natal and the breeding dispersal kernels for each bird species.
C_LIO_LIThe dispersal movements of the 234 European bird species analysed were statistically best explained by heavy-tailed kernels, meaning that while most individuals disperse over short distances, long-distance dispersal is a feature in almost all bird species. The overall phylogenetic signal in both median and long dispersal distances was low (Pagels {lambda} < 0.40), implying a high degree of taxonomic generality in our findings. As expected in birds, natal dispersal was 5 Km greater as an average than breeding dispersal for most species (88% species analysed).
C_LIO_LIOur comprehensive analysis of empirical kernels indicates that long-distance dispersal is common among European breeding bird species and across life stages. The dispersal estimates offer a first guide to selecting appropriate dispersal kernels in range expansion studies and provide new avenues to improve our understanding of the mechanisms and rules underlying dispersal events.
C_LI


title: Learning Feedback Molecular Network Models Using Integer Linear Programming

abstract: Analysis of intracellular molecular networks has many applications in understanding of the molecular bases of some complex diseases and finding the effective therapeutic targets for drug development. To perform such analyses, the molecular networks need to be converted into computational models. In general, network models constructed using literature and pathway databases may not accurately predict and reproduce experimental network data. This can be due to the incompleteness of literature on molecular pathways, the resources used to construct the networks, or some conflicting information in the resources. In this paper, we propose a network learning approach via an integer linear programming formulation that can efficiently incorporate biological dynamics and regulatory mechanisms of molecular networks in the learning process. Moreover, we present a method to properly take into account the feedback paths, while learning the network from data. Examples are also provided to show how one can apply the proposed learning approach to a network of interest. Overall, the proposed methods are useful for reducing the gap between the curated networks and experimental network data, and result in calibrated networks that are more reliable for making biologically meaningful predictions.

category: systems biology


title: A Computational Modeling Framework to Analyze Synovial-Tissue Based Drug Targets and Diagnostic Biomarkers in Rheumatoid Arthritis

abstract: Rheumatoid Arthritis (RA) is an inflammatory autoimmune disease that affects 23 million people worldwide. It is a clinically heterogeneous disorder characterized by the attack of inflammatory chemicals on the synovial tissue that lines joints. It is advantageous to develop effective, targeted treatments and identify specific diagnostic biomarkers for RA before extensive joint degradation, bone erosion, and cartilage destruction. Current modes of RA treatments have alleviated and notably halted the progression of RA. Despite this, not many patients reach low disease activity status after treatment, and a significant number of patients fail to respond to medication due to drug non-specificity. While the reasons for these rates remain unknown, the cellular and molecular signatures present in the synovial tissue for RA patients likely play a role in the varied treatment response. Thus, a drug that particularly targets specific genes and networks may have a significant effect in halting the progression of RA. This study evaluates and proposes potential drug targets through in silico mathematical modeling of various pathways of interest in RA. To understand how drugs interact with genes, we built a mathematical model with 30 two-gene and three-gene network interactions and analyzed the effect of 92 different perturbations to rate constants. We determined that inhibition of the LCK-CD4, VAV1-CD4, and MLT-ROR pathways could potentially serve as drug targets. We also found that increased activity of the DEC2-IL1{beta} and the NF-kB-interleukin pathway and the decreased activity of the TNF--REV-ERB pathway could serve as diagnostic biomarkers.


title: Low abundance members of the gut microbiome are potent drivers of immune cell education.

abstract: One of the main goals of microbiome research is to identify bacterial members that significantly affect host phenotypes and understand their contributions to disease pathogenesis. Studies identifying bacterial members that dictate host phenotype have focused mainly on the dominant members, and the role of low abundance microbes in determining host phenotypes and pathogenesis of diseases remains unexplored. In this study, we compared the gut bacterial community of mice with wide-ranging microbial exposure to determine if low abundance bacteria vary based on microbial exposure or remain consistent. We noted that similar to the high abundance bacterial community, a core community of low abundance bacteria made up a significant portion of the gut microbiome irrespective of microbial exposure. To determine the effect of low abundance bacteria on community structure and host gene expression, we devised a microbiome dilution strategy to "delete" out low abundance bacteria and engrafted the diluted microbiomes into germ-free mice. Our approach successfully excluded low abundance bacteria from small and large intestinal bacterial communities and induced global changes in microbial community structure and composition in the large intestine. Gene expression analysis of intestinal tissue revealed that loss of low abundance bacteria resulted in a drastic reduction in expression of multiple genes involved MHC class II antigen presentation pathway and T-cell cytokine production in the small intestine. The effect of low abundance bacteria on MHC class II expression was found specific to the intestinal epithelium at an early timepoint post-colonization and correlated with bacteria belonging to the family Erysipelotrichaceae. We conclude that low abundance bacteria have a significantly higher immuno-stimulatory effect compared to dominant bacteria and are thus potent drivers of early immune education in the gut. Therefore, characterizing immune interaction of low abundance bacteria with the host will offer greater insight into the intestinal immune landscape and disease pathogenesis.