title: Compared with SARS-CoV2 wild type's spike protein, the SARS-CoV2 omicron's receptor binding motif has adopted a more SARS-CoV1 and/or bat/civet-like structure.

abstract: Our study focuses on free energy calculations of SARS-CoV2 spike protein receptor binding motives (RBMs) from wild type and variants-of-concern with particular emphasis on currently emerging SARS- CoV2 omicron variants of concern (VOC). Our computational free energy analysis underlines the occurrence of positive selection processes that specify omicron host adaption and bring changes on the molecular level into context with clinically relevant observations. Our free energy calculations studies regarding the interaction of omicrons RBM with human ACE2 shows weaker binding to ACE2 than alphas, deltas, or wild types RBM. Thus, less virus is predicted to be generated in time per infected cell. Our mutant analyses predict with focus on omicron variants a reduced spike-protein binding to ACE2-receptor protein possibly enhancing viral fitness / transmissibility and resulting in a delayed induction of danger signals as trade-off. Finally, more virus is produced but less per cell accompanied with delayed Covid-19 immunogenicity and pathogenicity. Regarding the latter, more virus is assumed to be required to initiate inflammatory immune responses.


title: ZEB2 transduces HIF1α dependent regulation of Transglutaminase 2 in glomerular podocytes

abstract: Glomerular podocytes are instrumental in ensuring glomerular permselectivity and regulating the integrity of glomerular biology. However, podocytes are vulnerable to various noxious stimuli such as hypoxia, and podocyte injury presented with glomerulosclerosis and impaired kidney function. The mechanism of hypoxia-induced podocyte injury vis-a-vis glomerulosclerosis has remained enigmatic. Hypoxia inducible factor 1 (HIF1) that transduces hypoxic adaptations, induces Transglutaminase 2 (TG2), a calcium dependent enzyme that catalyzes intramolecular {varepsilon}-({gamma}-glutamyl) lysine cross-links of extracellular matrix (ECM) proteins. In this study, we investigated the mechanism of regulation of TG2 by HIF1. Stabilization of HIF1 by FG4592 (Roxadustat) and physiological hypoxia, resulted in elevated expression of ZEB2 (zinc-finger E-box-homeobox 2) and its downstream target TRPC6 (transient receptor potential channel 6). ZEB2 transcriptionally activates TG2 expression, whereas, via TRPC6, it induces calcium influx, inturn it increases the TG2 activity. Blocking the TRPC6 action or suppressing its expression only partially attenuated FG4592 induced TG2 activity, whereas suppression of ZEB2 expression significantly abolished TG2 activity. This study demonstrates that stabilization of HIF1 stimulates both TG2 expression and activity, whereas abrogation of HIF1 by metformin prevented HIF1 regulated TG2 and consequent glomerular injury.

category: cell biology


title: Photoaffinity capture compounds to profile the Magic Spot Nucleotide interactomes

abstract:
Magic Spot Nucleotides (MSN) regulate the stringent response, a highly conserved bacterial stress adaptation mechanism, enabling survival when confronted with adverse external challenges. In times of antibiotic crisis, a detailed understanding of the stringent response is of critical importance, as potentially new targets for pharmacological intervention could be identified. In this study, we delineate the MSN interactome in Escherichia coli and Salmonella typhimurium cell lysates applying a family of trifunctional photoaffinity capture compounds. We introduce different MSN probes covering diverse phosphorylation patterns, such as pppGpp, ppGpp, and pGpp. Our chemical proteomics approach provides datasets of diverse putative MSN receptors both from cytosolic and membrane fractions that, upon validation, unveil new MSN targets. We find, for example, that the dinucleoside polyphosphate hydrolase activity of the non-Nudix hydrolase ApaH is potently inhibited by pppGpp, which itself is converted to pGpp by ApaH. The photoaffinity capture compounds described herein will be useful to identify MSN interactomes under varying conditions and across bacterial species.

TOC

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC="FIGDIR/small/472736v1_ufig1.gif" ALT="Figure 1">
View larger version (17K):
org.highwire.dtl.DTLVardef@15cfc02org.highwire.dtl.DTLVardef@1a4ec1borg.highwire.dtl.DTLVardef@88fd27org.highwire.dtl.DTLVardef@1a42248_HPS_FORMAT_FIGEXP  M_FIG Molecular fishing: a family of trifunctional photoaffinity capture compounds enables the identification of Magic Spot Nucleotide receptors by a chemoproteomics approach.

C_FIG

category: biochemistry


title: Comparison of extraction methods for intracellular metabolomics

abstract: Measurements of metabolic compounds inside cells or tissues are of high informative potential since they represent the endpoint of biological information flow and a snapshot of the integration of many regulatory processes. However, it requires careful extraction to quantify their abundance. Here we present a comprehensive study using ten extraction protocols on four human sample types (liver tissue, bone marrow, HL60 and HEK cells) targeting 630 metabolites of different chemical classes. We show that the extraction efficiency and stability is highly variable across protocols and tissues by using different quality metrics including the limit of detection and variability between replicates as well as the sum of concentration as a global estimate of extraction stability. The profile of extracted metabolites depends on the used solvents - an observation which has implications for measurements of different sample types and metabolic compounds of interest. To identify the optimal extraction method for future metabolomics studies, the benchmark dataset was implemented in an easy-to-use, interactive and flexible online resource (R/shiny app MetaboExtract).


title: The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface

abstract: Chromosomes readily unlink from one another and segregate to daughter cells during cell division highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes mediate chromosome folding by DNA loop extrusion. In most bacteria, SMC complexes start loop extrusion at the ParB/parS partition complex formed near the replication origin. Whether they are recruited by recognizing a specific DNA structure in the partition complex or a protein component is unknown. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate chromosomes when transplanted into another organism. Using chimeric proteins and chemical cross-linking, we find that ParB binds to the Smc subunit directly. We map a binding interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex to initiate DNA loop extrusion.


title: Pseudomonas response regulators produced in an E. coli heterologous expression host exhibit host-derived post-translational phosphorylation

abstract: In this report, we systematically characterize 32 response regulators (RRs) from a metal tolerant groundwater isolate, Pseudomonas stutzeri RCH2 to assess the impact of host-derived post-translational phosphorylation. As observed by distinct shifted bands in a phos-tag gel, 12 of the 24 detected RRs show homogenous mixtures of phosphorylated proteins or heterogenous mixtures of unphosphorylated and phosphorylated proteins. By evaluating the phosphorylation state of CzcR and CopR II under varying assay parameters, we found that changes to pH and exogenous addition of phospho-donors (e.g. acetyl phosphate) have little to no effect on phosphorylation state. By applying protein production conditions that decrease the pool of intracellular acetyl-phosphate in E. coli, we found a reduction in the phosphorylated population of CopR II when magnesium was added to the media, but observed no change in phosphorylated population when CopR II is expressed in E. coli BL21 (DE3){Delta} pta, a mutant with a metabolic disruption to the acetyl-phosphate pathway. Therefore, the specific mechanism of post-translational phosphorylation of RRs in E. coli remains obscure. These findings show the importance of characterizing the phosphorylations state of proteins when heterologously expressed, since their biochemical and physiological properties are dependent on post-translational modification.


title: SARS-CoV-2 Spike protein activates TMEM16F-mediated platelet pro-coagulant activity

abstract:
BackgroundThrombosis of the lung micro-vasculature is a characteristic of COVID-19 disease, which is observed in large excess compared to other forms of acute respiratory distress syndrome and thus suggests a trigger for thrombosis endogenous to the lung. Our recent work has shown that the SARS-CoV-2 Spike protein activates the cellular TMEM16F chloride channel and scramblase. Through a screening on >3,000 FDA/EMA approved drugs, we identified Niclosamide and Clofazimine as the most effective molecules at inhibiting this activity. As TMEM16F plays an important role in the stimulation of the pro-coagulant activity of platelets, and considering that platelet abnormalities are common in COVID-19 patients, we investigated whether Spike directly affects platelet activation and pro-thrombotic function and tested the effect of Niclosamide and Clofazimine on these processes.

MethodsWe produced SARS-CoV-2 Spike or VSV-G protein-pseudotyped virions, or generated cells expressing Spike on their plasma membrane, and tested their effects on platelet adhesion (fluorescence), aggregation (absorbance), exposure of phosphatidylserine (flow cytometry for annexin V binding), calcium flux (flow cytometry for fluo-4 AM), and clot formation and retraction. These experiments were also conducted in the presence of the TMEM16F activity inhibitors Niclosamide and Clofazimine.

ResultsHere we show that exposure to SARS-CoV-2 Spike promotes platelet activation, adhesion and spreading, both when present on the envelope of virions or upon expression on the plasma membrane of cells. Spike was effective both as a sole agonist or by enhancing the effect of known platelet activators, such as collagen and collagen-related peptide. In particular, Spike exerted a noticeable effect on the procoagulant phenotype of platelets, by enhancing calcium flux, phosphatidylserine externalisation, and thrombin generation. Eventually, this resulted in a striking increase in thrombin-induced clot formation and retraction. Both Niclosamide and Clofazimine almost abolished this Spike-induced pro-coagulant response.

ConclusionsTogether, these findings provide a pathogenic mechanism to explain thrombosis associated to COVID-19 lung disease, by which Spike present in SARS-CoV-2 virions or exposed on the surface of infected cells, leads to local platelet stimulation and subsequent activation of the coagulation cascade. As platelet TMEM16F is central in this process, these findings reinforce the rationale of repurposing drugs targeting this protein, such as Niclosamide, for COVID-19 therapy.

category: pathology


title: Potential and action mechanism of favipiravir as an antiviral against Junin virus

abstract: Favipiravir is a nucleoside analogue that inhibits the replication and transcription of a broad spectrum of RNA viruses, including pathogenic arenaviruses. In this study, we isolated a favipiravir-resistant mutant of Junin virus (JUNV), which is the causative agent of Argentine hemorrhagic fever, and analyzed the antiviral mechanism of favipiravir against JUNV. Two amino acid substitutions, N462D in the RNA-dependent RNA polymerase (RdRp) and A168T in the glycoprotein precursor GPC, were identified in the mutant. GPC-A168T substitution enhanced the efficiency of JUNV internalization, which explains the robust replication kinetics of the mutant in the virus growth analysis. Although RdRp-N462D substitution did not affect polymerase activity levels in a minigenome system, comparisons of RdRp error frequencies showed that the virus with RdRp-D462 possessed a significantly higher fidelity. We also provided experimental evidence for the first time that favipiravir inhibited JUNV through the accumulation of transition mutations, confirming its role as a purine analogue against arenaviruses. Moreover, we showed that treatment with a combination of favipiravir and either ribavirin or remdesivir inhibited JUNV replication in a synergistic manner, blocking the generation of the drug-resistant mutant. Our findings provide new insights for the clinical management and treatment of Argentine hemorrhagic fever.

category: microbiology


title: The ColR/S two-component system is a conserved determinant of host association across Pseudomonas species

abstract: Members of the bacterial genus Pseudomonas form mutualistic, commensal and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system, part of the Pseudomonas core genome, is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens. Using plant rhizosphere colonization and virulence in a murine abscess model, we show that colR is required for commensalism with plants and virulence in animals. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not hostspecific, requirements for ColR-dependent genes. Collectively, our results suggest that ColR/S allows Pseudomonas to sense and respond to a host, but that the ColR-regulon has diverged between Pseudomonas strains with distinct lifestyles.


title: Manganese modulates metabolic activity and redox homeostasis in translationally-blocked Lactococcus cremoris, impacting metabolic persistence, cell-culturability, and flavor formation.

abstract: Manganese (Mn) is an essential trace element that is supplemented in microbial media with varying benefits across species and growth conditions. We found that growth of Lactococcus cremoris was unaffected by manganese omission from the growth medium. The main proteome adaptation to manganese omission involved increased manganese transporter production (up to 2000-fold), while the remaining 10 significant proteome changes were between 1.4 and 4 fold. Further investigation in translationally-blocked (TB), non-growing cells showed that Mn supplementation (20 M) led to approximately 1.5X faster acidification compared to Mn-free conditions. However, this faster acidification stagnated within 24 hours, likely due to draining of intracellular NADH that coincides with substantial loss of culturability. Conversely, without manganese, non-growing cells persisted to acidify for weeks, albeit at a reduced rate, but maintaining redox balance and culturability. Strikingly, despite being unculturable, -keto acid-derived aldehydes continued to accumulate in cells incubated in the presence of manganese, whereas without manganese cells predominantly formed the corresponding alcohols. This is most likely reflecting NADH availability for the alcohol dehydrogenase-catalyzed conversion. Overall, manganese influences the lactococcal acidification rate, and flavor formation capacity in a redox dependent manner. These are important industrial traits especially during cheese ripening, where cells are in a non-growing, often unculturable state.


title: Evolution of miRNA binding sites and regulatory networks in cichlids

abstract: The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA and TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.

category: molecular biology


title: Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting

abstract: Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in budding yeast to measure how transcriptional bursting changes upon single and double perturbations of chromatin remodeling factors, the transcription factor Gal4 and preinitiation complex (PIC) components. Using dynamic epistasis analysis, we reveal how remodeling of different nucleosomes regulates individual transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC acts synergistically with Gal4 binding to facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. In the absence of remodelers, nucleosomes at canonical TATA boxes are displaced by TBP binding to allow for transcription activation. Overall, our results reveal how promoter nucleosome remodeling, together with transcription factor and PIC binding regulates the kinetics of transcriptional bursting.


title: Arl15 upregulates the TGFβ family signaling by promoting the assembly of the Smad-complex

abstract: The hallmark event of the canonical transforming growth factor {beta} (TGF{beta}) family signaling is the assembly of the Smad-complex, consisting of the common Smad, Smad4, and phosphorylated receptor-regulated Smads. How the Smad-complex is assembled and regulated is still unclear. Here, we report that active Arl15, an Arf-like small G protein, specifically binds to the MH2 domain of Smad4 and colocalizes with Smad4 at the endolysosome. The binding relieves the autoinhibition of Smad4, which is imposed by the intramolecular interaction between its MH1 and MH2 domains. Activated Smad4 subsequently interacts with phosphorylated receptor-regulated Smads, forming the Smad-complex. Our observations suggest that Smad4 functions as an effector and a GTPase activating protein (GAP) of Arl15. Assembly of the Smad-complex enhances the GAP activity of Smad4 toward Arl15, therefore dissociating Arl15 before the nuclear translocation of the Smad-complex. Our data further demonstrate that Arl15 positively regulates the TGF{beta} family signaling.


title: DNMT3A knockouts in human iPSCs prevent de novo DNA methylation and reveal growth advantage during hematopoietic differentiation

abstract: DNA methyltransferase 3A (DNMT3A) is a frequently mutated gene in many hematological malignancies, indicating that it may be essential for hematopoietic differentiation. Here, we addressed the functional relevance of DNMT3A for differentiation of human induced pluripotent stem cells (iPSCs) by knocking out exon 2, 19, or 23. Exon 19-/- and 23-/- lines revealed absence of almost the entire de novo DNA methylation during mesenchymal and hematopoietic differentiation. Yet, differentiation was only slightly reduced in exon 19-/- and increased in exon 23-/- lines, whereas there was no significant impact on gene expression in hematopoietic progenitors (iHPCs). Notably, DNMT3A-/- iHPCs recapitulate some DNA methylation differences of acute myeloid leukemia with DNMT3A mutations. Furthermore, multicolor genetic barcoding revealed competitive growth advantage of exon 23-/- iHPCs. Our results demonstrate that de novo DNA methylation during hematopoietic differentiation of iPSCs is almost entirely dependent on DNMT3A and exon 23-/- iHPCs even gained growth advantage.


title: Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

abstract:
Understanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. In Gasterosteus aculeatus, a variant HOXDB allele is genetically linked to shortening an existing spine and adding a spine. In Apeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-coding HOXDB enhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independent cis-acting regulatory changes are linked to anterior expansion or contraction of HOXDB expression. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/472698v1_ufig1.gif" ALT="Figure 1">
View larger version (32K):
org.highwire.dtl.DTLVardef@8e6675org.highwire.dtl.DTLVardef@e89e13org.highwire.dtl.DTLVardef@1e1f1dcorg.highwire.dtl.DTLVardef@cdb6f8_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: evolutionary biology


title: Autophagy-related protein Atg11 preserves asymmetric inheritance of spindle microtubule-organizing centers

abstract: Asymmetric spindle pole body (SPB) inheritance requires a cascade of events that involve kinases, phosphatases and structural scaffold proteins including molecular motors and microtubule-associated proteins. Higher levels of an SPB component Spc72 and the spindle positioning factor Kar9 at the old SPB, which migrates to the daughter cell, ensure asymmetric SPB inheritance. In this study, by analyzing the protein interaction network of autophagy (Atg)-related proteins with those that constitute the chromosome segregation machinery, and growth inhibition kinetics in the presence of a microtubule poison, we identified Atg11 as a potential regulator of chromosome transmission from a cohort of 35 autophagy mutants in Saccharomyces cerevisiae. Cells lacking Atg11 did not show kinetochore defects but displayed a high rate of chromosome loss and delayed anaphase onset. Atg11 positively interacted with Kar9 and Kip2 and negatively with Dyn1 and Kar3 in mediating proper positioning and alignment of the mitotic spindle that was found to be under the surveillance of the spindle positioning checkpoint. Indeed, atg11{Delta} cells displayed an inverted SPB inheritance. Our experiments further revealed that via the Kar9 pathway, Atg11 promotes asymmetric localization of Spc72 and Kar9 on the old SPB. Atg11 physically interacted with Spc72 and transiently localized close to the old SPB during metaphase-to-anaphase progression. Thus, we uncover an autophagy-independent role of Atg11 in spindle alignment. This study emphasizes the importance of screens to identify factors mediating the complex and intricate crosstalk between biological processes fundamental to genomic integrity.

category: genetics


title: Atg11 promotes Kar9-mediated alignment of the mitotic spindle


title: Discovery of lipid-mediated protein-protein interactions in living cells using metabolic labeling with photoactivatable clickable probes

abstract: Protein-protein interactions (PPIs) are essential and pervasive regulatory elements in cell biology. Despite development of a range of techniques to probe PPIs in living systems, there is a dearth of approaches to capture interactions driven by specific post-translational modifications (PTMs). Myristoylation is a lipid PTM added to more than 200 human proteins, where it may regulate membrane localization, stability or activity. Here we report design and synthesis of a panel of novel photocrosslinkable and clickable myristic acid analog probes, and their characterization as efficient substrates for human N-myristoyltransferases NMT1 and NMT2, both biochemically and through X-ray co-crystallography. We demonstrate metabolic incorporation of probes to label NMT substrates in cell culture and in situ intracellular photoactivation to form a covalent crosslink between modified proteins and their interactors, capturing a snapshot of interactions driven by the presence of the lipid PTM. Proteomic analyses revealed both known and multiple novel interactors of a series of myristoylated proteins, including ferroptosis suppressor protein FSP1 and spliceosome-associated RNA helicase DDX46. The concept exemplified by these probes offers an efficient approach for exploring the PTM-specific interactome, which may prove broadly applicable to other PTMs.


title: Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex

abstract: The light-harvesting-reaction center (LH1-RC) core complex of purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides is characterized by the presence of both a dimeric form and a monomeric form. Following structure determination of the monomeric LH1-RC including its previously unrecognized component designated protein-U (Nat. Commun. 12, 6300, 2021), here we present cryo-EM structures of the dimeric LH1-RC from native Rba. sphaeroides IL106 at 2.75 [A] resolution and from an LH1-RC monomer lacking protein-U ({Delta}U) at 2.64 [A] resolution. The native dimeric core complex reveals many asymmetric features in the arrangement of its two monomeric components including the structural integrity of protein-U, the overall LH1 organization, and the rigidities of the proteins and pigments that form the complex. PufX polypeptides play a critical role in connecting two monomers, with one PufX interacting at its N-terminus with another PufX and an LH1 {beta}-polypeptide in another monomer, in good agreement with biochemical analyses. One of the proteins-U was only partially identified in the dimeric structure, signaling significantly different degrees of disorder in the two monomers. The {Delta}U LH1-RC monomer revealed a half-moon-shaped structure containing 11 - and 10 {beta}-polypeptides (compared with 14 of each in the wild type), indicating a critical role for protein-U in controlling the number of {beta}-subunits required for correct assembly and stabilization of the LH1-RC dimer. The structural features are discussed in relation to the unusual topology of intracytoplasmic photosynthetic membranes and an assembly model proposed for the native Rba. sphaeroides dimeric LH1-RC complex in membranes of wild-type cells.


title: Inferring the DNA replication origin density landscape in human cells from replication timing and fork directionality data

abstract: The determinants of the locations and firing times of the multiple replication origins are still elusive in human and other metazoan organisms. Experiments can independently profile mean replication timing (MRT) and replication fork directionality (RFD) genome-wide. In the hypothesis of a constant replication fork speed, MRT and RFD are related to each other by an analytical formula so are a priori equivalent. However, we show here that experimental noises result in MRT and RFD profiles containing information at different spatial frequencies. We further demonstrate that one can compute an origin density landscape that, when inserted in an appropriate simulation framework, jointly predicts experimental MRT and RFD profiles with an unprecedented precision. We also extract an analytical formula linking intrinsic origin efficiency with observed origin efficiency and MRT. We then compare the computed origin density landscape with experimental distributions of potential origins (ORC, MCM) or actual initiation events (Bubble-seq, SNS-seq, OK-seq). The results indicate that MRT and RFD data are highly consistent with each other, that our simple model suffices to capture the replication dynamics during S phase given an appropriate initiation probability landscape, but that the density of potential origins is not the sole determinant of this landscape.

category: biophysics


title: Simulation of the omicron variant of SARS-CoV-2 shows broad antibody escape, weakened ACE2 binding, and modest increase in furin binding

abstract: The recent emergence of the omicron variant of the SARS-CoV-2 virus with large numbers of mutations has raised concern about a potential new surge in infections. Here we use molecular dynamics to study the biophysics of the interface of the omicron spike protein binding to (i) the ACE2 receptor protein, (ii) antibodies from all known binding regions, and (iii) the furin binding domain. Our simulations suggest that while there is significant reduction of antibody binding strength corresponding to escape, the omicron spike pays a cost in terms of weaker receptor binding. The furin cleavage domain is the same or weaker binding than the alpha variant, suggesting less viral load and disease intensity than the extant delta variant.


title: Artificial intelligence to solve the X-ray crystallography phase problem: a case study report.

abstract:
The determination of three dimensional structures of macromolecules is one of the actual challenge in biology with the ultimate objective of understanding their function. So far, X-ray crystallography is the most popular method to solve structure, but this technique relies on the generation of diffracting crystals. Once a correct data set has been obtained, the calculation of electron density maps requires to solve the so-called <<phase problem >> using different approaches. The most frequently used technique is molecular replacement, which relies on the availability of the structure of a protein sharing strong structural similarity with the studied protein. Its success rate is directly correlated with the quality of the models used for the molecular replacement trials. The availability of models as accurate as possible is then definitely critical.

Very recently, a breakthrough step has been made in the field of protein structure prediction thanks to the use of machine learning approaches as implemented in the AlphaFold or RoseTTAFold structure prediction programs. Here, we describe how these recent improvements helped us to solve the crystal structure of a protein involved in the nonsense-mediated mRNA decay pathway (NMD), an mRNA quality control pathway dedicated to the elimination of eukaryotic mRNAs harboring premature stop codons.


title: Transient population dynamics drive the spread of invasive wild pigs in North America

abstract:
Invasion of nonindigenous species is considered one of the most urgent problems affecting native ecosystems and agricultural systems. Mechanistic models that account for short-term population dynamics can improve prediction because they incorporate differing demographic processes that link the environmental conditions of a spatial location explicitly with the invasion process. Yet short-term population dynamics are rarely accounted for in spatial models of invasive species spread.

Accounting for transient population dynamics, we predict the population growth rate and establishment probability of wild pigs following introduction into any location in North America. We compared predicted population growth rate with observed geographic rates of spread and found significant relationships between the annual rate of spread and population growth rates.

We used geospatial data on the distribution of mast producing tree species (a principle forage resource of wild pigs) and agricultural crops that can replace mast in their diets to predict population dynamics using transient population simulations. We simulated populations under different initial population sizes (i.e. number of introduced individuals, often termed propagule size) and for different amounts of time following introduction. By varying the initial population size and simulation time, we were able to identify areas in North America with high probability for establishment of wild pigs if introduced. Our findings can be used to inform surveillance and removal efforts to reduce the potential for establishment and spread of wild pigs.

category: ecology


title: Cell polarity determinant Dlg1 facilitates epithelial invagination by promoting tissue-scale mechanical coordination

abstract: Epithelial folding mediated by apical constriction serves as a fundamental mechanism to convert flat epithelial sheets into multilayered structures. It remains elusive whether additional mechanical inputs are required for folding mediated by apical constriction. Using Drosophila mesoderm invagination as a model, we identified an important role for the non-constricting, lateral mesodermal cells adjacent to the constriction domain ("flanking cells") in facilitating epithelial folding. We found that depletion of the basolateral determinant, Dlg1, disrupts the transition between apical constriction and invagination without affecting the rate of apical constriction. Strikingly, the observed delay in invagination is associated with ineffective apical myosin contractions in the flanking cells that lead to overstretching of their apical domain. The defects in the flanking cells impede ventral-directed movement of the lateral ectoderm, suggesting reduced mechanical coupling between tissues. Specifically disrupting the flanking cells in wildtype embryos by laser ablation or optogenetic depletion of cortical actin is sufficient to delay the apical constriction-to-invagination transition. Our findings indicate that effective mesoderm invagination requires intact flanking cells and suggest a role for tissue-scale mechanical coupling during epithelial folding.

category: developmental biology


title: Ecological landscapes guide the assembly of optimal microbial communities

abstract: Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.


title: Can associative learning be the general process for intelligent behavior in non-human animals?

abstract:
The general process- and adaptive specialization hypotheses represent two contrasting explanations for understanding intelligence in non-human animals. The general process hypothesis proposes that associative learning underlies all learning, whereas the adaptive specialization hypothesis suggests additional distinct learning processes required for intelligent behavior. Here, we use a selection of experimental paradigms commonly used in comparative cognition to explore these hypotheses. We tested if a novel computational model of associative learning -- A-learning -- could solve the problems presented in these tests. Results show that this formulation of associative learning suffices as a mechanism for general animal intelligence, without the need for adaptive specialization, as long as adequate motor- and perceptual systems are there to support learning. In one of the tests, however, the addition of a short-term trace memory was required for A-learning to solve that particular task. We further provide a case study showcasing the flexibility, and lack thereof, of associative learning, when looking into potential learning of self-control and the development of behavior sequences. From these simulations we conclude that the challenges do not so much involve the complexity of a learning mechanism, but instead lie in the development of motor- and perceptual systems, and internal factors that motivate agents to explore environments with some precision, characteristics of animals that have been fine-tuned by evolution for million of years.

Author summaryWhat causes animal intelligence? One hypothesis is that, among vertebrates, intelligence relies upon the same general processes for both memory and learning. A contrasting hypothesis states that important aspects of animal intelligence come from species- and problem specific cognitive adaptations. Here, we use a recently formulated model of associative learning and subject it, through computer simulations, to a battery of tests designed to probe cognitive abilities in animals. Our computer simulations show that this associative learning model can account well for how animals learn these various tasks. We conclude that a major challenge in understanding animal and machine intelligence lies in describing behavior systems. Specifically, how motor flexibility and perceptual systems together with internal factors allow animals and machines to navigate the world. As a consequence of our results, together with current progress in both animal- and machine learning, we cannot reject the idea that associative learning provides a general process for animal intelligence.

category: animal behavior and cognition


title: One of these morphs is not like the others: orange morphs exhibit different escape behavior than other morphs in a color polymorphic lizard

abstract: Variation in color morph behavior is an important factor in the maintenance of color polymorphism. Alternative anti-predator behaviors are often associated with morphological traits such as coloration, possibly because predator-mediated viability selection favors certain combinations of anti-predator behavior and color. The Aegean wall lizard, Podarcis erhardii, is color polymorphic and populations can have up to three monochromatic morphs: orange, yellow, and white. We investigated whether escape behaviors differ among coexisting color morphs, and if morph behaviors are repeatable across different populations with the same predator species. Specifically, we assessed color morph flight initiation distance (FID), distance to the nearest refuge (DNR), and distance to chosen refuge (DR) in two populations of Aegean wall lizards from Naxos island. We also analyzed the type of refugia color morphs selected and their re-emergence behavior following a standardized intrusion event. We found that orange morphs have different escape behaviors from white and yellow morphs, and these differences are consistent in both of the populations we sampled. Orange morphs have shorter FIDs, DNRs, and DRs, select different refuge types, and re-emerge less often after an intruder event compared to white and yellow morphs. Observed differences in color morph escape behaviors support the idea that morphs have evolved alternative behavioral strategies that may play a role in population-level morph maintenance and loss.


title: Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

abstract:
The de Bruijn graph has become a key data structure in modern computational genomics, and of keen interest is its compacted variant. The compacted de Bruijn graph provides a lossless representation of the graph, and it is often considerably more efficient to store and process than its non-compacted counterpart. Construction of the compacted de Bruijn graph resides upstream of many genomic analyses. As the quantity of sequencing data and the number of reference genomes on which to perform these analyses grow rapidly, efficient construction of the compacted graph becomes a computational bottleneck for these tasks.

We present CO_SCPLOWUTTLEFISHC_SCPLOW 2, significantly advancing the existing state-of-the-art methods for construction of this graph. On a typical shared-memory machine, it reduces the construction of the compacted de Bruijn graph for 661K bacterial genomes (2.58 Tbp of input reference genomes) from about 4.5 days to 17-23 hours. Similarly on sequencing data, it constructs the graph for a 1.52 Tbp white spruce read set in about 10 hours, while the closest competitor, which also uses considerably more memory, requires 54-58 hours.

category: bioinformatics


title: Label-free Cell Tracking Enables Collective Motion Phenotyping in Epithelial Monolayers

abstract:
Collective cell migration is an umbrella term for a rich variety of cell behaviors, whose distinct character is essential for biological function, notably for cancer metastasis. One essential feature of collective behavior is the motion of cells relative to their immediate neighbors. We introduce an AI-based pipeline to segment and track cell nuclei from phase contrast images. Nuclei segmentation is based on a U-Net convolutional neural network trained on images with nucleus staining. Tracking, based on the Crocker-Grier algorithm, quantifies nuclei movement and allows for robust downstream analysis of collective motion. Since the AI algorithm required no new training data, our approach promises to be applicable to and yield new insights for vast libraries of existing collective motion images. In a systematic analysis of a cell line panel with oncogenic mutations, we find that the collective rearrangement metric, D2min, which reflects non-affine motion, shows promise as an indicator of metastatic potential.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/472148v1_ufig1.gif" ALT="Figure 1">
View larger version (20K):
org.highwire.dtl.DTLVardef@82a35corg.highwire.dtl.DTLVardef@b31442org.highwire.dtl.DTLVardef@f703aborg.highwire.dtl.DTLVardef@1120d98_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIVersatile AI-based algorithm can robustly identify individual cells and track their motion from phase contrast images.
C_LIO_LIAnalysis of motion of cells relative to nearby neighbors distinguishes weakly tumorigenic (KRas) and metastatic (KRas/PTEN-/-) cell lines.
C_LI


title: Effective elasticity and persistence of strain in active filament-motor assemblies

abstract: Cross-linked, elastic, filamentous networks that are deformed by active molecular motors feature in several natural and synthetic settings. The effective active elasticity of these composite systems determines the length scale over which active deformations persist in fluctuating environments. This fundamental quantity has been studied in passive systems; however mechanisms determining and modulating this length-scale in active systems has not been clarified. Here, focusing on active arrayed filament-motor assemblies, we propose and analyze a minimal model in order to estimate the length scale over which imposed or emergent elastic deformations or stresses persist. We combine a mean-field continuum theory valid for weakly elastic assemblies with high dimensional Multi-Particle Collision (MPC) based Brownian simulations valid for moderate to strongly elastic and noisy systems. Integrating analytical and numerical results, we show that localized strains - steady or oscillatory - persist over well-defined length scales that dependent on motor activity, effective shear elasticity and filament extensibility. Extensibility is key even in very stiff filaments, and cannot be ignored when global deformations are considered. We clarify mechanisms by which motor derived active elasticity and passive shear elasticity of the filamentous backbone combine to effectively soften filaments. Surprisingly, the predictions of the mean-field theory agree qualitatively with results from stochastic discrete filament-motor model, even for moderately strong noise. We also find that athermal motor noise impacts the overall duty ratio of the motors and thereby the persistence length in these driven assemblies. Our study demonstrates how correlated activity in natural ordered active matter possesses a finite range of influence with clear testable experimental implications.


title: Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers

abstract:
BackgroundLiver cancer is the second leading cause of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) risk factors include chronic hepatitis, cirrhosis, and alcohol abuse, whereby tumorigenesis is induced through inflammation and subsequent fibrotic response. However, a subset of HCC arises in non-cirrhotic livers. We characterized the genomic and transcriptomic landscape of non-cirrhotic HCC to identify features underlying the diseases development and progression.

MethodsWhole genome and transcriptome sequencing was performed on 30 surgically resectable tumors comprised of primarily of non-cirrhotic HCC and adjacent normal tissue. Using somatic variants, capture reagents were created and employed on an additional 87 cases of mixed cirrhotic/non-cirrhotic HCC. Cases were analyzed to identify viral integrations, single nucleotide variants (SNVs), insertions and deletions (INDELS), copy number variants, loss of heterozygosity, gene fusions, structural variants, and differential gene expression.

ResultsWe detected 3,750 SNVs/INDELS and extensive CNVs and expression changes. Recurrent TERT promoter mutations occurred in >52% of non-cirrhotic discovery samples. Frequently mutated genes included TP53, CTNNB1, and APOB. Cytochrome P450 mediated metabolism was significantly downregulated. Structural variants were observed at MACROD2, WDPCP and NCKAP5 in >20% of samples. Furthermore, NR1H4 fusions involving gene partners EWSR1, GNPTAB, and FNIP1 were detected and validated in 2 non-cirrhotic samples.

ConclusionGenomic analysis can elucidate mechanisms that may contribute to non-cirrhotic HCC tumorigenesis. The comparable mutational landscape between cirrhotic and non-cirrhotic HCC supports previous work suggesting a convergence at the genomic level during disease progression. It is therefore possible genomic-based treatments can be applied to both HCC subtypes with progressed disease.

HighlightsO_LINon-cirrhotic HCC genomically resembles cirrhotic HCC
C_LIO_LIComprehensive genome- and transcriptome-wide profiling allows detection of novel structural variants, fusions, and undiagnosed viral infections
C_LIO_LINR1H4 fusions may represent a novel mechanism for tumorigenesis in HCC
C_LIO_LINon-cirrhotic HCC is characterized by genotoxic mutational signatures and dysregulated liver metabolism
C_LIO_LIClinical history and comprehensive omic profiling incompletely explain underlying etiologies for non-cirrhotic HCC highlighting the need for further research
C_LI

Short DescriptionThis study characterizes the genomic landscape of hepatocellular carcinomas (HCCs) in non-cirrhotic livers. Using 117 HCCs tumor/normal pairs, we identified 3,750 SNVs/INDELS with high variant frequency in TERT, TP53, CTNNB1, and APOB. CYP450 was significantly downregulated and many structural variants were observed. This characterization could assist in elucidating non-cirrhotic HCC tumorigenesis.

category: cancer biology


title: Discovery and synthesis of hydroxy-L-proline based blockers of the neutral amino acid transporters SLC1A4 (ASCT1) and SLC1A5 (ASCT2).

abstract: The conformationally restricted heterocycle hydroxy-L-proline is a versatile scaffold for the synthesis of diverse multi-functionalized pyrrolidines for probing the ligand binding sites of biological targets. With the goal to develop new inhibitors of the widely expressed amino acid transporters SLC1A4 and SLC1A5 (also known as ASCT1 and ASCT2), we synthesized and functionally screened a series of hydroxy-L-proline derivatives or  prolinols using electrophysiological and radio-labeled uptake assays on amino acid transporters from the SLC1, SLC7, and SLC38 solute carrier families. We identified a number of synthetic prolinols that act as selective high-affinity inhibitors of the SLC1 functional subfamily comprising the neutral amino acid transporters SLC1A4 and SLC1A5. The active and inactive prolinols were computationally docked into a threaded homology model and analyzed with respect to predicted molecular orientation and observed pharmacological activity. The series of hydroxy-L-proline derivatives identified here represents a new class of potential agents to pharmacologically modulate SLC1A4 and SLC1A5, amino acid exchangers that play important roles in a wide range of physiological and pathophysiological processes.

category: pharmacology and toxicology


title: The intrarenal renin-angiotensin system in hypertension: Insights from mathematical modelling

abstract: The renin-angiotensin system (RAS) plays a pivotal role in the maintenance of volume homeostasis and blood pressure. In addition to the well-studied systemic RAS, local RAS have been documented in various tissues, including the kidney. Given the role of the intrarenal RAS in the pathogenesis of hypertension, a role established via various pharmacologic and genetic studies, substantial efforts have been made to unravel the processes that govern intrarenal RAS activity. In particular, several mechanisms have been proposed to explain the rise in intrarenal angiotensin II (Ang II) that accompanies Ang II infusion, including increased angiotensin type 1 receptor (AT1R)-mediated uptake of Ang II and enhanced intrarenal Ang II production. However, experimentally isolating their contribution to the intrarenal accumulation of Ang II in Ang II-induced hypertension is challenging, given that they are fundamentally connected. Computational modelling is advantageous because the feedback underlying each mechanism can removed and the effect on intrarenal Ang II can be studied. In this work, the mechanisms governing the intrarenal accumulation of Ang II during Ang II infusion experiments are delineated and the role of the intrarenal RAS in Ang II-induced hypertension is studied. To accomplish this, a compartmental ODE model of the systemic and intrarenal RAS is developed and Ang II infusion experiments are simulated. Simulations indicate that AT1Rmediated uptake of Ang II is the primary mechanism by which Ang II accumulates in the kidney during Ang II infusion. Enhanced local Ang II production is unnecessary. The results demonstrate the role of the intrarenal RAS in the pathogenesis of Ang II-induced hypertension and consequently, clinical hypertension associated with an overactive RAS.

category: physiology


title: Proteome-wide cellular thermal shift assay reveals novel crosstalk between brassinosteroid and auxin signaling

abstract:
Despite the growing interest in using chemical genetics in plant research, small-molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass-spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or post-translational modifications allows the identification of drug targets, or the study of protein-metabolite and protein-protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal- and the phospho-proteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a novel substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf thus, revealing a novel crosstalk between brassinosteroid and auxin signaling.

Significance StatementChemical genetics, which investigates the biological processes using small molecules, is gaining interest in plant research. However, a major challenge is to uncover the mode of action of the small molecule. Here, we applied the cellular thermal shift assay coupled with mass spectrometry (CETSA MS) to intact Arabidopsis cells and showed that bikinin, the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, changed the thermal stability of some of its direct targets and putative GSK3 interacting proteins. In combination with phosphoproteomics, we also revealed that GSK3s phosphorylate the auxin carrier PIN-FORMED1 (PIN1) and regulated its polarity that is required for the vascular patterning in the leaf.

category: plant biology


title: Mice identify subgoal locations through an action-driven mapping process

abstract: Mammals instinctively explore and form mental maps of their spatial environments. Models of cognitive mapping in neuroscience mostly depict map-learning as a process of random or biased diffusion. In practice, however, animals explore spaces using structured, purposeful, sensory-guided actions. Here we test the hypothesis that executing specific exploratory actions is a key strategy for building a cognitive map. Previous work has shown that in arenas with obstacles and a shelter, mice spontaneously learn efficient multi-step escape routes by memorizing allocentric subgoal locations. We thus used threat-evoked escape to probe the relationship between ethological exploratory behavior and allocentric spatial memory. Using closed-loop neural manipulations to interrupt running movements during exploration, we found that blocking runs targeting an obstacle edge abolished subgoal learning. In contrast, blocking other movements while sparing edge-directed runs had no effect on memorizing subgoals. Finally, spatial analyses suggest that the decision to use a subgoal during escape takes into account the mouses starting position relative to the layout of the environment. We conclude that mice use an action-driven learning process to identify subgoals and that these subgoals are then integrated into a map-based planning process. We suggest a conceptual framework for spatial learning that is compatible with the successor representation from reinforcement learning and sensorimotor enactivism from cognitive science.

category: neuroscience


title: Interferon-γ Exposure of Human iPSC-derived Neurons Alters Major Histocompatibility Complex I and Synapsin I Protein Expression

abstract: Human epidemiological data links maternal immune activation during gestation with increased risk for neurodevelopmental disorders including schizophrenia. Animal models of maternal immune activation (MIA) provide causal evidence for this association and strongly suggest that inflammatory cytokines act is a critical link between maternal infection and aberrant offspring brain and behavior development. This includes evidence for reduced synapse formation, consistent with post-mortem and in vivo evidence of reduced synaptic density in schizophrenia. However, to what extent specific cytokines are necessary and sufficient for these effects remains unclear. Using a human cellular model, we recently demonstrated that acute exposure to interferon-{square} (IFN{square}) recapitulates molecular and cellular phenotypes associated with neurodevelopmental disorders. Here, we extend this work to test whether IFN{square} affects synapse formation in an induced neuron model that generates forebrain glutamatergic neurons. Using immunocytochemistry and quantitative PCR, we demonstrate that acute IFN{square} exposure results in significantly increased MHCI expression at the mRNA and protein level. Furthermore, acute IFN{square} exposure decreases synapsin I protein in neurons but does not affect synaptic gene mRNA levels. Interestingly, complement component 4A (C4A) mRNA is also significantly increased following acute IFN{square} exposure. This study builds on our previous work by showing that IFN{square}-mediated disruption of relevant synaptic proteins can occur at early stages of synapse formation, potentially contributing to neurodevelopmental disorder phenotypes such as schizophrenia.


title: The perceived position of a moving object is reset by temporal, not spatial limits

abstract: When the internal texture of a Gabor patch drifts orthogonally to its physical path, its perceived motion deviates dramatically from its physical path. The local position shifts accumulate to such an extent that a 45{degrees} oblique physical path appears to be vertical. However, at some point, a limit is reached and the path resets back to its veridical location, whereupon a new accumulation starts, making the new perceived path segment appear parallel to the pre-reset segment, but offset horizontally from it. Here, we tested whether spontaneous resets of this motion-induced position shift depend on the time or the distance over which position errors accrue, or both. We introduced a temporal gap in the middle of the path that forced the illusory path to reset back to its veridical physical position. This gap-triggered reset allowed us to measure the magnitude of the illusory offset up to that point. We found that perceived offset was less than expected for the angle of illusory drift, indicating that spontaneous resets had occurred prior to the gap-induced reset. The position offset decreased when the pre-gap duration increased but approximately doubled when the path length doubled. This pattern of perceived offsets is best accounted for by spontaneous resets that occur randomly over time at a constant rate, independently of the distance traveled. Our results suggest a temporal, not spatial, limit for the accumulation of position errors that underlies this illusion.


title: MIG-23 is involved in sperm migration in Ascaris suum

abstract:
In nematodes, spermiogenesis, which is also called sperm activation, is a process in which nonmotile spermatids are transformed into crawling spermatozoa, which is accompanied by a series of morphological, physiological and biochemical changes. Sperm motility acquisition during this process is essential for successful fertilization. However, the mechanisms of sperm motility regulation in nematodes remain to be clarified. Herein, we found that extracellular adenosine-5-triphosphate (ATP) level mediation by MIG-23, which is a homolog of human ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase), was required for major sperm protein (MSP) filament dynamics and sperm motility in the nematode Ascaris suum. MIG-23 was localized on the sperm plasma membrane. During sperm activation, mitochondrial activity was increased dramatically, and a large amount of ATP was produced and stored in refringent granules (RGs). In addition, a portion of the produced ATP was released to the extracellular space through ATP channels, which were composed of innexins and localized on the sperm plasma membrane. Spermatozoa, instead of spermatids, hydrolyzed exogenous ATP and processed ecto-ATPase activity. MIG-23 contributed to the ecto-ATPase activity of spermatozoa. Once MIG-23 activity was interrupted, spermatozoa also decreased their ATP hydrolysis activity. Blocking MIG-23 activity resulted in an increase in the depolymerization rate of MSP filaments in pseudopodia, which eventually affected nematode sperm migration. Overall, our data imply that MIG-23, which contributes to the ecto-ATPase activity of spermatozoa, regulates sperm migration by modulating extracellular ATP levels.

HighlightsO_LIATP is released to extracellular space through innexin channels which are identified in worm sperm.
C_LIO_LIWorm spematozoa show ecto-ATPase activity.
C_LIO_LIMIG-23 contributes to the ecto-ATPase activity of spermatozoa and regulates extracellular ATP level.
C_LIO_LIMIG-23 is required for MSP-based filament dynamics and sperm migration.
C_LI

category: cell biology


title: Plexins Promote Hedgehog Signaling Through Their Cytoplasmic GAP Activity

abstract:
Hedgehog signaling controls tissue patterning during embryonic and postnatal development and continues to play important roles throughout life. Characterizing the full complement of Hedgehog pathway components is essential to understanding its wide- ranging functions. Previous work has identified Neuropilins, established Semaphorin receptors, as positive regulators of Hedgehog signaling. Neuropilins require Plexin co- receptors to mediate Semaphorin signaling, but a role for Plexins in Hedgehog signaling has not yet been explored. Here, we provide evidence that multiple Plexins promote Hedgehog signaling in NIH/3T3 fibroblasts and that Plexin loss-of-function in these cells results in significantly reduced Hedgehog pathway activity. Catalytic activity of the Plexin GTPase activating protein (GAP) domain is required for Hedgehog signal promotion, and constitutive activation of the GAP domain further amplifies Hedgehog signaling. Additionally, we demonstrate that Plexins promote Hedgehog signaling at the level of GLI transcription factors and that this promotion requires intact primary cilia.

Finally, we find that Plexin loss-of-function significantly reduces the response to Hedgehog pathway activation in the mouse dentate gyrus. Together, these data identify Plexins as novel components of the Hedgehog pathway and provide insight into their mechanism of action.


title: A combined transcriptional and dynamic roadmap of single human pancreatic endocrine progenitors reveals proliferative capacity and differentiation continuum

abstract: Basic helix-loop-helix genes, particularly proneural genes, are well-described triggers of cell differentiation, yet limited information exists on their dynamics, notably in human development. Here, we focus on Neurogenin 3 (NEUROG3), which is crucial for pancreatic endocrine lineage initiation. Using a double reporter to monitor endogenous NEUROG3 transcription and protein expression in single cells in 2D and 3D models of human pancreas development, we show peaks of expression for the RNA and protein at 22 and 11 hours respectively, approximately two-fold slower than in mice, and remarkable heterogeneity in peak expression levels all triggering differentiation. We also reveal that some human endocrine progenitors proliferate once, mainly at the onset of differentiation, rather than forming a subpopulation with sustained proliferation. Using reporter index-sorted single-cell RNA-seq data, we statistically map transcriptome to dynamic behaviors of cells in live imaging and uncover transcriptional states associated with variations in motility as NEUROG3 levels change, a method applicable to other contexts.


title: Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration

abstract: Retinitis Pigmentosa (RP) is a wide array of progressive, debilitating visual disorders caused by mutations in a diverse set of genes. In both human patients and mouse models of RP, rod photoreceptor dysfunction leads to loss of night vision, and is followed by secondary cone photoreceptor dysfunction and degeneration, leading to loss of daylight color vision. A strategy to prevent secondary cone death could provide a generalized RP therapy to preserve daylight color vision regardless of the underlying mutation. In mouse models of RP, cones in the far peripheral retina survive long-term, despite complete rod loss. The mechanism for such peripheral cone survival had not been explored. Here, we found that active retinoic acid (RA) signaling in peripheral Muller glia is both sufficient and necessary for the extended cone survival. RA depletion by conditional knockout of RA synthesis enzymes, or overexpression of an RA degradation enzyme, abrogated peripheral cone survival. Conversely, constitutive activation of RA signaling in the central retina promoted long-term cone survival. These results indicate that RA signaling mediates the prolonged peripheral cone survival in the rd1 mouse model of retinal degeneration, and provide a basis for a generic strategy for cone survival in the many diseases that lead to loss of cone-mediated vision.


title: Prolyl-hydroxylase inhibitor-induced regeneration of alveolar bone and soft tissue in a mouse model of ligature-induced periodontitis

abstract:
Bone injuries and fractures reliably heal through a process of regeneration with restoration to original structure and function when the gap between adjacent sides of a fracture site is small. However, when there is significant volumetric loss of bone, bone regeneration usually does not occur.

In the present studies, we explore a particular case of volumetric bone loss in a mouse model of human periodontal disease (PD) in which alveolar bone surrounding teeth is permanently lost and not replaced. This model employs the placement a ligature around the upper second molar which leads to inflammation and bone breakdown and faithfully replicates the bacterially-induced inflammatory etiology of human PD to induce bone degeneration. After 10 days, the ligature is removed and the mice are treated with a timed-release formulation of a small molecule inhibitor of prolylhydroxylases (PHDi; 1,4-DPCA) previously shown to induce epimorphic regeneration of soft tissue in non-regenerating mice. This PHDi induces high expression of HIF-1 and the regenerative response is completely blocked by siHIF1a. Here, we observe that timed-release 1,4-DPCA rapidly and completely restores bone and soft tissue with normal anatomic fidelity and with increased stem cell markers due to stem cell migration into the site and/or de-differentiation of local tissue, PDL cell proliferation, and increased vascularization. In-vitro studies using gingival tissue show that 1,4-DPCA indeed induces de-differentiation and the expression of stem cell markers but does not exclude the role of migrating stem cells.


title: Areas Important for Ecological Connectivity Throughout Canada

abstract: Governments around the world have acknowledged the importance of conserving ecological connectivity to help reverse the decline of biodiversity. In this study we employed recent methodological developments in circuit theory to conduct the first pan-Canadian analysis of multi-species connectivity for all terrestrial regions of the country, at a spatial grain sufficient to support local land-management decisions. We developed a movement cost surface with a limited number of thematic categories using the most recently updated land cover data available for the country. We divided the country into 17 tiles and used a wall-to-wall, omnidirectional mode of Circuitscape on each tile in order to assess ecological connectivity throughout entire landscapes as opposed to strictly among protected areas. The resulting raw current density map of Canada revealed heterogenous patterns of current density across the country, strongly influenced by geography, natural barriers, and human development. We included a validation analysis of the output current density map with independent wildlife data from across the country and found that mammal and herpetofauna locations were predicted by areas of high current density. We believe our current density map can be used to identify areas important for connectivity throughout Canada and thereby contribute to efforts to conserve biodiversity.


title: Genome size distributions in bacteria and archaea are strongly linked to phylogeny

abstract:
The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses remain unclear. Moreover, statistical analyses on this topic have typically been limited to a narrow diversity of bacteria and archaea without considering the potential bias introduced by the shared recent ancestry of many lineages. In this study, we used a phylogenetic generalized least-squares (PGLS) analysis to evaluate the effect of different factors on the genome size of a broad diversity of bacteria and archaea. We used dN/dS to estimate the strength of purifying selection, and 16S copy number as a proxy for ecological strategy, which have both been postulated to play a role in shaping genome size. After model fit, Pagels lambda indicated a strong phylogenetic signal in genome size, suggesting that the diversification of this trait is strongly influenced by shared evolutionary histories. As a predictor variable, dN/dS showed a poor predictability and non-significance when phylogeny was considered, consistent with the view that genome reduction can occur under either weak or strong purifying selection depending on the ecological context. Copies of 16S rRNA showed poor predictability but maintained significance when accounting for non-independence in residuals, suggesting that ecological strategy as approximated from 16S rRNA copies might play a minor role in genome size variation. Altogether, our results indicate that genome size is a complex trait that is not driven by any singular underlying evolutionary force, but rather depends on lineage- and niche-specific factors that will vary widely across bacteria and archaea.

Author SummaryThe evolutionary forces driving genome size in bacteria and archaea have been subject to debate during the last decades. Independent comparative analyses have suggested that unique variables, such as the strength of selection, environmental complexity, and mutation rate, are the main drivers of this trait, which complicates generalizations across the Tree of Life. Here, we applied a phylogeny-based statistical approach to assess how tightly genome size is linked to evolutionary history in bacteria and archaea. Moreover, we also evaluated the predictability of genome size from the strength of purifying selection and ecological strategy on a broad diversity of bacteria and archaea genomes. Our approach indicates that genome size in prokaryotes is strongly dependent on phylogenetic history, and that genome size is the result of the interaction of variables like past events, current selection regimes, and environmental complexity that are clade dependent.


title: Patterns of parent and offspring gene expression reflect canalization, not plasticity, in response to environmental stress

abstract:
Parenting buffers offspring from hostile environments, but it is not clear how or if the genes that underlie parenting change their expression under environmental stress. We recently demonstrated that for the subsocial carrion beetle, Nicrophorus orbicollis, temperature during parenting does not affect parenting phenotypes. Here, we ask if transcriptional changes associated with parenting are likewise robust to environmental stress. The absence of a transcriptional response for parenting under stress would suggest that the genetic  programs for parenting and being parented are canalized. Conversely, a robust transcriptional response would suggest that plasticity of underlying gene expression is critical for maintaining behavioral stability, and that these mechanisms provide a potential target for selection in the face of environmental change. We test these alternatives by characterizing gene expression of parents and offspring with and without parent-offspring interactions under a benign and a stressful temperature. We found that parent-offspring interactions elicit distinct transcriptional responses of parents and larvae irrespective of temperature. We further detected robust changes of gene expression in beetles breeding at 24{degrees} C compared to 20{degrees} C irrespective of family interaction. However, no strong interaction between parent-offspring interaction and temperature was detected for either parents or larvae. We therefore conclude that canalization, not plasticity of gene expression, most likely explains the absence of behavioral plasticity under thermal stress. This result suggests that species may not have the genetic variation needed to respond to all environmental change, especially for complex phenotypes.

IMPACT STATEMENTParenting is thought to evolve to buffer offspring from harsh or inhospitable conditions. However, once evolved, does parenting continue to buffer against new environmental challenges such as might occur under global warming? One way organisms achieve different phenotypes without evolving different genes for each trait is by changing timing or extent of gene expression. Changes in gene expression influencing physiological traits such as hypoxia have been shown to facilitate adaptation to changing environments. It is less clear if changes in gene expression are also important for behavioral plasticity in complex social traits, such as parental care. In this study, we ask whether families of the subsocial burying beetle, Nicrophorus orbicollis, show altered expression of parent or offspring genes that may help compensate for reduced offspring success under global warming. To test the extent that gene expression underlies behavioral plasticity in parenting and offspring responses to parenting, we characterize the gene expression profiles of whole families (males, females, and larvae) with and without parent-offspring interactions under two thermal conditions: 20{degrees} C and 24{degrees} C. We found that heat stress predominantly induced downregulation of genes, consistent with a constrained acclimation response. However, when temperature was considered in conjunction with parent-offspring interactions, genetic plasticity was extremely limited. That is, the genes underlying parent-offspring interactions did not show strong signatures of differential expression under more stressful thermal conditions. Given that we previously found no effects of temperature on parental behavior, we suggest that constrained, not plastic gene expression, underpins stability of parent-offspring interactions and limits the buffering capacity for family interactions under environmental stress. Insights from this study deepen our understanding of the interplay between genetic and phenotypic plasticity in complex behavioral traits and how traits such as parenting may limit responses to novel environmental challenges.


title: Gene expression underlying parenting and being parented reflect canalization, not plasticity, in response to environmental stress


title: Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

abstract: Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.


title: Dynamic interplay between structural variations and 3D chromosome organization in pancreatic cancer

abstract: Structural variations (SVs) are the greatest source of variation in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human pancreatic cancer remain largely undefined due to technological limitations. Here, we investigate the spectrum of SVs and three-dimensional (3D) chromatin architecture in human pancreatic ductal epithelial cell carcinogenesis by using state-of-the-art long- read single-molecule real-time (SMRT) and high-throughput chromosome conformation capture (Hi-C) sequencing techniques. We find that the 3D genome organization is remodeled and correlated with gene expressional change. The bulk remodeling effect of cross-boundary SVs in the 3D genome partly depends on intercellular genomic heterogeneity. Meanwhile, contact domains tend to minimize these disrupting effects of SVs within local adjacent genomic regions to maintain overall stability of 3D genome organization. Moreover, our data also demonstrates complex genomic rearrangements involving two key driver genes CDKN2A and SMAD4, and elucidates their influence on cancer-related gene expression from both linear view and 3D perspective. Overall, this study provides a valuable resource and highlights the impact, complexity and dynamicity of the interplay between SVs and 3D genome organization, which further expands our understanding of pathogenesis of SVs in human pancreatic cancer.


title: GiPS: Genomics-informed parent selection uncovers the breeding value of wheat genetic resources

abstract: The great efforts spent in the maintenance of past diversity in genebanks are rationalized by the potential role of plant genetic resources in future crop improvement - a concept whose practical implementation has fallen short of expectations. Here, we implement genomics-informed parent selection to expedite pre-breeding without discriminating against non-adapted germplasm. We collect dense genetic profiles for a large winter wheat collection and evaluate grain yield and resistance to yellow rust in representative coresets. Genomic prediction within and across genebanks identified the best parents for PGR x elite derived crosses that outyielded current elite cultivars in multiple field trials.

category: genomics


title: Comprehensive Benchmarking of CITE-seq versus DOGMA-seq Single Cell Multimodal Omics

abstract: The recently developed transcription, epitopes, and chromatin accessibility by sequencing (TEA-seq) and similar DOGMA-seq single-cell trimodal omics assays provide unprecedented opportunities for understanding cell biology, but independent optimization, benchmarking and evaluation are lacking. We explored the utility, pros and cons of DOGMA-seq compared to the bimodal cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) assay in activated and stimulated human peripheral blood T cells. We identified an optimal incubation time and concentration of digitonin (DIG) for cell permeabilization and found that single-cell trimodal omics measurements after DIG permeabilization were generally better than after an alternative "low-loss lysis" (LLL) permeabilization condition. Next, we found that DOGMA-seq with optimized DIG permeabilization and its ATAC library provides more information, even though its mRNA and cell surface protein antibody-derived tag (ADT) libraries have slightly inferior quality, compared to CITE-seq. Finally, we recognized the additional value of DOGMA-seq for studying lineage-specific T helper cells.


title: A framework for research into continental ancestry groups of the UK Biobank

abstract:
BackgroundThe UK Biobank is a large prospective cohort, based in the United Kingdom, that has deep phenotypic and genomic data on roughly a half a million individuals. Included in this resource are data on approximately 78,000 individuals with "non-white British ancestry". Whilst most epidemiology studies have focused predominantly on populations of European ancestry, there is an opportunity to contribute to the study of health and disease for a broader segment of the population by making use of the UK Biobanks "non-white British ancestry" samples. Here we present an empirical description of the continental ancestry and population structure among the individuals in this UK Biobank subset.

ResultsReference populations from the 1000 Genomes Project for Africa, Europe, East Asia, and South Asia were used to estimate ancestry for each individual. Those with at least 80% ancestry in one of these four continental ancestry groups were taken forward (N=62,484). Principal component and K-means clustering analyses were used to identify and characterize population structure within each ancestry group. Of the approximately 78,000 individuals in the UK Biobank that are of "non-white British" ancestry, 50,685, 6,653, 2,782, and 2,364 individuals were associated to the European, African, South Asian, and East Asian continental ancestry groups, respectively. Each continental ancestry group exhibits prominent population structure that is consistent with self-reported country of birth data and geography.

ConclusionsMethods outlined here provide an avenue to leverage UK Biobanks deeply phenotyped data allowing researchers to maximise its potential in the study of health and disease in individuals of non-white British ancestry.


title: The Blepharisma stoltei macronuclear genome: towards the origins of whole genome reorganization

abstract: Massive DNA excision occurs regularly in ciliates, ubiquitous microbial eukaryotes with somatic and germline nuclei in the same cell. Tens of thousands of internally eliminated sequences (IESs) scattered throughout a copy of the ciliate germline genome are deleted during development of the streamlined somatic genome. Blepharisma represents one of the two earliest diverging ciliate classes, and, unusually, has dual pathways of somatic nuclear development, making it ideal for investigating the functioning and evolution of these processes. Here, we report the somatic genome assembly of Blepharisma stoltei strain ATCC 30299 (41 Mb), arranged as numerous alternative telomere-capped minichromosomes. This genome encodes eight PiggyBac transposase homologs liberated from transposons. All are subject to purifying selection, but just one, the putative IES excisase, has a complete catalytic triad. We propose PiggyBac homologs were ancestral excisases that enabled evolution of extensive, natural genome editing.


title: Genome editing excisase origins illuminated by somatic genome of Blepharisma


title: Alternation emerges as a multi-modal strategy for turbulent odor navigation

abstract: Foraging mammals exhibit a familiar yet poorly characterized phenomenon, "alternation", a momentary pause to sniff in the air often preceded by the animal rearing on its hind legs or raising its head. Intriguingly, rodents executing an olfactory search task spontaneously exhibit alternation in the presence of airflow, suggesting that alternation may serve an important role during turbulent plume-tracking. To test this hypothesis, we combine fully-resolved numerical simulations of turbulent odor transport and Bellman optimization methods for decision-making under partial observability. We show that an agent trained to minimize search time in a realistic odor plume exhibits extensive alternation together with the characteristic cast-and-surge behavior commonly observed in flying insects. Alternation is tightly linked with casting and occurs more frequently when the agent is far downwind of the source, where the likelihood of detecting airborne cues is higher relative to cues close to the ground. Casting and alternation emerge as complementary tools for effective exploration when cues are sparse. We develop a model based on marginal value theory to capture the interplay between casting, surging and alternation. More generally, we show how multiple sensorimotor modalities can be fruitfully integrated during complex goal-directed behavior.


title: Epigenetic remodeling during monolayer cell expansion reduces therapeutic potential

abstract:
Understanding how cells remember previous mechanical environments to influence their fate, or mechanical memory, informs the design of biomaterials and therapies in medicine. Current regeneration therapies require two-dimensional (2D) cell expansion processes to achieve large cell populations critical for the repair of damaged (e.g. connective and musculoskeletal) tissues. However, the influence of mechanical memory on cell fate following expansion is unknown, and mechanisms defining how physical environments influence the therapeutic potential of cells remain poorly understood. Here, we show that the organization of histone H3 trimethylated at lysine 9 (H3K9me3) and expression of tissue-identifying genes in primary cartilage cells (chondrocytes) transferred to three-dimensional (3D) hydrogels depends on the number of previous population doublings on tissue culture plastic during 2D cell expansion. Decreased levels of H3K9me3 occupying promoters of dedifferentiation genes after the 2D culture were also retained in 3D culture. Suppression of H3K9me3 during expansion of cells isolated from a murine model similarly resulted in the loss of the chondrocyte phenotype and global remodeling of nuclear architecture. In contrast, increasing levels of H3K9me3 through inhibiting H3K9 demethylases partially rescued the chondrogenic nuclear architecture and gene expression, which has important implications for tissue repair therapies, where expansion of large numbers of phenotypically-suitable cells is required. Overall, our findings indicate mechanical memory in primary cells is encoded in the chromatin architecture, which impacts cell fate and the phenotype of expanded cells.

SIGNIFICANCE STATEMENTTissue regeneration procedures, such as cartilage defect repair (e.g. Matrix-induced Autologous Chondrocyte Implantation) often require cell expansion processes to achieve sufficient cells to transplant into an in vivo environment. However, the chondrocyte cell expansion on 2D stiff substrates induces epigenetic changes that persist even when the chondrocytes are transferred to a different (e.g. 3D) or in vivo environment. Treatments to alter epigenetic gene regulation may be a viable strategy to improve existing cartilage defect repair procedures and other tissue engineering procedures that involve cell expansion.

category: bioengineering


title: Identifying target sites for placental therapeutics through the comparison of normal term pregnancies and intrauterine growth restricted proteomes

abstract:
A variety of pathologies, including intrauterine growth restriction (IUGR), have been linked to placental insufficiencies as important causal factors, however, little has been done to develop therapeutics that may improve placental development, structure and function. The placenta offers the opportunity to manipulate the in-utero environment without directly intervening with the fetus, accessible from the maternal circulation, a vital but temporary organ, the placenta is no longer required after birth. Developing therapeutics must involve multiple aspects of targeting and safety to ensure no off-target impact on the pregnant person or fetus as well as enhance efficiency of delivery. In addition to our studies on nanoparticle delivery to the placenta [1] we are developing targeting strategies to allow peripheral delivery via the maternal circulation. In this study we have performed the isolation of the microvillous membrane from human placental syncytiotrophoblast (the targeting cell) and via proteomic analysis identified potential targeting moieties, we have then compared this to publicly available data from pregnancies complicated by fetal growth restriction to ensure that we do not identify targets which would be reduced in FGR, resulting in less efficient targeting.

HighlightsO_LIProteomic analysis detected key genes, proteins, and pathways present in the syncytiotrophoblast membrane of normal placentas.
C_LIO_LISpecific membrane proteins identified show promise for future characterization of placental pathologies, such as IUGR.
C_LIO_LIProteomes of normal and diseased placentas require further study to better understand the etiology of certain conditions.
C_LI


title: Modeling the Three-Dimensional Chromatin Structure from Hi-C Data with Transfer Learning

abstract: Recent studies have revealed the importance of three-dimensional (3D) chromatin structure in the regulation of vital biological processes. Contrary to protein folding, no experimental procedure that can directly determine ground-truth 3D chromatin coordinates exists. Instead, chromatin conformation is studied implicitly using high-throughput chromosome conformation capture (Hi-C) methods that quantify the frequency of all pairwise chromatin contacts. Computational methods that infer the 3D chromatin structure from Hi-C data are thus unsupervised, and limited by the assumption that contact frequency determines Euclidean distance. Inspired by recent developments in deep learning, in this work we explore the idea of transfer learning to address the crucial lack of ground-truth data for 3D chromatin structure inference. We present a novel method, Transfer learning Encoder for CHromatin 3D structure prediction (TECH-3D) that combines transfer learning with creative data generation procedures to reconstruct chromatin structure. Our work outperforms previous deep learning attempts for chromatin structure inference and exhibits similar results as state-of-the-art algorithms on many tests, without making any assumptions on the relationship between contact frequencies and Euclidean distances. Above all, TECH-3D presents a highly creative and novel approach, paving the way for future deep learning models.


title: Caveats to deep learning approaches to RNA secondary structure prediction

abstract: Machine learning (ML) and in particular deep learning techniques have gained popularity for predicting structures from biopolymer sequences. An interesting case is the prediction of RNA secondary structures, where well established biophysics based methods exist. These methods even yield exact solutions under certain simplifying assumptions. Nevertheless, the accuracy of these classical methods is limited and has seen little improvement over the last decade. This makes it an attractive target for machine learning and consequently several deep learning models have been proposed in recent years. In this contribution we discuss limitations of current approaches, in particular due to biases in the training data. Furthermore, we propose to study capabilities and limitations of ML models by first applying them on synthetic data that can not only be generated in arbitrary amounts, but are also guaranteed to be free of biases. We apply this idea by testing several ML models of varying complexity. Finally, we show that the best models are capable of capturing many, but not all, properties of RNA secondary structures. Most severely, the number of predicted base pairs scales quadratically with sequence length, even though a secondary structure can only accommodate a linear number of pairs.


title: A Precision Medicine Approach to Metabolic Therapy for Breast Cancer in Mice

abstract:
Increasing evidence highlights the possibility for approaches targeting metabolism as potential adjuvants to cancer therapy. Sodium-glucose transport protein 2 (SGLT2) inhibitors are the newest class of antihyperglycemic therapies, and have recently been highlighted as a novel therapeutic approach to breast cancer. To our knowledge, however, SGLT2 inhibitors have not been applied in the neoadjuvant setting as a precision medicine approach to combining metabolic therapy with standard of care therapy for this devastating disease. In this study we combine the SGLT2 inhibitor dapagliflozin with paclitaxel chemotherapy in both lean and obese mice. We show that dapagliflozin enhances the efficacy of paclitaxel, reducing tumor glucose uptake and prolonging survival in an insulin-dependent manner in some but not all breast tumors. Our data find a genetic signature for breast tumors most likely to respond to dapagliflozin in combination with paclitaxel. Tumors driven by mutations upstream of canonical insulin signaling pathways are likely to respond to such treatment, whereas tumors driven by mutations downstream of canonical insulin signaling are not. These data demonstrate that dapagliflozin enhances the response to chemotherapy in mice with breast cancer and suggest that breast cancer patients with driver mutations upstream of canonical insulin signaling may be most likely to benefit from this neoadjuvant approach. A clinical trial is currently in preparation, with an application recently submitted for Yale Human Investigations Committee approval, to test this hypothesis in breast cancer patients.

One Sentence SummaryWe identify a driver mutation signature by which glucose-wasting metabolic therapy (dapagliflozin) enhances the efficacy of chemotherapy in mice with breast cancer.


title: Paw placement during walking is altered by analgesic doses of opioids and post-surgical injury in mice

abstract: Hind paw-directed assays are commonly used to study the analgesic effects of opioids in mice. However, opioid-induced hyper-locomotion can obscure results of such assays. We aimed to overcome this potential confound by using gait analysis to observe hind paw usage during walking in mice. We measured changes in paw print area following induction of post-surgical pain (using the paw incision model) and treatment with oxycodone. Paw incision surgery reduced the paw print area of the injured hind paw as the mice avoided placing the incised section of the paw on the floor. Surprisingly, oxycodone caused a tiptoe-like gait in mice, resulting in a reduced paw print area in both hind paws. Further investigation of this opioid-induced phenotype revealed that analgesic doses of oxycodone or morphine dose-dependently reduced hind paw print area in uninjured mice. The gait changes were not dependent on opioid-induced increases in locomotor activity; speed and paw print area had no correlation in opioid-treated mice, and other analgesic compounds that alter locomotor activity did not affect paw print area. Unfortunately, the opioid-induced "tiptoe" gait phenotype prevented gait analysis from being a viable metric for demonstrating opioid analgesia in injured mice. However, this work reveals an important, previously uncharacterized effect of treatment with analgesic doses of opioids on paw placement. Our characterization of how opioids affect gait has important implications for the use of mice to study opioid pharmacology and suggests that scientists should use caution when using hind paw-directed nociceptive assays to test opioid analgesia in mice.


title: Qualifying a human Liver-Chip for predictive toxicology: Performance assessment and economic implications

abstract: Human organ-on-a-chip (Organ-Chip) technology has the potential to disrupt preclinical drug discovery and improve success in drug development by recapitulating organ-level pathophysiology and clinical responses. The Innovation and Quality (IQ) consortium formed by multiple pharmaceutical and biotechnology companies to confront this challenge has published guidelines that define criteria for qualifying preclinical models, however, systematic and quantitative evaluation of the predictive value of Organ-Chips has not yet been reported. Here, 780 Liver-Chips were analyzed to determine their ability to predict drug-induced liver injury caused by small molecules identified as benchmarks by the IQ consortium. The Liver-Chip met the qualification guidelines across a blinded set of 27 known hepatotoxic and non-toxic drugs with a sensitivity of 80%, increasing to 87% when protein binding is corrected, and a specificity of 100%. A computational economic value analysis suggests that with this performance the Liver-Chip could generate $3 billion annually for the pharmaceutical industry due to increased R&D productivity.