title: A distributed residue network permits conformational binding specificity in a conserved family of actin remodelers

abstract: Metazoan proteomes contain many paralogous proteins that have evolved distinct functions. The Ena/VASP family of actin regulators consists of three members that share an EVH1 interaction domain with a 100% conserved binding site. A proteome-wide screen revealed ciliary protein PCARE as a high-affinity ligand for ENAH EVH1. Here we report the surprising observation that PCARE is ~100-fold specific for ENAH over paralogs VASP and EVL and can selectively bind and inhibit ENAH-dependent adhesion in cells. Specificity arises from a mechanism whereby PCARE stabilizes a conformation of the ENAH EVH1 domain that is inaccessible to family members VASP and EVL. Structure-based modeling rapidly identified seven residues distributed throughout EVL that are sufficient to differentiate binding by ENAH vs. EVL. By exploiting the ENAH-specific conformation, we rationally designed the tightest and most selective ENAH binder to date. Our work uncovers a conformational mechanism of interaction specificity that distinguishes highly similar paralogs and establishes tools for dissecting specific Ena/VASP functions in processes including cancer cell invasion.

category: biochemistry


title: The stiffness-sensitive transcriptome of human tendon stromal cells

abstract: Matrix stiffness and its effects on tensional homeostasis act as major regulators of cellular states in health and disease. Stiffness-sensing studies are typically performed using cells that have acquired "mechanical memory" through prolonged propagation in rigid mechanical environments, e.g. tissue culture plastic (TCP). This may potentially mask the full extent of the stiffness-driven mechanosensing programs. To address this, we developed a biomaterial system composed of two-dimensional mechano-variant silicone substrates that is permissive to large-scale cell culture expansion processes. We broadly mapped the stiffness-mediated mechano-responses by performing RNA sequencing on human tendon-derived stromal cells. We find that matrix rigidities approximating tendon microscale stiffness range (E. ~35 kPa) distinctly favor programs related to chromatin remodeling and Hippo signaling; whereas more compliant stiffnesses (E. 2 kPa) were enriched in responses related to pluripotency, synapse assembly and angiogenesis. We also find that tendon stromal cells undergo dramatic phenotypic drift on conventional TCP, with near-complete suppression of tendon-related genes and emergence of expression signatures skewed towards fibro-inflammatory and metabolic activation. Strikingly, mechano-variant substrates abrogate fibroblasts activation, with tenogenic stiffnesses inducing a transcriptional program that strongly correlate with established tendon tissue-specific signatures. Computational inference predicted that AKT1 and ERK1/2 are major signaling hubs mediating stiffness-sensing in tendon cells. Together, our findings highlight how the underlying biophysical cues may dictate the transcriptional identity of resident cells, and how matrix mechano-reciprocity regulates diverse sets of previously underappreciated mechanosensitive processes in tendon stromal fibroblasts.

category: bioengineering


title: Protein corona modulates interaction of spiky nanoparticles with lipid bilayers

abstract: The impact of protein corona on the interactions of nanoparticles (NPs) with cells remains an open question. This question is particularly relevant to NPs which sizes, ranging from tens to hundreds nanometers, are comparable to the sizes of most abundant proteins in plasma. Protein sizes match with typical thickness of various coatings and ligands layers, usually present at the surfaces of larger NPs. Such size match may affect the properties and the designed function of NPs. We offer a direct demonstration of how protein corona can dramatically change the interaction mode between NPs and lipid bilayers. To this end, we choose the most extreme case of NP surface modification: nanostructures in the form of rigid spikes of 10-20 nm length at the surface of gold nanoparticles. In the absence of proteins we observe the formation of reversible pores when spiky NPs absorb on lipid bilayers. In contrast, the presence of bovine serum albumin (BSA) proteins adsorbed at the surface of spiked NPs, effectively reduce the length of spikes exposed to the interaction with lipid bilayers. Thus, protein corona changes qualitatively the dynamics of pore formation, which is completely suppressed at high protein concentrations. These results suggest that protein corona can not only be critical for interaction of NPs with membranes, it may change their mode of interaction, thus offsetting the role of surface chemistry and ligands.

category: biophysics


title: Personalized chordoma organoids for drug discovery studies

abstract: Chordomas are rare tumors of notochordal origin, most commonly arising in the sacrum or skull base. Primary treatment of chordoma is surgery, however complete resection is not always feasible due to their anatomic location, and recurrence rates remain high. Chordomas are considered insensitive to conventional chemotherapy, and their rarity complicates running timely and adequately powered trials to identify effective regimens. Therefore, there is a need for discovery of novel therapeutic approaches. Drug discovery efforts in chordoma have been mostly limited to cell line models. Patient-derived organoids can accelerate drug discovery studies and predict patient responses to therapy. In this proof-of-concept study, we successfully established organoids from seven chordoma tumor samples obtained from five patients presenting with tumors in different sites and stages of disease. The organoids recapitulated features of the original parent tumors and inter-as well as intra-patient heterogeneity. High-throughput screenings performed on the organoids highlighted targeted agents such as PI3K/mTOR, EGFR, and JAK2/STAT3 inhibitors among the most effective molecules. Pathway analysis underscored how the NF-kB and IGF-1R pathways are sensitive to perturbations and potential targets to pursue for combination therapy of chordoma.

category: cancer biology


title: Predicting phenotypes from genetic, environment, management, and historical data using CNNs

abstract: Predicting phenotypes from genetic (G), environmental (E), and management (M) conditions is a long-standing challenge with implications to agriculture, medicine, and conservation. Most methods reduce the factors in a dataset (feature engineering) in a subjective and potentially oversimplified manner. Convolutional Neural Networks (CNN) can overcome this by allowing the data itself to determine which factors are most important. CNN models were developed for predicting agronomic yield from a combination of replicated trials and historical yield survey data. The results were more accurate than standard methods when tested on heldout G, E, and M data (r=0.5 vs r=0.4), and performed slightly worse than standard methods when only G was held out (r=0.74 vs r=0.78). Pre-training on historical data increased accuracy by 1-36% compared to trial data alone. Saliency map analysis indicated the CNN has "learned" to prioritize many factors of known agricultural importance.

category: plant biology


title: Parameterization of regulatory nodes for engineering broad host range heterologous gene expression

abstract: By building on the SEVA (Standard European Vector Architecture) format we have refactored a number of regulatory nodes recruited from both Gram-negative and Gram-positive bacteria for rigorously comparing and parameterizing five expression devices that respond to diverse and unrelated chemical inducers, i.e. LacIq-Ptrc, XylS-Pm, AlkS-PalkB, CprK-PDB3 and ChnR-PchnB. These were assembled as cargoes following the SEVA standard within exactly the same vector backbone and bearing the different functional segments arrayed in an invariable DNA scaffold. Their performance in an Escherichia coli strain of reference was then analyzed through the readout a fluorescence reporter gene that contained strictly identical translation signal elements in all cases and in the same DNA context. This study allowed us to describe and compare the cognate expression systems with unprecedented quantitative detail. The systems under scrutiny diverged considerably in their capacity, expression noise, inducibility and OFF/ON ratios. These features, along with the absence of physiological effects caused by the inducers and the lack of cross-regulation offer a panoply of choices to potential users and help interoperability of the specific constructs.

category: synthetic biology


title: Neural correlates and determinants of approach-avoidance conflict in the prelimbic prefrontal cortex

abstract: The recollection of environmental cues associated with threat or reward allows animals to select the most appropriate behavioral responses. Neurons in the prelimbic cortex (PL) respond to both threat- and reward-associated cues. However, it remains unknown whether PL regulates threat-avoidance vs. reward-approaching responses when an animals decision depends on previously associated memories. Using a conflict model in which male Long-Evans rats retrieve memories of shock- and food-paired cues, we observed two distinct phenotypes during conflict: i) rats that continued to press a lever for food (Pressers); and ii) rats that exhibited a complete suppression in food seeking (Non-Pressers). Single-unit recordings revealed that increased risk-taking behavior in Pressers is associated with persistent food-cue responses in PL, and reduced spontaneous activity in PL glutamatergic (PLGLUT) neurons during conflict. Activating PLGLUT neurons in Pressers attenuated food-seeking responses in a neutral context, whereas inhibiting PLGLUT neurons in Non-Pressers reduced defensive responses and increased food approaching during conflict. Our results establish a causal role for PLGLUT neurons in mediating individual variability in memory-based risky decision making by regulating threat-avoidance vs. reward-approach behaviors.

category: neuroscience


title: Successful IL-12 cancer immunotherapy requires NK cell-derived CCL5 for anti-tumor DC-T cell crosstalk

abstract:
T cell-directed cancer immunotherapy often fails to generate lasting tumor control. Harnessing additional effectors of the immune response against tumors may strengthen the clinical benefit of immunotherapies. Here, we demonstrate that therapeutic targeting of the IFN{gamma}-IL-12 pathway relies on the ability of a population of tissue-resident NK (trNK) cells to orchestrate an anti-tumor microenvironment. Particularly, utilizing an engineered adenoviral platform, we show that paracrine IL-12 enhances functional DC-CD8 T cell interactions to generate adaptive anti-tumor immunity. This effect depends on the abundance of trNK cells and specifically their capacity to produce the cDC1-chemoattractant CCL5. Failure to respond to IL-12 and other IFN{gamma}-inducing therapies such as immune checkpoint blockade in tumors with low trNK cell infiltration could be overcome by intra-tumoral delivery of CCL5. Our findings reveal a novel barrier for T cell-focused therapies and offer mechanistic insights into how T cell-NK cell-DC crosstalk can be enhanced to promote anti-tumor immunity and overcome resistance.

SignificanceWe identified the lack of CCL5-producing, tissue-resident NK (trNK) cells as a barrier to T cell-focused therapies. While IL-12 induces anti-tumoral DC-T cell crosstalk in trNK cellrich tumors, resistance to IL-12 or anti-PD-1 in trNK cellpoor tumors can be overcome by the additional delivery of CCL5.

category: immunology


title: Adaptive anti-tumor immunity is orchestrated by a population of CCL5-producing tissue-resident NK cells


title: The homologous recombination complex of the Rad51 paralogs Rad55-Rad57 avoids translesion DNA polymerase recruitment and counterbalances mutagenesis induced by UV radiation

abstract:
The bypass of DNA lesions that block replicative polymerases during DNA replication relies on DNA damage tolerance pathways. The error-prone translesion synthesis (TLS) pathway relies on specialized DNA polymerases that incorporate nucleotides in front of base lesions, potentially inducing mutagenesis. Two error-free pathways can bypass the lesions: the template switching pathway, which uses the sister chromatid as a template, and the homologous recombination pathway (HR), which also can use the homologous chromosome as template. The balance between error-prone and error-free pathways controls the mutagenesis level. Therefore, it is crucial to precisely characterize factors that influence the pathway choice to better understand genetic stability at replication forks. In yeast, the complex formed by the Rad51 paralogs Rad55 and Rad57 promotes HR and template-switching at stalled replication forks. At DNA double-strand breaks (DSBs), this complex promotes Rad51 filament formation and stability, notably by counteracting the Srs2 anti-recombinase. To explore the role of the Rad55-Rad57 complex in error-free pathways, we monitored the genetic interactions between Rad55-Rad57, the translesion polymerases Pol{zeta} or Pol{eta}, and Srs2 following UV radiation that induces mostly single-strand DNA gaps. We found that the Rad55-Rad57 complex was involved in three ways. First, it protects Rad51 filaments from Srs2, as it does at DSBs. Second, it promotes Rad51 filament stability independently of Srs2. Finally, we observed that UV-induced HR is almost abolished in Rad55-Rad57 deficient cells, and is partially restored upon Pol{zeta} or Pol{eta} depletion. Hence, we propose that the Rad55-Rad57 complex is essential to promote Rad51 filament stability on single-strand DNA gaps, notably to counteract the error-prone TLS polymerases and mutagenesis.

Author summaryProcessive and accurate DNA polymerases replicate genomic DNA during the S phase of each cell cycle. DNA base lesions on template DNA block these polymerases and result in an accumulation of single-stranded DNA gaps behind moving replication forks. These gaps are filled-in by error-prone and error-free pathways. In this work, we show that the complex made by the Rad51 paralogs Rad55 and Rad57 is essential for the error-free homologous recombination gap-filling pathway when DNA replication is stalled by UV-induced DNA lesions, but not for DNA double strand break repair. Interestingly, we found that homologous recombination is efficiently outcompeted by error-prone translesion DNA polymerases in Rad55-Rad57-deficient cells. We propose that the Rad55-Rad57 complex is essential for Rad51 filament stability at UV-induced DNA gaps to promote efficient error-free homologous recombination. Furthermore, our study in yeast predicts that inhibitors of error-prone DNA polymerases might selectively target cancer cells in which RAD51 paralogs are mutated.

category: genetics


title: Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps


title: Integrating digital and field surveillance to complement efforts to manage epidemic diseases of livestock: African swine fever as a case study

abstract: The SARS-CoV-2 pandemic has unveiled the importance of stakeholders and ordinary citizens in managing infectious disease emergencies. Efficient management of infectious diseases requires a top-down approach which must be complemented with a bottom-up response to be effective. Here we investigate a novel approach to surveillance for transboundary animal diseases using African Swine fever as a model. We were able to collect data at a population level on information-seeking behavior and at a local level through a targeted questionnaire-based survey to relevant stakeholders such as farmers and veterinary authorities. Our study shows how information-seeking behavior and resulting public attention during an epidemic, can be addressed through novel data streams from digital platforms such as Wikipedia. We also bring evidence on how field surveys aimed at local workers (e.g. farmers) and public authorities remain a crucial tool to assess more in-depth preparedness and awareness among front-line actors. We conclude that they should be used in combination to maximize the outcome of surveillance and prevention activities for selected transboundary animal diseases.

category: scientific communication and education


title: Distinct Neural Representations of Decision Uncertainty in Metacognition and Mentalizing

abstract: Metacognition and mentalizing are both associated with meta-level mental state representations. Specifically, metacognition refers to monitoring ones own cognitive processes, while mentalizing refers to monitoring others cognitive processes. However, this self-other dichotomy is insufficient to delineate the two high-level mental processes. We here used functional magnetic resonance imaging (fMRI) to systematically investigate the neural representations of different levels of decision uncertainty in monitoring different targets (the current self, the past self, and others) performing a perceptual decision-making task. Our results reveal diverse formats of intrinsic mental state representations of decision uncertainty in mentalizing, separate from the associations with external information. External information was commonly represented in the right inferior parietal lobe (IPL) across the mentalizing tasks. However, the meta-level mental states of decision uncertainty attributed to others were uniquely represented in the dorsomedial prefrontal cortex (dmPFC), rather than the temporoparietal junction (TPJ) that also equivalently represented the object-level mental states of decision inaccuracy attributed to others. Further, the object-level and meta-level mental states of decision uncertainty, when attributed to the past self, were represented in the precuneus and the lateral frontopolar cortex (lFPC), respectively. In contrast, the dorsal anterior cingulate cortex (dACC) consistently represented both decision uncertainty in metacognition and estimate uncertainty during monitoring the different mentalizing processes, but not the inferred decision uncertainty in mentalizing. Hence, our findings identify neural signatures to clearly delineate metacognition and mentalizing and further imply distinct neural computations on the mental states of decision uncertainty during metacognition and mentalizing.


title: Separation of multiple motor memories through implicit and explicit processes

abstract: Acquisition of multiple motor skills without interference is a remarkable ability in sport and daily life. During adaptation to opposing perturbations, a common paradigm to study this ability, each perturbation can be successfully learned when a dynamical contextual cue, such as a follow-through movement, is associated with the direction of the perturbation. It is still unclear, however, to what extent this context-dependent learning engages the cognitive strategy-based explicit process and the implicit process that occurs without conscious awareness. Here, we designed four reaching experiments to untangle the individual contributions of the explicit and implicit components while participants learned opposing visuomotor perturbations, with a second unperturbed follow-through movement that served as a contextual cue. In Exp. 1 we replicated previous adaptation results and showed that follow-through movements also allow learning for opposing visuomotor rotations. For one group of participants in Exp. 2 we isolated strategic explicit learning by inducing a 2-sec time delay between movement and end-point feedback, while for another group we isolated the implicit component using the task-irrelevant error-clamp paradigm, in which participants were firmly instructed to aim their reaches directly to the target. Our data showed that opposing perturbations could be fully learned by explicit strategies; but when strategy was restricted, distinct implicit processes contributed to learning. In Exp.3, we examined whether the learned motor behaviors are influenced by the disparity between the follow-through contexts. We found that the location of follow-through targets had little effect on total learning, yet it led to more instances in which participants failed to learn the task. In Exp. 4, we explored the generalization capability to untrained novel targets. Participants showed near-flat generalization of the implicit and explicit processes to adjacent targets. Overall, our results indicate that follow-through contextual cues influence activity of both implicit and explicit processes during separation of motor memories. Furthermore, the follow-through context might activate, in part, top-down cognitive factors that influence not only the dynamics of the explicit learning but also the implicit process.


title: Distinct threat and valence signals in rat nucleus accumbens core

abstract: Appropriate responding to threat and reward is essential to survival. The nucleus accumbens core (NAcc) is known to support and organize reward behavior. More recently our laboratory has shown the NAcc is necessary to discriminate cues for threat and safety. To directly reveal NAcc threat responding, we recorded single-unit activity from 7 female rats undergoing Pavlovian fear discrimination. Rats fully discriminated cues for danger, uncertainty, and safety. Demonstrating direct threat responding, most NAcc neurons showed greatest firing changes to danger and uncertainty. Heterogeneity in cue and reward firing led to the detection of multiple, functional populations. One NAcc population specifically decreased firing to threat (danger and uncertainty). A separate population bi-directionally signaled valence through firing decreases to negative valence events (danger and uncertainty) and opposing firing increases to positive valence events (reward and safety onset). The findings point to the NAcc as a neural source of threat information and a more general valence hub.


title: Investigation of extramammary sources of Group B Streptococcus reveals its unusual ecology and epidemiology in camels

abstract: Camels are vital to food production in the drylands of the Horn of Africa, with milk as their main contribution to food security. A major constraint to camel milk production is mastitis, inflammation of the mammary gland. The condition negatively impacts milk yield and quality as well as household income. The leading cause of mastitis in dairy camels is Streptococcus agalactiae, group B Streptococcus (GBS), which is also a commensal and pathogen of humans. It has been suggested that extramammary reservoirs for this pathogen may contribute to the occurrence of mastitis in camels. We explored the molecular epidemiology of GBS in camels using a cross-sectional study design for sample collection and phenotypic, genomic and phylogenetic analysis of isolates. Among 88 adult camels and 93 calves from six herds in Laikipia County, Kenya, GBS was detected in 20% of 50 milk samples, 25% of 152 nasal swabs, 8% of 90 oral swabs and 3% of 90 rectal swabs, but not in vaginal swabs. Per camel herd, two to four sequence types (ST) were present. More than half of the isolates belonged to ST617 or its single-locus variant, ST1652, with these STs found across all sample types. Serotype VI was detected in 30 of 58 isolates. In three herds, identical STs were detected in milk and swab samples, suggesting that extramammary sources of GBS may contribute to the maintenance and spread of GBS within camel herds. This needs to be considered when developing prevention and control strategies. In addition, the high nasal carriage rate, low recto-vaginal carriage rate, and high prevalence of serotype VI for GBS in camels are in stark contrast to the distribution of GBS in humans and reveal hitherto unknown ecological and molecular features of this bacterial species.

category: microbiology


title: Genome-Wide DNA Methylation Profiles of Neurodevelopmental Disorder Genes in Mouse Placenta and Fetal Brain Following Prenatal Exposure to Polychlorinated Biphenyls

abstract:
BackgroundPolychlorinated biphenyls (PCBs) are developmental neurotoxicants implicated as environmental risk factors for neurodevelopmental disorders (NDD), including autism spectrum disorders (ASD).

ObjectiveWe examined the effects of prenatal exposure to a human-relevant mixture of PCBs on the DNA methylome of fetal mouse brain and placenta to determine if there was a shared subset of differentially methylated regions (DMRs).

MethodsA PCB mixture formulated to model the 12 most abundant congeners detected in the serum of pregnant women from a prospective high-risk ASD cohort was administered to female mice prior to and during pregnancy. Whole-genome bisulfite sequencing (WGBS) was performed to assess genome-wide DNA methylation profiles of placenta and brain on gestational day 18.

ResultsWe found thousands of significant (empirical p < 0.05) DMRs distinguishing placentas and brains from PCB-exposed embryos from sex-matched vehicle controls. In both placenta and brain, PCB-associated DMRs were significantly (p < 0.005) enriched for functions related to neurodevelopment, cellular adhesion, and cellular signaling, and significantly (Odds Ratio > 2.4, q < 0.003) enriched for bivalent chromatin marks. The placenta and brain PCB DMRs overlapped significantly (Z-score = 4.5, p = 0.0001) by genomic coordinate and mapped to a shared subset of genes significantly (q < 0.05) enriched for Wnt signaling, Slit/Robo signaling, and genes differentially expressed in multiple NDD/ASD models. The placenta and brain DMRs also significantly (q < 0.05) overlapped by genomic coordinate with brain samples from humans with Rett syndrome and Dup15q syndrome.

DiscussionThese results demonstrate that placenta can be used as a surrogate for embryonic brain DNA methylation changes over genes relevant to NDD/ASD in a mouse model of prenatal PCB exposure.

category: genomics


title: Additive Effects of Cognitive Load, Motor Demand, and Environmental Complexity on Attention: A Real-World EEG-study

abstract: The capacity to regulate ones attention in accordance with fluctuating task demands and environmental contexts is an essential feature of adaptive behavior. Although the electrophysiological correlates of attentional processing have been extensively studied in the laboratory, relatively little is known about the way they unfold under more variable, ecologically-valid conditions. Accordingly, this study employed a  real-world EEG design to investigate how attentional processing varies under increasing cognitive, motor, and environmental demands. Forty-four participants were exposed to an auditory oddball task while (1) sitting in a quiet room inside the lab, (2) walking around a sports field, and (3) wayfinding across a university campus. In each condition, participants were instructed to either count or ignore oddball stimuli. While behavioral performance was similar across the lab and field conditions, oddball count accuracy was significantly reduced in the campus condition. Moreover, event-related potential components (mismatch negativity and P3) elicited in both  real-world settings differed significantly from those obtained under laboratory conditions. These findings demonstrate the impact of environmental factors on attentional processing during simultaneously-performed motor and cognitive tasks, highlighting the value of incorporating dynamic and unpredictable contexts within naturalistic designs.


title: EEG and behavioral correlates of attentional processing while walking and navigating naturalistic environments


title: Chop-n-drop: in silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection

abstract: The identification of proteins at the single-molecule level would open exciting new venues in biological research and disease diagnostics. Previously we proposed a nanopore-based method for protein identification called chop-n-drop fingerprinting, in which the fragmentation pattern induced and measured by a proteasome-nanopore construct is used to identify single proteins. However whether such fragmentation patterns are sufficiently characteristic of proteins to identify them in complex samples remained unclear. In the simulation study presented here, we show that 97.9% of human proteome constituents are uniquely identified under close to ideal measuring circumstances, using a simple alignment-based classification method. We show that our method is robust against experimental error, as 78.8% can still be identified if the resolution is twice as low as currently attainable and 10% of proteasome restriction sites and protein fragments are randomly ignored. Based on these results and our experimental proof-of-concept, we argue that chop-n-drop fingerprinting has the potential to make cost-effective single-molecule protein identification feasible in the near future.

category: bioinformatics


title: Genetic Variation as a Long-Distance Modulator of RAD21 Expression in Humans

abstract: Mutations and changes in expression in RAD21 are common across cancers types and outside of cancer can result in cohesinopathy. As such, exploration of variants that modify RAD21 enhancer activity, across the genome, may also provide insights into mechanisms by which distinct variants impact healthy human development and disease. We searched 42,953,834 genomic variants for a spatial-eQTL association with the transcription of RAD21. We identified 123 significant associations (FDR < 0.05), which are local (cis) or long-distance (trans) regulators of RAD21 expression. The 123 variants co-regulate a further seven genes, enriched for having Sp2 transcription factor binding sites in their promoter regions. The Sp2 transcription factor and six of the seven genes had previously been associated with cancer onset, progression, and metastasis. Our results suggest that genome-wide variation in non-coding regions impacts on RAD21 transcript levels in addition to other genes, which then could impact on oncogenesis and the process of ubiquitination. This identification of distant co-regulation of oncogenes represents a strategy for discovery of novel genetic regions which impact cancer onset and a potential for diagnostics.


title: Molecular Systems Predict Equilibrium Distributions of Phenotype Diversity Available for Selection

abstract:
Two long standing challenges in theoretical population genetics and evolution are predicting the distribution of phenotype diversity generated by mutation and available for selection and determining the interaction of mutation, selection, and drift to characterize evolutionary equilibria and dynamics. More fundamental for enabling such predictions is the current inability to causally link population genetic parameters, selection and mutation, to the underlying molecular parameters, kinetic and thermodynamic. Such predictions would also have implications for understanding cryptic genetic variation and the role of phenotypic robustness.

Here we provide a new theoretical framework for addressing these challenges. It is built on Systems Design Space methods that relate system phenotypes to genetically-determined parameters and environmentally-determined variables. These methods, based on the foundation of biochemical kinetics and the deconstruction of complex systems into rigorously defined biochemical phenotypes, provide several innovations that automate (1) enumeration of the phenotypic repertoire without knowledge of kinetic parameter values, (2) representation of phenotypic regions and their relationships in a System Design Space, and (3) prediction of values for kinetic parameters, concentrations, fluxes and global tolerances for each phenotype.

We now show that these methods also automate prediction of phenotype-specific mutation rate constants and equilibrium distributions of phenotype diversity in populations undergoing steady-state exponential growth. We introduce this theoretical framework in the context of a case study involving a small molecular system, a primordial circadian clock, compare and contrast this framework with other approaches in theoretical population genetics, and discuss experimental challenges for testing predictions.

category: evolutionary biology


title: Natural variation at the Drosophila melanogaster Or22 odorant receptor locus is associated with changes in olfactory behaviour

abstract: In insects many critical olfactory behaviours are mediated by the large odorant receptor (Or) gene family, which determine the response properties of different classes of olfactory receptor neurons (ORNs). While ORN responses are generally conserved within and between Drosophila species, variant alleles of the D.melanogaster Or22 locus have previously been shown to the response profiles of an ORN class called ab3A. These alleles show potential clinal variation, suggesting that selection is acting at this locus. Here, we investigated if the changes seen in ab3A responses lead to changes in olfactory-related behaviours. We show that variation at the Or22 locus and in the ab3A neurons are not fully compensated for by other ORNs and lead to overall changes in antennal odorant detection. We further show that this correlates with differences in odorant preference behaviour and with differences in oviposition site preference, with flies that have the chimaeric short allele strongly preferring to oviposit on banana. These findings indicate that variation at the Or22 locus leads to changes in olfactory-driven behaviours that could be under selective pressure, and add support to the idea that the ab3A neurons are of especial importance to the ecology of Drosophila flies.


title: Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper

abstract:
MotivationIdentifying gene clusters of interest in phylogenetically proximate and distant taxa can help to infer phenotypes of interest. Conserved gene clusters may differ by only a few genes, which can be biologically meaningful, such as the formation of pseudogenes or insertions interrupting regulation. These qualities may allow for unsupervised clustering of similar gene clusters into bins that provide a population-level understanding of the genetic variation in similar gene clusters.

ResultsWe developed GeneGrouper, a command-line tool that uses a density-based clustering method to group gene clusters into bins. GeneGrouper demonstrated high recall and precision in benchmarks for the detection of the 23-gene Salmonella enterica LT2 Pdu gene cluster and four-gene Pseudomonas aeruginosa PAO1 Mex gene cluster in 435 genomes containing mixed taxa. In a subsequent application investigating the diversity and impact of gene complete and incomplete LT2 Pdu gene clusters in 1130 S. enterica genomes, GeneGrouper identified a novel, frequently occurring pduN pseudogene. When replicated in vivo, disruption of pduN with a frameshift mutation negatively impacted microcompartment formation. We next demonstrated the versatility of GeneGrouper by clustering both distant homologous gene clusters and variable gene clusters found in integrative and conjugative elements.

AvailabilityGeneGrouper software and code are publicly available at https://github.com/agmcfarland/GeneGrouper.


title: Oligodendrocyte precursor cells guide the migration of cortical interneurons by unidirectional contact repulsion

abstract: The cerebral cortex is built by neural cells that migrate away from their birthplace. In the forebrain, ventrally-derived oligodendrocyte precursor cells (vOPCs) travel tangentially together with cortical interneurons (cINs) to reach the cortex. After birth, vOPCs form transient synapses with cINs before engaging later into myelination. Here we tested whether these populations interact during embryogenesis while migrating. By coupling histological analysis of mouse genetic models with live imaging, we showed that, while responding to the chemokine Cxcl12, vOPCs and cINs occupy mutually-exclusive forebrain territories. Moreover, vOPCs depletion selectively disrupts the migration and distribution of cINs. At the cellular level, we found that by promoting unidirectional contact-repulsion (UCoRe) of cINs, vOPCs steer their migration away from blood vessels and contribute to their allocation to proper migratory streams. UCoRe is thus an efficient strategy to spatially control the competition for a shared chemoattractant, thereby allowing cINs to reach proper cortical territories.


title: Modulation of the host cell transcriptome and epigenome by Fusobacterium nucleatum

abstract: Fusobacterium nucleatum (Fn) is a ubiquitous opportunistic pathogen with an emerging role as an oncomicrobe in colorectal and other cancer types. Fn can adhere to and invade host cells in a manner that varies across Fn strains and host cell phenotypes. Here we performed pairwise co-cultures between three Fn strains and two immortalized primary host cell types (colonic epithelial cells and vascular endothelial cells) followed by RNA-seq and ChIP-seq to investigate transcriptional and epigenetic host cell responses. We observed that Fn-induced host cell transcriptional modulation involves strong upregulation of genes related to immune migration and inflammatory processes, such as TNF, CXCL8, CXCL1, and CCL20. Further, we identified genes strongly upregulated specifically in conditions of host cell invasion, including overexpression of both EFNA1 and LIF, two genes commonly upregulated in colorectal cancer and associated with poor patient outcomes, and PTGS2 (COX2), a gene associated with the protective effect of aspirin in the colorectal cancer setting. Interestingly, we also observed downregulation of numerous histone modification genes upon Fn exposure. To further explore this relationship, we used the ChIP-seq data to annotate chromatin states genome-wide. We found significant chromatin remodeling following Fn exposure in conditions of host cell invasion, with substantial increases in the frequency of states corresponding to active enhancers as well as low signal or quiescent states. Thus, our results highlight increased inflammation and chemokine gene expression as conserved host cell responses to Fn exposure, and extensive host cell epigenomic changes associated with Fn host cell invasion. These results extend our understanding of Fn as an emerging pathogen and highlight the importance of considering strain heterogeneity and host cell phenotypic variation when exploring pathogenic mechanisms of Fn.


title: Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements

abstract: Neuronal activity induced by brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin-to-gene expression programs. Enhancer activation is an early event in the regulatory control of BDNF-treated neurons, where the bZIP motif-binding Fos protein pioneered chromatin opening and cooperated with co-regulatory transcription factors (Homeobox, EGRs, and CTCF) to induce transcription. Deleting cis-regulatory sequences decreased BDNF-mediated Arc expression, a regulator of synaptic plasticity. BDNF-induced accessible regions are linked to preferential exon usage by neurodevelopmental disorder-related genes and heritability of neuronal complex traits, which were validated in human iPSC-derived neurons. Thus, we provide a comprehensive view of BDNF-mediated genome regulatory features using comparative genomic approaches to dissect mammalian neuronal activity.


title: Cooperativity of catalytic and lectin-like domain of T. congolense trans-sialidase modulates its catalytic activity

abstract:
Trans-sialidases (TS) represent a multi-gene family of unusual enzymes, which catalyse the transfer of terminal sialic acids from sialoglycoconjugates to terminal galactose or N-acetylgalactosamine residues of oligosaccharides without the requirement of CMP-Neu5Ac, the activated Sia used by typical sialyltransferases. Most work on trypanosomal TS has been done on enzymatic activities of TS from T. cruzi (causing Chagas disease in Latin America), subspecies of T. brucei, (causing human sleeping sickness in Africa) and T. congolense (causing African Animal Trypanosomosis in livestock). Previously, we demonstrated that T. congolense TS (TconTS) lectin domain (LD) binds to several carbohydrates, such as 1,4-{beta}-mannotriose.

To investigate the influence of TconTS-LD on enzyme activities, we firstly performed in silico analysis on structure models of TconTS enzymes. Findings strongly supports the potential of domain swaps between TconTS without structural disruptions of the enzymes overall topologies. Recombinant domain swapped TconTS1a/TS3 showed clear sialidase and sialic acid (Sia) transfer activities, when using fetuin and lactose as Sia donor and acceptor substrates, respectively. While Sia transfer activity remained unchanged from the level of TconTS1a, hydrolysis was drastically reduced. Presence of 1,4-{beta}-mannotriose during TS reactions modulates enzyme activities favouring trans-sialylation over hydrolysis.

In summary, this study provides strong evidence that TconTS-LDs play pivotal roles in modulating enzyme activity and biological functions of these and possibly other TS, revising our fundamental understanding of TS modulation and diversity.


title: Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation

abstract: Although most eukaryotic mRNAs require a 5'-cap for translation initiation, some can also be translated through a poorly studied cap-independent pathway. Here we developed a circRNA-based system and unbiasedly identified more than 10,000 sequences in the human transcriptome that contain Cap-independent Translation Initiators (CiTIs). Surprisingly, most of the identified CiTIs are located in 3'UTRs, which mainly promote translation initiation in mRNAs bearing highly structured 5'UTR. Mechanistically, CiTI recruits several translation initiation factors including eIF3 and DHX29, which in turn unwind 5'UTR structures and facilitate ribosome scanning. Functionally, we showed that the translation of HIF1A mRNA, an endogenous DHX29 target, is antagonistically regulated by its 5'UTR structure and a new 3'-CiTI in response to hypoxia. Therefore, deletion of 3'-CiTI suppresses cell growth in hypoxia and tumor progression in vivo. Collectively, our study uncovers a new regulatory mode for translation where the 3'UTR actively participate in the translation initiation.

category: molecular biology


title: Physically active lifestyle is associated with attenuation of hippocampal dysfunction in healthy older adults

abstract: Alterations in hippocampal function have been shown in older adults, expressed as changes in hippocampal activity and connectivity. While hippocampal activation during memory demands have been demonstrated to decrease with age, some older individuals present increased activity, or hyperactivity, of the hippocampus which is associated with increased neuropathology and poorer memory function. In addition, lower functional coherence between the hippocampus and core hubs of the default mode network (DMN), namely the posteromedial and medial prefrontal cortices, as well as increased local intrahippocampal connectivity, were also demonstrated in cognitively intact older adults. Aerobic exercise has been shown to elicit neuroprotective effects on hippocampal structure and vasculature in aging, and improvements in maximal aerobic capacity (MAC) have been suggested to mediate these exercise-related effects. However, how these lifestyle factors relate to hippocampal function is not clear. Fifty-two cognitively intact older adults (age 65-80) have been recruited and divided into physically active (n=29) or non-active (n=23) groups based on their aerobic activity lifestyle habits. Participants underwent resting-state as well as task-based fMRI experiments which included an associative memory encoding paradigm followed by a post-scan memory recognition test. In addition, forty-four participants also performed cardiopulmonary exercise tests to evaluate MAC. While both groups demonstrated increased anterior hippocampal activation during memory encoding, physically active lifestyle was associated with significantly lower activity level and higher memory performance in the recognition task. In addition, the physically active group also demonstrated higher functional connectivity of the anterior and posterior hippocampi with the core hubs of the DMN, and lower local intra-hippocampal connectivity within and between hemispheres. MAC was negatively associated with hippocampal activation level and demonstrated positive correlation with hippocampal-DMN connectivity. According to these findings, aerobically active lifestyle may be associated with attenuation of hippocampal dysfunction in cognitively healthy older adults.


title: Naturalized Dolichogenidea gelechiidivoris Marsh (Hymenoptera: Braconidae) complement the resident parasitoid complex of Tuta absoluta (Meyrick) (Lepidopera:Gelechiidae) in Spain

abstract: Our study aimed to assess the contribution of natural parasitism due to Necremnus tutae Ribes & Bernardo (Hymenoptera: Eulophidae) to the biological control of Tuta absoluta (Meyrick) (Lepidopera:Gelechiidae) in commercial plots where an IPM program based on the use of predatory mirid bugs was implemented. During the samplings, the presence of another parasitoid was detected and, therefore, a second part of our study intended to identify this species and to evaluate the importance of its natural populations in the biological control of the pest. Leaflets with T. absoluta galleries were collected during 2017-2020 from commercial tomato plots in the horticultural production area of Catalonia (Northeast Spain), including greenhouses, open fields, and roof covered tunnels that lack side walls. In the laboratory, T. absoluta larvae were classified as ectoparasitized, alive, or dead. Reared parasitoids from ectoparasitized larvae were mostly morphologically identified as Necremnus sp. with parasitism rates that peaked in summer months with values between 9 and 15%. Some of these ectoparasitized larvae also yielded another parasitoid identified as Dolichogenidea gelechiidivoris Marsh (Hymenoptera: Braconidae) by both morphological and molecular-DNA barcoding methods. In 2020, parasitism rates due to D. gelechiidivoris that increased with season up to 22%. Our work reports for the first time in Europe the presence of the neotropical species D. gelechiidivoris adding this biocontrol agent to the resident parasitoid complex of T. absoluta in Spain.

category: ecology


title: Fitness Landscapes Reveal Context-Dependent Benefits of Oviposition Choice

abstract:
Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Are such context-dependent behaviours adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition choice reflects distinct, context-specific local fitness peaks. Manipulating female egg allocation in a habitat containing optimal and suboptimal resource patches, we measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference). Females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components that are linked in a tradeoff. With increasing age and prior exposure to competition, they produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naive females produce many slow-developing offspring, beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts.

Preprint available at - https://www.biorxiv.org/content/10.1101/2021.05.27.445916v1.full

Citation - Vrinda Ravi Kumar, Gaurav Agavekar, Deepa Agashe; bioRxiv 2021.05.27.445916; doi: https://doi.org/10.1101/2021.05.27.445916


title: Pathways of forest savannization in a mesic African savanna-forest mosaic

abstract:
O_LIFires in savannas limit tree cover, thereby promoting flammable grass accumulation and fuelling further frequent fires. Meanwhile, forests and thickets form dense canopies that reduce C4-grass fuel loads and creating a humid microclimate, thereby excluding fires under typical climatic conditions.
C_LIO_LIHowever, extreme fires occasionally burn into these closed-canopy systems. Although these rare fires cause substantial tree mortality and can make repeat fires more likely, the long-term consequences of an extreme fire for closed canopy vegetation structure and potential to convert to savanna (hereafter "savannization") remain largely unknown.
C_LIO_LIHere, we analysed whether an extreme fire could, alone, alter species composition, vegetation structure, and fire regimes of closed-canopy ecosystems in an intact savanna-forest-thicket mosaic, or whether successive fires after an initial extreme fire were necessary to trigger a biome transition between from forest to savanna.
C_LIO_LIWe found that forests that only burned once recovered, whereas those that burned again following an initial extreme fire transitioned from closed-canopy forests towards open, grassy savannas.
C_LIO_LIWhile thickets had less tree mortality in fires than forests, repeat fires nonetheless precipitated a transition towards savannas.
C_LIO_LIColonization of the savanna tree community lagged behind the grass community, but also began to transition.
C_LI

SynthesisOur results suggest that rare extreme fires, followed by repeated burning can indeed result in savannization in places where savanna and forest represent alternative stable states.


title: Pathways of savannization in a mesic African savanna-forest mosaic


title: Pathways of savannization in a mesic African savanna-forest mosaic following an extreme fire


title: Pheromone Receptors Help Cnaphalocrocis medinalis Avoid Competition in Rice Fields

abstract: Cnaphalocrocis medinalis (Guenee) (Lepidoptera: Pyralidae) is one of the most important insect pests that attack the rice crop, Oryza sativa L., in China, feeding on rice leaves. Chilo suppressalis and Sesamia inferens are two common insects living within the same ecological system that feed on rice stalks. Their behavior could affect C. medinaliss choice of oviposition place, so we tested the electroantennogram (EAG) response of C. medinalis to a conspecific sex pheromone (Z11-18:OH; Z11-18:Ald; Z13-18:OH; Z13-18:Ald) and two other insects pheromone compounds (Z9-16:Ald; Z11-16Ald; Z11-16:OH;Z11-16:Ac and 16:Ald). The results indicate C. medinalis can detect those pheromones and is sensitive to Z11-16:Ald and Z9-16:Ald. In the heterologous expression system of Xenopus oocytes, we cloned three pheromone receptor genes, CmedPR1, CmedPR2, and CmedPR3. These had the same electroantennogram response, in addition to the response to the conspecific pheromone. CmedPR2 and CmedPR3 displayed strong sensitivity to Z11-16Ald and Z9-16:Ald. These results may contribute to clarifying how C. medinalis recognizes pheromones and interspecies communication.


title: Genomic insights into longan evolution from a chromosome-level genome assembly and population analysis of longan accessions

abstract: Longan (Dimocarpus longan) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. High-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of contiguity (contig N50=12.1 Mb, scaffold N50= 29.5 Mb) over a previous draft assembly. A total of 40,420 protein-coding genes were predicted in D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.


title: Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions


title: Jasmine: Population-scale structural variant comparison and analysis

abstract: The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes.


title: IN VIVO ANALYSIS OF THE ROLE OF GASDERMIN-B (GSDMB) IN CANCER USING NOVEL KNOCK-IN MOUSE MODELS

abstract:
BackgroundGasdermin-B gene (GSDMB) is frequently over-expressed in tumors, and its shortest translated variant (isoform 2; GSDMB2) increases aggressive behavior in breast cancer cells. Paradoxically, GSDMB could have either pro-tumor or tumor suppressor properties depending on the biological context. Since GSDMB gene is not present in the mouse genome, deciphering fully the functional roles of GSDMB in cancer requires novel in vivo models.

MethodsWe first generated by gene targeting a conditional knock-in mouse model (R26-STOP-GB2) harboring human GSDMB2 transcript within the ROSA26 locus. We next derived the R26-GB2 model ubiquitously expressing GSDMB2 in multiple tissues (confirmed by western blot and immunohistochemistry) and performed a comprehensive histopathological analysis in multiple tissues from 75 male and female mice up to 18 months of age. Additionally, we produced the double transgenic model R26-GB2/MMTV-PyMT, co-expressing GSDMB2 and the Polyoma-Middle-T oncogene, and assessed breast cancer generation and progression in GSDMB2-homozygous (n=10) and control (n=17) female mice up to 15 weeks of age.

ResultsIn the R26-GB2 model, which showed different GSDMB2 cytoplasmic and/or nuclear localization among tissues, we investigated if GSDMB2 expression had intrinsic tumorigenic activity. 41% of mice developed spontaneous lung tumors, but neither the frequency nor the histology of these neoplasias was significantly different from wildtype animals. Strikingly, while 17% control mice developed gastric carcinomas, no GSDMB2-positive mice did. No other tumor types or additional histological alterations were frequently seen in these mice. In the R26-GB2/MMTV-PyMT model, the strong nucleus-cytoplasmic GSDMB2 expression in breast cancer cells did not significantly affect cancer formation (number of tumors, latency, tumor weight, histology or proliferation) or lung metastasis potential compared to controls.

ConclusionsGSDMB2 expression alone does not have an overall tumorigenic potential in mice, but it might reduce gastric carcinogenesis. Contrary to human cancers, GSDMB2 upregulation does not significantly affect breast cancer generation and progression in mouse models. However, to evidence the GSDMB functions in cancer and other pathologies in vivo may require the presence of specific stimulus or cellular contexts. Our novel mouse strains will serve as the basis for the future development of more precise tissue-specific and context-dependent cancer models.


title: Case study: Digital spatial profiling of metastatic clear cell carcinoma reveals intra-tumor heterogeneity in epithelial-mesenchymal gradient.

abstract: Intrinsic intra-tumor heterogeneity (ITH) has been linked to worse patient outcomes. The development of spatial profiling technology has enabled the deciphering of ITH with multiple analysis readouts. Advanced ovarian clear cell carcinoma (OCCC), known to harbor ITH, is chemoresistant, poor prognostic, and possesses distinct molecular and histological characteristics. However, detailed spatial information of the nature of ITH within OCCC remains unclear. Here, we utilized the NanoString Digital spatial profiling (DSP) GeoMx platform to perform multiplex protein expression analysis on tumor samples of primary and colonic metastatic sites from one advanced OCCC patient. The spatial resolution revealed the existence of an epithelial-mesenchymal (EM) gradient within the metastatic tumor but not the primary tumor, and similar EM gradient was not observed within the primary tumor. The EM gradient exhibited a distinct pattern from the periphery to the core of the metastatic tumor. Compared to tumor cells at the primary site, there was an intermediate zone in between the tumor periphery and the tumor core in the colonic metastasis with differential expression patterns of pan-cytokeratin (PanCK), fibronectin (FN), smooth muscle actin (SMA), neural cell adhesion molecule (NCAM), integrin alpha X (ITGAX), and Ki-67. Our study provides the first spatially resolved in situ evidence of intermediate or hybrid EM states within the tumor samples of similar morphology. This not only demonstrates the promising applications of spatial profiling in precision medicine but also provides an unprecedented view of the EM gradient during the progression of cancer such as OCCC.


title: A generic systems-theoretic approach to identify biological networks capable of adaptation

abstract: Constructing biological networks capable of performing specific biological functionalities has been of sustained interest in synthetic biology. Adaptation is one such ubiquitous functional property, which enables every living organism to sense a change in its surroundings and return to its operating condition prior to the disturbance. In this paper, we present a generic systems theory-driven method for designing adaptive protein networks. First, we translate the necessary qualitative conditions for adaptation to mathematical constraints using the language of systems theory, which we then map back as  design requirements for the underlying networks. We go on to prove that a protein network with different input-output nodes (proteins) needs to be at least of third-order in order to provide adaptation. Next, we show that the necessary design principles obtained for a three-node network in adaptation consist of negative feedback or a feed-forward realization. Interestingly, the design principles obtained by the proposed method remain the same for a network of arbitrary size and connectivity. Finally, we prove that the motifs discovered for adaptation are non-retroactive for a canonical downstream connection. This result explains how complex biological networks achieve robustness while keeping the core motifs unchanged in the context of a particular functionality. We corroborate our theoretical results with detailed and thorough numerical simulations. Overall, our results present a generic, systematic and robust framework for designing various kinds of biological networks.

category: systems biology


title: Functional connectome reorganization relates to post-stroke motor recovery and structural disconnection

abstract: Motor recovery following ischemic stroke is contingent on the ability of surviving brain networks to compensate for damaged tissue. In rodent models, sensory and motor cortical representations have been shown to remap onto intact tissue around the lesion site, but remapping to more distal sites (e.g. in the contralesional hemisphere) has also been observed. Resting state functional connectivity (FC) analysis has been employed to study compensatory network adaptations in humans, but mechanisms and time course of motor recovery are not well understood. Here, we examine longitudinal FC in 23 first-episode ischemic pontine stroke patients (34-74 years old; 8 female, 15 male) and utilize a graph matching approach to identify patterns of regional functional connectivity reorganization during recovery. We quantified functional reorganization between several intervals ranging from 1 week to 6 months following stroke, and demonstrated that the areas that undergo functional reorganization most frequently are in cerebellar/subcortical networks. Brain regions with more structural connectome disruption due to the stroke also had more functional remapping over time. Finally, we show that the amount of functional reorganization between time points is correlated with the extent of motor recovery observed between those time points in the early to late subacute phases, and, furthermore, individuals with greater baseline motor impairment demonstrate more extensive early subacute functional reorganization (from one to two weeks post-stroke) and this reorganization correlates with better motor recovery at 6 months. Taken together, these results suggest that our graph matching approach can quantify recovery-relevant, whole-brain functional connectivity network reorganization after stroke.


title: Synaptic density and neuronal metabolic function measured by PET in the unilateral 6-OHDA rat model of Parkinson's disease

abstract:
Parkinsons disease (PD) is caused by progressive neurodegeneration and characterised by motor dysfunction. Neurodegeneration of dopaminergic neurons also causes aberrations within the cortico-striato-thalamo-cortical (CSTC) circuit, which has been hypothesised to lead to non-motor symptoms such as depression. Individuals with PD have both lower synaptic density and changes in neuronal metabolic function in the basal ganglia, as measured using [11C]UCB-J and [18F]FDG positron emission tomography (PET), respectively. However, the two radioligands have not been directly compared in the same PD subject or in neurodegeneration animal models. Here, we investigate [11C]UCB-J binding and [18F]FDG uptake in the CSTC circuit following a unilateral dopaminergic lesion in rats and compare it to sham lesioned rats.

Rats received either a unilateral injection of 6-hydroxydopamine (6-OHDA) or saline in the medial forebrain bundle and rostral substantia nigra (n=4/group). After three weeks, all rats underwent two PET scans using [18F]FDG, followed by [11C]UCB-J on a separate day. [18F]FDG uptake and [11C]UCB-J binding were both lower in the ipsilateral striatal regions compared to the contralateral regions. Using [11C]UCB-J, we could detect an 8.7% decrease in the ipsilateral ventral midbrain, compared to a 2.9% decrease in ventral midbrain using [18F]FDG. Differential changes between hemispheres for [11C]UCB-J and [18F]FDG outcomes were also evident in the CSTC circuits cortical regions, especially in the orbitofrontal cortex and medial prefrontal cortex where higher synaptic density yet lower neuronal metabolic function was observed, following lesioning.

In conclusion, [11C]UCB-J and [18F]FDG PET can detect divergent changes following a dopaminergic lesion in rats, especially in cortical regions that are not directly affected by the neurotoxin. These results suggest that combined [11C]UCB-J and [18F]FDG scans could yield a better picture of the heterogeneous cerebral changes in neurodegenerative disorders.


title: Motivated semantic control: Exploring the effects of extrinsic reward and self-reference on semantic retrieval in semantic aphasia

abstract: Recent insights show increased motivation can benefit executive control, but this effect has not been explored in relation to semantic cognition. Patients with deficits of controlled semantic retrieval in the context of semantic aphasia (SA) after stroke may benefit from this approach since  semantic control is considered an executive process. Deficits in this domain are partially distinct from domain-general deficits of cognitive control. We assessed the effect of both extrinsic and intrinsic motivation in healthy controls and semantic aphasia patients. Experiment 1 manipulated extrinsic reward using high or low levels of points for correct responses during a semantic association task. Experiment 2 manipulated the intrinsic value of items using self-reference; allocating pictures of items to the participant ( self) or researcher ( other) in a shopping game before people retrieved their semantic associations. These experiments revealed that patients, but not controls, showed better performance when given an extrinsic reward, consistent with the view that increased external motivation may help to ameliorate patients semantic control deficits. However, while self-reference was associated with better episodic memory, there was no effect on semantic retrieval. We conclude that semantic control deficits can be reduced when extrinsic rewards are anticipated; this enhanced motivational state is expected to support proactive control, for example, through the maintenance of task representations. It may be possible to harness this modulatory impact of reward to combat the control demands of semantic tasks in SA patients.


title: A machine learning approach for MRI-based classification of individuals with mild cognitive impairment

abstract: Diagnosis criteria for Mild Cognitive Impairment (MCI) rely on cognitive symptoms and do not require specific biomarker evidence of pathology. Nevertheless, patients may still have subtle brain changes that are identifiable with neuroimaging. To classify MCI patients vs. healthy age-matched controls, two algorithms--Multilayer Perceptron (MLP) and Support Vector Machine (SVM)--were applied to structural MRI data from the OASIS-1 cohort (https://www.oasis-brains.org/). Despite their comparable performance in some measures, the MLP algorithm was preferable due to superior recall of MCI cases.


title: Parasite-driven cascades or hydra effects: susceptibility and foraging depression shape parasite-host-resource interactions

abstract:
O_LIWhen epidemics kill hosts and increase their resources, should the density of hosts decrease (with a resource increase, this constitutes a trophic cascade) or increase (a hydra effect)? Seeking answers, we integrate trait measurements, a resource-host-parasite model, and experimental epidemics with plankton. This combination reveals how a spectrum from cascades to hydra effects can arise. It reflects tension between parasite-driven mortality (a density-mediated effect) and foraging depression upon contact with parasite propagules (a trait-mediated one).
C_LIO_LIIn the model, mortality rises when higher susceptibility to infection increases infection prevalence. Epidemics release resources while suppressing hosts (creating a cascade). In contrast, when hosts are less susceptible and parasites depress their foraging, a resource feedback can elevate host density during epidemics (creating a hydra effect), particularly at higher carrying capacity of resources. This combination elevates primary production relative to per-host consumption of resources (two key determinants of host density).
C_LIO_LIWe test these predictions of the qualitative effects of host traits and resource carrying capacity with trait measurements and a mesocosm experiment. Trait measurements show clonal lines of zooplankton hosts differ in their foraging depression and susceptibility. We seeded resource-host-parasite mesocosms with different host genotypes and provided different nutrient supplies to test model predictions. Hydra effects and trophic cascades arose under different conditions, as predicted by the model.
C_LIO_LIHence, tension between trait-mediated and density-mediated effects of parasites governs the fate of host density during epidemics - from cascades to hydra effects - via feedbacks with resources.
C_LI


title: Graminoids vary in functional traits, carbon dioxide and methane fluxes in a restored peatland: implications for modeling carbon storage

abstract: One metric of peatland restoration success is the re-establishment of a carbon sink, yet considerable uncertainty remains around the timescale of carbon sink trajectories. Conditions post-restoration may promote the establishment of vascular plants such as graminoids, often at greater density than would be found in undisturbed peatlands, with consequences for carbon storage. Although graminoid species are often considered as a single plant functional type (PFT) in land-atmosphere models, our understanding of functional variation among graminoid species is limited, particularly in a restoration context. We used a traits-based approach to evaluate graminoid functional variation and to assess whether different graminoid species should be considered a single PFT or multiple types. We tested hypotheses that greenhouse gas fluxes (CO2, CH4) would vary due to differences in plant traits among five graminoid species in a restored peatland in central Alberta, Canada. We further hypothesized that species would form two functionally distinct groupings based on taxonomy (grass, sedge). Differences in gas fluxes among species were primarily driven by variation in leaf physiology related to photosynthetic efficiency and resource-use, and secondarily by plant size. Multivariate analyses did not reveal distinct functional groupings based on taxonomy or environmental preferences. Rather, we identified functional groups defined by continuous plant traits and carbon fluxes that are consistent with ecological strategies related to differences in growth rate, resource-acquisition, and leaf economics. These functional groups displayed larger carbon storage potential than currently-applied graminoid PFTs. Existing PFT designations in peatland models may be more appropriate for pristine or high-latitude systems than those under restoration. Although replacing PFTs with continuous plant traits remains a challenge in peatlands, traits related to leaf physiology and growth rate strategies offer a promising avenue for future applications.


title: Chromosome X-wide analysis of positive selection in human populations: from common and private signals to selection impact on inactivated genes and enhancers-like signatures

abstract: The ability of detecting adaptive (positive) selection in the genome has opened the possibility of understanding the genetic bases of population-specific adaptations genome-wide. Here we present the analysis of recent selective sweeps specifically in the X chromosome in different human populations from the third phase of the 1000 Genomes Project using three different haplotype-based statistics. We describe numerous instances of genes under recent positive selection that fit the regimes of hard and soft sweeps, showing a higher amount of detectable sweeps in sub-Saharan Africans than in non-Africans (Europe and East Asia). A global enrichment is seen in neural-related processes while numerous genes related to fertility appear among the top candidates, reflecting the importance of reproduction in human evolution. Commonalities with previously reported genes under positive selection are found, while particularly strong new signals are reported in specific populations or shared across different continental groups. We report an enrichment of signals in genes that escape X chromosome inactivation, which may contribute to the differentiation between sexes. We also provide evidence of a widespread presence of soft-sweep-like signatures across the chromosome and a global enrichment of highly scoring regions that overlap potential regulatory elements. Among these, enhancers-like signatures seem to present putative signals of positive selection that might be in concordance with selection in their target genes. Also, particularly strong signals appear in regulatory regions that show differential activities, which might point to population-specific regulatory adaptations.


title: hei-tag: a highly efficient tag to boost targeted genome editing

abstract:
Precise, targeted genome editing by CRISPR/Cas9 is key for basic research and translational approaches in model and non-model systems1. While active in all species tested so far, editing efficiencies still leave room for improvement. To reach its target, the bacterial Cas9 needs to be efficiently shuttled into the nucleus as attempted by fusion of nuclear localization signals (NLSs) to the Cas9 protein2. Additional domains such as FLAG- or myc-tags are added for immediate detection or straight-forward purification3. To avoid steric hinderance impacting on activity, amino acid linkers are employed connecting Cas9 and additional domains.

We present the  hei-tag (high efficiency-tag), boosting the activity of the wide variety of CRISPR/Cas genome editing tools. The addition of the hei-tag to Cas9 or a C-to-T base editor dramatically enhances the respective targeting efficiency in model systems ranging from fish to mammals, including tissue culture applications. This allows to instantly upgrade existing and potentially highly adapted systems as well as establish novel highly efficient tools.


title: Deciphering signatures of natural selection via deep learning

abstract: Identifying genomic regions influenced by natural selection provides fundamental insights into a wide range of problems including human health, animal and plant breeding, and the understanding of local adaptation. We propose a new method, DeepGenomeScan, that can be used to address all these problems. It is based on the principle that the genotypes of individuals can be used to predict any associated trait; not only their phenotype but also their spatial location or the environmental attributes of the habitat they live in. We, therefore, implemented a deep learning method to detect candidate regions under selection by identifying loci that contribute the most to the predictive power of the deep neural network. Using simulations, we show that our method can successfully identify loci underlying quantitative traits subject to complex spatial patterns of selection. We apply DeepGenomeScan to a European human genetic variation dataset and posit that the loci that contribute the most to the prediction of latitude and longitude are located in genomic regions under selection. Using this approach, we identified many SNPs located within well-known genes, some of which were not identified using existing population genetics approaches, e.g. MCM6, MGAT5, TMEM163.


title: Predictive Modeling of Pseudomonas syringae Virulence on Bean using Gradient Boosted Decision Trees

abstract:
Pseudomonas syringae is a genetically diverse bacterial species complex responsible for numerous agronomically important crop diseases. Individual P. syringae isolates are typically given pathovar designations based on their host of isolation and the associated disease symptoms, and these pathovar designations are often assumed to reflect host specificity although this assumption has rarely been rigorously tested. Here we developed a rapid seed infection assay to measure the virulence of 121 diverse P. syringae isolates on common bean (Phaseolus vulgaris). This collection includes P. syringae phylogroup 2 (PG2) bean isolates (pathovar syringae) that cause bacterial spot disease and P. syringae phylogroup 3 (PG3) bean isolates (pathovar phaseolicola) that cause the more serious halo blight disease. We found that bean isolates in general were significantly more virulent on bean than non-bean isolates and observed no significant virulence difference between the PG2 and PG3 bean isolates. However, when we compared virulence within PGs we found that PG3 bean isolates were significantly more virulent than PG3 non-bean isolates, while there was no significant difference in virulence between PG2 bean and non-bean isolates. These results indicate that PG3 strains have a higher level of host specificity than PG2 strains. We then employed machine learning to investigate if we could use genomic data to predict virulence on bean. We used gradient boosted decision trees to model the virulence using whole genome kmers, type III secreted effector kmers, and the presence/absence of type III effectors and phytotoxins. Our model performed best using whole genome data and was able to predict virulence with high accuracy (mean absolute error = 0.05). Finally, we functionally validated the model by predicting virulence for 16 strains and found that 15 (94%) had virulence levels within the bounds of estimated predictions. This study demonstrates the power of machine learning for predicting host specific adaptation and strengthens the hypothesis that P. syringae PG2 strains have evolved a different lifestyle than other P. syringae strains.

AUTHOR SUMMARYPseudomonas syringae is a genetically diverse Gammaproteobacterial species complex responsible for numerous agronomically important crop diseases. Strains in the P. syringae species complex are frequently categorized into pathovars depending on pathogenic characteristics such as host of isolation and disease symptoms. Common bean pathogens from P. syringae are known to cause two major diseases: the halo blight disease, which is characterized by large necrotic lesions surrounded by a chlorotic zone or halo of yellow tissue; and the bacterial spot disease, which is characterized by brown leaf spots. While halo blight can cause serious crop losses, bacterial spot disease is generally of minor agronomic concern. The application of statistical genetic and machine learning approaches to genomic data has greatly increased our power to identify genes underlying traits of interest, such as host specificity. Machine learning models can be used to predict outcomes from new samples or to identify the genetic feature(s) that carry the most importance when predicting a particular phenotype. Here, we implemented a rapid method for screening a proxy of virulence for P. syringae isolates on common bean, and used this screen to assess virulence of P. syringae strains on bean. We found that halo blight pathogens display a stronger degree of host specificity compared to brown spot pathogens, and that genomic kmers and virulence factors can be used to predict the virulence of P. syringae isolates on bean using machine learning models.


title: Identifying and Classifying Goals For Scientific Knowledge

abstract:
MotivationScience progresses by posing good questions, yet work in biomedical text mining has not focused on them much. We propose a novel idea for biomedical natural language processing: identifying and characterizing the questions stated in the biomedical literature. Formally, the task is to identify and characterize ignorance statements, statements where scientific knowledge is missing or incomplete. The creation of such technology could have many significant impacts, from the training of PhD students to ranking publications and prioritizing funding based on particular questions of interest. The work presented here is intended as the first step towards these goals.

ResultsWe present a novel ignorance taxonomy driven by the role ignorance statements play in the research, identifying specific goals for future scientific knowledge. Using this taxonomy and reliable annotation guidelines (inter-annotator agreement above 80%), we created a gold standard ignorance corpus of 60 full-text documents from the prenatal nutrition literature with over 10,000 annotations and used it to train classifiers that achieved over 0.80 F1 scores.

AvailabilityCorpus and source code freely available for download at https://github.com/UCDenver-ccp/Ignorance-Question-Work. The source code is implemented in Python.

ContactMayla.Boguslav@CUAnshcutz.edu


title: Surveillance of in situ tumor arrays reveals early environmental control of cancer immunity

abstract:
The immune phenotype of a tumor is a key predictor of its response to immunotherapy1-4. Patients who respond to immune checkpoint blockade generally present with tumors that are infiltrated by activated T cells, a tumor-immune phenotype referred to as  immune inflamed5-7. However, not all immune inflamed tumors respond to therapy, and in addition the majority of patients presents with tumors that lack T cells ( immune desert) or that exclude T cells in the periphery of the tumor islet ( immune excluded)8. Despite the importance of these tumor-immune phenotypes in patients, little is known about their development, heterogeneity or dynamics due to an inability to model these features pre-clinically.

Here, we describe an approach designated STAMP (skin tumor array by micro-poration), which combines in vivo noninvasive, high-throughput time-lapse imaging with excisional biopsies and next generation sequencing to characterize the establishment of the immunological niche and follow its evolution during immunotherapy. STAMP involves the seeding of dozens to hundreds clonal tumors in the superficial dermis of a single mouse ear that can be visualized in situ over weeks to months. Using this approach, we found that genetically identical tumors could display surprisingly different immune phenotypes. Although individual tumors of the same array were populated by the same T cell clonotypes, regression or progression of individual tumors were associated with distinct patterns of spatial organization of the T cells. In situ imaging of 14K tumors revealed that immune phenotypes were not static over-time but could rather evolve with tumor growth and response to treatment. Therapy-induced or spontaneous early conversion to the immune inflamed phenotype correlated with tumor regression and enhanced cytotoxic T cell activity. Therefore, STAMP provides a flexible approach to study the relationship between tumor evolution, immune cell dynamics, and tumor microenvironment with therapeutic response.


title: ZHX2 Promotes HIF1α Oncogenic Signaling in Triple-Negative Breast Cancer

abstract: Triple-negative breast cancer (TNBC) is an aggressive and highly lethal disease, which warrants the critical need to identify new therapeutic targets. We show that Zinc Fingers And Homeoboxes 2 (ZHX2) is amplified or overexpressed in TNBC cell lines and patients. Functionally, depletion of ZHX2 inhibited TNBC cell growth and invasion in vitro, orthotopic tumor growth and spontaneous lung metastasis in vivo. Mechanistically, ZHX2 bound with hypoxia inducible factor (HIF) family members and positively regulated HIF1 activity in TNBC. Integrated ChIP-Seq and gene expression profiling demonstrated that ZHX2 co-occupied with HIF1 on transcriptionally active promoters marked by H3K4me3 and H3K27ac, thereby promoting gene expression. Furthermore, multiple residues (R491, R581 and R674) on ZHX2 are important in regulating its phenotype, which correspond with their roles on controlling HIF1 activity in TNBC cells. These studies establish that ZHX2 activates oncogenic HIF1 signaling, therefore serving as a potential therapeutic target for TNBC.


title: Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis

abstract: Pediatric ulcerative colitis (UC) is a distinct type of inflammatory bowel disease with severe disease activity and rapid progression, which can lead to detrimental life-long consequences. The pathogenesis of pediatric UC remains unclear, although dysbiosis of the gut microbiota has been considered an important factor. In this study, we used mass spectrometry-based glycomic approaches to examine the N-glycans that were associated with the intestinal mucosal-luminal interface microbiota cells of treatment-naive pediatric UC or control patients. We observed abundant paucimannosidic and other truncated N-glycans that were associated with the microbiota and found that the pediatric UC microbiota samples contained significantly higher levels of these atypical N-glycans compared to those of controls. This study indicates that intestinal N-glycans may be used as novel UC biomarker candidates and the aberrant metabolism of glycans by gut microbiota may be involved in the pathogenesis of UC in children.


title: Estradiol Influences Adenosinergic Signaling and NREM Sleep Need in Adult Female Rats

abstract:
Studies report estradiol (E2) suppresses sleep in females; however, the mechanisms of E2 action remain largely undetermined. Our previous findings suggest that the median preoptic nucleus (MnPO) is a key nexus for E2 action on sleep. Here, using behavioral, neurochemical and pharmacological approaches, we investigated whether E2 influenced the sleep homeostat as well as adenosinergic signaling in the MnPO of adult female rats. During the Light Phase, where rats accumulate the majority of sleep, E2 markedly reduced NREM-SWA (a measure of the homeostatic sleep need). Following 6-hours of sleep deprivation, levels of NREM-SWA were significantly increased compared to baseline sleep. However, the NREM-SWA levels were not different between E2 and control treatment despite a significant increase in wake at the expense of NREM sleep. Analysis of NREM-SWA differences between baseline and recovery sleep following sleep deprivation demonstrated that E2 induced a 2-fold increase in delta power compared to controls suggesting that E2 significantly expanded the dynamic range for the sleep homeostat. Correlated with E2-induced changes in physiological markers of homeostatic sleep was a marked increase in extracellular adenosine (a molecular marker of homeostatic sleep need) during unrestricted and recovery sleep following a 6-hour deprivation. Additionally, E2 blocked the ability of an adenosine A2A receptor agonist (CGS-21680) to increase NREM sleep compared to controls. Thus, taken together, the findings that E2 increased extracellular adenosine content, while blocking A2A signaling in the MnPO suggests a potential mechanism for how estrogens impact sleep in the female brain.

Statement of SignificanceWhile gonadal steroids and gender are implicated as risk factors for sleep disruptions and insomnia, the relationship between ovarian steroids and sleep is poorly understood. Understanding the mechanisms through which estradiol (E2) is working to influence sleep-wake behavior is a critical first step toward a better understanding of the role of estrogens in sleep pathologies. Using a rodent model, the current study presents novel findings suggesting that estradiol (E2) is influencing adenosinergic actions in the MnPO. The ability of E2 to attenuate the local effects of the A2A receptors in the MnPO suggests that E2 modulation of A2A receptor signaling may underlie estrogenic suppression of sleep behavior as well as changes in homeostatic sleep need.


title: A deep-learning-based toolbox for Automated Limb Motion Analysis (ALMA) in murine models of neurological disorders

abstract: In neuroscience research, the refined analysis of rodent locomotion is complex and cumbersome, and access to the technique is limited because of the necessity for expensive equipment. In this study, we implemented a new deep-learning-based toolbox for Automated Limb Motion Analysis (ALMA) that requires only basic behavioral equipment and an inexpensive camera. The ALMA toolbox enables the unbiased and comprehensive analyses of locomotor kinematics and paw placement and can be applied to neurological conditions affecting the brain and spinal cord. We demonstrated that the ALMA toolbox can (1) robustly track the evolution of locomotor deficits after spinal cord injury, (2) sensitively detect locomotor abnormalities after traumatic brain injury, and (3) correctly predict disease onset in a multiple sclerosis model. We, therefore, established a broadly applicable automated and standardized approach that requires minimal financial and time commitments to facilitate the comprehensive analysis of locomotion in rodent disease models.


title: Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects

abstract: The prevalence of clonal haematopoiesis of indeterminate potential (CHIP) in healthy individuals increases rapidly from age 60 onwards and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in stem cells that are also drivers of myeloid malignancies. Since mutations in stem cells often drive leukaemia, we hypothesised that stem cell fitness substantially contributes to transformation from CHIP to leukaemia. Stem cell fitness is defined as the proliferative advantage over cells carrying no or only neutral mutations. It is currently unknown whether mutations in different CHIP genes lead to distinct fitness advantages that could form the basis for patient stratification. We set out to quantify the fitness effects of CHIP drivers over a 12 year timespan in older age, using longitudinal error-corrected sequencing data. We developed a new method based on drift-induced fluctuation (DIF) filtering to extract fitness effects from longitudinal data, and thus quantify the growth potential of variants within each individual. Our approach discriminates naturally drifting populations of cells and faster growing clones, while taking into account individual mutational context. We show that gene-specific fitness differences can outweigh inter-individual variation and therefore could form the basis for personalised clinical management.

category: cell biology


title: Complex and long-range linkage disequilibrium and its relationship with QTL for Marek's Disease resistance in chicken populations

abstract: Chicken long-range linkage disequilibrium (LRLD) and LD blocks, and their relationship with previously described Mareks Disease (MD) quantitative trait loci regions (QTLRs), were studied in an F6 population from a full-sib advanced intercross line (FSAIL), and in eight commercial pure layer lines. Genome wide LRLD was studied in the F6 population by random samples of non-syntenic and syntenic marker pairs genotyped by Affymetrix HD 600K SNP array. To illustrate the relationship with QTLRs, LRLD and LD blocks in and between the MD QTLRs were studied by all possible marker pairs of all array markers in the QTLRs, using the same F6 QTLR genotypes and genotypes of the QTLR elements markers in the eight lines used in the MD mapping study. LRLD was defined as r2 [≥] 0.7 over a distance [≥] 1 Mb, and 1.5% of all syntenic marker pairs were classified as LRLD. Complex fragmented and interdigitated LD blocks were found, over distances ranging from a few hundred to a few million bases. Vast high, long-range, and complex LD was found between two of the MD QTLRs. Cross QTLRs STRING networks and gene interactions suggested possible origins of this exceptional QTLRs LD. Thus, causative mutations can be located at a much larger distance from a significant marker than previously appreciated. LRLD range and LD block complexity may be used to identify mapping errors, and should be accounted for while interpreting genetic mapping studies. All sites with high LD with a significant marker should be considered as candidate for the causative mutation.


title: Protein structural consequences of DNA mutational signatures: A meta-analysis of somatic variants and deep mutational scanning data

abstract: AO_SCPLOWBSTRACTC_SCPLOWSignatures of DNA motifs associated with distinct mutagenic exposures have been defined for somatic variants, but little is known about the consequences different mutational processes pose to the cell, especially how mutagens exert damage on specific proteins and their three-dimensional structures. Here we identify a DNA mutational signature which corresponds to damaging protein variants. We show that this mutational signature is under-sampled in sequencing data from tumour cohorts, constituting the "dark matter" of the mutational landscape which could only be accessed using deep mutational scanning (DMS) data. By training a set of gradient boosting classifiers, we illustrate that DMS data from only a handful ({approx} 10) of experiments can accurately predict variant impact, and that DNA mutational signatures embed information about the protein-level impact of variants. We bridge the gap between DNA sequence variations and protein-level consequences, discuss the significance of this signature in informing protein design and molecular principles of protein stability, and clarify the relationship between disease association and the true impact mutations bring to protein function.


title: The "dark matter" of protein variants carries a distinct DNA signature and predicts damaging variant effects


title: Spontaneous polarization and cell guidance on asymmetric nanotopography

abstract: Asymmetric nanotopography with sub-cellular dimensions has recently been demonstrated to be able to provide a unidirectional bias in the migration of cells. The details of this guidance depend both on the type of cell studied and the design of the nanotopography. This behavior is not yet well understood, so there is a pressing need for a predictive description of cell migration on such nanotopography that captures both the initiation of migration and the manner in which cell migration evolves. Here, we employ a three-dimensional, physics-based model to study cell guidance on asymmetric nanosawteeth. In agreement with experimental data, our model predicts that asymmetric sawteeth lead both to spontaneous motion and changes in motion phenotypes. Our model demonstrates that asymmetric nano-sawteeth induce a unidirectional bias in guidance direction that is dependent upon the actin polymerization rate and the sawtooth dimensions. Motivated by this model, an analysis of previously reported experimental data indicates that the degree of guidance by asymmetric nanosawteeth increases with the cell velocity.


title: Levelling out differences in aerobic glycolysis neutralizes the competitive advantage of oncogenic PIK3CA mutant progenitors in the esophagus

abstract: Normal human tissues progressively accumulate cells carrying mutations. Activating mutations in PIK3CA generate large clones in the aging human esophagus, but the underlying cellular mechanisms are unclear. Here, we tracked mutant PIK3CA esophageal progenitor cells in transgenic mice by lineage tracing. Expression of an activating heterozygous Pik3caH1047R mutation in single progenitor cells tilts cell fate towards proliferation, generating mutant clones that outcompete their wild type neighbors. The mutation leads to increased aerobic glycolysis through the activation of Hif1 transcriptional targets compared with wild type cells. We found that interventions that level out the difference in activation of the PI3K/HIF1/aerobic glycolysis axis between wild type and mutant cells attenuate the competitive advantage of Pik3caH1047R mutant cells in vitro and in vivo. Our results suggest that clinically feasible interventions that even out signaling imbalances between wild type and mutant cells may limit the expansion of oncogenic mutants in normal epithelia.


title: Physachenolide C induces complete regression of established murine melanoma tumors via apoptosis and cell cycle arrest

abstract: Melanoma is an aggressive skin cancer that metastasizes to other organs. While immune checkpoint blockade with anti-PD-1 has transformed the treatment of advanced melanoma, many melanoma patients fail to respond to anti-PD-1 therapy or develop acquired resistance. Thus, effective treatment of melanoma still represents an unmet clinical need. Our prior studies support the anti-cancer activity of the 17{beta}-hydroxywithanolide class of natural products, including physachenolide C (PCC). As single agents, PCC and its semi-synthetic analog demonstrated direct cytotoxicity in a panel of murine melanoma cell lines, which share common driver mutations with human melanoma; the IC50 values ranged from 0.18 - 1.7 {micro}M. PCC treatment induced apoptosis of tumor cells both in vitro and in vivo. In vivo treatment with PCC alone caused the complete regression of established melanoma tumors in all mice, with a durable response in 33% of mice after discontinuation of treatment. T cell-mediated immunity did not contribute to the therapeutic efficacy of PCC or prevent tumor recurrence in YUMM2.1 melanoma model. In addition to apoptosis, PCC treatment induced G0-G1 cell cycle arrest of melanoma cells, which upon removal of PCC, re-entered the cell cycle. PCC-induced cycle cell arrest likely contributed to the in vivo tumor recurrence in a portion of mice after discontinuation of treatment. Thus, 17{beta}-hydroxywithanolides have the potential to improve the therapeutic outcome for patients with advanced melanoma.