title: Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen

abstract: While most productivity on the surface of the Earth today is fueled by oxygenic photosynthesis, during the early parts of Earth history it is thought that anoxygenic photosynthesis--using compounds like ferrous iron or sulfide as electron donors--drove most global carbon fixation. Anoxygenic photosynthesis is still performed by diverse bacteria in niche environments today. Of these, the Chlorobi (formerly green sulfur bacteria) are often interpreted as being particularly ancient and are frequently proposed to have fueled the biosphere early in Earth history before the rise of oxygenic photosynthesis. Here, we perform comparative genomic, phylogenetic, and molecular clock analyses to determine the antiquity of the Chlorobi and their characteristic phenotypes. We show that contrary to common assumptions, the Chlorobi clade is relatively young, with anoxygenic phototrophy, carbon fixation via the rTCA pathway, and iron oxidation all significantly postdating the rise of oxygen ~2.3 billion years ago. The Chlorobi therefore could not have fueled the Archean biosphere, but instead represent a relatively young radiation of organisms which likely acquired the capacity for anoxygenic photosynthesis and other traits via horizontal gene transfer sometime after the evolution of oxygenic Cyanobacteria.


title: CropMetaPop: a population genetics program to simulate the evolution of crop metapopulations

abstract:
Stochastic simulation programs are useful to study the evolution of crop populations in changing environments. These programs require to take into account some specific features characterizing farmers practices such as seed circulation or seed mixing. However such human-mediated evolutionary processes are different from the classical colonization or migration models used in most existing stochastic simulation programs for quantitative population genetics.

To fill this gap, CropMetaPop is an individual based forward-time simulation program for quantitative population genetics developed to represent a diversity of socially established rules underlying seed circulation between farmers. For instance, one farmer can give seeds to neighbours according to his stock and receive from them according to his needs. Crop-Metapop also takes into account other important evolutionary forces encountered in crop diversity management systems, such as different population sizes and selection modalities for different populations.

CropMetaPop makes it possible to study the impacts of different crop biodiversity management strategies. For this purpose, it simulates the genetic evolution over time of several crop populations submitted to genetic drift and selection and linked by explicitly modeled seed circulation and mixtures.

category: evolutionary biology


title: Genome-wide analysis of mobile element insertions in human genomes

abstract: Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36,699 non-reference MEIs constructed from 5,675 genomes, comprising 2,998 Chinese samples ([~]26.2X, NyuWa) and 2,677 samples from the 1000 Genomes Project ([~]7.4X, 1KGP). We discovered that LINE-1 insertions were highly enriched at centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.

category: genomics


title: Integrated evaluation of telomerase activation and telomere maintenance across cancer cell lines

abstract: In cancer, telomere maintenance is critical for the development of replicative immortality. Using genome sequences from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer Project, we calculated telomere content across 1,299 cancer cell lines. We find that telomerase reverse transcriptase (TERT) expression correlates with telomere content in lung, central nervous system, and leukemia cell lines. Using CRISPR/Cas9 screening data, we show that lower telomeric content is associated with dependency of CST telomere maintenance components. Increased dependencies of shelterin members are associated with wild-type TP53 status. Investigating the epigenetic regulation of TERT, we find widespread allele-specific expression in promoter-wildtype contexts. TERT promoter-mutant cell lines exhibit hypomethylation at PRC2-repressed regions, suggesting a cooperative global epigenetic state in the reactivation of telomerase. By incorporating telomere content with genomic features across comprehensively characterized cell lines, we provide further insights into the role of telomere regulation in cancer immortality.

category: cancer biology


title: ENOX2 NADH Oxidase: A BCR-ABL1-dependent cell surface and secreted redox protein in chronic myeloid leukemia (CML)

abstract: Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm caused by the acquisition of BCR-ABL1 fusion in a hematopoietic stem cell. We identified the ENOX2 gene as up-regulated in BCR-ABL1-expressing UT-7 cell lines through a transcriptome assay. The oncofoetal ENOX2 protein (Ecto-Nicotinamide Adenine Dinucleotide Oxidase Disulfide Thiol Exchanger 2) is expressed on the external plasma membrane surface of cancer cells and can be released in cancer patients serum. Considering these data, we studied ENOX2 expression in CML cell lines and patients using quantitative RT-PCR, western-blots, the ELISA method, and transcriptomic dataset reanalysis. We confirmed increased ENOX2 mRNA expression in the BCR-ABL1-expressing UT-7 cell line. Comparable results were obtained in CML patients at diagnosis. Western-blot analyses on UT-7 and TET-inducible Ba/F3 cell lines established the up-regulation of ENOX2 protein. BCR-ABL1 has been found to induce ENOX2 overexpression in a kinase-dependent manner. In a series of 41 patients with CML, ELISA assays showed a highly significant increase of ENOX2 protein levels in the plasma of patients with CML (p < 0.0001) as compared to controls (n=28). Transcriptomic dataset (GSE4170) reanalyzes have shown specific ENOX2 mRNA overexpression in the chronic phase of the disease. Bioinformatic analyses identified several genes whose mRNA expression was positively correlated to ENOX2. Some of them encode proteins involved in cellular functions compatible with the growth deregulation observed in CML. All in all, our results demonstrate for the first time the upregulation of a secreted Redox protein in a BCR-ABL1-dependent manner in CML. Our data suggest that ENOX2 (through its transcriptional program) plays a significant role in the BCR-ABL1 leukemogenesis. Further studies are required to clarify the relationship between BCR-ABL1 and ENOX2.


title: Network-based modeling of herb combinations in Traditional Chinese Medicine

abstract: Traditional Chinese Medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein-protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.

category: systems biology


title: Spinal V1 neurons inhibit motor targets locally and sensory targets distally to coordinate locomotion

abstract: Rostro-caudal coordination of spinal motor output is essential for locomotion. Most spinal interneurons project axons longitudinally to govern locomotor output, yet their connectivity along this axis remains unclear. In this study, we use larval zebrafish to map synaptic outputs of a major inhibitory population, V1 (Eng1+) neurons, which are implicated in dual sensory and motor functions. We find that V1 neurons exhibit long axons extending rostrally and exclusively ipsilaterally for an average of 6 spinal segments; however, they do not connect uniformly with their post-synaptic targets along the entire length of their axon. Locally, V1 neurons inhibit motor neurons (both fast and slow) and other premotor targets including V2a, V2b and commissural pre-motor neurons. In contrast, V1 neurons make robust inhibitory contacts throughout the rostral extent of their axonal projections onto a dorsal horn sensory population, the Commissural Primary Ascending neurons (CoPAs). In a computational model of the ipsilateral spinal network, we show that this pattern of short range V1 inhibition to motor and premotor neurons is crucial for coordinated rostro-caudal propagation of the locomotor wave. We conclude that spinal network architecture in the longitudinal axis can vary dramatically, with differentially targeted local and distal connections, yielding important consequences for function.

category: neuroscience


title: Modeling autism-associated SHANK3 deficiency using human cortico-striatal organoids generated from single neural rosettes

abstract: Our understanding of the human brain is limited by the lack of experimental models to mechanistically probe the properties of brain cells at different developmental stages under normal and pathological conditions. We developed a new method for generating human cortico-striatal organoids from stem cell-derived single neural rosettes (SNRs) and used it to investigate cortico-striatal development and deficits caused by the deficiency of an autism- and intellectual disability-associated gene SHANK3. We show that SNR-derived organoids consist of different cortico-striatal cells, including pallial and subpallial progenitors, primary cortical and striatal neurons, interneurons, as well as macroglial and mural cells. We also demonstrate that neurons in SNR-derived organoids are predictably organized, functionally mature, and capable of establishing functional neural networks. Interestingly, we found that the cellular and electrophysiological deficits in SHANK3-deficient SNR-derived organoids are dependent on the level of SHANK3 expression and that organoids with complete hemizygous SHANK3 deletion have disrupted expression of several clustered protocadherins and multiple primate-specific zinc-finger genes. Together, this study describes a new method for using SNRs to generate organoids, provides new insights into the cell lineages associated with human cortico-striatal development, and identifies specific molecular pathways disrupted by hemizygous SHANK3 deletion, which is the most common genetic abnormality detected in patients with 22q13 deletion syndrome.


title: Postdiction: when temporal regularity drives space perception through pre-stimulus alpha oscillations

abstract:
During postdiction, the last stimulus of a sequence changes the perception of the preceding ones: in the rabbit illusion, a three-flash series presented regularly in time, but not in space, is - illusory - perceived as spatially regular. Such a reorganization of (spatial) perception could be driven by internal priors, e.g. favoring slow motion for the rabbit illusion. Although postdiction is a ubiquitous phenomenon, its neural underpinnings remain poorly understood. Here, we focused on the role of priors during postdiction and hypothesized that these could be reflected by alpha oscillations (8-12Hz), previously observed to correlate with idiosyncratic biases. We presented human participants with ambiguous visual stimuli that elicited the rabbit illusion on about half the trials, allowing us to contrast MEG-EEG brain responses to the same physical events causing distinct percepts. Given that a strong prior will increase the overall probability of perceiving the illusion, we used the percentage of perceived illusion as a proxy for an individuals prior. We found that high fronto-parietal alpha power was associated with perceiving the sequence according to individual biases: participants with high susceptibility to the illusion would report the illusion, while participants with low susceptibility would report the veridical sequence. Additionally, we found that pre-stimulus alpha phase in occipital and frontal areas dissociated illusory from non-illusory trials. These results point to a dissociated relation of the power and timing of alpha band activity to illusory perception, with power reflecting prior expectations and phase influencing behavioral performance, potentially due to the modulation of sensory uncertainty.

Significance StatementLate events may sometimes influence how earlier events are perceived, as if the arrow of time was reversed in the brain. This surprising phenomenon, called postdiction, is observed in the rabbit illusion, and highlights a predominant mechanism for perceptual processes. Perception builds up from the combination of prior expectations with incoming sensory evidence, which takes time. We showed that pre-stimulus neural activity, and more specifically alpha oscillations (8-12Hz), play a double role in postdiction. Fronto-parietal alpha power reflects individual prior expectation, while occipital and frontal alpha phase predicts illusory perception. Postdiction might actually be a means of compensating for the neural delays inherent in perceptual processes, so that the arrow of perceptual time matches the arrow of physical time.


title: Identification of candidate susceptibility genes to Puccinia graminis f. sp. tritici in wheat

abstract: Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.

category: plant biology


title: Discerning amyloid network in plants

abstract: Amyloids are proteinaceous fibrillar structures and are known for their pathogenic and functional roles across the kingdoms. Besides proteinaceous deposits, amyloid-like structures are present in small metabolite assemblies and fibrillar hydrogels. Recent cryoelectron microscopy studies have shed light on the heterogeneous nature of the amyloid structures and their association with carbohydrate or lipid molecules, suggesting that amyloids are not exclusively proteinaceous. The association of amyloids with carbohydrates is further supported because the gold-standard dye of amyloid detection, Congo red, also binds to carbohydrates, probably due to similar stacking interactions. We name the association between amyloids, carbohydrates and other biomolecules as amyloid-network and propose that plants might contain such structures. Specifically, we hypothesize that cereal seeds containing glutamine-repeat-rich granules of storage proteins may have amyloid-like structures. This is because, polyQ repeats are associated with protein aggregation and amyloid formation in humans and are linked to multiple neurodegenerative conditions. Also seed storage proteins and seed cell wall proteins possess carbohydrate affinity. Thus, plant seeds might contain an intercalated network of proteins and carbohydrates, lending strength, stability and dynamics to these structures. In this paper, we show that, plant seeds have a mesh-like network that shows apple-green birefringence on staining with Congo red, a characteristic of amyloids. This congophilic network is more prominent in protein-rich seed sections of wheat and lentils, as compared to starch-rich compartments of potato. The findings suggest an amyloid network in the seeds and might be extended to other plant tissues. Further investigation with mass spectrometry and other techniques would detail the exact compositional analysis of these networks.


title: NCodR: A multi-class SVM classification to distinguish between non-coding RNAs in Viridiplantae

abstract: Non-coding RNAs (ncRNAs) are major players in the regulation of gene expression. This study analyses seven classes of ncRNAs in plants using sequence and secondary structure-based RNA folding measures. We observe distinct regions in the distribution of AU content along with overlapping regions for different ncRNA classes. Additionally, we find similar averages for minimum folding energy index across various ncRNAs classes except for pre-miRNAs and lncRNAs. Various RNA folding measures show similar trends among the different ncRNA classes except for pre-miRNAs and lncRNAs. We observe different k-mer repeat signatures of length three among various ncRNA classes. However, in pre-miRs and lncRNAs, a diffuse pattern of k-mers is observed. Using these attributes, we train eight different classifiers to discriminate various ncRNA classes in plants. Support-vector machines employing radial basis function show the highest accuracy (average F1 of ~91%) in discriminating ncRNAs, and the classifier is implemented as a web server, NCodR.


title: Effects of carbon, nitrogen, phosphorus, and potassium on flowering and Fruiting of Glycyrrhiza uralensis

abstract:
AbstractCarbon (C), nitrogen (N), phosphorus (P), and potassium (K) play an important role in flower bud differentiation and seed-filling; however, the effects of these elements on the flowering and fruiting of Glycyrrhiza uralensis Fisch. are not known. In this study, we evaluated the differences in the C, N, P, and K levels between the fruiting and nonfruiting plants of G. uralensis at different growth stages. The correlations between the elements C, N, P, and K and the flower and fruit falling rates, rate of empty seeds, rate of shrunken grains, and thousand kernel weight (TKW) were also determined. The results show that the P and K levels and C:N, P:N, and K:N ratios of flowering plants are significantly higher than those of nonflowering plants; N level of flowering plants is significantly lower than that of nonflowering plants at the flower bud differentiation stage. The number of inflorescences was positively correlated with C and K levels and C:N and K:N ratios. A low level of C, P, and K and high level of N in flowering and pod setting stage may lead to the flower and fruit drop of G. uralensis. The K level is significantly negatively correlated with the rates of empty and shrunken seeds. The N level is significantly positively correlated with TKW. Thus, high levels of C, P, and K might be beneficial to flower bud differentiation, while higher levels of N is not beneficial to the flower bud formation of G. uralensis. Higher levels of N and K at the filling stage were beneficial to the seed setting and seed-filling of G. uralensis.

HighlightHigh levels of C, P, and K might be beneficial to flower bud differentiation, while higher levels of N is not beneficial to the flower bud formation of G. uralensis. Higher levels of N and K at the filling stage were beneficial to the seed setting and seed-filling of G. uralensis.


title: Homozygosity at its Limit: Inbreeding Depression in Wild Arabidopsis arenosa Populations

abstract: New combinations of genetic material brought together through hybridization can lead to unfit offspring as a result of outbreeding or inbreeding depression. In selfing plants such as Arabidopsis thaliana, outbreeding depression is typically the result of pairwise deleterious epistatic interactions between two alleles that can geographically co-occur. What remains elusive is how often alleles resulting in genetic incompatibilities co-occur in natural populations of outcrossing plant species. To address this question, we screened over two thousand five hundred wild Arabidopsis arenosa hybrid plants in search for potential genetic mismatches. We show that although abnormal deleterious phenotypes are common, the transcriptional profiles of these abnormal A. arenosa plants differ substantially from those seen in incompatible A. thaliana hybrids. The abnormal hybrid phenotypes in A. arenosa had different underlying genetic architectures, yet a repeated theme was increased homozygosity, indicating that inbreeding rather than outbreeding depression gives rise to some of the deleterious phenotypes segregating in wild A. arenosa populations.


title: Overcoming the impacts of two-step batch effect correction on gene expression estimation and inference

abstract: Non-ignorable technical variation is commonly observed across data from multiple experimental runs, platforms, or studies. These so-called batch effects can lead to difficulty in merging data from multiple sources, as they can severely bias the outcome of the analysis. Many groups have developed approaches for removing batch effects from data, usually by accommodating batch variables into the analysis (one-step correction) or by preprocessing the data prior to the formal or final analysis (two-step correction). One-step correction is often desirable due it its simplicity, but its flexibility is limited and it can be difficult to include batch variables uniformly when an analysis has multiple stages. Two-step correction allows for richer models of batch mean and variance. However, prior investigation has indicated that two-step correction can lead to incorrect statistical inference in downstream analysis. Generally speaking, two-step approaches introduce a correlation structure in the corrected data, which, if ignored, may lead to either exaggerated or diminished significance in downstream applications such as differential expression analysis. Here, we provide more intuitive and more formal evaluations of the impacts of two-step batch correction compared to existing literature. We demonstrate that the undesired impacts of two-step correction (exaggerated or diminished significance) depend on both the nature of the study design and the batch effects. We also provide strategies for overcoming these negative impacts in downstream analyses using the estimated correlation matrix of the corrected data. We compare the results of our proposed workflow with the results from other published one-step and two-step methods and show that our methods lead to more consistent false discovery controls and power of detection across a variety of batch effect scenarios. Software for our method is available through GitHub (https://github.com/jtleek/sva-devel) and will be available in future versions of the sva R package in the Bioconductor project (https://bioconductor.org/packages/release/bioc/html/sva.html). Batch effect; Two-step batch adjustment; ComBat; Sample correlation adjustment; Generalized least squares

category: bioinformatics


title: Computational reconstruction of clonal hierarchies from bulk sequencing data of acute myeloid leukemia samples

abstract: Acute myeloid leukemia is an aggressive cancer of the blood forming system. The malignant cell population is composed of multiple clones that evolve over time. Clonal data reflect the mechanisms governing treatment response and relapse. Single cell sequencing provides most direct insights into the clonal composition of the leukemic cells, however it is still not routinely available in clinical practice. In this work we develop a computational algorithm that allows identifying all clonal hierarchies that are compatible with bulk variant allele frequencies measured in a patient sample. The clonal hierarchies represent descendance relations between the different clones and reveal the order in which mutations have been acquired. The proposed computational approach is tested using single cell sequencing data that allow comparing the outcome of the algorithm with the true structure of the clonal hierarchy. We investigate which problems occur during reconstruction of clonal hierarchies from bulk sequencing data. Our results suggest that in many cases only a small number of possible hierarchies fits the bulk data. This implies that bulk sequencing data can be used to obtain insights in clonal evolution.


title: Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain

abstract:
BackgroundTransposable elements (TEs) widely contributed to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However a specific search for the existence of full-length transpositionally competent TEs has not been performed in this genus.

ResultsHere we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be active driving germline polymorphisms among individuals and somatic polymorphisms in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes.

ConclusionsThe neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full lenght LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.


title: Ubiquitin ligase RIPLET mediates polyubiquitination of RIG-I and LGP2 and regulates the innate immune responses to SARS-CoV-2 infection

abstract: RIG-I, a cytoplasmic viral RNA sensor, is crucial for innate antiviral immune responses; however, there are controversies about RIG-Is regulatory mechanism by several ubiquitin ligases and LGP2. Our genetic study revealed that the RIPLET ubiquitin ligase was a general activating factor for RIG-I signaling, whereas another ubiquitin ligase, TRIM25, activated RIG-I in a cell-type-specific manner. These RIPLET and TRIM25 functions were modulated by accessory factors, such as ZCCH3C and NLRP12. Interestingly, we found an additional role of RIPLET in innate immune responses. RIPLET induced delayed polyubiquitination of LGP, resulting in the attenuation of excessive cytokine expression at the late phase. Moreover, RIPLET was involved in the innate immune responses against SARS-CoV-2 infection, a cause of the recent COVID-19 pandemic. Our data indicate that RIPLET fine-tunes innate immune responses via polyubiquitination of RIG-I and LGP2 against virus infection, including SARS-CoV-2.

category: immunology


title: A multiscale model suggests that a moderately weak inhibition of SARS-CoV-2 replication by type I IFN could accelerate the clearance of the virus

abstract: AO_SCPLOWBSTRACTC_SCPLOWSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible RNA virus that emerged in China at the end of 2019 and caused a large global outbreak. The interaction between SARS-CoV-2 and the immune response is complex because it is regulated by various processes taking part at the intracellular, tissue, and host levels. To gain a better understanding of the pathogenesis and progression of COVID-19, we formulate a multiscale model that integrate the main mechanisms which regulate the immune response to SARS-CoV-2 across multiple scales. The model describes the effect of type I interferon on the replication of SARS-CoV-2 inside cells. At the tissue level, we simulate the interactions between infected cells and immune cells using a hybrid agent-based representation. At the same time, we model the dynamics of virus spread and adaptive immune response in the host organism. After model validation, we demonstrate that a moderately weak inhibition of virus replication by type I IFN could elicit a strong adaptive immune response which accelerates the clearance of the virus. Furthermore, numerical simulations suggest that the deficiency of lymphocytes and not dendritic cells could lead to unfavourable outcomes in the elderly population.


title: Next generation vaccine platform: polymersomes as stable nanocarriers for a highly immunogenic and durable SARS-CoV-2 spike protein subunit vaccine

abstract: Multiple successful vaccines against SARS-CoV-2 are urgently needed to address the ongoing Covid-19 pandemic. In the present work, we describe a subunit vaccine based on the SARS-CoV-2 spike protein co-administered with CpG adjuvant. To enhance the immunogenicity of our formulation, both antigen and adjuvant were encapsulated with our proprietary artificial cell membrane (ACM) polymersome technology. Structurally, ACM polymersomes are self-assembling nanoscale vesicles made up of an amphiphilic block copolymer comprising of polybutadiene-b-polyethylene glycol and a cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane. Functionally, ACM polymersomes serve as delivery vehicles that are efficiently taken up by dendritic cells, which are key initiators of the adaptive immune response. Two doses of our formulation elicit robust neutralizing titers in C57BL/6 mice that persist at least 40 days. Furthermore, we confirm the presence of memory CD4+ and CD8+ T cells that produce Th1 cytokines. This study is an important step towards the development of an efficacious vaccine in humans.


title: Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

abstract: The SARS-CoV-2 spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2 infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. We demonstrate that S must be processed at the S1/S2 border in order to mediate cell-cell fusion, and that mutations at potential cleavage sites within the S2 subunit alter S processing at the S1/S2 border, thus preventing cell-cell fusion. We also identify residues within the internal fusion peptide and the cytoplasmic tail that modulate S cell-cell fusion. Additionally, we examine S stability and protein cleavage kinetics in a variety of mammalian cell lines, including a bat cell line related to the likely reservoir species for SARS-CoV-2, and provide evidence that proteolytic processing alters the stability of the S trimer. This work therefore offers insight into S stability, proteolytic processing, and factors that mediate S cell-cell fusion, all of which help give a more comprehensive understanding of this highly sought-after therapeutic target.

category: microbiology


title: Lost in translation: codon optimization inactivates SARS-CoV-2 RdRp

abstract:
The catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), Nsp12, has a unique NiRAN domain that transfers nucleoside monophosphates to the Nsp9 protein. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation) Nsp12 exists in inactive state in which NiRAN/RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or NTPs partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN/RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically-linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and design of its inhibitors.

HighlightsO_LICodon-optimization of Nsp12 triggers misfolding and activity loss
C_LIO_LISlow translation, accessory Nsp7 and Nsp8 subunits, and NTPs rescue Nsp12
C_LIO_LINon-substrate nucleotides activate RNA chain synthesis, likely via NiRAN domain
C_LIO_LICrosstalk between two Nsp12 active sites that bind the same ligands
C_LI

category: molecular biology


title: Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides


title: Molecular Dynamics Reveals the Effects of Temperature on Critical SARS-CoV-2 Proteins

abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly identified RNA virus that causes the serious infection Coronavirus Disease 2019 (COVID-19). The incidence of COVID-19 is still increasing worldwide despite the summer heat and cool winter. However, little is known about seasonal stability of SARS-CoV-2. Herein, we employ Molecular Dynamics (MD) simulations to explore the effect of temperature on four critical SARS-CoV-2 proteins. Our work demonstrates that the spike Receptor Binding Domain (RBD), Main protease (Mpro), and nonstructural protein 3 (macro X) possesses extreme thermos-stability when subjected to temperature variations rendering them attractive drug targets. Furthermore, our findings suggest that these four proteins are well adapted to habitable temperatures on earth and are largely insensitive to cold and warm climates. Furthermore, we report that the critical residues in SARS-CoV-2 RBD were less responsive to temperature variations as compared to the critical residues in SARS-CoV. As such, extreme summer and winter climates, and the transition between the two seasons, are expected to have a negligible effect on the stability of SARS-CoV-2 which will marginally suppress transmission rates until effective therapeutics are available world-wide.


title: Excitable axonal domains adapt to sensory deprivation in the olfactory system

abstract: The axon initial segment, nodes of Ranvier, and the oligodendrocyte-derived myelin sheath have significant influence on the firing patterns of neurons and the faithful, coordinated transmission of action potentials to downstream brain regions. In the olfactory bulb, olfactory discrimination tasks lead to adaptive changes in cell firing patterns, and the output signals must reliably travel large distances to other brain regions along highly myelinated tracts. Whether myelinated axons adapt to facilitate olfactory sensory processing is unknown. Here, we investigate the morphology and physiology of mitral cell axons in the adult olfactory system, and show that unilateral sensory deprivation causes system-wide adaptations in axons. Mitral cell spiking patterns and action potentials also adapted to sensory deprivation. Strikingly, both axonal morphology and mitral cell physiology were altered on both the deprived and non-deprived sides, indicating system level adaptations to reduced sensory input. Our work demonstrates a previously unstudied mechanism of plasticity in the olfactory system.


title: SENP1 in the retrosplenial agranular cortex regulates core autistic-like symptoms in mice

abstract: Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder, in which core symptoms are defects of social interaction and evidently repetitive behaviors. Although around 50-70 % of ASD patients have comorbidity of intellectual disabilities (ID) or developmental delay (DD), there are some ASD patients who exhibit only core symptoms but without ID/DD, raising the question whether there are genetic components and neural circuits specific for core symptoms of ASD. Here, by focusing on ASD patients who do not show compound ID or DD, we identified a de novo heterozygous gene-truncating mutation of the Sentrin-specific peptidase1 (SENP1) gene, coding the small ubiquitin-like modifiers (SUMO) deconjugating enzyme, as a potentially new candidate gene for ASD. We found that Senp1 haploinsufficient mice exhibited core symptoms of autism such as deficits in social interaction and repetitive behaviors, but normal learning and memory ability. Moreover, we found that the inhibitory and excitatory synaptic functions were severely affected in the retrosplenial agranular (RSA) cortex of Senp1 haploinsufficient mice. Lack of Senp1 led to over SUMOylation and degradation of fragile X mental retardation protein (FMRP) proteins, which is coded by the FMR1 gene, also implicated in syndromic ASD. Importantly, re-introducing SENP1 or FMRP specifically in RSA fully rescued the defects of synaptic functions and core autistic-like symptoms of Senp1 haploinsufficient mice. Together, these results demonstrated that disruption of the SENP1-FMRP regulatory axis in the RSA may cause core autistic symptoms, which provide a candidate brain region of ASD for potential therapeutic intervene by neural modulation approaches.


title: CTP and parS control ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning

abstract: ParABS partition systems, comprising the centromere-like DNA sequence parS, the parS-binding ParB-CTPase and the nucleoid-binding ParA-ATPase, ensure faithful segregation of bacterial chromosomes and low-copy-number plasmids. F-plasmid partition complexes containing ParBF and parSF move by generating and following a local concentration gradient of nucleoid-bound ParAF. However, the process through which ParBF activates ParAF-ATPase has not been defined. We studied CTP- and parSF-modulated ParAF--ParBF complex assembly, in which DNA-bound ParAF-ATP dimers are activated for ATP hydrolysis by interacting with two ParBF N-terminal domains. CTP or parSF enhances the ATPase rate without significantly accelerating ParAF--ParBF complex assembly. Together, parSF and CTP accelerate ParAF--ParBF assembly without further significant increase in ATPase rate. Magnetic-tweezers experiments showed that CTP promotes multiple ParBF loading onto parSF-containing DNA, generating condensed partition complex-like assemblies. We propose that ParBF in the partition complex adopts a conformation that enhances ParBF--ParBF and ParAF--ParBF interactions promoting efficient partitioning.

category: cell biology


title: CTP and parS coordinate ParB partition complex dynamics and ParA-ATPase activation for ParABS-mediated DNA partitioning


title: Neuronal post-developmentally acting SAX-7S/L1CAM can function as cleaved fragments to maintain neuronal architecture in C. elegans

abstract: Whereas remarkable advances have uncovered mechanisms that drive nervous system assembly, the processes responsible for the lifelong maintenance of nervous system architecture remain poorly understood. Subsequent to its establishment during embryogenesis, neuronal architecture is maintained throughout life in the face of the animals growth, maturation processes, the addition of new neurons, body movements, and aging. The C. elegans protein SAX-7, homologous to the vertebrate L1 protein family, is required for maintaining the organization of neuronal ganglia and fascicles after their successful initial embryonic development. To dissect the function of sax-7 in neuronal maintenance, we generated a null allele and sax-7S-isoform-specific alleles. We find that the null sax-7(qv30) is, in some contexts, more severe than previously described mutant alleles, and that the loss of sax-7S largely phenocopies the null, consistent with sax-7S being the key isoform in neuronal maintenance. Using a sfGFP::SAX-7S knock-in, we observe sax-7S to be predominantly expressed across the nervous system, from embryogenesis to adulthood. Yet, its role in maintaining neuronal organization is ensured by post-developmentally acting SAX-7S, as larval transgenic sax-7S(+) expression alone is sufficient to profoundly rescue the null mutants neuronal maintenance defects. Moreover, the majority of the protein SAX-7 appears to be cleaved, and we show that these cleaved SAX-7S fragments together, not individually, can fully support neuronal maintenance. These findings contribute to our understanding of the role of the conserved protein SAX-7/L1CAM in long-term neuronal maintenance, and may help decipher processes that go awry in some neurodegenerative conditions.

category: developmental biology


title: Profiling transcription factor sub-networks in type I interferon signaling and in response to SARS-CoV-2 infection

abstract: Type I interferons (IFN /{beta}) play a central role in innate immunity to respiratory viruses, including coronaviruses. Genetic defects in type I interferon signaling were reported in a significant proportion of critically ill COVID-19 patients. Extensive studies on interferon-induced intracellular signal transduction pathways led to the elucidation of the Jak-Stat pathway. Furthermore, advances in gene expression profiling by microarrays have revealed that type I interferon rapidly induced multiple transcription factor mRNA levels. In this study, transcription factor profiling in the transcriptome was used to gain novel insights into the role of inducible transcription factors in response to type I interferon signaling in immune cells and in lung epithelial cells after SARS-CoV-2 infection. Modeling the interferon-inducible transcription factor mRNA data in terms of distinct sub-networks based on biological functions such as antiviral response, immune modulation, and cell growth revealed enrichment of specific transcription factors in mouse and human immune cells. The evolutionarily conserved core type I interferon gene expression consists of the inducible transcriptional factor mRNA of the antiviral response sub-network and enriched in granulocytes. Analysis of the type I interferon-inducible transcription factor sub-networks as distinct protein-protein interaction pathways revealed insights into the role of critical hubs in signaling. Interrogation of multiple microarray datasets revealed that SARS-CoV-2 induced high levels of IFN-beta and interferon-inducible transcription factor mRNA in human lung epithelial cells. Transcription factor mRNA of the three major sub-networks regulating antiviral, immune modulation, and cell growth were differentially regulated in human lung epithelial cell lines after SARS-CoV-2 infection and in the tissue samples of COVID-19 patients. A subset of type I interferon-inducible transcription factors and inflammatory mediators were specifically enriched in the lungs and neutrophils of COVID-19 patients. The emerging complex picture of type I IFN transcriptional regulation consists of a rapid transcriptional switch mediated by the Jak-Stat cascade and a graded output of the inducible transcription factor activation that enables temporal regulation of gene expression.


title: Laser ablation of the apical sensory organ of Hydroides elegans does not inhibit detection of metamorphic cues

abstract:
Larvae of many marine invertebrates bear an anteriorly positioned apical sensory organ (ASO) presumed to be the receptor for settlement- and metamorphosis-inducing environmental cues, based on its structure, position and observed larval behavior. Larvae of the polychaete Hydroides elegans are induced to settle by bacterial biofilms, which they explore with their ASO and surrounding anteroventral surfaces. A micro-laser was utilized to destroy the ASO and other anterior ciliary structures in competent larvae of H. elegans. After ablation, larvae were challenged with bacterial biofilmed or clean surfaces and percent metamorphosis was determined. Ablated larvae were also assessed for cellular damage by applying fluorescently tagged FMRF-amide antibodies and observing the larvae by laser-scanning confocal microscopy. While the laser pulses caused extensive damage to the ASO and surrounding cells, they did not inhibit metamorphosis. We conclude that the ASO is not a required receptor site for cues that induce metamorphosis.

Summary StatementLarvae of the polychaete Hydroides elegans retain the capacity to sense biofilm cues and metamorphose despite removal of their apical sensory organs, the supposed sensors for settlement cues.

category: zoology


title: Idiosyncratic learning performance in flies generalizes across modalities

abstract: Individuals vary in their innate behaviors, even when they have the same genome and have been reared in the same environment. The extent of individuality in plastic behaviors, like learning, is less well characterized. Also unknown is the extent to which intragenotypic differences in learning generalize: if an individual performs well in one assay, will it perform well in other assays? We investigated this using the fruit fly Drosophila melanogaster, an organism long-used to study the mechanistic basis of learning and memory. We found that isogenic flies, reared in identical lab conditions, and subject to classical conditioning that associated odorants with electric shock, exhibit clear individuality in their learning responses. Flies that performed well when an odor was paired with shock tended to perform well when other odors were paired with shock, or when the original odor was paired with bitter taste. Thus, individuality in learning performance appears to be prominent in isogenic animals reared identically, and individual differences in learning performance generalize across stimulus modalities. Establishing these results in flies opens up the possibility of studying the genetic and neural circuit basis of individual differences in learning in a highly suitable model organism.


title: Computational structural genomics unravels common folds and predicted functions in the secretome of fungal phytopathogen Magnaporthe oryzae

abstract: Magnaporthe oryzae relies on a diverse collection of secreted effector proteins to reprogram the host metabolic and immune responses for the pathogens benefit. Characterization of the effectors is thus critical for understanding the biology and host infection mechanisms of this phytopathogen. In rapid, divergent effector evolution, structural information has the potential to illuminate the unknown aspects of effectors that sequence analyses alone cannot reveal. It has recently become feasible to reliably predict the protein structures without depending on homologous templates. In this study, we tested structure modeling on 1854 secreted proteins from M. oryzae and evaluated success and obstacles involved in effector structure prediction. With sensitive homology search and structure-based clustering, we defined both distantly related homologous groups and structurally related analogous groups. With this dataset, we propose sequence-unrelated, structurally similar effectors are a common theme in M. oryzae and possibly in other phytopathogens. We incorporated the predicted models for structure-based annotations, molecular docking and evolutionary analyses to demonstrate how the predicted structures can deepen our understanding of effector biology. We also provide new experimentally testable structure-derived hypotheses of effector functions. Collectively, we propose that computational structural genomic approaches can now be an integral part of studying effector biology and provide valuable resources that were inaccessible before the advent of reliable, machine learning-based structure prediction.


title: HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells

abstract: Human immunodeficiency virus type 1 (HIV-1) replicates in CD4+ T cells leading to profound T cell loss, immunological dysfunction and AIDS. Determining how HIV-1 shapes the immunological niche in which it resides to create a permissive environment is central to informing efforts to limit pathogenesis, disturb viral reservoirs and achieve a cure. A key roadblock in understanding HIV-T cell interactions is the requirement to activate CD4+ T cells in vitro in order to make them permissive to infection. This dramatically alters T cell biology, obscuring native virus-host interactions. Here we show that HIV-1 cell-to-cell spread permits efficient and productive infection of resting CD4+ T cells without the need for prior activation. Infection is preferential for resting memory T cells, is observed with both CXCR4-tropic virus and CCR5-tropic transmitter-founder viruses and results in virus production and onward spreading infection. Strikingly, we find that HIV-1 infection of resting memory CD4+ T cells primes for induction of a tissue-resident memory (TRM)-like phenotype evidenced by upregulation of TRM markers CD69/CXCR6 alongside co-expression of CD49a, PD-1, CD101 as well as transcription factor Blimp-1. Furthermore, we reveal that HIV-1 initiates a transcriptional program that overlaps with the core TRM transcriptional signature. This reprograming depends on the HIV-1 accessory protein Vpr. We propose that HIV-1 infection drives a CD4+ TRM-phenotype potentially sequestering infected cells within tissues to support viral replication and persistence.


title: Design of a novel DNA Gyrase B inhibitor with a rhodanine scaffold: in silico and in vitro approaches

abstract: Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin intermediate-resistant Staphylococcus aureus (VRSA) is one among the WHO high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The de novo ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic in silico screening process, the hit molecules were screened for their synthetic accessibility, drug likeliness and pharmacokinetics properties in addition to its target specific interactions. Of the total 374 hit molecules obtained through de novo ligand design, qsl-304 emerged as the most promising ligand. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the in vitro activity was proven, with an IC50 of 31.23 g/mL against the novobiocin resistant clinical isolate of Staphylococcus aureus sa-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance.


title: The CovR regulatory network drives the evolution of Group B Streptococcus virulence

abstract: Virulence of the neonatal pathogen Group B Streptococcus depends on the master regulator CovR. Inactivation of CovR leads to large-scale transcriptome remodeling and impairs almost every step of the interaction between the pathogen and the host. However, comparative analyses suggested a plasticity of the CovR signalling pathway in clinical isolates, probably due to the host selective pressure and leading to phenotypic heterogeneity in the bacterial population. Here, we characterize the CovR regulatory network in a strain representative of the hypervirulent lineage responsible of the majority of late-onset meningitidis. Genome-wide binding and transcriptome analysis demonstrated that CovR acts as a direct and global repressor of virulence genes, either as a primary regulator or with specialized co-regulators. Remarkably, CovR directly regulates genes of the pan-genome, including the two specific hypervirulent adhesins and horizontally acquired genes, as well as core-genes showing mutational biases in the population. Parallel analysis of the CovR network in a second isolate links strain-specificities to micro-evolutions in CovR-regulated promoters and to broad difference due to variability in CovR activation by phosphorylation. Our results highlight the direct, coordinated, and strain-specific regulation of virulence genes by CovR. This intra-species evolution of the signalling network reshapes bacterial-host interactions, increasing the potential for adaptation and the emergence of clone associated with specific diseases.


title: Shifts in marine invertebrate bacterial assemblages associated with tissue necrosis during a heatwave

abstract: Marine heatwaves (MHWs) are periods of extremely high seawater temperature that affect marine ecosystems in several ways. Anthozoans (corals and gorgonians) and Porifera (sponges) are usually among the taxa most affected by MHWs. Both are holobiont entities that form complex interactions with a wide range of microbes, which are an essential part of these organisms and play key roles in their health status. Here, we determine microbial community changes suffered in two corals (Cladocora caespitosa and Oculina patagonica), one gorgonian (Leptogorgia sarmentosa), and one sponge (Sarcotragus fasciculatus) during the 2015 MHW. The microbial communities were different among hosts and displayed shifts related to host health status, with a higher abundance in necrosed tissues of Ruegeria species or of potential pathogens like Vibrio. We also carry out a meta-analysis using 93 publicly accessible 16S rRNA gene libraries from O. patagonica, C. caespitosa and L. sarmentosa to establish a Mediterranean core microbiome in these species. We have identified one Ruegeria OTU that maintained a stable and consistent association with these species, which was also related with tissue necrosis in their hosts. Therefore, Ruegeria sp. could play an important and still underexplored role in the health status of its hosts.


title: Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset

abstract: Functional and lasting immune responses to the novel coronavirus (SARS-CoV-2) are currently under intense investigation as antibody titers in plasma have been shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we sought to determine the presence of SARS-CoV-2-specific memory B cells in COVID-19 convalescent patients. In this study, we report on the evolution of the overall humoral immune responses on 101 blood samples obtained from 32 COVID-19 convalescent patients between 16 and 233 days post-symptom onset. Our observations indicate that anti-Spike and anti-RBD IgM in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity in convalescent plasma declines rapidly compared to Fc-effector functions. Concomitantly, the frequencies of RBD-specific IgM+ B cells wane significantly when compared to RBD-specific IgG+ B cells, which increase over time, and the number of IgG+ memory B cells which remain stable thereafter for up to 8 months after symptoms onset. With the recent approval of highly effective vaccines for COVID-19, data on the persistence of immune responses are of central importance. Even though overall circulating SARS-CoV-2 Spike-specific antibodies contract over time during convalescence, we demonstrate that RBD-specific B cells increase and persist up to 8 months post symptom onset. We also observe modest increases in RBD-specific IgG+ memory B cells and importantly, detectable IgG and sustained Fc-effector activity in plasma over the 8-month period. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for the prevention of secondary infections, vaccine efficacy and herd immunity against COVID-19.


title: TRPM7 is critical for short-term synaptic depression by regulating synaptic vesicle endocytosis

abstract: TRPM7 contributes to a variety of physiological and pathological processes in many tissues and cells. With a widespread distribution in the nervous system, TRPM7 is involved in animal behaviors and neuronal death induced by ischemia. However, the physiological role of TRPM7 in CNS neuron remains unclear. Here, we identify endocytic defects in neuroendocrine cells and neurons from TRPM7 knockout (KO) mice, indicating a role of TRPM7 in synaptic vesicle endocytosis. Our experiments further pinpoint the importance of TRPM7 as an ion channel in synaptic vesicle endocytosis. Ca2+ imaging detects a defect in presynaptic Ca2+ dynamics in TRPM7 KO neuron, suggesting an importance of Ca2+ influx via TRPM7 in synaptic vesicle endocytosis. Moreover, the short-term depression is enhanced in both excitatory and inhibitory synaptic transmission from TRPM7 KO mice. Taking together, our data suggests that Ca2+ influx via TRPM7 may be critical for short-term plasticity of synaptic strength by regulating synaptic vesicle endocytosis in neurons.


title: Proteins observed in scalp hair from preschool children

abstract:
Early childhood experiences have long-lasting effects on subsequent mental and physical health, education, and employment. Measurement of these effects relies on insensitive behavioral signs, subjective assessments by adult observers, neuroimaging and neurophysiological studies, or remote epidemiologic outcomes. Despite intensive search, no biomarkers for developmental changes in the brain have been identified. We analyzed scalp hair from healthy children and their mothers using an unbiased proteomics platform to reveal 1368 hair proteins commonly observed in children, 1438 proteins commonly observed in mothers, and 1288 proteins observed sporadically in individual subjects. Mothers showed higher numbers of peptide spectral matches and hair proteins compared to children, with important age-related differences between mothers and children. Age-related differences were also observed in children, with differential protein expression patterns between younger (2 years and below) and older children (3-5 years). Boolean analyses showed greater conservation of hair protein patterns between mothers and their biological children as compared to mothers and unrelated children. The top 5% proteins driving population variability represent biological pathways associated with brain development, immune signaling, and stress response regulation. Non-structural proteins observed in scalp hair may include promising biomarkers to investigate the developmental changes associated with early childhood experiences.

One Sentence SummaryThe non-structural proteins observed in scalp hair from preschool children show evidence for heritability, reflect biological functions such as brain development, or immune function and regulation of stress responses, and exhibit age- and sex-related differences across periods of early childhood development.


title: DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as Alk target in the Drosophila visceral mesoderm.

abstract: Development of the midgut visceral muscle of Drosophila crucially depends on Anaplastic Lymphoma Kinase (Alk) receptor tyrosine kinase (RTK) signalling, which is needed to specify founder cells (FCs) in the circular visceral mesoderm (VM). While activation of the Alk receptor by its ligand Jelly Belly (Jeb) is well characterized, only a small number of target molecules have been identified. Here, we assayed RNA polymerase II (Pol II) occupancy in VM cells by using the targeted DamID (TaDa) approach. To identify Alk targets we employed comparative analysis of embryos overexpressing Jeb versus embryos with abrogated Alk activity, revealing differential expression of a number of genes, including the Snail/Scratch family transcription factor Kahuli (Kah). Upon further in vivo validation, we confirmed that Alk signalling regulates Kah mRNA expression in the VM. We show that Kah mutants display defects in the formation of midgut constrictions, similar to that of pointed (pnt) mutants. Analysis of publicly available ChIP data defined a Kah target-binding site similar to that of Snail. In addition, we compared genes that were differentially expressed in Kah mutants with publicly available Kah- and Pnt-ChIP datasets identifying a set of common target genes putatively regulated by Kah and Pnt in midgut constriction. Taken together, we (i) report a rich dataset of Alk responsive loci in the embryonic VM, (ii) provide the first functional characterization of the Kah transcription factor, identifying a role in embryonic midgut constriction, and (iii) suggest a model in which Kah and Pnt cooperate in embryonic midgut morphogenesis.


title: Dynamics of sex-biased gene expression over development in the stick insect Timema californicum

abstract: AO_SCPLOWBSTRACTC_SCPLOWSexually dimorphic phenotypes are thought to arise primarily from sex-biased gene expression during development. Major changes in developmental strategies, such as the shift from hemimetabolous to holometabolous development, are therefore expected to have profound consequences for the dynamics of sex-biased gene expression. However, no studies have previously examined sex-biased gene expression during development in hemimetabolous insects, precluding comparisons between developmental strategies. Here we characterized sex-biased gene expression at three developmental stages in a hemimetabolous stick insect (Timema californicum): hatchlings, juveniles, and adults. As expected, the proportion of sex-biased genes gradually increased during development, mirroring the gradual increase of phenotypic sexual dimorphism. Sex-biased genes identified at early developmental stages were generally consistently male- or female-biased at later stages, suggesting their importance in sexual differentiation. Additionally, we compared the dynamics of sex-biased gene expression during development in T. californicum to those of the holometabolous fly Drosophila melanogaster by reanalyzing publicly available RNA-seq data from third instar larval, pupal and adult stages. In D. melanogaster, 84% of genes were sex-biased at the adult stage (compared to only 20% in T. californicum), and sex-biased gene expression increased abruptly at the adult stage when morphological sexual dimorphism is manifested. Our findings are consistent with the prediction that the dynamics of sex-biased gene expression during development differ extensively between holometabolous and hemimetabolous insect species.


title: Elucidation of an anaerobic pathway for metabolism of L-carnitine-derived γ-butyrobetaine to trimethylamine in human gut bacteria

abstract:
Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient L-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent L-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the L-carnitine-derived metabolite {gamma}-butyrobetaine ({gamma}bb) by the human gut bacterium Emergencia timonensis. We identify a set of genes upregulated by {gamma}bb and demonstrate that the enzymes encoded by the induced {gamma}bb utilization (bbu) gene cluster convert {gamma}bb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a flavin cofactor to catalyze a redox neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic {gamma}bb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from L-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of L-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.

SIGNIFICANCETrimethylamine (TMA) is a disease-associated metabolite produced in the human body exclusively by microbes. Gut microbes generate TMA from essential nutrients consumed in the human diet, including L-carnitine. However, our understanding of the biochemical mechanisms involved in these transformations is incomplete. In this work, we define the biochemical pathway and genetic components in gut bacteria required for anaerobic production of TMA from {gamma}-butyrobetaine, a metabolite derived from L-carnitine. This discovery identifies a new type of TMA-producing enzyme and fills a critical gap in our knowledge of L-carnitine metabolism to TMA in the anaerobic environment of the human gut. This knowledge will enable evaluation of the link between L-carnitine metabolism and human disease, and the design of potential therapeutics.

category: biochemistry


title: SARS-CoV-2 receptor binding mutations and antibody mediated immunity.

abstract: SARS-CoV-2 mutations can impact infectivity, viral load, and overall morbidity/mortality during infection. In this analysis, we look at the mutational landscape of the SARS-CoV-2 receptor binding domain, a structure that is antigenic and allows for viral binding to the host. We analyze 104193 GISAID sequences acquired on October 15th, 2020 with a majority of sequences (96%) containing point mutations. We report high frequency mutations with improved binding affinity to ACE2 including S477N, N439K, V367F, and N501Y and address the potential impact of RBD mutations on antibody binding. The high frequency S477N mutation is present in 6.7% of all SARS-CoV-2 sequences, co-occurs with D614G, and is currently present in 14 countries. To address RBD-antibody interactions we take a subset of human derived antibodies and define their interacting residues using PDBsum. Our analysis shows that adaptive immunity against SARS-CoV-2 enlists broad coverage of the RBD suggesting that antibody mediated immunity should be sufficient to resolve infection in the presence of RBD point mutations that conserve structure.


title: Evaluation of Drug/Ligand Binding Constants for Human Serum Albumin Using Differential Scanning Calorimetry

abstract: This paper reports utilization of differential scanning calorimetry measurements to evaluate binding constants for Human Serum Albumin of 28 different drug ligands. Protein/ligand mixtures were prepared at various ligand concentrations and subjected to thermal denaturation analysis by calorimetry. From the measurements, the melting temperature, Tm, and free-energy{Delta} Gcal(37{degrees}C) for melting ligand-bound Albumin were evaluated as a function of ligand concentration. Concentration dependent behaviors of{Delta} Gcal(37{degrees}C) and Tm derived from protein/ligand mixtures were used to construct dose-response curves. Model fits of dose-response curves yielded quantitative evaluation of the ligand binding constant, KD, and semi-quantitative estimates of the binding stoichiometry, n. Many of the ligands had known binding affinity for Albumin with binding constants reported in the literature. Evaluated Albumin binding parameters for the ligands impressively agreed with reported literature values determined using other standard experimental methods. These results demonstrated utility of our calorimetry-based process for applications in pre-clinical drug screening.

category: biophysics


title: Tumor Microenvironment Alters Chemoresistance of Hepatocellular Carcinoma Through CYP3A4 Metabolic Activity

abstract: Variations in tumor biology from patient to patient combined with the low overall survival rate of hepatocellular carcinoma (HCC) present significant clinical challenges. During the progression of chronic liver diseases from inflammation to the development of HCC, microenvironmental properties, including tissue stiffness and oxygen concentration, change over time. This can potentially impact drug metabolism and subsequent therapy response to commonly utilized therapeutics, such as doxorubicin, multi-kinase inhibitors (e.g., sorafenib), and other drugs, including immunotherapies. In this study, we utilized four common HCC cell lines embedded in 3D collagen type-I gels of varying stiffnesses to mimic normal and cirrhotic livers with environmental oxygen regulation to quantify the impact of these microenvironmental factors on HCC chemoresistance. In general, we found that HCC cells with higher baseline levels of cytochrome p450-3A4 (CYP3A4) enzyme expression, HepG2 and C3Asub28, exhibited a cirrhosis-dependent increase in doxorubicin chemoresistance. Under the same conditions, HCC cell lines with lower CYP3A4 expression, HuH-7 and Hep3B2, showed a decrease in doxorubicin chemoresistance in response to an increase in microenvironmental stiffness. This differential therapeutic response was correlated with the regulation of CYP3A4 expression levels under the influence of stiffness and oxygen variation. In all tested HCC cell lines, the addition of sorafenib lowered the required doxorubicin dose to induce significant levels of cell death, demonstrating its potential to help reduce systemic doxorubicin toxicity when used in combination. These results suggest that patient-specific tumor microenvironmental factors, including tissue stiffness, hypoxia, and CYP3A4 activity levels, may need to be considered for more effective use of chemotherapeutics in HCC patients.


title: Induction of peri-implantation stage synthetic embryos using reprogramming paradigms in ESCs

abstract: Blastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that synthetic embryo-like structures are generated solely based on transcription factor-mediated molecular reprogramming of embryonic stem cells in a simple 3D co-culture system. ESCs in these cultures self-organize into elongated, compartmentalized synthetic embryo-like structures over the course of reprogramming exhibiting anterior visceral endoderm formation and symmetry breaking. Single-cell RNA-Seq reveals transcriptional profiles resembling epiblast, visceral endoderm, and extraembryonic ectoderm of early murine embryos around E4.5-E5.5. Within the epiblast, compartment marker gene expression supports primordial germ cell specification. After transplantation, synthetic embryo-like structures implant in uteri and initiate the formation of decidual tissues. This system allows for fast and reproducible generation of synthetic embryo-like structures, providing further insights into synthetic embryology.

category: synthetic biology


title: Evaluation of deep convolutional neural networks for in situ hybridization gene expression image representation

abstract: High resolution in situ hybridization (ISH) images of the brain capture spatial gene expression at cellular resolution. These spatial profiles are key to understanding brain organization at the molecular level. Previously, manual qualitative scoring and informatics pipelines have been applied to ISH images to determine expression intensity and pattern. To better capture the complex patterns of gene expression in the human cerebral cortex, we applied a machine learning approach. We propose gene re-identification as a contrastive learning task to compute representations of ISH images. We train our model on a ISH dataset of ~1,000 genes obtained from postmortem samples from 42 individuals. This model reaches a gene re-identification rate of 38.3%, a 13x improvement over random chance. We find that the learned embeddings predict expression intensity and pattern. To test generalization, we generated embeddings in a second dataset that assayed the expression of 78 genes in 53 individuals. In this set of images, 60.2% of genes are re-identified, suggesting the model is robust. Importantly, this dataset assayed expression in individuals diagnosed with schizophrenia. Gene and donor-specific embeddings from the model predict schizophrenia diagnosis at levels similar to that reached with demographic information. Mutations in the most discriminative gene, SCN4B, may help understand cardiovascular associations with schizophrenia and its treatment. We have publicly released our source code, embeddings, and models to spur further application to spatial transcriptomics. In summary, we propose and evaluate gene re-identification as a machine learning task to represent ISH gene expression images.


title: Sexual dimorphism in outcomes of non-muscle invasive bladder cancer: a role of CD163+ M2 macrophages, B cells and PD-L1 immune checkpoint.

abstract: Non-muscle invasive bladder cancer (NMIBC) is significantly more common in men than women. However, female patients with NMIBC often present with more aggressive disease and do not respond as well to immunotherapy treatments. We hypothesized that sexual dimorphism in the tumor immune microenvironment (TIME) may contribute to the inferior clinical outcomes observed in female patients. To test this hypothesis, we interrogated the expression patterns of genes associated with specific immune cell types and immune regulatory pathways using tumor whole transcriptome profiles from male (n=357) and female (n=103) patients with NMIBC. High-grade tumors from female patients exhibited significantly increased expression of CD40, CTLA4, PDCD1, LAG3 and ICOS immune checkpoint genes. Based on the significant differences in expression profiles of these genes and the cell types that most commonly express these in the TIME, we evaluated the density and spatial distribution of CD8+Ki67+ (activated cytotoxic T cells), FoxP3+ (regulatory T cells), CD103+ (tissue resident T cells), CD163+ (M2-like tumor associated macrophages), CD79a+ (B cells), PD-L1+ (Programmed-Death Ligand-1) and PD-1+ cells using multiplexed immunofluorescence in an independent cohort of 332 patient tumors on a tissue microarray (n=259 males and n=73 females). Tumors from female patients showed significantly higher infiltration of CD163+ macrophages and PD-L1+ cells compared to tumors from male patients. Notably, increased infiltration of CD163+ macrophages and CD79a+ B cells independently associated with decreased recurrence free survival. Not only do these results have the potential to inform the rational utilization of immunomodulatory therapies based on the TIME of both male and female patients with NMIBC, these novel findings highlight the necessity of considering sexual dimorphism in the design of future immunotherapy trials.


title: The quorum sensing system NprR-NprRB contributes to spreading and fitness in colony biofilms of Bacillus thuringiensis.

abstract: Quorum sensing (QS) are intercellular communication mechanisms to coordinate bacterial gene expression in response to signaling molecules. In Bacillus thuringiensis the QS system NprR-NprRB (receptor protein-signaling peptide) regulates the expression of genes related to nutrient scavenging during necrotrophism and also modulates sporulation onset. However, the relevance of QS in free-living stages of B. thuringiensis is less known. In this work, we depict the contribution of this QS system to spreading in colony biofilms. Through a spreading assay in spotted colonies of B. thuringiensis Bt8741 Wt and derived mutants, we find that the spreading phenotype depends on the NprR regulator and on the extracellular signaling NprRB peptide. We also show that this phenotype is associated to an increased fitness of the bacterium in these experimental conditions. Exogenous addition of a lipopeptide surfactant was sufficient to recover spreading in the {Delta}nprR-nprRB mutant, indicating that the phenotype could be mediated by the lipopeptide kurstakin. Finally, we suggest that the spreading is relevant in nature, since it occurs in the sole presence of soil nutrients, and it is conserved in several species of Bacillus commonly found in soil. This novel function of NprR-NprRB highlights the relevance of this QS system on the evolution and on the free-lifestyle ecology of B. thuringiensis.


title: A Catalog of the Diversity and Ubiquity of Metabolic Organelles in Bacteria

abstract: Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways, which are incompatible with surrounding metabolism. In contrast to their eukaryotic counterparts, the selectively permeable membrane of BMCs, the shell, is composed of protein. While the sequestered enzymes vary among functionally distinct BMCs, the proteins that form diverse BMC shells are structurally homologous; this enables the bioinformatic identification of the organelles by locating genes encoding shell proteins, which are typically proximal to those for the encapsulated enzymes. With recent advances in genome-resolved metagenomics and the emphasis on "microbial dark matter", many new genome sequences from diverse and obscure bacterial clades have become available. We find the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014. Moreover, the addition of new types we uncovered doubles the number of distinct BMC types known. These expand the range of catalysis encapsulated in BMCs, underscoring that there is dark biochemistry that is compartmentalized in bacterial organelles yet to be discovered through genome sequencing. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, and experimental characterization, and broadens the foundation for the development of BMC-based nanoarchitectures for biomedical and bioengineering applications.


title: Mycorrhizal dominance reduces forest-tree species diversity

abstract: Ectomycorrhizas and arbuscular mycorrhizas, the two most widespread plant-fungal symbioses, are thought to differentially influence tree species diversity, with positive plant-soil feedbacks favoring locally abundant ectomycorrhizal tree species and negative feedbacks promoting species coexistence and diversity in arbuscular mycorrhizal forests. While seedling recruitment studies and cross-biome patterns of plant diversity and mycorrhizal dominance support this hypothesis, it remains to be tested at the forest stand level over continental scales. Here, we analyze [~]85,000 forest plots across the United States to show that both ectomycorrhizal-dominated and arbuscular mycorrhizal-dominated forests show relatively low tree diversity, while forests with a mixture of mycorrhizal strategies support a higher number of tree species. Our findings suggest that mycorrhizal dominance, rather than mycorrhizal type, shapes tree diversity in forests.

category: ecology


title: An Alternative, Cas12a-based CRISPR Interference System for Mycobacteria

abstract: The introduction of CRISPR interference (CRISPRi) has made gene repression in mycobacteria much more efficient, but technical challenges of the prototypical Cas9-based platform, for example in multigene regulation, remain. Here, we introduce an alternative CRSPRi platform that uses the minimal Cas12a enzyme in combination with synthetic CRISPR arrays. This system is simple, tunable, and can regulate multiple genes simultaneously, providing a new tool to probe higher-order genetic interactions in mycobacteria including Mycobacterium tuberculosis (Mtb).

category: genetics


title: CONTROLLING COCKROACH POPULATIONS IN HUMAN AND ANIMAL HABITATIONS BY REDUCING FOOD AVAILABILITY

abstract:
BackgroundCockroaches, carriers of pathogenic organisms that cause human and animal disease, typically have access to human or pet food in bowls, allowing cockroaches to expand their colonies and infestations.

HypothesisWe hypothesized that existing anti-ant technology could be converted to anti-cockroach technology by simple design changes.

MethodsA base of various heights was affixed to the bottom of an anti-ant bowl to increase the distance of the anti-ant shield from the native height "x" to the hypothesized cockroach-resistant height "z". The effects of z =0, 12.7, 15.9, 19.1, 25.4, 44.5, and 57.2 mm were studied. 118.3 cc (4 oz) of dry cat food was used as cockroach bait. The modified anti-ant bowls were placed in a high-intensity cockroach environment during summer nights where the temperatures varied between 23.9-29.4 degrees Celsius for 3 hours and then cockroach counts were performed. Ten runs at each height z were performed.

ResultsMean numbers of infesting cockroaches {+/-} SD at each height z were 21.3{+/-}2.9 at 0 mm, 22.0{+/-}2.9 at 12.7 mm, 11.2{+/-}2.6 at 15.9 mm, 0.9{+/-}0.8 at 19.1mm, 0.4{+/-}0.5 at 25.4 mm, 0{+/-}0 at 44.5 mm, and 0{+/-}0 at 57.2 mm (p<0.001 with z[≥]15.9 mm for all). Cockroach numbers began declining when z = 15.9 mm and declined to only large cockroaches at z = 25.4 mm. The cockroaches that were able to overcome the z =25.4 mm were the larger American cockroaches that can exceed 76.2 mm (3 inch) in length. However, at z = 44.5 mm and 57.2 mm no cockroaches penetrated the modified bowl.

ConclusionsTo defeat the majority of species of cockroaches the anti-insect shield should be at a height of at least 25.4 mm and to defeat the larger American cockroaches preferably greater than 25.4 mm with 44.5 mm and 57.2 mm defeating all tested cockroaches

category: animal behavior and cognition


title: Cellular crowd control: overriding endogenous cell coordination makes cell migration more susceptible to external programming

abstract: As collective cell migration is essential in biological processes spanning development, healing, and cancer progression, methods to externally program cell migration are of great value. However, problems can arise if the external commands compete with strong, pre-existing collective behaviors in the tissue or system. We investigate this problem by applying a potent external migratory cue--electrical stimulation and electrotaxis--to primary mouse skin monolayers where we can tune cell-cell adhesion strength to modulate endogenous collectivity. Monolayers with high cell-cell adhesion showed strong natural coordination and resisted electrotactic control, with this conflict actively damaging the leading edge of the tissue. However, reducing pre-existing coordination in the tissue by specifically inhibiting E-cadherin-dependent cell-cell adhesion, either by disrupting the formation of cell-cell junctions with E-cadherin specific antibodies or rapidly dismantling E-cadherin junctions with calcium chelators, significantly improved controllability. Finally, we applied this paradigm of weakening existing coordination to improve control to demonstrate accelerated wound closure in vitro. These results are in keeping with those from diverse, non-cellular systems, and confirm that endogenous collectivity should be considered as a key, quantitative design variable when optimizing external control of collective migration.

category: bioengineering


title: Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model

abstract: Protein-protein interaction (PPI) networks have proven to be a valuable tool in systems biology to facilitate the discovery and understanding of protein function. Unfortunately, experimental PPI data remains sparse in most model organisms and even more so in other species. Existing methods for computational prediction of PPIs seek to address this limitation, and while they perform well when sufficient within-species training data is available, they generalize poorly to new species or often require specific types and sizes of training data that may not be available in the species of interest. We therefore present D-SCRIPT, a deep learning method for predicting a physical interaction between two proteins given just their sequences. Compared to existing methods, D-SCRIPT generalizes better to new species and is robust to limitations in training data size. Our approach encodes the intuition that for two proteins to physically interact, a subset of amino acids from each protein should be in contact with the other. The intermediate stages of D-SCRIPT directly implement this intuition; the penultimate stage in D-SCRIPT is a rough estimate of the inter-protein contact map of the protein dimer. This structurally-motivated design enables interpretability of our model and, since structure is more conserved evolutionarily than sequence, improves generalizability across species. We show that a D-SCRIPT model trained on 38,345 human PPIs enables significantly improved functional characterization of fly proteins compared to the state-of-the-art approach. Evaluating the same D-SCRIPT model on protein complexes with known 3-D structure, we find that the inter-protein contact map output by D-SCRIPT has significant overlap with the ground truth. Our work suggests that recent advances in deep learning language modeling of protein structure can be leveraged for protein interaction prediction from sequence. D-SCRIPT is available at http://dscript.csail.mit.edu.


title: FILER: large-scale, harmonized FunctIonaL gEnomics Repository

abstract:
MotivationQuerying massive collections of functional genomic and annotation data, linking and summarizing the query results across data sources and data types are important steps in high-throughput genomic and genetic analytical workflows. However, accomplishing these steps is difficult because of the heterogeneity and breadth of data sources, experimental assays, biological conditions (e.g., tissues, cell types), data types, and file formats.

ResultsFunctIonaL gEnomics Repository (FILER) is a large-scale, harmonized functional genomics data catalog uniquely providing: 1) streamlined access to >50,000 harmonized, annotated functional genomic and annotation datasets across >20 integrated data sources, >1,100 biological conditions/tissues/cell types, and >20 experimental assays; 2) a scalable, indexing-based genomic querying interface; 3) ability for users to analyze and annotate their own experimental data against reference datasets. This rich resource spans >17 Billion genomic records for both GRCh37/hg19 and GRCh38/hg38 genome builds. FILER scales well with the experimental (query) data size and the number of reference datasets and data sources. When evaluated on large-scale analysis tasks, FILER demonstrated great efficiency as the observed running time for querying 1000x more genomic intervals (106 vs. 103) against all 7x109 hg19 FILER records increased sub-linearly by only a factor of 15x. Together, these features facilitate reproducible research and streamline querying, integrating, and utilizing large-scale functional genomics and annotation data.

Availability and implementationFILER can be 1) freely accessed at https://lisanwanglab.org/FILER, 2) deployed on cloud or local servers (https://bitbucket.org/wanglab-upenn/FILER), and 3) integrated with other pipelines using provided scripts.

Contactlswang@pennmedicine.upenn.edu


title: Molecular Dynamics Simulations of Phytopthora sojae Avirulence Factor 5, PsAvh5, Define Membrane Binding and Inositolphosphate-3'-phosphate Interactions and Protein Mechanics

abstract: Phytopthora Avirulence proteins are a primary target for development of rational chemical and biological control of some of the most devastating plant pathogens. Despite the sequencing of entire genomes, and characterization of many of these proteins at the chemical level, many questions remain regarding actual chemical and biological interactions involved. In addition, disputed roles of ligands, such as Inositolphosphate-3-phosphate and amino acids of important function remain unclear. To address some of these issues, we developed molecular models from structural elements and published data for Phytopthora sojae avirulence protein 5. Molecular dynamics simulations are used to study protein function, interactions involved primarily with lipids and membranes, and inositol derivatives. Our findings indicate that the protein is stable as a monomer, and in a dimeric form. Also, that these proteins interact with Inositolphosphate-3phosphate as a necessary membrane element, in binding. We identified several amino acids of importance, additional to defining the mechanical features of the protein within the binding process to different membranes. A high affinity, comparable to other membrane surface binding molecules of -219.54 Kcal for the dimer, and -176.61 for the monomer were determined. With either form, we found the inositolphosphate-3-phosphate to be essential in the membrane binding process. Our findings answer some of the debated questions while creating a point to further test avirulence proteins in general for functional aspects. Additionally, the structures and data can be utilized to provide a better starting point for rational design approaches to control this pathogen.


title: Molecular Dynamics Simulations of Phytopthora sojae Avirulence Factor 5, PsAvh5, Define Membrane Binding, Inositolphosphate-3'-phosphate Interactions and Protein Mechanics


title: Identifying the Link Between Chemical Exposures and Breast Cancer in African American Women via ToxCast High Throughput Screening Data

abstract: Among women, breast cancer is the most prevalent form of cancer worldwide and has the second highest mortality rate of any cancer in the United States. The breast cancer related death rate is 40% higher in African American women compared to European American women. The incidence of triple negative breast cancer (TNBC), an aggressive subtype of breast cancer for which there is no targeted therapy, is approximately three times higher in non-Hispanic Black women (NHBW) compared to non-Hispanic White women (NHWW). The drivers of these differences in breast cancer incidence and mortality are still poorly understood, and likely lie in an interaction between genetic and environmental factors. Here, we aimed to identify chemical exposures which may play a role in breast cancer disparities. Using chemical biomonitoring data from the National Health and Nutrition Examination Survey (NHANES) and biological activity data from the EPAs ToxCast program, we assessed the toxicological profiles of chemicals with higher biomarker concentrations in US NHBW. We conducted a literature search to identify a gene set of breast cancer targets included in ToxCast to analyze the response of prioritized chemicals in these assays. Forty-three chemical biomarkers are significantly higher in NHBW. Investigation of these chemicals in ToxCast resulted in a total of 32,683 assays for analysis, 5,172 of which contained nonzero values for the concentration at which the dose-response fitted model reaches the cutoff considered "active" and the scaled top value of dose response curve. Of these chemicals BPA, PFOS, and thiram are most comprehensively assayed. 2,5-dichlorophenol, 1,4-dichlorobenzene, and methyl and propyl parabens had higher biomarker concentrations in NHBW and moderate testing and activity in ToxCast. The distribution of active concentrations for these chemicals in ToxCast assays are comparable to biomarker concentrations in NHBW. Through this integrated analysis, we have identified that multiple chemicals, including thiram, propylparaben, and p,p DDE, with disproportionate exposures in NHBW, have breast cancer associated biological activity at human exposure relevant doses.

category: pharmacology and toxicology


title: Tapping into the aging brain: In vivo microdialysis reveals mirroring pathology between preclinical models and patients with Alzheimer's disease

abstract: Preclinical models of Alzheimers disease (AD) can provide valuable insights into the onset and progression of the disease, such as changes in concentrations of amyloid-{beta} (A{beta}) and tau in cerebrospinal fluid (CSF). However, such models are currently underutilized due to limited advancement in techniques that allow for longitudinal monitoring of CSF akin to methods employed in AD patients. An elegant way to understand the biochemical environment in the diseased brain is intracerebral microdialysis, a method that has until now been limited to short-term observations, or snapshots, of the brain microenvironment. Our novel push-pull microdialysis method in AD mice permits in vivo longitudinal monitoring of dynamic changes of A{beta} and tau in CSF and allows for better translational understanding of CSF biomarkers. Specifically, we demonstrate that CSF concentrations of A{beta} and tau along disease progression in transgenic mice mirror what is observed in patients, with a decrease in CSF A{beta} observed when plaques are deposited, and an increase in CSF tau once tau pathology is present in the brain. We found that a high molecular weight cut-off membrane allowed for simultaneous sampling of A{beta} and tau, comparable to lumbar puncture CSF collection in patients. We furthermore provide specific recommendations for optimal application of our novel microdialysis method, such as achieving optimal recovery of analytes, which depends heavily on the flow rate of perfusion, probe properties and perfusate composition. Our approach can further advance AD research by following evolving neuropathology along the disease cascade via consecutive sampling from the same animal, and can additionally be used to administer pharmaceutical compounds and assess their efficacy in treating AD.

category: neuroscience


title: Paradoxical stabilization of relative position in moving frames

abstract: To capture where things are and what they are doing, the visual system may extract the position and motion of each object relative to its surrounding frame of referencee.g., 1,2. Here we report a particularly powerful example where a paradoxical stabilization is produced by a moving frame. We first take a frame that moves left and right and we flash its right edge before, and its left edge after, the frames motion. For all frame displacements tested, the two edges are perceived as stabilized, with the left edge on the left and right edge on the right, separated by the frames width as if the frame were not moving. This illusory stabilization holds even when the frame travels farther than its width, reversing the actual spatial order of the two flashes. Despite this stabilization, the motion of the frame is still seen, albeit much reduced, and this hides the paradoxical standstill of relative positions. In a second experiment, two probes are flashed inside the frame at the same physical location before and after the frame moves. Despite being physically superimposed, the probes are perceived widely separated, again as if they were seen in the frames coordinates and the frame were stationary. This illusory separation is set by the distance of the frames travel, independently of its speed. This paradoxical stabilization suggests a link to visual constancy across eye movements where the displacement of the entire visual scene may act as a frame to stabilize the perception of relative locations.


title: Achieving natural behavior in a robot using neurally inspired hierarchical control

abstract: Terrestrial locomotion presents tremendous computational challenges on account of the enormous degrees of freedom in legged animals, and the complex and unpredictable properties of the natural environment and the effectors. Yet the nervous system can achieve locomotion with ease. Here we introduce a quadrupedal robot capable of goal-directed posture control and locomotion over rough terrain. The underlying control architecture is a hierarchical network of simple negative feedback control systems inspired by the organization of the vertebrate nervous system. Without using an internal model or feedforward planning, and without any training, our robot shows robust posture control and locomotor behavior in novel environments with unpredictable disturbances.