title: 3,3'-Diindolylmethane induces apoptosis and autophagy in fission yeast

abstract: 3,3-Diindolylmethane (DIM) is a compound derived from the digestion of indole-3-carbinol, found in the broccoli family. It induces apoptosis and autophagy in some types of human cancer. DIM extends lifespan in the fission yeast Schizosaccharomyces pombe. The mechanisms by which DIM induces apoptosis and autophagy in humans and expands lifespan in fission yeasts are not fully understood. Here, we show that DIM induces apoptosis and autophagy in log-phase cells, which is dose-dependent in fission yeast. A high concentration of DIM disrupted the nuclear envelope (NE) structure and induced chromosome condensation at an early time point. In contrast, a low concentration of DIM induced autophagy but did not disrupt NE structure. The mutant defective in autophagy was more sensitive to a low concentration of DIM, demonstrating that the autophagic pathway contributes to the survival of cells against DIM. Moreover, our results showed that the lem2 mutant is more sensitive to DIM. NE in the lem2 mutant was disrupted even at the low concentration of DIM. Our results demonstrate that the autophagic pathway and NE integrity are important to maintain viability in the presence of a low concentration of DIM. The mechanism of apoptosis and autophagy induction by DIM might be conserved in fission yeast and humans. Further studies will contribute to the understanding of the mechanism of apoptosis and autophagy by DIM in fission yeast and humans.

category: molecular biology


title: MotSASi: Functional Short Linear Motifs (SLiMs) prediction based on genomic single nucleotide variants and structural data

abstract:
Short linear motifs (SLiMs) are key to cell physiology mediating reversible protein-protein interactions. Precise identification of SLiMs remains a challenge, being the main drawback of most bioinformatic prediction tools their low specificity (high number of false positives). An important, usually overlooked, aspect is the relation between SLiMs mutations and disease. The presence of variants in each residue position can be used to assess the relevance of the corresponding residue(s) for protein function, and its (in)tolerance to change.

In the present work, we combined sequence variant information and structural analysis of the energetic impact of single amino acid substitution (SAS) in SLiM-Receptor complex structure, and showed that it significantly improves prediction of true functional SLiMs. Our strategy is based on building a SAS tolerance matrix that shows, for each position, whether one of the possible 19 SAS is tolerated or not. Herein we present the MotSASi strategy and analyze in detail 4 SLiMs involved in intracellular protein trafficking. Our results show that inclusion of variant and sequence information significantly improves both prediction of true SLiMs and rejection of false positives, while also allowing better classification of variants inside SLiMs, a results with a direct impact in clinical genomics.


title: Assessing spatial segregation of beluga whales (Delphinapterus leucas) in Western Hudson Bay estuaries

abstract: Segregation of older adult males from females and immature males is known to occur in some beluga whale populations, but it is unclear if adults accompanied by calves segregate in Hudson Bay, where the largest summering population is found. Using imagery from a photographic aerial survey conducted in August 2015, we considered a number of environmental variables that might explain distribution by age class of beluga near two of three main estuaries (Churchill and Seal River) used by Western Hudson Bay belugas in the summer season. Belugas were identified and classified by age manually using an identification decision tree and GPS coordinates were plotted in ArcGIS. Distribution by age class was examined in relation to distance to coastal habitat and bathymetry to test the predation risk hypothesis, sea surface temperature (thermal advantage hypothesis), and extent of river plume (forge-selection hypothesis). Habitat characteristics and the proportion of age classes in both estuaries were similar between age class groups (with and without calves) indicating no segregation and suggesting the environmental data assessed were not driving patterns of distribution and density of age classes at the spatial and temporal scale being investigated. Results provide a greater understanding of spatial patterns of beluga whale habitat use in western Hudson Bay and information useful in conservation and management advice.

category: ecology


title: Co-translational biogenesis of lipid droplet integral membrane proteins

abstract:
Membrane proteins destined for lipid droplets (LDs), a major intracellular storage site for neutral lipids, are inserted into the endoplasmic reticulum (ER) and then trafficked to LDs where they reside in a hairpin loop conformation. Here, we show that LD membrane proteins can be delivered to the ER either co- or post-translationally and that their membrane-embedded region specifies pathway selection. The co-translational route for LD membrane protein biogenesis is insensitive to a small molecule inhibitor of the Sec61 translocon, Ipomoeassin F, and instead relies on the ER membrane protein complex (EMC) for membrane insertion. Strikingly, this route can also result in a transient exposure of the short N-termini of LD membrane proteins to the ER lumen, followed by topological rearrangements that enable their transmembrane segment to form a hairpin loop and N-termini to face the cytosol. Our study reveals an unexpected complexity to LD membrane protein biogenesis and identifies a role for the EMC during their co-translational insertion into the ER.

SUMMARY STATEMENTInsertion of many lipid droplet membrane proteins into the endoplasmic reticulum (ER) is co-translational, mediated by the ER membrane protein complex (EMC) and involves topology reorientation.

category: biochemistry


title: Constructing a warhead of PROTAC with aptamer for tumor-selective degradation of nucleolin

abstract: PROteolysis TArgeting Chimeras (PROTACs) induce targeted protein degradation by hijacking the intracellular ubiquitin proteasome system, thus emerging as a new strategy for drug development. However, most PROTACs generated lack cell-type selectivity and have poorly soluble in water. To address this drawback, we developed a novel PROTAC ZL216 using aptamer AS1411 as a targeting ligand of nucleolin to conjugate with a small molecule ligand of E3 ligase VHL, which shows high aqueous solubility and serum stability. Based on the differential expression of nucleolin on the cell surface, ZL216 could bind to and internalize into breast cancer cells, but not normal breast cells. Furthermore, we revealed that ZL216 promoted the formation of a nucleolin-ZL216-VHL ternary complex in breast cancer cells and potently induced nucleolin degradation in vitro and in vivo. As a result, ZL216 inhibited the proliferation and migration of breast cancer cells. These studies demonstrate that in addition to peptides and small molecule compounds, nuclei acid aptamers can also be used to generate PROTACs, which broadens the toolbox constructing PROTACs and provides a promising strategy for development of tumor-selective PROTACs.


title: Development of a novel PROTAC using the nucleic acid aptamer as a targeting ligand for tumor-selective degradation of nucleolin


title: Development of a Novel PROTAC using the Nucleic Acid Aptamer as a Targeting Ligand for Tumor Selective Degradation of Nucleolin


title: Design of Transmembrane Mimetic Structural Probes to Trap Different Stages of γ-Secretase-Substrate Interaction

abstract: The transmembrane domain (TMD) of the amyloid precursor protein of Alzheimers disease is processively cut by {gamma}-secretase through endoproteolysis and tricarboxypeptidase "trimming". We recently developed a prototype substrate TMD mimetic for structural analysis--composed of a helical peptide inhibitor linked to a transition-state analog--that simultaneously engages a substrate exosite and the active site and is pre-organized to trap the carboxypeptidase transition state. Here we developed variants of this prototype designed to allow visualization of transition states for endoproteolysis, TMD helix unwinding, and lateral gating of substrate, identifying potent inhibitors for each class. These TMD mimetics exhibited non-competitive inhibition and occupy both exosite and active site as demonstrated by inhibitor cross competition experiments and photoaffinity probe binding assays. The new probes should be important structural tools for trapping different stages of substrate recognition and processing via ongoing cryo-electron microscopy with {gamma}-secretase, ultimately aiding rational drug design.


title: Effects of enhanced insect feeding on the faecal microbiota and transcriptome of a family of captive common marmosets (Callithrix jacchus)

abstract: Common marmosets have been widely used in biomedical research for years. Nutritional control is an important factor in managing their health, and insect intake would be beneficial for that purpose because common marmosets frequently feed on insects in natural habitats. Here, we examined the effect of enhanced insect feeding on the gut by analysing the faecal microbiota and transcripts of captive marmosets. A family consisting of six marmosets was divided into two groups. During the seven-day intervention period, one group (the insect feeding group, or Group IF) was fed one cricket and one giant mealworm per marmoset per day, while the other (the control group, or Group C) was not fed these insects. RNA was extracted from faecal samples to evaluate the ecology and transcripts of the microbiota, which were then compared among time points before (Pre), immediately after (Post), and two weeks after intervention (After) by total RNA sequencing. The gut microbiota of marmosets showed Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria as dominant phyla. Linear discriminant analysis showed differential characteristics of microbiota with and without insect feeding treatment. Further analysis of differentially expressed genes revealed increases and decreases in Bacteroidetes and Firmicutes, respectively, corresponding to the availability of insects under both Post and After conditions. Significant changes specific to insect feeding were also detected within the transcriptome, some of which were synchronized with the fluctuations in the microbiota, suggesting a functional correlation or interaction between the two. The rapid changes in the microbiota and transcripts may be deeply connected to the original microbiota community shaped by marmoset feeding ecology in the wild. The results were informative for identifying the physiological impact of insect feeding to produce a better food regimen and for detecting transcripts that are currently unidentifiable.

category: physiology


title: The road not taken: disconnection of a human-unique cortical pathway in schizophrenia and its effects on naturalistic social cognition

abstract:
BackgroundEfficient processing of complex and dynamic social scenes relies on intact connectivity of many underlying cortical areas and networks, but how connectivity deficits affect this functioning in social cognition remains unknown. Here we measure these relationships using functionally based localization of social cognition areas, resting-state functional connectivity, and movie-watching data.

MethodsIn 42 schizophrenia participants (SzP) and 41 healthy controls (HC), we measured the functional connectivity of areas localized by face-emotion processing, theory-of-mind, and attention tasks. We quantified the weighted shortest path length between visual and medial prefrontal theory-of-mind areas in both populations to assess the impact of functional connectivity deficits on network structure. We then correlated connectivity along the shortest path in each group with movie-evoked activity in a key node of the theory-of-mind network (TPJp).

ResultsSzP had pronounced connectivity deficits in temporoparietal junction/posterior superior temporal sulcus (TPJ-pSTS) areas involved in face-emotion processing (t(81)=4.4, p=0.00002). In HC the shortest path connecting visual and medial prefrontal theory-of-mind areas passed through TPJ-pSTS, whereas in SzP the shortest path passed through prefrontal cortex (PFC). While movie-evoked TPJp activity correlated with connectivity along the TPJ-pSTS pathway in both groups (r=0.43, p=0.002), it additionally correlated with connectivity along the PFC pathway only in SzP (rSzP=0.56, p=0.003).

ConclusionsConnectivity along the human-unique TPJ-pSTS pathway affects both the network architecture and functioning of areas involved in processing complex dynamic social scenes. These results demonstrate how focal deficits can have widespread impacts across cortex.

category: neuroscience


title: KIF2C regulates synaptic plasticity and cognition by mediating dynamic microtubule invasion of dendritic spines

abstract: Dynamic microtubules play a critical role in cell structure and function. In nervous system, microtubules specially extend into and out of synapses to regulate synaptic development and plasticity. However, the detailed polymerization especially the depolymerization mechanism that regulates dynamic microtubules in synapses is still unclear. In this study, we find that KIF2C, a dynamic microtubule depolymerization protein without known function in the nervous system, plays a vital role in the structural and functional plasticity of synapses and regulates cognitive function. Using RNAi knockdown and conditional knockout approaches, we showed that KIF2C regulates spine morphology and synaptic membrane expression of AMPA (-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid) receptors. Moreover, KIF2C deficiency leads to impaired excitatory transmission, long-term potentiation, and altered cognitive behaviors in mice. Mechanistically, KIF2C regulates microtubule dynamics and microtubule invasion of spines in neurons by its microtubule depolymerization capability in a neuronal activity-dependent manner. This study explores a novel function of KIF2C in the nervous system and provides an important regulatory mechanism on how microtubule invasion of spines regulates synaptic plasticity and cognition behaviors.


title: Brain Laterality Dynamics Support Human Cognition

abstract: Hemispheric lateralization constitutes a core architectural principle of human brain organization underlying cognition, often argued to represent a stable, trait-like feature. However, emerging evidence underlines the inherently dynamic nature of brain networks, in which time-resolved alterations in functional lateralization remain uncharted. Integrating dynamic network approaches with the concept of hemispheric laterality, we map the spatiotemporal architecture of whole-brain lateralization in a large sample of high-quality resting-state fMRI data (N=991, Human Connectome Project). We reveal distinct laterality dynamics across lower-order sensorimotor systems and higher-order associative networks. Specifically, we expose two aspects of the laterality dynamics: laterality fluctuations, defined as the standard deviation of laterality time series, and laterality reversal, referring to the number of zero-crossings in laterality time series. These two measures are associated with moderate and extreme changes in laterality over time, respectively. While laterality fluctuations depict positive association with language function and cognitive flexibility, laterality reversal shows a negative association with the same neurocognitive factors. These opposing interactions indicate a dynamic balance between intra- and inter-hemispheric communication, i.e., segregation and integration of information across hemispheres. Furthermore, in their time-resolved laterality index, the default-mode and language networks correlate negatively with visual/sensorimotor and attention networks, indicating flexible while parallel processing capabilities that are linked to better out-of-scanner cognitive performance. Finally, the laterality dynamics correlate with regional metabolism and structural connectivity and showed significant heritability. Our results provide insights into the adaptive nature of the lateralized brain and new perspectives for future studies of human cognition, genetics and brain disorders.


title: Distinct Roles of Dopamine D1 and D2 Receptor-expressing Neurons in the Nucleus Accumbens for a Strategy Dependent Decision Making

abstract: To optimize decision making, animals need to execute not only a strategy to choose a good option but sometimes also one to avoid a bad option. A psychological study indicates that positive and negative information is processed in a different manner in the brain. The nucleus accumbens (NAc) contains two different types of neurons, dopamine D1 and D2 receptor-expressing neurons which are implicated in reward-based decision making and aversive learning. However, little is known about the neural mechanisms by which D1 or D2 receptor-expressing neurons in the NAc contribute to the execution of the strategy to choose a good option or one to avoid a bad option under decision making. Here, we have developed two novel visual discrimination tasks for mice to assess the strategy to choose a good option and one to avoid a bad option. By chemogenetically suppressing the subpopulation of the NAc neurons, we have shown that dopamine D2 receptor-expressing neurons in the NAc selectively contribute to the strategy to avoid a bad option under reward-based decision making. Furthermore, our optogenetic and calcium imaging experiments indicate that dopamine D2 receptor-expressing neurons are activated by error choices and the activation following an error plays an important role in optimizing the strategy in the next trial. Our findings suggest that the activation of D2 receptor-expressing neurons by error choices through learning enables animals to execute the appropriate strategy.


title: The orphan drug dichloroacetate reduces amyloid beta-peptide production whilst promoting non-amyloidogenic proteolysis of the amyloid precursor protein

abstract: The amyloid cascade hypothesis proposes that excessive accumulation of amyloid beta-peptides is the initiating event in Alzheimers disease. These neurotoxic peptides are generated from the amyloid precursor protein via sequential cleavage by {beta}- and {gamma}-secretases in the  amyloidogenic proteolytic pathway. Alternatively, the amyloid precursor protein can be processed via the  non-amyloidogenic pathway which, through the action of the -secretase a disintegrin and metalloproteinase (ADAM) 10, both precludes amyloid beta-peptide formation and has the additional benefit of generating a neuroprotective soluble amyloid precursor protein fragment, sAPP. In the current study, we investigated whether the orphan drug, dichloroacetate, could alter amyloid precursor protein proteolysis. In SH-SY5Y neuroblastoma cells, dichloroacetate enhanced sAPP generation whilst inhibiting {beta}-secretase processing of endogenous amyloid precursor protein and the subsequent generation of amyloid beta-peptides. Over-expression of the amyloid precursor protein partly ablated the effect of dichloroacetate on amyloidogenic and non-amyloidogenic processing whilst over-expression of the {beta}-secretase only ablated the effect on amyloidogenic processing. Similar enhancement of ADAM-mediated amyloid precursor protein processing by dichloroacetate was observed in unrelated cell lines and the effect was not exclusive to the amyloid precursor protein as an ADAM substrate, as indicated by dichloroacetate-enhanced proteolysis of the Notch ligand, Jagged1. Despite altering proteolysis of the amyloid precursor protein, dichloroacetate did not significantly affect the expression of -, {beta}- or {gamma}-secretases. In conclusion, dichloroacetate can inhibit amyloidogenic and promote non-amyloidogenic proteolysis of the amyloid precursor protein. As the drug is already used for the treatment of lactic acidosis and is known to cross the blood-brain-barrier, it might represent a cheap and effective therapy for slowing the progression of Alzheimers disease.

category: cell biology


title: Pollen meta-barcoding reveals foraging preferences of honeybees (Apis mellifera L.) along space-time gradient in Japan

abstract: The availability of pollen in urban-rural landscapes is an essential factor that influences the population dynamics of insect pollinators. The amount and diversity of pollen play a pivotal role in the foraging ecology of pollinators for their growth and health, but investigations on the spatio-temporal patterns of foraged plants remain rare, especially in cities as neo-ecosystems. Here, we explored the temporal foraging habits of a highly polylectic pollinator (Apis mellifera L.) in a study area, including different landscape classes from rural to urban areas. Mixed-pollen in each month and each location (N = 17) were analysed using DNA meta-barcoding to identify plants visited by honeybees. The results showed that the landscape class (rural, suburban and urban areas) explains spatial variations in the plant composition foraged by honeybees, but not in taxa richness. Furthermore, pollen diversity and plant composition showed a strong seasonal dependence. Furthermore, a higher plant richness and foraged woody taxa was found to occur in spring, which was mainly dominated by the genera Prunus and Acer. In summer and autumn, the genera Trifolium and Plantago of the herbaceous stratum were the most visited plants. The Fabaceae, Rosaceae, Brassicaceae, Plantaginaceae, and Onagraceae plant families were the most frequently observed in all combined samples. The present study contributes to a broader understanding of the ecology and floral preferences of honeybees, on which urban planning can rely to promote biodiversity in cities.


title: The pink salmon genome: uncovering the genomic consequences of a strict two-year life-cycle

abstract: Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A strict two-year life-history of most pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of centromere drive or a combination or reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

category: genomics


title: Inhibitory effect of  an anti-prokineticin-1 antibody on liver metastasis in mice injected with human colorectal cancer cell lines

abstract: Controlling hematogenous metastases is an effective treatment strategy for colorectal cancer. Multidisciplinary treatment for colorectal cancer has made great strides, and molecularly-targeted drugs have greatly improved the prognosis of patients. However, currently accepted molecularly- targeted therapeutic agents require concomitant use with anticancer agents. Thus, new molecularly-targeted drugs need to be developed. The prokineticin family of angiogenic factors has the potential of becoming target molecules. Among them, prokineticin-1 (PROK1) is involved in the promotion of angiogenesis, tumor growth, and liver metastases in colorectal cancer. We manufactured our own anti-PROK1 antibody and verified its effect in inhibiting liver metastases and prolonging survival. The method involved creating liver metastasis model mice using human colorectal cancer cell lines. These mice were divided into anti-PROK1 antibody administration and control groups. Mice were treated intraperitoneally with antibodies or phosphate-buffered saline (control) every 3 days. The number of liver metastatic lesions and survival time of each group were compared. The number of metastatic lesions decreased, and survival time was significantly prolonged in the antibody-treated group. Furthermore, using microarray and immunostaining in both groups, we confirmed the effect of administering the anti-PROK1 antibody on the oxidation, reduction, and apoptotic processes, and cell division of tumors, and that alterations were suppressed in 72.1% of the genes examined. The expression of transforming growth factor-{beta} (TGF-{beta}), a tumor suppressor gene, was increased. The increased expression of TGF-{beta} via PROK1 antibody administration may suppress the cancer cell proliferation ability, leading to liver metastasis suppression and prolonging the survival time of mice.

category: cancer biology


title: Embedded 3D printing in self-healing annealable composites for functional patterning of human neural constructs

abstract: Human in vitro models of neural tissue with controllable cellular identity, tunable microenvironment, and defined spatial arrangement are needed to facilitate studies of brain development and disease. Towards this end, embedded printing in jammed microgel supports (i.e., granular gels) holds great promise as it allows precise and programmable patterning of extremely soft and compliant tissue constructs. However, in contrast to the vast material landscape available for bulk hydrogels, granular printing support formulations are restricted to a handful of materials without the ability for facile adjustment of biofunctional properties of the cellular microenvironment. Therefore, there has been a need for novel materials that take advantage of versatile biomimicry of bulk hydrogels while providing high-fidelity support for embedded printing akin to granular gels. To address this need, we present a modular platform for bioengineering of neuronal networks via direct embedded 3D printing of human stem cells inside Self-Healing Annealable Particle-Extracellular matrix (SHAPE) composites. SHAPE composites consist of soft microgels immersed in viscous extracellular-matrix solution to enable precise freeform patterning of human stem cells and consequent generation and long-term maintenance of mature subtype-specific neurons that extend projections within the volume of the annealed support. The developed approach further allows multi-ink deposition, live spatial and temporal monitoring of oxygen levels, as well as creation of vascular channels. Due to its modularity, SHAPE biomanufacturing toolbox not only offers a solution for functional modeling of mechanically sensitive neural constructs, but also has potential to be applied to a wide range of biomaterials with different crosslinking mechanisms to model tissues and diseases where recapitulation of complex architectural features and topological cues is essential.

category: bioengineering


title: Embedded 3D printing in self-healing annealable composites for precise patterning of functionally mature human neural constructs


title: Multiscale model of the physiological control of myocardial perfusion to delineate putative metabolic feedback mechanisms

abstract: Coronary blood flow is tightly regulated to ensure that myocardial oxygen delivery meets local metabolic demand via the concurrent action of myogenic, neural, and metabolic mechanisms. While several competing hypotheses exist, the specific nature of the local metabolic mechanism(s) remains poorly defined. To gain insights into the viability of putative metabolic feedback mechanisms and into the coordinated action of parallel regulatory mechanisms, we applied a multi-scale modeling framework to analyze experimental data on coronary pressure, flow, and myocardial oxygen delivery in the porcine heart in vivo. The modeling framework integrates a previously established lumped-parameter model of myocardial perfusion used to account for transmural hemodynamic variations and a simple vessel mechanics model used to simulate the vascular tone in each of three myocardial layers. Vascular tone in the resistance vessel mechanics model is governed by input stimuli from the myogenic, metabolic, and autonomic control mechanisms. Seven competing formulations of the metabolic feedback mechanism are implemented in the modeling framework, and associated model simulations are compared to experimental data on coronary pressures and flows under a range of experimental conditions designed to interrogate the governing control mechanisms. Analysis identifies a maximally likely metabolic mechanism among the seven tested models, in which production of a metabolic signaling factor is proportional to MVO2 and delivery proportional to flow. Finally, the identified model is validated based on comparisons of simulations to data on the myocardial perfusion response to conscious exercise that were not used for model identification.


title: Extracellular and intracellular components of theimpedance of neural tissue

abstract:
Electric phenomena in brain tissue can be measured using extracellular potentials, such as the local field potential, or the electro-encephalogram. The interpretation of these signals depend on the electric structure and properties of extracellular media, but the measurements of these electric properties are still debated. Some measurements point to a model where the extracellular medium is purely resistive, and thus parameters such as electric conductivity and permittivity should be independent of frequency. Other measurements point to a pronounced frequency dependence of these parameters, with scaling laws that are consistent with capacitive or diffusive effects. However, these experiments correspond to different preparations, and it is unclear how to correctly compare them. Here, we provide for the first time, impedance measurements (in the 1-10 KHz frequency range) using the same set-up in various preparations, from primary cell cultures to acute brain slices, with a comparison with similar measurements performed in artificial cerebrospinal fluid with no biological material. The measurements show that when the current flows across a cell membrane, the frequency dependence of the macroscopic impedance between intracellular and extracellular electrodes is significant, and cannot be captured by a model with resistive media. Fitting a mean-field model to the data shows that this frequency dependence could be explained by the ionic diffusion mainly associated to Debye layers surrounding the membranes. We conclude that neuronal membranes and their ionic environment induce strong deviations to resistivity, that should be taken into account to correctly interpret extracellular potentials generated by neurons.

SignificanceThe electro-encephalogram recorded at the scalp surface and local-field potentials recorded within neural tissue are generated by electric currents in neurons, and thus depend on the impedance of neural tissue. Different measured values were proposed, and it is currently unclear what is the real impedance of neural tissue. Here, we show that the impedance depends on the measurement technique. If the measurement is exclusively extracellular, the system appears as equivalent to a simple resistor. However, if the measurement includes an intracellular electrode, a more complex impedance is observed, because the current has to flow through the membrane, as happening in the brain. Thus, we provide an explanation for apparent disagreements, and indicate in which cases each impedance should be used.


title: Extracellular and intracellular components of the impedance of neural tissue


title: Precision dynamical mapping using topological data analysis reveals a unique hub-like transition state at rest

abstract: Even in the absence of external stimuli, neural activity is both highly dynamic and organized across multiple spatiotemporal scales. The continuous evolution of brain activity patterns during rest is believed to help maintain a rich repertoire of possible functional configurations that relate to typical and atypical cognitive phenomena. Whether these transitions or "explorations" follow some underlying arrangement or instead lack a predictable ordered plan remains to be determined. Here, using a precision dynamics approach, we aimed at revealing the rules that govern transitions in brain activity at rest at the single participant level. We hypothesized that by revealing and characterizing the overall landscape of whole brain configurations (or states) we could interpret the rules (if any) that govern transitions in brain activity at rest. To generate the landscape of whole-brain configurations we used Topological Data Analysis based Mapper approach. Across all participants, we consistently observed a rich topographic landscape in which the transition of activity from one state to the next involved a central hub-like "transition state." The hub topography was characterized as a shared attractor-like basin where all canonical resting-state networks were represented equally. The surrounding periphery of the landscape had distinct network configurations. The intermediate transition state and traversal through it via a topographic gradient seemed to provide the underlying structure for the continuous evolution of brain activity patterns at rest. In addition, differences in the landscape architecture were more consistent within than between subjects, providing evidence of idiosyncratic dynamics and potential utility in precision medicine.


title: Cellular heterogeneity and molecular reprogramming of host response during influenza acute lung injury

abstract: Acute lung injury (ALI) caused by influenza A virus (IAV or influenza) manifests from dysregulated cellular interactions between hematopoietic and non-hematopoietic cells that develop into a pathologic host response. However, the lungs diverse cellular framework that dictates the pathologic host response and acute lung injury remains incompletely understood. We performed a single-cell RNA-seq (scRNA-seq) analysis of total lung cells in mice from severe influenza to examine the cellular heterogeneity and cell-specific regulation of host response. We observed that IAV infection resulted in significant myelopoiesis, predominantly monocyte, and macrophage subsets, which constituted over 50% of total immune cells. IAV infection resulted in the significant loss of endothelial and fibroblast cells, representing the most predominant non-hematopoietic cells and crucial to regulating inflammatory response and barrier integrity. We also show the cell-cell communication dynamics of interferon and chemokine signaling and global regulation of these responses in transition from homeostatic to IAV infection state. These data highlight a robust application of scRNA-seq technology in establishing the atlas of cellular heterogeneity from its homeostatic transition to infection state and the host response regulation in IAV-mediated lung pathology.

category: immunology


title: Sterol scarcity primes p38 immune defenses through a TIR-1/SARM1 phase transition

abstract: Intracellular signaling regulators can be concentrated into membrane-free, higher-ordered protein assemblies to initiate protective responses during stress -- a process known as phase transition. Here, we show that a phase transition of the Caenorhabditis elegans Toll/interleukin-1 receptor domain protein (TIR-1), an NAD+ glycohydrolase homologous to mammalian sterile alpha and TIR motif-containing 1 (SARM1), underlies p38 PMK-1 immune pathway activation in C. elegans intestinal epithelial cells. Through visualization of fluorescently labeled TIR-1/SARM1 protein, we demonstrate for the first time that physiologic stresses, both pathogen and non-pathogen, induce multimerization of TIR-1/SARM1 into visible puncta within intestinal epithelial cells. In vitro enzyme kinetic analyses revealed that, like mammalian SARM1, the NAD+ glycohydrolase activity of C. elegans TIR-1 is dramatically potentiated by protein oligomerization and a phase transition. Accordingly, C. elegans with genetic mutations that specifically block either multimerization or the NAD+ glycohydrolase activity of TIR-1/SARM1 fail to induce p38 PMK phosphorylation, are unable to increase immune effector expression, and are dramatically susceptible to bacterial infection. Finally, we demonstrate that the TIR-1/SARM1 phase transition is modified by dietary cholesterol, revealing a new adaptive response that allows a metazoan host to anticipate pathogen threats during micronutrient deprivation, a time of relative susceptibility to infection. When cholesterol is limited, TIR-1/SARM1 oligomerizes into puncta in intestinal epithelial cells and engages its NAD+ glycohydrolase activity, which increases p38 PMK-1 phosphorylation, and primes immune effector induction in a manner that promotes pathogen clearance from the intestine during a subsequent infection. Thus, a phase transition of TIR-1/SARM1 as a prerequisite for its NAD+ glycohydrolase activity is strongly conserved across millions of years of evolution and is essential for diverse physiological processes in multiple cell types.


title: A TIR-1/SARM1 phase transition underlies p38 immune pathway activation in the C. elegans intestine


title: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin

abstract: Nucleolus is the organelle for ribosome biogenesis and for sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive 2-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the nucleolar integrity mediated by rRNA biogenesis maintains the normal liquid-liquid phase separation (LLPS) of nucleolus and the formation of peri-nucleolar heterochromatin (PNH). Upon rRNA biogenesis defect, the natural LLPS of nucleolus is disrupted, causing dissociation of NCL/TRIM28 complex from PNH and changes of epigenetic states and reorganization of the 3D structure of PNH, which leads to Dux, a 2C program transcription factor gene, to be released from the PNH region and activation of 2C-like program. Correspondingly, embryos with rRNA biogenesis defect are incompatible to develop from 2-cell (2C) to 4-cell embryos, with delayed repression of 2C/ERV genes and a transcriptome skewed toward earlier cleavage embryo signatures. Our results highlight that rRNA-mediated nucleolar integrity and 3D structure reshaping of PNH compartment regulates the fate transition of mES cells to 2C-like cells, and that rRNA biogenesis is a critical regulator during the 2-cell-to-4-cell transition of murine pre-implantation embryo development.


title: Does the rainbow trout ovarian fluid guide the spermatozoon on its way to the egg?

abstract: Fertilization of freshwater fish occurs in an environment that may negatively affect the gametes; therefore, the specific mechanisms triggering the encounters of gametes would be highly expedient. The egg and ovarian fluid (OF) are likely the primary sources of these triggers in fish that we confirmed here for rainbow trout Oncorhynchus mykiss. The ovarian fluid significantly affected the spermatozoa performance: it supported high velocity for a more extended period and changed the motility pattern from tumbling in water to straightforward moving in the ovarian fluid. Rainbow trout OF induced a trapping chemotaxis-like effect on activated male gametes, and this effect depended on the properties of the activating media. The interaction of the spermatozoa with the attracting agents was accompanied by their "turn-and-run" behavior involving asymmetric flagellar beating and Ca2+ concentration bursts in the bent flagella segment, characteristic of the chemotactic response. Collectively, the ovarian fluid creates the optimal environment for rainbow trout spermatozoa performance, being an effective promoter of fertilization. The individual peculiarities of the egg (ovarian fluid) - sperm interaction in rainbow trout reflect the specific features of the spawning process in this species.


title: Protist.guru: a comparative transcriptomics database for the protist kingdom

abstract:
SummaryDuring the last few decades, the study of microbial ecology has been enabled by molecular and genomic data. DNA sequencing has revealed the surprising extent of microbial diversity and how microbial processes run global ecosystems. However, significant gaps in our understanding of the microbial world remain, and one example is that microbial eukaryotes, or protists, are still neglected. To address this gap, we used gene expression data from 15 distinct protist species to create protist.guru: an online database equipped with tools for identifying functional co-expression networks, gene families, and enriched gene clusters. Here, we show how our database can be used to reveal genes involved in essential pathways, such as the synthesis of secondary carotenoids in Haematococcus lacustris. We expect protist.guru to serve as a valuable resource for protistologists, as well as a catalyst for discoveries and new insights into the biological processes of microbial eukaryotes.

AvailabilityThe database and co-expression networks are freely available from http://protist.guru/. The expression matrices and sample annotations are found in the supplementary data.

category: evolutionary biology


title: Molecular Evolution across Mouse Spermatogenesis

abstract: Genes involved in spermatogenesis tend to evolve rapidly, but we still lack a clear understanding of how different components of molecular evolution vary across this complex developmental process. We used fluorescence activated cell sorting (FACS) to generate expression data for both early (meiotic) and late (postmeiotic) cell types across thirteen inbred strains of mice (Mus) spanning ~7 million years of evolution. We used these comparative developmental data to investigate the evolution of lineage-specific expression, protein-coding sequences, and expression levels. We found increased lineage specificity and more rapid protein-coding and expression divergence during late spermatogenesis, suggesting that signatures of rapid testis molecular evolution are punctuated across sperm development. Despite strong overall developmental parallels in these components of molecular evolution, protein and expression divergences were only weakly correlated across genes. We detected more rapid protein evolution on the X chromosome relative to the autosomes, while X-linked gene expression tended to be relatively more conserved likely reflecting chromosome-wide regulatory constraints. Using allele-specific FACS expression data from crosses between four strains, we found that the relative contributions of different regulatory mechanisms also differed between cell-types. Genes showing cis-regulatory changes were more common late in spermatogenesis, and tended to be associated with larger differences in expression levels and greater expression divergence between species. In contrast, genes with trans-acting changes were more common early and tended to be more conserved across species. Our findings advance understanding of gene evolution across spermatogenesis and underscore the fundamental importance of developmental context in molecular evolutionary studies.


title: Evolution of a costly immunity to cestode parasites is a pyrrhic victory

abstract:
Parasites impose fitness costs on their hosts. Biologists therefore tend to assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests selection may instead favor loss of resistance. Immune costs are rarely documented in nature, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes they gained resistance to the freshwater-associated tapeworm, Schistocephalus solidus. Extensive peritoneal fibrosis and inflammation contribute to suppression of cestode growth and viability, but also impose a substantial cost of reduced fecundity. Combining genetic mapping and population genomics, we find that the immune differences between tolerant and resistant populations arise from opposing selection in both populations acting, respectively, to reduce and increase resistance consistent with divergent optimization.

One Sentence SummaryRecently-evolved freshwater populations of stickleback frequently evolve increased resistance to tapeworms, involving extensive fibrosis that suppresses parasite growth; because this fibrosis greatly reduces fish fecundity, in some freshwater populations selection has favored an infection-tolerant strategy with fibrosis suppression.


title: Genetic load and extinction in peripheral populations: the roles of migration, drift and demographic stochasticity

abstract: We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic vs. demographic effects of migration. Our analysis is based on a  semi-deterministic analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients.


title: Trophic specialization on unique resources in one of the most celebrated examples of sympatric speciation, Barombi Mbo crater lake cichlids

abstract: Divergent ecological selection often results in trophic niche partitioning and is one of the central processes underlying sympatric speciation. However, there are still few studies of niche partitioning in putative examples of sympatric speciation in the wild. Here we conducted the first quantitative study of dietary niche partitioning in one of the most celebrated examples of sympatric speciation, Barombi Mbo cichlids, using stomach contents and stable isotope analyses. We found little evidence for trophic niche partitioning among any Barombi Mbo cichlids, even among the nine species coexisting in sympatry in the littoral zone. Stable isotope analyses supported these conclusions of minimal dietary overlap. However, we did find extraordinary dietary specialization in some species, including spongivory and feeding on terrestrial ants, both unique feeding strategies among freshwater fishes. Stomach contents of the spongivore (Pungu maclareni) were 20% freshwater sponge, notable considering that only 0.04% of all fishes consume sponges. Overall, we conclude that while there is less trophic niche partitioning than expected among Barombi Mbo cichlids, there is evidence for dietary specialization on rare resources in support of Liems paradox.


title: Red queen's race: rapid evolutionary dynamics of an expanding family of meiotic drive factors and their hpRNA suppressors

abstract: Meiotic drivers are a class of selfish genetic elements that are widespread across eukaryotes. As their activities are often detrimental to organismal fitness, opposing regulatory mechanisms are usually required to silence them, to ensure fair segregation during meiosis. Accordingly, the existence of such selfish elements is frequently hidden in genomes, and their molecular functions are little known. Here, we trace evolutionary steps that generated the Dox meiotic drive system in Drosophila simulans (Dsim), which distorts male:female balance (sex-ratio) by depleting male progeny. We show that Dox emerged via stepwise mobilization and acquisition of portions of multiple D. melanogaster genes, notably including from protamine, which replaces histones in haploid sperm and mediates the highly condensed state of sperm chromatin. Moreover, we reveal novel Dox homologs in Dsim and massive, recent, amplification of Dox superfamily genes specifically on X chromosomes of its closest sister species D. mauritiana (Dmau) and D. sechellia (Dsech). The emergence of Dox superfamily genes is tightly associated with 359-bp repeats (in the 1.688 family of satellite repeats) that flank de novo genomic copies. In concert, we find coordinated emergence and diversification of autosomal hairpin RNA-class siRNA loci that target subsets of Dox superfamily genes across simulans clade species. Finally, an independent set of protamine amplifications on the Y chromosome of D. melanogaster indicates that protamine genes are frequent and recurrent players in sex chromosome dynamics. Overall, we reveal fierce genetic arms races between meiotic drive factors and siRNA suppressors associated with recent speciation.


title: Multivariate Genomewide Association Analysis with IHT

abstract: 1In genome-wide association studies (GWAS), analyzing multiple correlated traits is potentially superior to conducting multiple univariate analyses. Standard methods for multivariate GWAS operate marker-by-marker and are computationally intensive. We present a penalized regression algorithm for multivariate GWAS based on iterative hard thresholding (IHT) and implement it in a convenient Julia package MendelIHT.jl (https://github.com/OpenMendel/MendelIHT.jl). In simulation studies with up to 100 traits, IHT exhibits similar true positive rates, smaller false positive rates, and faster execution times than GEMMAs linear mixed models and mv-PLINKs canonical correlation analysis. On UK Biobank data, our IHT software completed a 3-trait joint analysis in 20 hours and an 18-trait joint analysis in 53 hours, requiring up to 80GB of computer memory. In short, our software enables geneticists to fit a single regression model that simultaneously considers the effect of all SNPs and dozens of traits.

category: genetics


title: Multivariate Genomewide Association Analysis by Iterative Hard Thresholding


title: The genetic etiology of longitudinal measures of predicted brain ageing in a population-based sample of mid to late-age males

abstract:
Magnetic resonance imaging data are being used in statistical models to predicted brain ageing (PBA) and as biomarkers for neurodegenerative diseases such as Alzheimers Disease. Despite their increasing application, the genetic and environmental etiology of global PBA indices is unknown. Likewise, the degree to which genetic influences in PBA are longitudinally stable and how PBA changes over time are also unknown. We analyzed data from 734 men from the Vietnam Era Twin Study of Aging with repeated MRI assessments between the ages 52 to 72 years. Biometrical genetic analyses  twin models revealed significant and highly correlated estimates of additive genetic heritability ranging from 59% to 75%. Multivariate longitudinal modelling revealed that covariation between PBA at different timepoints could be explained by a single latent factor with 73% heritability. Our results suggest that genetic influences on PBA are detectable in midlife or earlier, are longitudinally very stable, and are largely explained by common genetic influences.

HighlightsWe explored the genetic and environmental etiology of MRI-based predicted brain age (PBA) in a longitudinal sample of males starting in midlife. Genetic influences on PBA are detectable in midlife or earlier, are longitudinally very stable, and largely explained by common genetic influences.


title: The lesser Pacific striped octopus, Octopus chierchiae: an emerging laboratory model for the study of octopuses

abstract: Cephalopods have the potential to become useful experimental models in various fields of science, particularly in neuroscience, physiology, and behavior. Their complex nervous systems, intricate color- and texture-changing body patterns, and problem-solving abilities have attracted the attention of the biological research community, while the high growth rates and short life cycles of some species render them suitable for laboratory culture. Octopus chierchiae is a small octopus native to the central Pacific coast of North America whose predictable reproduction, short time to maturity, small adult size, and ability to lay multiple egg clutches (iteroparity) make this species ideally suited to laboratory culture. Here we describe novel methods for culture of O. chierchiae, with emphasis on enclosure designs, feeding regimes, and breeding management. Our results demonstrate the feasibility of multigenerational culture of O. chierchiae. Specifically, O. chierchiae bred in the laboratory grows from a 3.5-millimeter mantle length at hatching to an adult mantle length of approximately 20-30 millimeters in 250-300 days, with 14-15% survivorship to over 400 days of age in first and second generations. O. chierchiae sexually matures at around an estimated six months of age and, unlike most octopus species, can lay multiple clutches of eggs, approximately every 30-90 days. Eggs are large and hatchlings emerge as direct developing octopuses. Based on these results, we propose that O. chierchiae possesses both the practical and biological features needed for a model octopus that can be cultured repeatedly to address a wide range of fundamental biological questions.

category: animal behavior and cognition


title: Transient late gestation prenatal hypoxic insult results in functional deficits but not gross neuroanatomic deficits in mice

abstract: Intrauterine hypoxia is a common cause of brain injury in children resulting in a broad spectrum of long-term neurodevelopmental sequela, including life-long disabilities that can occur even in the absence of severe neuroanatomic damage. Postnatal hypoxia-ischemia rodent models are commonly used to understand the effects of ischemia and transient hypoxia on the developing brain. Postnatal models, however, have some limitations. First, they do not test the impact of placental pathologies on outcomes from hypoxia. Second, they primarily recapitulate severe injury because they provoke substantial cell death, which is not seen in children with mild hypoxic injury. Lastly, they do not model preterm hypoxic injury. Prenatal models of hypoxia in mice may allow us to address some of these limitations to expand our understanding of developmental brain injury. The published rodent models of prenatal hypoxia employ multiple days of hypoxic exposure or complicated surgical procedures, making these models challenging to perform consistently in mice. Furthermore, large animal models suggest that transient prenatal hypoxia without ischemia is sufficient to lead to significant functional impairment to the developing brain. However, these large animal studies are resource-intensive and not readily amenable to mechanistic molecular studies. Therefore, here we characterized the effect of late gestation (embryonic day 17.5) transient prenatal hypoxia (5% inspired oxygen) on long-term anatomical and neurodevelopmental outcomes in mice. Late gestation transient prenatal hypoxia increased hypoxia-inducible factor 1 alpha protein levels (a marker of hypoxic exposure) in the fetal brain. Hypoxia exposure predisposed animals to decreased weight at postnatal day 2, which normalized by day 8. However, hypoxia did not affect gestational age at birth, litter size at birth, or pup survival. No differences in fetal brain cell death or long-term gray or white matter changes resulted from hypoxia. Animals exposed to prenatal hypoxia did have several long-term functional consequences, including sex-dichotomous changes. Hypoxia exposure was associated with a decreased seizure threshold and abnormalities in hindlimb strength and repetitive behaviors in males and females. Males exposed to hypoxia had increased anxiety-related deficits, whereas females had deficits in social interaction. Neither sex developed any motor or visual learning deficits. This study demonstrates that late gestation transient prenatal hypoxia in mice is a simple, clinically relevant paradigm for studying putative environmental and genetic modulators of the long-term effects of hypoxia on the developing brain.


title: Deficits in seizure threshold and other behaviors in adult mice without gross neuroanatomic injury after late gestation transient prenatal hypoxia


title: Direct focus sensing and shaping for high-resolution multi-photon imaging in deep tissue

abstract: High-resolution optical imaging of deep tissue in-situ such as the living brain is fundamentally challenging because of the aberration and scattering of light. In this work, we develop an innovative adaptive optics three-photon microscope based on direct focus sensing and shaping that can accurately measure and effectively compensate for both low- and high-order specimen-induced aberrations and recover near-diffraction-limited performance at depth. A conjugate adaptive optics configuration with remote focusing enables in vivo imaging of fine neuronal structures in the mouse cortex through the intact skull up to a depth of 750 {micro}m below pia, making high-resolution microscopy in cortex near non-invasive. Functional calcium imaging with high sensitivity and accuracy, and high-precision laser-mediated microsurgery through the intact skull were demonstrated. Moreover, we also achieved in vivo high-resolution imaging of the deep cortex and subcortical hippocampus up to 1.1 mm below pia within the intact brain.


title: Quantitative Phase Velocimetry for Label-Free Measurement of Intracellular Mass Transport Velocity

abstract: Transport of mass within cells helps maintain homeostasis and is disrupted by disease and stress. Here, we develop quantitative phase velocimetry (QPV) as a label-free approach to make the invisible flow of mass within cells visible and quantifiable. We benchmark our approach against alternative image registration methods, a theoretical error model, and synthetic data. Our method tracks not just individual labeled particles or molecules, but the entire flow of bulk material through the cell. This enables us to measure diffusivity within distinct cell compartments using a single approach, which we use here for direct comparison of nuclear and cytoplasmic diffusivity. As a label-free method, QPV can be used for long-term tracking to capture dynamics through the cell cycle.


title: A comparison of data integration methods for single-cell RNA sequencing of cancer samples

abstract: Tumours are routinely profiled with single-cell RNA sequencing (scRNA-seq) to characterize their diverse cellular ecosystems of malignant, immune, and stromal cell types. When combining data from multiple samples or studies, batch-specific technical variation can confound biological signals. However, scRNA-seq batch integration methods are often not designed for, or benchmarked, on datasets containing cancer cells. Here, we compare 5 data integration tools applied to 171,206 cells from 5 tumour scRNA-seq datasets. Based on our results, STACAS and fastMNN are the most suitable methods for integrating tumour datasets, demonstrating robust batch effect correction while preserving relevant biological variability in the malignant compartment. This comparison provides a framework for evaluating how well single-cell integration methods correct for technical variability while preserving biological heterogeneity of malignant and non-malignant cell populations.

category: bioinformatics


title: VistoSeg: a MATLAB pipeline to process, analyze and visualize high resolution histology images for Visium spatial transcriptomics data

abstract:
MotivationRecent advances in spatially-resolved transcriptomics technologies such as 10x Genomics Visium platform have enabled the generation of transcriptome-wide spatial expression maps within intact tissue. However, steps for processing the high-resolution histology images, extracting relevant features from the images, and integrating them with the gene expression data remain unresolved.

ResultsWe describe VistoSeg, a MATLAB pipeline to process, analyze, and interactively visualize the high-resolution images from the 10x Genomics Visium platform. The output from VistoSeg can then be integrated with the spatial-molecular information in downstream analyses using any programming language, such as R or Python.

AvailabilityVistoSeg is available at https://github.com/LieberInstitute/VistoSeg (DOI: 10.5281/zenodo.5156783) with a tutorial at http://research.libd.org/VistoSeg

Supplementary informationSupplementary data are available at Bioinformatics online.


title: EnGRNT: Inference of gene regulatory networks using ensemble methods and topological feature extraction

abstract: The development of computational methods to predict gene regulatory networks (GRNs) from gene expression data is a challenging task. Many machine learning methods have been developed, including supervised, unsupervised, and semi-supervised to infer gene regulatory networks. Most of these methods ignore the class imbalance problem which can lead to decreasing the accuracy of predicting regulatory interactions in the network. Therefore, developing an effective method considering imbalanced data is a challenging task. In this paper, we propose EnGRNT approach to infer GRNs with high accuracy that uses ensemble-based methods. The proposed approach, as well as the gene expression data, considers the topological features of GRN. We applied our approach to the simulated Escherichia coli dataset. Experimental results demonstrate that the appropriateness of the inference method relies on the size and type of expression profiles in microarray data. Except for multifactorial experimental conditions, the proposed approach outperforms unsupervised methods. The obtained results recommend the application of EnGRNT on the imbalanced datasets.


title: Energetics of a protein disorder-order transition in small molecule recognition

abstract: Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered  lid region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.

category: biophysics


title: RPnet: A Reverse Projection Based Neural Network for Coarse-graining Metastable Conformational States for Protein Dynamics

abstract: Markov State Model (MSM) is a powerful tool for modeling the long timescale dynamics based on numerous short molecular dynamics (MD) simulation trajectories, which makes it a useful tool for elucidating the conformational changes of biological macromolecules. By partitioning the phase space into discretized states and estimate the probabilities of inter-state transitions based on short MD trajectories, one can construct a kinetic network model that could be used to extrapolate long time kinetics if the Markovian condition is met. However, meeting the Markovian condition often requires hundreds or even thousands of states (microstates), which greatly hinders the comprehension of conformational dynamics of complex biomolecules. Kinetic lumping algorithms can coarse grain numerous microstates into a handful of metastable states (macrostates), which would greatly facilitate the elucidation of biological mechanisms. In this work, we have developed a reverse projection based neural network (RPnet) method to lump microstates into macrostates, by making use of a physics-based loss function based on the projection operator framework of conformational dynamics. By recognizing that microstate and macrostate transition modes can be related through a projection process, we have developed a reverse projection scheme to directly compare the microstate and macrostate dynamics. Based on this reverse projection scheme, we designed a loss function that allows effectively assess the quality of a given kinetic lumping. We then make use of a neural network to efficiently minimize this loss function to obtain an optimized set of macrostates. We have demonstrated the power of our RPnet in analyzing the dynamics of a numerical 2D potential, alanine dipeptide, and the clamp opening of an RNA polymerase. In all these systems, we have illustrated that our method could yield comparable or better results than competing methods in terms of state partitioning and reproduction of slow dynamics. We expect that our RPnet holds promise in analyzing conformational dynamics of biological macromolecules.


title: Cancer Cells Viscoelasticity Measurement by Quantitative Phase and Flow Stress Induction

abstract:
Cell viscoelastic properties are affected by the cell cycle, differentiation, pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotypisation are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative Phase Imaging (QPI) is used for image acquisition because this technique enables to quantify optical path length delays introduced by the sample, thus providing a label-free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live cell experiments and even through a time-lapse, where we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters like circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, where an increase of stiffness corresponded to actin repolymerisation in time.

SIGNIFICANCEWe present an approach for viscoelasticity measurement using QPI and shear stress induction by fluid flow. Our system builds and extends a recently published approach by parametric deconvolution, which allows us to eliminate the influence of the fluidic system and reliably measure both the shear modulus and viscosity of the cells in high throughput. Additionally, the proposed method enables to simultaneously determine cell refractive index map, cell dry mass map, and morphology, thereby enabling a multimodal cellular characterisation in a single measurement.


title: Coordinated Cross-Talk Between the Myc and Mlx Networks in Liver Regeneration and Neoplasia

abstract:
Background & AimsThe c-Myc (Myc) bHLH-ZIP transcription factor is deregulated in most cancers. In association with Max, Myc controls target genes that supervise metabolism, ribosome biogenesis, translation and proliferation. This "Myc Network" cross-talks with the "Mlx Network", which consists of the Myc-like proteins MondoA and ChREBP and Max-like Mlx. Together, this "Extended Myc Network" regulates both common and distinct genes targets. Here we studied the consequence of Myc and/or Mlx ablation in the liver, particularly those pertaining to hepatocyte proliferation, metabolism and spontaneous tumorigenesis.

MethodsWe examined the ability of hepatocytes lacking Mlx (MlxKO) or Myc+Mlx (double KO or DKO) to repopulate the liver over an extended period of time in a murine model of Type I tyrosinemia. We also compared this and other relevant behaviors, phenotypes and transcriptomes of the livers to those from previously characterized MycKO, ChrebpKO and MycKO x ChrebpKO mice.

ResultsHepatocyte regenerative potential deteriorated as the Extended Myc Network was progressively dismantled. Genes and pathways dysregulated in MlxKO and DKO hepatocytes included those pertaining to translation, mitochondrial function and non-alcoholic fatty liver disease (NAFLD). The Myc and Mlx Networks were shown to cross-talk, with the latter playing a disproportionate role in target gene regulation. All cohorts also developed NAFLD and molecular evidence of early steatohepatitis. Finally, MlxKO and DKO mice displayed extensive hepatic adenomatosis.

ConclusionsIn addition to demonstrating cooperation between the Myc and Mlx Networks, this study revealed the latter to be more important in maintaining proliferative, metabolic and translational homeostasis, while concurrently serving as a suppressor of benign tumorigenesis.

SynopsisThe Myc and Mlx Networks exhibit extensive cross-talk and regulate distinct but overlapping sets of transcriptional targets. The current work demonstrates the cooperation between these two Networks in supporting the regenerative capabilities of normal hepatocytes while also revealing that the Mlx Network serves as a suppressor of spontaneous hepatic adenomatosis


title: Pancreatic Brsk2 amplifies parasympathetic signals to promote type 2 diabetes

abstract: The parasympathetic nervous system (PNS) modulates postprandial glucose metabolism via innervating pancreas; however, its significance in the pathogenesis of type 2 diabetes (T2DM) remains unclear. Here we show that brain-specific serine/threonine-protein kinase 2 (Brsk2), accumulated in obese mouse islets, responds to PNS activation and initiates pre-absorptive insulin release. In inducible mouse models, excessive Brsk2 amplifies parasympathetic signaling to {beta} cells and increases their secretion, ensuing insulin resistance and T2DM. Conversely, Brsk2 inhibition prevents and treats HFD-induced metabolic abnormities via avoiding {beta}-cell oversecretion. Mechanistically, parasympathetic acetylcholine activates cholinergic receptor M3 (Chrm3), then Chrm3 recruits and stabilizes Brsk2, which in turn phosphorylates phospholipase A2 activating protein (Plaa). A Chrm3-Brsk2-Plaa axis stimulates {beta}-cell hypersecretion during both pre-absorptive and absorptive stages in HFD-feeding mice, thus imposing insulin resistance and {beta}-cell dysfunction. Blocking parasympathetic signaling to {beta} cells by Brsk2 protein restoration, autonomic mediation drugs, or vagotomy restricted diabetes development. Moreover, three human BRSK2 variants are associated with hyperinsulinemia, insulin resistance, and T2DM in the Chinese population. These findings reveal that Brsk2 links parasympathetic nervous system to nutrition-overload induced T2DM.

category: pathology


title: The synergistic effect of circRNA methylation promotes pulmonary fibrosis

abstract:
RationaleN6-Methyladenosine (m6A) is the most common type of RNA methylation modification, mainly occurring on mRNA. Whether m6A-modified circRNAs are involved in different settings of pulmonary fibrosis remains unclear.

Methods and ResultsUsing an m6A-circRNA epitranscriptomic chip, candidate circRNAs were selected, in which hsa_circ_0000672 and hsa_circ_0005654 were specifically involved in SiO2-induced pulmonary fibrosis by targeting the same protein, eIF4A3, indicating that the m6A modification of these two circRNAs has a synergistic effect on fibroblast dysfunction induced by SiO2. A mechanistic study revealed that the m6A modification of circRNAs was mainly mediated by the methyltransferase METTL3. Furthermore, METTL3 promoted the activation, migration and activity of pulmonary fibroblasts and participated in SiO2-induced pulmonary fibrosis via circRNA m6A modification.

Conclusionm6A methylation of circRNAs mediates silica-induced fibrosis via synergistic effects, enriching the understanding of circRNAs and uncovering a potential new target to treat fibrosis-related diseases.

category: pharmacology and toxicology


title: Mucin-mimetic action of capsaicin improves high fat diet-induced gut barrier dysfunction in mice colon

abstract:
The gut barrier - including tight junction proteins and mucus layers, is the first line of defense against physical, chemical, or pathogenic incursions. This barrier is compromised in various health disorders. Capsaicin, a dietary agonist of Transient receptor potential vanilloid 1 (TRPV1) channel, is reported to alleviate the complications of obesity. While its mode of action is well established to enhance energy expenditure, metabolism and prevent dysbiosis, the more local effects on the host gut - particularly the gut barrier and mucus system remain elusive.

We employed a diet-induced obesity model to investigate the effect of capsaicin on the gut barrier and mucus production and to understand the involvement of mucus, bacteria, and TRPV1 in these phenomena. Mucin feeding reflected most of the effects produced by capsaicin, indicating that mucus modulation by capsaicin plays a crucial role in its anti-obesity effects. Capsaicin, bacteria and the host mucus system seem to act in a cyclic cascade involving TRPV1, which can be activated by capsaicin and various bacteria. These findings provide new insight into the role of TRPV1 in maintaining a healthy gut environment.

HIGHLIGHTSO_LIExogenous mucin feeding produced anti-obesity effects similar to capsaicin in mice.
C_LIO_LIMucin and capsaicin improved TJP expression, intestinal permeability and gut microbial diversity.
C_LIO_LICapsaicin modulated bacterial diversity in vitro, independently of the host.
C_LIO_LIProbiotic bacteria and butyrate activated TRPV1 in transfected HEK cells.
C_LIO_LIAnti-obesity action of capsaicin is not exclusive to TRPV1 agonism.
C_LIO_LICapsaicins action as colonic mucus secretagogue - plays a crucial part in its anti-obesity benefits.
C_LI


title: Mixed matrix factorization: a novel algorithm for the extraction of kinematic-muscular synergies

abstract: Synergistic models have been employed to investigate motor coordination separately in the muscular and kinematic domains. However, the relationship between muscle synergies, constrained to be non-negative, and kinematic synergies, whose elements can be positive and negative, has received limited attention. Existing algorithms for extracting synergies from combined kinematic and muscular data either do not enforce non-negativity constraints or separate non-negative variables into positive and negative components. We propose a mixed matrix factorization (MMF) algorithm based on a gradient descent update rule which overcomes these limitations. It allows to directly assess the relationship between kinematic and muscle activity variables, by enforcing the non-negativity constrain on a subset of variables. We validated the algorithm on simulated kinematic-muscular data generated from known spatial synergies and temporal coefficients, by evaluating the similarity between extracted and ground truth synergies and temporal coefficients when the data are corrupted by different noise levels. We also compared the performance of MMF to that of non-negative matrix factorization applied to separate positive and negative components (NMFpn). Finally, we factorized kinematic and EMG data collected during upper-limb movements to demonstrate the potential of the algorithm. MMF achieved almost perfect reconstruction on noiseless simulated data. It performed better than NMFpn in recovering the correct spatial synergies and temporal coefficients with noisy simulated data. It also allowed to correctly select the original number of ground truth synergies. We showed meaningful applicability to real data; MMF can also be applied to any multivariate data that contains both non-negative and unconstrained variables.


title: Genes for tRNA recycling are upregulated in response to infection with Theiler's mouse encephalitis virus

abstract: The concept of tRNA recycling has recently emerged from the studies of ribosome-associated quality control. Therein tRNase ZS removes the 2', 3'>p from the ANKZF1-cleaved tRNA and the subsequent TRNT1 action re-generates the intact tRNA. To know the roles of the tRNA recycling in vivo, we investigated how viral infection affects the tRNA recycling system by analyzing the mRNA levels of tRNase ZS and TRNT1. We found that both genes in HeLa cells are upregulated in response to infection of Theilers mouse encephalitis virus but not to that of an influenza A virus. Upregulation was also observed in cells infected with encephalomyocarditis virus with reduced efficiency. The levels of the IFN-{beta} mRNA appeared to positively correlate with those of the tRNase ZS and TRNT1 mRNAs. The tRNase ZS gene may be regulated post-transcriptionally in the cells infected with Theilers mouse encephalitis virus.


title: Role of autophagy in sepsis-induced skeletal muscle dysfunction, whole-body metabolism, and survival

abstract: Septic patients frequently develop skeletal muscle wasting and weakness, resulting in severe clinical consequences and adverse outcomes. Autophagy is a stress-induced degradative process essential to cell survival. Recent studies have demonstrated that sepsis triggers sustained induction of autophagy in skeletal muscles, although the impact of this enhanced autophagy on sepsis-induced muscle dysfunction remains unclear. Atg7 is an autophagy gene that plays a major role in autophagosome formation. Using an inducible and muscle-specific Atg7 knockout mouse model (Atg7iSkM-KO), we investigated the functional importance of skeletal muscle autophagy in sepsis. Sepsis was induced using cecal ligation and perforation (CLP) with a sham operation serving as a control. Atg7iSkM-KO mice exhibited a more severe phenotype in response to sepsis, marked by severe muscle wasting and contractile dysfunction, hypoglycemia, higher ketone levels and a decreased in survival as compared to mice with intact Atg7. Several genes that encode 26S proteasome subunits were upregulated, suggesting that activation of the ubiquitin-proteasome system is responsible for the severe muscle atrophy that was seen in these mice. Sepsis and Atg7 deletion resulted in the accumulation of mitochondrial dysfunction, although sepsis did not further worsen mitochondrial dysfunction in Atg7iSkM-KO mice. Overall, our study demonstrates that autophagy inactivation in skeletal muscles triggers significant worsening of sepsis-induced contractile and metabolic dysfunctions and negatively impacts survival. Induction of autophagy in skeletal muscles in response to sepsis thus represents a protective mechanism.


title: Balancing conservation priorities for grassland and forest specialist bird communities in agriculturally dominated landscapes

abstract: Effective conservation planning often requires difficult decisions when at-risk species inhabit economically valuable landscapes or if the needs of multiple threatened species do not align. In the agriculture-dominated landscape of eastern Ontario and southwestern Quebec, Canada, conflicting habitat requirements exist between threatened grassland birds benefiting from certain agriculture practices and those of a diverse woodland bird community dependent on forest recovery. Using multi-scale species distribution models with Breeding Bird Survey (BBS) data, we assessed habitat suitability for 8 threatened grassland and forest specialists within this region. We also identified landscapes that jointly maximize occurrence of the 8 focal species and diversity of the overall grassland and forest communities. Influential habitat associations differed among species at the territory (200m radius) and landscape level (1km), highlighting the importance of considering multiple spatial scales. Species diversity was maximized when forest or grassland/pasture cover approached 40-50%, indicating a positive response to land cover heterogeneity. We identified species diversity hotspots near Lake Huron, as well as along the shore and southeast of the St. Lawrence River. These areas represent mosaic landscapes, balancing forest patches, wetland, grassland/pasture, and row crops such as corn, soybean, and cereals. Despite drastic landscape changes associated with agroecosystems, we demonstrate that targeted habitat protection and enhancement that prioritizes land cover diversity can maximize protection of bird communities with directly contrasting needs. We highlight multiple pathways to achieve this balance, including forest retention or separating row crops with hedgerows and wooded fence-lines, improving flexibility in conservation approaches.


title: Response to nitrogen and salinity in Rhizophora mangle propagules varies by maternal family and population of origin

abstract: Many coastal foundation plant species thrive across a range of environmental conditions, often displaying dramatic phenotypic variation in response to environmental variation. We characterized the response of propagules from six populations of the foundation species Rhizophora mangle L. to full factorial combinations of two levels of salt (15 ppt and 45 ppt) reflecting the range of salinity measured in the field populations, and two levels of nitrogen (N; no addition and amended at approximately 3 mg N per pot each week) equivalent to comparing ambient N to a rate of addition of 75 kg per hectare per year. The response to increasing salt included significant plasticity in succulence. Propagules also showed plasticity in maximum photosynthetic rate in response to N amendment, but the responses depended on the level of salt and varied by population of origin. Generally, survival was lower in high salt and high N, but the impact varied among populations. Overall, this study revealed significant phenotypic plasticity in response to salt and N level. Propagules from different populations differed in all traits measured. Variation in phenotypic plasticity and propagule survival in R. mangle may contribute to adaptation to a complex mosaic of environmental conditions and response to climate change.


title: Mites alight! Sunflower crop area and pollen supplementation enhance honey bee resistance to Varroa destructor

abstract:
Anthropogenic landscape changes can affect parasite epidemiology in wild and agricultural animals. Honey bees are agricultural animals whose services are threatened by loss of floral resources and by parasites, most notably the invasive mite Varroa destructor. Existing mite control strategies rely heavily on chemical treatments that can adversely affect bees. Alternative, pesticide-free control methods are urgently needed to maintain effective pollination services. Many flowering plants provide nectar and pollen that enhance resistance to parasites in animals. Enrichment of landscapes with antiparasitic floral resources could therefore provide a sustainable means of parasite control in pollinators.

Floral rewards of Asteraceae plants have been shown to reduce parasitic infection in diverse bee species, including honey and bumble bees. Here, we tested the effects of sunflower (Helianthus annuus) cropland and pollen supplementation on honey bee resistance to macro- and microparasites. Our results show that each doubling of sunflower crop area is associated with a 28% reduction in mite infestation intensity. Late-summer supplementation of colonies with sunflower pollen reduced mite infestation by 2.75-fold relative to an artificial pollen. Our findings suggest the potential for sunflower plantings or pollen supplements to counteract a main driver of honey bee losses worldwide.


title: Assembling an illustrated family-level tree of life for exploration in mobile devices

abstract: Since the concept of the tree of life was introduced by Darwin about a century and a half ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive tree of life for its exploration has been a difficult task to achieve due to two main obstacles: i) information is scattered into a plethora of individual sources and ii) practical visualization tools for exceptionally large trees are lacking. To overcome both challenges, we aimed to synthetize a family-level tree of life by compiling over 1400 published phylogenetic studies, ensuring that the source trees represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the synthetic tree by employing over 550 secondary-calibration points, using publicly available sequences for more than 5000 taxa, and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app (Tree of Life) for smartphones in order to facilitate the visualization and interactive exploration of the resulting tree. Interactive features include an easy exploration by zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, a timescale to determine extinction and divergence dates, and quick links to Wikipedia. Small illustrations of organisms are displayed at the tips of the branches, to better visualize the morphological diversity of life on earth. Our assembled Tree of Life currently includes over 7000 taxonomic families (about half of the total family-level diversity) and its content will be gradually expanded through regular updates to cover all life on earth at family-level.


title: Near-Zero Phase-Lag Hyperscanning in a Novel Wireless EEG System

abstract: Hyperscanning is an emerging technology that concurrently scans the neural dynamics of multiple individuals to study interpersonal interactions. In particular, hyperscanning with wireless electroencephalography (EEG) is increasingly popular owing to its mobility and ability to decipher social interactions in natural settings at the millisecond scale. To align multiple EEG time series with sophisticated event markers in a single time domain, a precise and unified timestamp is required for stream synchronization. This study proposed a clock-synchronized method using a custom-made RJ45 cable to coordinate the sampling between wireless EEG amplifiers to prevent incorrect estimation of interbrain connectivity due to asynchronous sampling. In this method, analog-to-digital converters are driven by the same sampling clock. Additionally, two clock-synchronized amplifiers leverage additional RF channels to keep the counter of their receiving dongles updated, guaranteeing that binding event markers received by the dongle with the EEG time series have the correct timestamp. The results of two simulation experiments and one video gaming experiment revealed that the proposed method ensures synchronous sampling in a system with multiple EEG devices, achieving near-zero phase-lag and negligible amplitude difference between signals. According to all of the signal-similarity metrics, the suggested method is a promising option for wireless EEG hyperscanning and can be utilized to precisely assess the interbrain couplings underlying social-interaction behaviors.


title: Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates

abstract:
AO_SCPLOWBSTRACTC_SCPLOWSinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are "active," since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these "active sinking particles," has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. "Scale-free vertical tracking microscopy." Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached Vorticella cause substantial changes to the flow around aggregates in a dynamic manner and reshape mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking significantly changes how aggregates interact with the water-column at larger scales by modifying the encounter and plume cross-sections and by inducing sustained aggregate rotations. In this way our work suggests an important role of biological activity in understanding the growth, degradation, composition and sinking speeds of aggregates with consequences for predicting vertical material fluxes in marine, freshwater and man-made environments.

1 Significance StatementSinking aggregates are a critical part of aquatic ecosystems. Plentiful sinking aggregates account for the majority of carbon sequestration in the oceans. These aggregates are densely colonized by microorganisms, including many that generate feeding currents. Utilizing a novel instrument for high resolution imaging of sinking particles, we demonstrate that these feeding currents significantly change how water flows near the aggregates. We show that these changes in flow are likely to affect aquatic system processes, including aggregation rates, degradation rates, sinking speeds, and aggregate composition. Our work provides a starting point for exploring the larger-scale implications of attached organisms on these system processes, which, in turn, are critical for understanding carbon sequestration in the oceans or efficiency in waste-water treatment plants.


title: Functional multi-omics reveals genetic and pharmacologic regulation of surface CD38 in multiple myeloma

abstract: CD38 is a surface ectoenzyme expressed at high levels on myeloma plasma cells and is the target for the monoclonal antibodies (mAbs) daratumumab and isatuximab. CD38 density on tumor cells is an important determinant of mAb efficacy, and CD38 loss after mAb treatment may play a role in resistance. Several small molecules have been found to increase tumor surface CD38, with the goal of boosting mAb efficacy in a co-treatment strategy. Here we sought to extend our currently limited insight into CD38 surface expression by using a multi-omics approach. Genome-wide CRISPR-interference screens integrated with patient-centered epigenetic analysis confirmed known regulators of CD38, such as RARA, while revealing XBP1 and SPI1 as other key transcription factors governing surface CD38 levels. CD38 knockdown followed by cell surface proteomics demonstrated no significant remodeling of the myeloma "surfaceome" after genetically-induced loss of this antigen. Integrated transcriptome and surface proteome data confirmed high specificity of all-trans retinoic acid in upregulating CD38 in contrast to broader effects of azacytidine and panobinostat. Finally, unbiased phosphoproteomics identified inhibition of MAP kinase pathway signaling in tumor cells after daratumumab treatment. Our work provides a resource to design strategies to enhance efficacy of CD38-targeting immunotherapies in myeloma.


title: Sex-dependent development of Kras-induced anal squamous cell carcinoma in mice

abstract: Anal squamous cell carcinoma (SCC) will be diagnosed in an estimated 9,080 adults in the United States this year, and rates have been rising over the last several decades. Most people that develop anal SCC have associated human papillomavirus (HPV) infection ([~]85-95%), with approximately 5-15% of anal SCC cases occurring in HPV-negative patients from unknown etiology. This study identified and characterized a Kras-driven, female sex hormone-dependent development of anal squamous cell carcinoma (SCC) in the LSL-KrasG12D ; Pdx1-Cre (KC) mouse model that is not dependent on papillomavirus infection. One hundred percent of female KC mice develop anal SCC, while no male KC mice develop tumors. Both male and female KC anal tissue express Pdx1 and Cre-recombinase mRNA, and the activated mutant KrasG12D gene. Although the driver gene mutation KrasG12D is present in anus of both sexes, only female KC mice develop Kras-mutant induced anal SCC. To understand the sex-dependent differences, KC male mice were castrated and KC female mice were ovariectomized. Castrated KC males displayed an unchanged phenotype with no anal tumor formation. In contrast, ovariectomized KC females demonstrated a marked reduction in anal SCC development, with only 15% developing anal SCC. Finally, exogenous administration of estrogen rescued the tumor development in ovariectomized KC female mice and induced tumor development in castrated KC males. These results confirm that the anal SCC is estrogen mediated. The delineation of the role of female sex hormones in mediating mutant Kras to drive anal SCC pathogenesis highlights a subtype of anal SCC that is independent of papillomavirus infection. These findings may have clinical applicability for the papillomavirus-negative subset of anal SCC patients that typically respond poorly to standard of care chemoradiation.


title: Phenolic profiles and antioxidant activities of Saskatchewan (Canada) bred haskap (Lonicera caerulea) berries

abstract: Phenolic extracts from five Saskatoon, Saskatchewan, bred and grown haskap berry varieties (Aurora, Blizzard, Honey Bee, Indigo Gem, and Tundra) were characterized via liquid chromatography with photodiode array detection (HPLC-PDA) and mass spectrometry (HPLC-MS/MS). Tundra had the highest phenolic content (727.0 mg/100 g FW) while Indigo Gem had the highest anthocyanin content (447.8 mg/100 g FW). HPLC-MS/MS identified two previously unreported anthocyanins (Tundra variety): delphinidin-sambubioside and a peonidin-pentoside. Fruit extracts were fractionated to produce an anthocyanin rich (40% ethanol) and flavanol/flavonol rich (100% ethanol) fraction. This process affords the ability to isolate/concentrate specific subclasses for nutraceutical applications. High in vitro radical scavenging was observed for all haskap phenolic extracts. An extract from the Tundra variety delayed borage oil oxidation more effectively than commercial antioxidants (BHT and Rosamox). These results show the high phenolic content of these haskaps along with their capacity for radical scavenging/delaying lipid oxidation, indicating potential commercial value.

category: plant biology


title: The ethanol tolerance in Saccharomyces cerevisiae under a phenomics perspective

abstract: Ethanol (EtOH) is a substantial stressor for Saccharomyces cerevisiae. Data integration from strains with different phenotypes, including EtOH stress-responsive lncRNAs, are still not available. We covered these issues seeking systems modifications that drive the divergences between higher (HT) and lower (LT) EtOH tolerant strains under their highest stress conditions. We showed that these phenotypes are neither related to high viability nor faster population rebound after stress relief. LncRNAs work on many stress-responsive systems in a strain-specific manner promoting the EtOH tolerance. Cells use membraneless RNA/protein storage and degradation systems to endure the stress harming, and lncRNAs jointly promote EtOH tolerance. CTA1 and longevity are primer systems promoting phenotype-specific gene expression. The lower cell viability and growth under stress is a byproduct of sphingolipids and inositol phosphorylceramide dampening, acerbated in HTs by sphinganine, ERG9, and squalene overloads; LTs diminish this harm by accumulating inositol 1-phosphate. The diauxic shift drives an EtOH buffering by promoting an energy burst under stress, mainly in HTs. Analysis of mutants showed genes and lncRNAs in three strains critical for their EtOH tolerance. Finally, longevity, peroxisome, energy and lipid metabolisms, RNA/protein degradation and storage systems are the main pathways driving the EtOH tolerance phenotypes.

category: systems biology