title: The Parastagonospora nodorum necrotrophic effector SnTox5 targets the wheat gene Snn5 and facilitates entry into the leaf mesophyll

abstract: Parastagonospora nodorum, causal agent of septoria nodorum blotch, is a destructive necrotrophic fungal pathogen of wheat. P. nodorum is known to secrete several necrotrophic effectors that target wheat susceptibility genes that trigger classical biotrophic resistance responses but resulting in susceptibility rather than resistance. SnTox5 targets the wheat susceptibility gene Snn5 to induce necrosis. In this study, we used full genome sequences of 197 P. nodorum isolates collected from the US and their disease phenotyping on the Snn5 differential line LP29, to perform genome wide association study analysis to localize the SnTox5 gene to chromosome 8 of P. nodorum. SnTox5 was validated using gene transformation and CRISPR-Cas9 based gene disruption. SnTox5 encoded a small secreted protein with a 22 and 45 amino acid secretion signal and a pro sequence, respectively. The SnTox5 gene is under purifying selection in the Upper Midwest but under strong diversifying selection in the South/East regions of the US. Comparison of wild type and SnTox5-disrupted strains on wheat lines with and without the susceptibility target Snn5 showed that SnTox5 has two functions, 1) facilitating colonization of the mesophyll layer, and 2) targeting Snn5 to induce programmed cell death to provide cellular nutrient to complete its necrotrophic life cycle.

category: pathology


title: Small-molecule-mediated OGG1 inhibition attenuates pulmonary inflammation and lung fibrosis

abstract: Interstitial lung diseases such as idiopathic pulmonary fibrosis (IPF) are caused by persistent micro-injuries to alveolar epithelial tissues together with aberrant repair processes. Despite substantial advancement in our understanding of IPF progression, numerous questions remain concerning disease pathology. IPF is currently treated with pirfenidone and nintedanib, compounds which slow the rate of disease progression but fail to treat underlying causes of disease. The DNA repair enzyme 8-oxoguanine DNA glycosylase-1 (OGG1) is upregulated following TGF-{beta} exposure in several fibrosis-associated cell types. Currently, no pharmaceutical solutions targeting OGG1 have been utilized in the treatment of IPF. In this study, a novel small molecule OGG1 inhibitor, TH5487, decreased myofibroblast transition and associated pro-fibrotic markers in fibroblast cells. In addition, TH5487 decreased pro-inflammatory cytokine production, inflammatory cell infiltration, and lung remodeling in a murine model of bleomycin-induced pulmonary fibrosis. Taken together, these data strongly suggest that TH5487 is a potent, specific, and clinically-relevant treatment for IPF.

category: pharmacology and toxicology


title: Evaluation of the growth performance, physiological traits, antioxidant indices, and heat shock protein 70 to dietary supplementation of stinging nettle (Urtica dioica) in broilers exposed to chronic heat stress

abstract: Heat stress is known as one of the most prevalent environmental stressors in poultry production, which is associated with oxidative stress. Stinging nettle is a medicinal herb with strong antioxidant properties. The present study was conducted to evaluate the effects of dietary stinging nettle at two different levels (2% and 4%) on growth performance and oxidative stress indices of broilers exposed to chronic heat stress. On day 14, a total of 240 broiler chickens were randomly assigned to 6 treatment groups as follows: 1) NC: negative control; 2) HS: heat-stressed broiler; 3) HS-SN2: heat-stressed broiler fed by 2% dietary stinging nettle; 4) HS-SN4: heat-stressed broilers fed by 4% stinging nettle; 5) SN2: no heat-stressed broilers fed by 2% dietary stinging nettle; 6) SN4: no heat-stressed broilers fed by 4% dietary stinging nettle. Diet supplementation with stinging nettle was performed from days 14 to 35 and a chronic heat stress was induced from days 22 to 29. The growth performance and oxidative indices were evaluated on days 14, 21, 29, and 35. Rectal temperature and panting frequency were assessed on days 22, 25, and 29. As a result, weight gain and food intake decreased in the HS compared to the NC, and these parameters increased in the HS-SN2 and HS-SN4 compared to the HS (P<0.05). The HS, HS-SN2, and HS-SN4 groups had a significantly higher rectal temperature and panting frequency. The HS had the higher circulating MDA and HSP70, and lower T-AOC, SOD, and GSH-Px compared to the treatments. The HS-SN4 had a significantly lower MDA and HSP70, and higher T-AOC, GSH-Px, and SOD compared to the HS and HS-SN2. In conclusion, the addition of 4% stinging nettle powder to the broilers diet improved the oxidative status in heat-stressed birds. Furthermore, this herb could be utilized as a feed additive in poultry diet to improve birds health and defense mechanisms under stressful conditions.

category: physiology


title: The scaffold-dependent function of RIPK1 in dendritic cells promotes injury-induced colitis

abstract: Receptor interacting protein kinase 1 (RIPK1) is a cytosolic multidomain protein that controls cell life and death. While RIPK1 promotes cell death through its kinase activity, it also functions as a scaffold protein to promote cell survival by inhibiting FADD-caspase 8-dependent apoptosis and RIPK3-MLKL-dependent necroptosis. This pro-survival function is highlighted by excess cell death and a perinatal lethality in Ripk1-/- mice. Recently, loss of function mutation of RIPK1 was found in patients with immunodeficiency and inflammatory bowel diseases. Hematopoietic stem cell transplantation restored not only immunodeficiency but also intestinal inflammatory pathology, indicating that RIPK1 in hematopoietic cells is critical to maintain intestinal immune homeostasis. Here, we generated dendritic cell (DC)-specific Ripk1-/- mice in a genetic background with loss of RIPK1 kinase activity and found that the mice developed spontaneous colonic inflammation characterized by increased neutrophil infiltration. In addition, these mice were highly resistant to injury-induced colitis. The increased neutrophil infiltration in the colon and the resistance to colitis were restored by dual inactivation of RIPK3 and FADD, but not by inhibition of RIPK3, MLKL, or ZBP1 alone. Altogether, these results reveal a scaffold activity-dependent role of RIPK1 in protecting colonic DCs from apoptotic insults and maintenance of colonic immune homeostasis.

category: immunology


title: Allelic and Genotypic Frequencies of NAT2, CYP2E1 and AADAC genes in a cohort of Peruvian Tuberculosis Patients

abstract:
BackgroundWe determined the frequency of genetic polymorphisms in three anti-TB drug metabolic proteins previously reported: N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1) and arylacetamide deacetylase (AADAC) within a Peruvian population in a cohort of TB patients. We included 395 participants completed their anti-tuberculosis treatment.

Results[~]74% of the participants are carriers of slow metabolizer genotypes: NAT2*5, NAT2*6 and NAT2*7, which increase the sensitivity of INH at low doses and increase the risk of drug-induced liver injuries. [~] 64% are homozygous for the wild-type CYP2E1*1A allele, which could increase the risk of hepatotoxicity. However, 16% had a NAT2 fast metabolizer phenotype which could increase the risk of acquiring resistance to INH, thereby increasing the risk of multidrug-resistant (MDR) or treatment failure. The frequency of rs1803155 (AADAC*2 allele) was higher (99.9%) in Peruvians than in in European American, African American, Japanese, and Korean populations.

ConclusionsThis high prevalence of slow metabolizers for Isoniazid in the Peruvian population should be further studied and considered to help individualize drug regimens, especially in countries with a great genetic diversity like Peru. These data will help the Peruvian National Tuberculosis Control Program develop new strategies for therapies.

category: genetics


title: Comprehensive Profiling of Plasma Exosomes Using Data Independent Acquisitions, New Tools for Aging Cohort Studies

abstract: Aging is a complex biological process associated with progressive loss of physiological function and susceptibility to several diseases, such as cancer and neurodegeneration. Exosomes are involved in many cellular signaling pathways, and their cargo may serve as promising disease or aging biomarkers. These membrane-bound extracellular vesicles facilitate the transport of intracellular contents to proximal and distal cells in the body. Here, we investigated two omics approaches for exosome analysis. To overcome the challenges of plasma exosome contamination with abundant soluble plasma proteins, we developed a high-throughput method to isolate highly purified exosomes from human plasma by sequential size-exclusion chromatography and ultrafiltration. First, we used data-dependent acquisitions from offline high-pH reversed-phase fractions of exosome lysate to generate a deep spectral library comprising [~]2,300 exosome proteins. Second, in a pilot aging study, we used comprehensive data-independent acquisitions to compare plasma exosomes from young (20-26 yrs) and old (60-66 yrs) individuals. We quantified 1,318 exosome proteins, and levels of 144 proteins were significantly different in young and old plasma groups (Q<0.05 and >1.5-fold change). We also analyzed exosome miRNA cargo and detected 331 miRNAs. Levels of several were significantly different in young and old individuals. In addition, 88 and 17 miRNAs were unique to old and young individuals, respectively. Plasma exosome biomarkers have great potential for translational studies investigating biomarkers of aging and age-related diseases and to monitor therapeutic aging interventions.

category: cell biology


title: Brazil Nut Effect Drives Pattern Formation in Early Mammalian Embryos

abstract: The formation of three-dimensional ordered spatial patterns, which is essential for embryonic development, tissue regeneration, and cancer metastasis, is mainly guided by the chemical concentration gradient of morphogens. However, since no chemical concentration gradient has been observed in the early embryonic development (pre-implantation) of mammals, the pattern formation mechanism has been unsolved for a long time. During the second cell fate decision of mouse embryos, the inner cell mass (ICM) segregates into topographically regionalized epiblast (EPI) and primitive endoderm (PrE) layers. Here, we report that the segregation process of PrE/EPI precursors coincides with an emerged periodic expansion-contraction vibration of the blastocyst cavity, which induces phase transition in the ICM compartment to a higher fluidity state and generates directional tissue flows. By experiments and modeling, we demonstrate that the spatial segregation of PrE and EPI precursors is mediated by a "Brazil nut effect"-like viscous segregation mechanism in which PrE precursors with low affinity gradually migrate to the surface of ICM along with the tissue flow, while EPI precursors with high affinity remains inside ICM under cavity vibration. Artificially manipulation of the frequency and amplitude of cavity vibration could control the process of spatial separation as well as lineage specification of PrE/EPI. Furthermore, disruption of the cavity vibration in the initial stage after segregation could reverse the ICM cells back to a mixed state. Therefore, this study reveals a fundamental mechanism that guarantees the robustness of cell segregation and pattern formation without specific morphogens in early mammalian embryos. Our model also emphasizes a conserved function of cavity structure that widely exists in organisms as an energy reservoir and converter between different forms, such as chemical and mechanical energy.

category: developmental biology


title: A new murine Rpl5 (uL18) mutation provides a unique model of variably penetrant Diamond Blackfan Anemia

abstract: Ribosome dysfunction is implicated in multiple abnormal developmental and disease states in humans. Heterozygous germline mutations in genes encoding ribosomal proteins (RPs) are found in the majority of individuals with Diamond Blackfan anemia (DBA) while somatic mutations have been implicated in a variety of cancers and other disorders. Ribosomal protein-deficient animal models show variable phenotypes and penetrance, similar to human DBA patients. The spontaneous anemia remission observed in some DBA patients occurs via unknown mechanism(s) and has not been previously described in animal models. Here we characterized a novel ENU mouse mutant (Skax23m1Jus) with growth and skeletal defects, cardiac malformations and increased mortality. Following genetic mapping and whole exome sequencing, we identified an intronic Rpl5 mutation, which segregated with all affected mice. This mutation was associated with decreased ribosome generation, consistent with Rpl5 haploinsufficiency. Rpl5Skax23-Jus mutant animals had a profound delay in erythroid maturation and increased mortality at embryonic day E12.5, which improved by E14.5. Surviving mutant animals had a macrocytic anemia at birth as well as evidence of ventricular septal defect (VSD). Surviving adult and aged mice exhibited no hematopoietic defect or VSD. We propose that this novel Rpl5Skax23-Jus mutant mouse will be useful to study the factors influencing the variable penetrance and anemia remission that are observed in DBA.


title: A synthetic RNA-mediated evolution system in yeast

abstract: Laboratory evolution is a powerful approach to search for genetic adaptations to new or improved phenotypes, yet either relies on labour-intensive human-guided iterative rounds of mutagenesis and selection, or prolonged adaptation regimes based on naturally evolving cell populations. Here we present CRISPR- and RNA-assisted in vivo directed evolution (CRAIDE) of genomic loci using evolving chimeric donor gRNAs continuously delivered from an error-prone T7 RNA polymerase, and directly introduced as RNA repair donors into genomic targets under either Cas9 or dCas9 guidance. We validate CRAIDE by evolving novel functional variants of an auxotrophic marker gene, and by conferring resistance to a toxic amino acid analogue in bakers yeast Saccharomyces cerevisiae with a mutation rate >3,000-fold higher compared to spontaneous native rate, thus enabling the first demonstrations of in vivo delivery and information transfer from long evolving RNA donor templates into genomic context without the use of in vitro supplied and pre-programmed repair donors.

category: bioengineering


title: Mapping yeast mitotic 5' resection at base resolution reveals the sequence and positional dependence of nucleases in vivo

abstract: Resection of the 5-terminated strand at DNA double strand breaks (DSBs) is the critical regulated step in the transition to homologous recombination. Biochemical and genetic studies have led to a multi-step model of DSB resection in which endonucleolytic cleavage mediated by Mre11 in partnership with Sae2 is coupled with exonucleolytic cleavage mediated by redundant pathways catalyzed by Exo1 and Sgs1/Dna2. These models have not been well tested at mitotic DSBs in vivo because most methods used to monitor resection cannot precisely map early cleavage events. Here we report resection monitoring with high-throughput sequencing in which molecular identifiers allow exact counting of cleaved 5 ends at base pair resolution. Mutant strains, including exo1{Delta}, mre11-H125N, exo1{Delta} and exo1{Delta} sgs1{Delta}, revealed a major Mre11-dependent cleavage position 60 to 70 bp from the DSB end whose exact position depended on local sequence and tracked a possible motif. They further revealed an Exo1-dependent pause point approximately 200 bp from the DSB. Suppressing resection extension in exo1{Delta} sgs1{Delta} yeast exposed a footprint of regions where cleavage was restricted within 119 bp of the DSB. These results provide detailed in vivo support of prevailing models of DSB resection and extend them to show the combined influence of sequence specificity and access restrictions on Mre11 and Exo1 nucleases.


title: A partially sex-reversed giant kelp sheds light into the mechanisms of sexual differentiation in a UV sexual system

abstract: In UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the brown algal model Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and suggested that the female developmental program may occur by  default, triggered in the absence of the male master sex determination gene(s). Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental program is however incomplete, because gametes of this feminised male are unable to produce the sperm-attracting pheromone lamoxirene. We identify the transcriptomic patterns underlying the male and female specific developmental programs, and reveal the faster evolutionary rates of male-biased genes compared to female-biased and unbiased genes. Moreover, we show that the phenotypic feminisation of the variant strain is associated with both feminisation and de-masculinisation of gene expression patterns. Importantly, the feminisation phenotype was associated with the dramatic downregulation of two V-specific genes including a candidate sex-determining gene on the V-specific region. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system with marked sexual dimorphism, and contribute to disentangling the role of sex-linked genes and autosomal gene expression in the initiation of the male and female developmental programs. Overall, the data presented here imply that the U-specific region in the giant kelp is not required to initiate the female developmental program, but is critical to produce fully functional eggs, arguing against the idea that female is the  default sex in this species.

category: evolutionary biology


title: Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

abstract:
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) approaches capture the broadest perspective on community composition, culture-dependent (CD) methods can capture low abundance taxa that are missed using CI approaches. The aim of this study was to assess microbial diversity in tropical marine sediments collected from five shallow water sites in Belize using both CD and CI approaches. CD methods captured approximately 3% of the >800 genera detected across the five sites. Additionally, 39 genera were only detected using CD approaches revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in the delineation of sediment communities. This study provides important baseline data describing shallow water sediment microbial communities and evidence that standard cultivation techniques may be more effective than previously recognized.

Originality-Significance StatementMarine sediments host some of the most diverse microbial communities on the planet. While these communities are critical for global nutrient cycling, the oceanic food web, and the maintenance of ecosystem dynamics, they remain poorly studied. Studies that have assessed sediment communities typically use culture-independent approaches, which have known biases and can miss ecologically important taxa. Here we describe microbial diversity in marine sediments using both culture-dependent and culture-independent approaches. Our culturing approach, sequencing communities as opposed to individual colonies, revealed an additional 39 genera that were not detected with culture-independent methods. Additionally, we cultured numerous, as-yet undescribed species, suggesting that traditional culturing practices can be more efficient than commonly thought. Moreover, our results indicate rare taxa play an important role in distinguishing microbial communities at different sites, thus highlighting the importance of deep sequencing and incorporating culture-dependent approaches for diversity assessments.

category: microbiology


title: De novo purine nucleotide biosynthesis mediated by amidophosphoribosyl transferase is required for conidiation and essential for the successful host colonization of Magnaporthe oryzae

abstract: Amidophosphoribosyl transferase catalyzes the first step of the purine nucleotide biosynthesis by converting 5-phosphoribosyl-1-pyrophosphate into 5-phosphoribosyl-1-amine. In this study, we identified and characterized the functions of MoAde4, an ortholog of yeast Ade4 in the rice blast fungus. MoAde4 is a 537-amino acid protein containing the GATase_6 and pribosyltran domains. Quantitative real-time PCR analysis showed MoADE4 transcripts were highly expressed during conidiation, early-infection, and late-infection stages of the fungus. Disruption of MoADE4 gene resulted in {Delta}Moade4 mutant exhibiting adenine, adenosine, and hypoxanthine auxotrophy on MM. Conidia quantification assays showed {Delta}Moade4 mutant was significantly reduced in sporulation. The conidia of {Delta}Moade4 mutant could still form appressoria but mostly failed to penetrate the rice cuticle. Pathogenicity test showed {Delta}Moade4 was completely nonpathogenic on rice and barley leaves which was attributed by failure of its infectious hyphae to colonize the host cells. The {Delta}Moade4 was defective in induction of strong host immunity and had its purine transporter genes repressed during in planta infection. Addition of exogenous adenine partially rescued conidiation and pathogenicity defects of the {Delta}Moade4 mutant on the barley and rice leaves. Localization assays showed that MoAde4 is located in the cytoplasm. Taken together, our results demonstrate that purine biosynthesis orchestrated by MoAde4 is required for fungal development, conidiation, more importantly, we found it to be essential for fungal pathogenicity not because of the appressorial formation, but appressorium penetration and host colonization during the plant infection of M. oryzae. Thus this findings suggests that purine biosynthesis could act as an important target for combating recalcitrant plant fungal pathogens.

category: molecular biology


title: Post-transcriptional dysregulation in autism, schizophrenia and bipolar disorder

abstract: Post-transcriptional gene regulation (PTGR) contributes to numerous aspects of RNA metabolism. While multiple regulators of PTGR have been associated with the occurrence and development of psychiatric disorders, a systematic investigation of the role of PTGR in the context of neuropsychiatric disorders is still lacking. In this work, we developed a new transcriptome -based algorithm to estimate PTGR and applied it to an RNA-Seq dataset of 2160 brain samples from individuals with autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BD) and controls. The results showed that the contribution of PTGR abnormality to gene differential expression between three common psychiatric disorders and controls was about 30% of that of transcriptional gene regulation (TGR) abnormality. Besides, aberrant PTGR tended to decrease RNA stability in SCZ/BD, while increase RNA stability in ASD, implicating contrasting pathologies among diseases. The abnormal alteration of PTGR in SCZ/BD converged on the inhibition of neurogenesis and neural differentiation, whereas dysregulation of PTGR in ASD induced enhanced activity of apoptosis. This suggested that heterogeneity in disease mechanism and clinical manifestation across different psychiatric disorders may be partially attributed to the diverse role of PTGR. Intriguingly, we identified a promising RBP (RNA bind protein) ELAVL3 (ELAV-Like Protein 3) that have a profound role in all three psychiatric disorders. Our systematic study expands the understanding of the link between PTGR and psychiatric disorders and also open a new avenue for deciphering the pathogenesis of psychiatric disorders.

category: genomics


title: Neuronal activity patterns regulate BDNF expression in cortical neurons via synaptic connections and calcium signaling

abstract: During development, cortical circuits are remodeled by spontaneous and sensory-evoked activity via alteration of the expression of wiring molecules. An intriguing question is how physiological neuronal activity modifies the expression of these molecules in developing cortical networks. Here, we addressed this issue, focusing on brain-derived neurotrophic factor (BDNF), one of the factors underlying cortical wiring. Real-time imaging of Bdnf promoter activity in organotypic slice cultures revealed that patterned stimuli differentially regulated the increase and the time course of the promoter activity in upper layer neurons. Calcium imaging further demonstrated that stimulus-dependent increases in the promoter activity were roughly proportional to the increase in intracellular Ca2+ concentration per unit time. Finally, optogenetic stimulation showed that the promoter activity was increased efficiently by patterned stimulation in defined cortical circuits. These results suggest that physiological stimulation patterns differentially tune activity-dependent gene expression in developing cortical neurons via cortical circuits, synaptic responses, and alteration of intracellular calcium signaling.

category: neuroscience


title: Concurrent feature-specific reactivation within the hippocampus and neocortex facilitates episodic memory retrieval

abstract: The hippocampus is a key brain region for the storage and retrieval of episodic memories, but how it performs this function is unresolved. According to the hippocampal indexing theory, the hippocampus stores an event-specific index of the pattern of neocortical activity that occurred during perception. During retrieval, reactivation of the index by a partial cue facilitates the reactivation of the associated neocortical pattern. Therefore, event-specific retrieval requires joint reactivation of the hippocampal index and the associated neocortical networks. To test this theory, we examine the relation between performance on a recognition memory task requiring retrieval of image-specific visual details and feature-specific reactivation within the hippocampus and neocortex. We show that trial-by-trial recognition accuracy correlates with neural reactivation of low-level features (e.g. luminosity and edges) within the posterior hippocampus and early visual cortex for participants with high recognition lure accuracy. As predicted, the two regions interact, such that recognition accuracy correlates with hippocampal reactivation only when reactivation co-occurs within the early visual cortex (and vice-versa). In addition to supporting the hippocampal indexing theory, our findings show large individual differences in the features underlying visual memory and suggest that the anterior and posterior hippocampus represents gist-like and detailed features, respectively.


title: DLL4 and PDGF-BB regulate migration of human iPSC-derived skeletal myogenic progenitors

abstract: Muscle satellite stem cells (MuSCs) are responsible for skeletal muscle growth and regeneration. Despite their differentiation potential, human MuSCs have limited in vitro expansion and in vivo migration capacity, limiting their use in cell therapies for diseases affecting multiple skeletal muscle groups such as muscular dystrophies. Several protocols have been developed to derive progenitor cells similar to MuSCs from human induced pluripotent stem cells (hiPSCs), in order to establish a source of myogenic cells with controllable proliferation and differentiation capacity. However, currently available hiPSC myogenic derivatives also suffer from limitations of cell migration, ultimately delaying their clinical translation. Here we provide evidence that activation of NOTCH and PDGF pathways with DLL4 and PDGF-BB improves migration of hiPSC-derived myogenic progenitors in vitro. Transcriptomic and functional analyses demonstrate that this property is conserved across species and multiple hiPSC lines, including genetically-corrected hiPSC derivatives from a patient with Duchenne muscular dystrophy. DLL4 and PDGF-BB treatment had no negative impact on cell proliferation; cells maintained their myogenic memory, with differentiation fully rescued by NOTCH inhibition. RNAseq analysis indicate that pathways involved in cell migration are modulated in treated myogenic progenitors, consistent with results from functional profiling of cell motility at single cell resolution. Notably, treated cells also showed enhanced trans-endothelial migration in transwell assays. Enhancing extravasation is a key translational milestone for intravascular delivery of hiPSC myogenic derivatives: our study establishes the foundations of a transgene-free, developmentally inspired strategy to achieve this goal, moving hiPSCs one step closer to future muscle gene and cell therapies.


title: How does the magnitude of genetic variation affect eco-evolutionary dynamics in character displacement?

abstract: AO_SCPLOWBSTRACTC_SCPLOWWhile previous studies on character displacement tended to focus on trait divergence and convergence as a result of long-term evolution, recent studies suggest that character displacement can be a special case of evolutionary rescue, where rapid evolution prevents population extinction by weakening negative interspecific interactions. When the magnitude of genetic variation is small, however, the speed of trait divergence can be slow and populations may go extinct before the completion of character displacement. Here we analyzed a simple model to examine how the magnitude of genetic variation affects evolutionary rescue via ecological and reproductive character displacement that weakens resource competition and reproductive interference, respectively. We found that the large additive genetic variance is more important for preventing extinction in reproductive character displacement than in ecological character displacement. This is because reproductive interference produces a locally stable coexistence equilibrium with positive frequency-dependence (i.e., minority disadvantage) whereas ecological character displacement results in a globally stable coexistence equilibrium. Furthermore, population extinction becomes less likely when ecological and reproductive character displacement occur simultaneously due to positive covariance between ecological and reproductive traits. Our results suggest that while reproductive character displacement may be rarer than ecological character displacement, it is more likely to occur when there exists positive trait covariance, such as the case of a magic trait in reinforcement of speciation processes.

category: ecology


title: The intestinal microbiota-driven dopamine level influences social interaction and innate color preference in zebrafish larvae

abstract: Gut microbiota influence neurodevelopment of brain and programing of behaviors. However, the mechanism underlining the relationship between shoals behaviors and intestinal microbiota remain controversial and the roles of neurotransmitters are still unclear. Here we show that, shoaling behavior affected the innate color preference of shoals, indicating that shoals tended to choose a favorable color environment that benefits social contact. Meanwhile, administration of D1-R antagonist disrupted the social interaction which led to the deficits of color preference. More importantly, the altered microbiota caused by an antibiotic OTC decreased the sociability and weakened shoals color preference. When given a supplement of LGG after OTC exposure, fish exhibited an unexpectedly recovery capability in social cohesion and color preference. Our findings show that dopamine level of brain could mediate both social recognition and color preference, and highlight the pathway of microbial metabolites through the microbiota-gut-brain axis that coordinate the production of dopamine.

category: animal behavior and cognition


title: Data variability in standardised cell culture experiments

abstract: Despite much debate about a perceived  reproducibility crisis in the life sciences, it remains unclear what level of replicability is technically possible [1,2]. Here, we analysed the variation among drug response data of the NCI60 project, which for decades has tested anti-cancer agents in a 60-cell line panel following a standardised protocol [3]. In total, 2.8 million compound/cell line experiments are available in the NCI60 resource CellMiner [4]. The largest fold change between the lowest and highest GI50 (concentration that reduces cell viability by 50%) in a compound/cell line combination was 3.16 x 1010. All compound/cell line combinations with >100 experiments displayed maximum GI50 fold changes >5, 99.7% maximum fold changes >10, 87.3% maximum fold changes >100, and 70.5% maximum fold changes >1000. FDA-approved drugs and experimental agents displayed similar variation. The variability remained very high after removal of outliers and among experiments performed in the same month. Hence, our analysis shows that high variability is an intrinsic feature of experimentation in biological systems, even among highly standardised experiments in a world-leading research environment. Thus, a narrow focus on experiment standardisation does not ensure a high level of replicability on its own.


title: Identification of Kinases Activated by Multiple Pro-Angiogenic Growth Factors

abstract: Antiangiogenic therapy began as an effort to inhibit VEGF signaling, which was thought to be the sole factor driving tumor angiogenesis. It has become clear that there are more pro-angiogenic growth factors that can participate in and can substitute for VEGF during tumor vascularization. This has led to the development of multi-kinase inhibitors that simultaneously target multiple growth factor receptors. These inhibitors perform better than monotherapies yet to date no multi-kinase inhibitor targets all receptors known to be involved in pro-angiogenic signaling and resistance inevitably occurs. Given the large number of pro-angiogenic growth factors identified, it may be impossible to simultaneously target all pro-angiogenic growth factor receptors with a single agent. Here we search downstream of the receptors for kinase targets that would be critical to endothelial cell proliferation, irrespective of the growth factor signal. To do this systematically we develop a quantitative endothelial cell proliferation assay and combine it with "kinome regression" or KIR, a recently developed computational and kinase screening method capable of identifying kinases that influence any measurable and quantitative phenotype, such as proliferation. We report the result of this analysis. The kinases implicated by KIR are both expected and unexpected intracellular kinases. Using RNA interference we provide orthogonal evidence of their importance in endothelial cell proliferation. This approach points to a new strategy that can be employed to develop a more complete anti-angiogenic blockade.

category: systems biology


title: Increased region of surround stimulation enhances contextual feedback and feedforward processing in human V1

abstract:
The majority of synaptic inputs to the primary visual cortex (V1) are non-feedforward, instead originating from local and anatomical feedback connections. Animal electrophysiology experiments show that feedback signals originating from higher visual areas with larger receptive fields modulate the surround receptive fields of V1 neurons. Theories of cortical processing propose various roles for feedback and feedforward processing, but systematically investigating their independent contributions to cortical processing is challenging because feedback and feedforward processes coexist even in single neurons. Capitalising on the larger receptive fields of higher visual areas compared to primary visual cortex (V1), we used an occlusion paradigm that isolates top-down influences from feedforward processing. We utilised functional magnetic resonance imaging (fMRI) and multi-voxel pattern analysis methods in humans viewing natural scene images. We parametrically measured how the availability of contextual information determines the presence of detectable feedback information in non-stimulated V1, and how feedback information interacts with feedforward processing. We show that increasing the visibility of the contextual surround increases scene-specific feedback information, and that this contextual feedback enhances feedforward information. Our findings are in line with theories that cortical feedback signals transmit internal models of predicted inputs.

Significance StatementThe visual system has circuit mechanisms for processing scene context. These circuits involve lateral and feedback inputs to neurons. These inputs interact with feedforward inputs and modulate neuronal responses to visual stimuli presented outside their receptive fields. Systematically investigating independent contributions of feedback and feedforward processes is challenging because they coexist even in single neurons. Here we use an occlusion paradigm to isolate feedback and lateral signals in human participants viewing natural scene images in fMRI. We show that increasing the visibility of the contextual surround increases scene-specific feedback information, which also enhances feedforward signals. Our findings are in line with theories that cortical feedback signals carry abstract internal models that combine with more detailed representations in primary visual cortex.


title: Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters

abstract: In invasive electrophysiological recordings, a variety of neuronal oscillations can be detected across the cortex, with overlap in space and time. This overlap complicates measurement of neuronal oscillations using standard referencing schemes, like common average or bipolar referencing. Here, we illustrate the effects of spatial mixing on measuring neuronal oscillations in invasive electrophysiological recordings and demonstrate the benefits of using data-driven referencing schemes in order to improve measurement of neuronal oscillations. We discuss referencing as the application of a spatial filter. Spatio-spectral decomposition is used to estimate data-driven spatial filters, a computationally fast method which specifically enhances signal-to-noise ratio for oscillations in a frequency band of interest. We show that application of these data-driven spatial filters has benefits for data exploration, investigation of temporal dynamics and assessment of peak frequencies of neuronal oscillations. We demonstrate multiple use cases, exploring between-participant variability in presence of oscillations, spatial spread and waveform shape of different rhythms as well as narrowband noise removal with the aid of spatial filters. We find high between-participant variability in the presence of neural oscillations, a large variation in spatial spread of individual rhythms and many non-sinusoidal rhythms across the cortex. Improved measurement of cortical rhythms will yield better conditions for establishing links between cortical activity and behavior, as well as bridging scales between the invasive intracranial measurements and noninvasive macroscale scalp measurements.


title: Visual stimulation with blue wavelength light drives V1 effectively eliminating stray light contamination during two-photon calcium imaging

abstract:
BACKGROUNDBrain visual circuits are often studied in vivo by imaging Ca2+ indicators with green-shifted emission spectra. Polychromatic white visual stimuli have a spectrum that partially overlaps indicators emission spectra, resulting in significant contamination of calcium signals.

NEW METHODTo overcome light contamination problems we choose blue visual stimuli, having a spectral composition not overlapping with Ca2+ indicators emission spectrum. To compare visual responsiveness to blue and white stimuli we used electrophysiology (visual evoked potentials-VEPs) and 3D acousto-optic two-photon(2P) population Ca2+ imaging in mouse primary visual cortex (V1).

RESULTSVEPs in response to blue and white stimuli had comparable peak amplitudes and latencies. Ca2+ imaging revealed that the populations of neurons responding to blue and white stimuli were largely overlapping, that their responses had similar amplitudes, and that functional response properties such as orientation and direction selectivities were also comparable.

COMPARISON WITH EXISTING METHODSMasking or shielding the microscope are often used to minimize the contamination of Ca2+ signal by white light, but they are time consuming, bulky and thus can limit experimental design, particularly in the more and more frequently used awake set-up. Blue stimuli not interfering with imaging allow to omit shielding without affecting V1 physiological responsiveness.

CONCLUSIONSOur results show that the selected blue light stimuli evoke physiological responses comparable to those evoked by white stimuli in mouse V1. This will make complex designs of imaging experiments in behavioral set-ups easier, and facilitate the combination of Ca2+ imaging with electrophysiology and optogenetics.

HighlightsO_LIWhite and blue light trigger VEPs with similar amplitudes and latencies in mouse V1
C_LIO_LIBlue-and white-responding neurons are two largely overlapping neuronal populations
C_LIO_LIBlue and white evoke Ca2+ responses similar in magnitude and latency
C_LIO_LIBlue and white evoke Ca2+ responses similar in orientation/direction selectivity
C_LIO_LIBlue stimuli could be an alternative to white ones in behavior and opto-physiological tests
C_LI

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title: Poly(rC)-binding protein 1 limits hepatitis C virus assembly and egress

abstract: The hepatitis C virus (HCV) co-opts numerous cellular elements - including proteins, lipids, and microRNAs - to complete its viral life cycle. The cellular RNA-binding protein, poly(rC)-binding protein 1 (PCBP1), was previously reported to bind to the 5 untranslated region (UTR) of the HCV genome; however, its importance in the viral life cycle has remained unclear. Herein, we sought to clarify the role of PCBP1 in the HCV life cycle. Using the HCV cell culture (HCVcc) system, we found that knockdown of endogenous PCBP1 resulted in an overall decrease in viral RNA accumulation, yet resulted in an increase in extracellular viral titers. To dissect PCBP1s specific role in the HCV life cycle, we carried out assays for viral entry, translation, genome stability, RNA replication, as well as virion assembly and secretion. We found that PCBP1 knockdown did not directly affect viral entry, translation, RNA stability, or RNA replication, but resulted in an overall increase in infectious particle secretion. This increase in virion secretion was evident even when viral RNA synthesis was inhibited, and blocking virus secretion could partially restore the viral RNA accumulation decreased by PCBP1 knockdown. We therefore propose a model where endogenous PCBP1 normally limits virion assembly and secretion, which increases viral RNA accumulation in infected cells by preventing the departure of viral genomes packaged into virions. Overall, our findings improve our understanding of how cellular RNA-binding proteins influence viral genomic RNA utilization during the HCV life cycle.


title: Poly(rC)-binding protein 1 limits hepatitis C virus assembly and secretion


title: Alanine cross-feeding determines Escherichia coli colony growth dynamics

abstract: Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.


title: Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies


title: The gene expression profile of the song control nucleus HVC shows sex specificity, hormone responsiveness, and species specificity among songbirds

abstract: Singing occurs in songbirds of both sexes, but some species show typical degrees of sex-specific performance. We studied the transcriptional sex differences in the HVC, a brain nucleus critical for song pattern generation, of the forest weaver (Ploceus bicolor), the blue-capped cordon-bleu (Uraeginthus cyanocephalus), and the canary (Serinus canaria), which are species that show low, medium, and high levels of sex-specific singing, respectively. We observed persistent sex differences in gene expression levels regardless of the species-specific sexual singing phenotypes. We further studied the HVC transcriptomes of defined phenotypes of canary, known for its testosterone-sensitive seasonal singing. By studying both sexes of canaries during both breeding and nonbreeding seasons, nonbreeding canaries treated with testosterone, and spontaneously singing females, we found that the circulating androgen levels and sex were the predominant variables associated with the variations in the HVC transcriptomes. The comparison of natural singing with testosterone-induced singing in canaries of the same sex revealed considerable differences in the HVC transcriptomes. Strong transcriptional changes in the HVC were detected during the transition from nonsinging to singing in canaries of both sexes. Although the sex-specific genes of singing females shared little resemblance with those of males, our analysis showed potential functional convergences. Thus, male and female songbirds achieve comparable singing behaviours with sex-specific transcriptomes.


title: A role for Gcn5 in heterochromatin structure, gene silencing and NER at the HML locus in budding yeast

abstract: Histone acetyltransferase Gcn5 plays an important role in transcription activation, DNA replication-coupled nucleosome assembly and nucleotide excision repair (NER). However, its functions on the heterochromatin are unexplored. Here, we find that removal of Gcn5 leads to more condensed heterochromatin structure, as revealed by topology analysis of HML circles. Importantly, the altered heterochromatin structure is restored by re-expression of Gcn5 in the gcn5{Delta} cells. As a result of the more compact heterochromatin, gene silencing at the HML locus is increased and NER efficiency at HML is impaired in the absence of Gcn5. Interestingly, while the association of SIR complex with HML is enhanced in cells lacking Gcn5, the altered compaction of HML heterochromatin is also observed due to the deletion of Gcn5 from Sir- cells. These findings reveal a role of Gcn5 in the regulation of heterochromatin structure, gene silencing and NER efficiency at the heterochromatic HML locus in yeast.


title: Development of the foregut in Katharina tunicata (Mollusca; Polyplacophora)

abstract: As a highly diverse phyla, Mollusca is both intriguing to study and difficult to define. No single common feature distinguishes the phyla, but the most common and recognizable is the radula. Throughout Molluscan history, there have been many developments to the radular structure. Evolutionary development of unique radular structures may have been made possible by developmental modularity. This histological study examines the development of polyplacophoran internal gut development. Here, I describe the developmental sequence of chiton feeding structures for the first time. Feeding structures are present by 10 days post hatch. Future research should examine larval stages prior to this in order to determine whether developmental modularity exists in polyplacophorans.


title: PDX1 directs a core developmentally and evolutionarily conserved gene program in the pancreatic islet

abstract: Pancreatic and duodenal homeobox 1 (PDX1) is crucial for pancreas organogenesis, yet the dynamic changes in PDX1 targets in mouse or human pancreas development have not been examined. We integrated the PDX1 cistrome with cell lineage-specific gene expression in both mouse and human developing pancreas. We identified a core set of developmentally and evolutionarily conserved PDX1 bound genes that reveal the broad multifaceted role of PDX1 in pancreas development. Despite the well-known, dramatic changes in PDX1 function and expression, we showed that PDX1 binding is largely stable from embryonic pancreas to adult islet. This may point towards a dual role of PDX1, activating or repressing the expression of its targets at different ages, dependent on other functionally-congruent or directly-interacting partners. Our work also suggests that PDX1 functions not only in initiating pancreas differentiation, but also as a potential keepsake of the progenitor program in the adult beta cells.


title: Is bigger always better? Neither body size nor aggressive behavior are good predictors to measure the degree of specialization of hummingbird interaction networks in rocky outcrops

abstract: Interspecific competition can strongly influence community structure and shape niche breadth and overlap. One of the main factors that determine the hummingbird community structure is competition for food. Hummingbirds functional attributes, such as beak length and body mass, influence nectar acquisition in the flowers, shaping foraging niches according to hummingbird dominance and foraging strategy. This study evaluates how the hummingbirds functional and behavioral attributes are related to plants assemblage in rocky outcrops habitats. We tested the following hypothesis: H1) Functional traits (beak length and body mass) are related to the richness and frequency of pollen grain morphotypes carried by hummingbirds; H2) Dominant and territorial hummingbirds carry a lower richness and frequency of pollen types when compared to subordinate hummingbirds, and H3) Hummingbird species carry different types of pollen grains. We conducted the study between September 2018 and March 2019 in a Campo Rupestre (rocky outcrops) in Southeastern Brazil. Hummingbirds were captured with a trap built based on trapdoors. We recorded their beak size and body masses, marked with commercial bird rings and ink on parts of the body, and then released. Behavioral responses to artificial feeders were collected regarding each visits time and duration and the outcome of aggressive interactions. The pollen adhered to the body parts was collected and identified in the laboratory. Our results showed that neither body size nor aggressive behaviors influenced pollen richness and frequency in rocky outcrops. Beak length was the most important hummingbirds attribute that influenced pollen richness, but not pollen frequency. Short-billed hummingbirds carried the greatest richness of pollen grains. Pollen grain richness and frequency were not related to hummingbird body mass or aggressive behavior. The hummingbird-pollen grain interaction network has shown to be generalized in the pollen grain transport. We conclude that hummingbirds beak length is the central morphological variable to measure pollen grain transport. It has direct implications for the pollination of different plant species.


title: HNF4α isoforms regulate the circadian balance between carbohydrate and lipid metabolism in the liver

abstract: Hepatocyte Nuclear Factor 4 (HNF4), a master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2). P1-HNF4 is the major isoform in the adult liver while P2-HNF4 is thought to be expressed only in fetal liver and liver cancer. Here, we show that P2- HNF4 is expressed at ZT9 and ZT21 in the normal adult liver and orchestrates a distinct transcriptome and metabolome via unique chromatin and protein-protein interactions. We demonstrate that while P1-HNF4 drives gluconeogenesis, P2-HNF4 drives ketogenesis and is required for elevated levels of ketone bodies in females. Exon swap mice expressing only P2- HNF4 exhibit subtle differences in circadian gene regulation and disruption of the clock increases expression of P2-HNF4. Taken together, we propose that the highly conserved two-promoter structure of the Hnfa gene is an evolutionarily conserved mechanism to maintain the balance between gluconeogenesis and ketogenesis in the liver in a circadian fashion.


title: Informative Regions In Viral Genomes

abstract: Viruses, far from being just parasites affecting hosts fitness are major players in any microbial ecosystem. In spite of their broad abundance, viruses, in particular bacteriophages remain largely unknown since only about 20% of sequences obtained from viral community DNA surveys could be annotated by comparison to public databases. In order to shed some light into this genetic dark matter we expanded the search of orthologous groups as potential markers to viral taxonomy from bacteriophages and included eukaryotic viruses, establishing a set of 31,150 ViPhOGs. To this, we examine the non-redundant viral diversity stored in public databases, predict proteins in genomes lacking such information and all annotated and predicted proteins were used to identify potential protein domains. Clustering of domains and unannotated regions into orthologous groups was done using cogSoft. Finally, we employed a supervised classification method by using a Random Forest implementation to classify genomes into their taxonomy and found that the presence/absence of ViPhOGs is significantly associated with their taxonomy. Furthermore, we established a set of 1,457 ViPhOGs that given their importance for the classification could be considered as markers/signatures for the different taxonomic groups defined by the ICTV at the Order, Family, and Genus levels. Both, the ViPhOGs and informative ViPhOGs sets are available at the Open Science Framwork (OSF) under the ViPhOGs project (https://osf.io/2zd9r/).

category: bioinformatics


title: MAPK Pathway Inhibition as A Rational Therapeutic Strategy for MiR-138-5p/PAQR3 Dysregulation-mediated Epirubicin Resistance in Triple-negative Breast Cancer

abstract: Anthracyclines, such as epirubicin, activate the mitogen-activated protein kinase (MAPK) pathway in breast cancer (BC). Better predictors of tumor response are needed to guide de-intensification of anthracyclines when used in BC treatment. Here, we aimed to see if MAPK activation was responsible and targetable for epirubicin resistance, and to explore mechanisms and predictive markers for resistance. MAPK pathway inhibitors were used to ameliorate epirubicin resistance. Negative regulators of MAPK were screened to identify the essential gene cascades required for activation of the pathway. In vitro and in vivo approaches were applied to investigate epirubicin resistance. The regulatory miRNA was identified through bioinformatics-based screening and luciferase reporter assay. 114 estrogen receptor negative patients who received epirubicin monotherapy were included to evaluate predictive markers for tumor response. The MAPK pathway was activated in cells resistant to epirubicin; MAPK inhibition ameliorated epirubicin resistance. In triple-negative breast cancer (TNBC), progestin and adipoQ receptor 3 (PAQR3) were the most significantly decreased negative MAPK regulators. PAQR3 increased epirubicin sensitivity and suppressed MAPK activation in resistant cells. MiR-138-5p was increased in epirubicin resistant cells, and was shown to downregulate PAQR3, causing resistance in epirubicin resistant cells. PAQR3 was an independent factor in predicting response to epirubicin (OR=4.86, 95%CI=1.13-20.87, P=0.034), and possessed a high negative predictive value (NPV) (0.93; 95%CI=0.83-0.97). In addition, PAQR3 exhibited a better predictive value in patients older than 50 years (12.92 (95% CI, 1.43-116.78, P = 0.023). The combinative use of PAQR3 and topoisomerase II- (TOP2A) led to an increased specificity (0.70; 95%CI=0.61-0.79), when compared with either PAQR3 or TOP2A alone. MAPK inhibition ameliorated epirubicin resistance. MiR-138-5p-induced PAQR3 reduction causes epirubicin resistance in TNBC via activation of MAPK cascades. PAQR3 is an independent and favorable predictor response to epirubicin in BC.

category: cancer biology


title: VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer

abstract: A comprehensive understanding of androgen receptor (AR) signalling mechanisms during prostate carcinogenesis is instrumental in developing novel therapies. Studies have shown glycosylation as a key androgen regulated process and that O-GlcNAc transferase (OGT), the enzyme that catalyses the covalent addition of UDP-N-acetylglucosamine (UDP-GlcNAc) to serine and threonine residues of proteins, is often up-regulated in prostate cancer (PCa) with its expression correlated with high Gleason score. In this study we have identified an AR and OGT co-regulated factor, VPRBP also known as DCAF1. We show that VPRBP is regulated by the AR at the transcript level, and stabilized by OGT at the protein level. VPRBP knockdown in PCa cells led to a significant decrease in cell proliferation, p53 stabilization, nucleolar fragmentation and increased p53 recruitment to the chromatin. In human prostate tumor samples, VPRBP protein overexpression correlated with AR amplification, OGT overexpression, early biochemical relapse and poor clinical outcome. Analysis of TCGA datasets found a positive correlation of VPRBP with AR mRNA expression. Furthermore, AR activity gene signature analysis revealed a positive correlation of VPRBP with a subset of AR target genes implying that VPRBP has a preferential regulatory impact on part of the AR regulome. In conclusion, we have shown that VPRBP/DCAF1 promotes PCa cell proliferation by restraining p53 activation under the influence of the AR and OGT as well as uncovered a unique subset of AR activity gene signature that correlates with VPRBP expression with the potential for new avenues for patient stratification and treatment.


title: Rapid stress hardening in the Antarctic midge improves male fertility by increasing courtship success and preventing the decline of accessory gland proteins following cold exposure

abstract: Rapid hardening is a process that quickly improves an animals performance following exposure to a potentially damaging stress. Features of reproduction can be improved by rapid hardening, but little is known about how rapid hardening may contribute to physiological responses in the cold environment of Antarctica. In this study of the Antarctic midge, Belgica antarctica (Diptera, Chironomidae), we examine how rapid hardening in response to dehydration (RDH) or cold (RCH) improves male pre- and post-copulatory function related to fertility when the insects are subsequently subjected to a damaging cold exposure. Neither RDH nor RCH improved survival in response to lethal cold stress, but male activity following sublethal cold exposure was enhanced. Both RCH and RDH improved mating success of males compared to those subjected directly to a sublethal bout of cold. Egg viability decreased following direct exposure to sublethal cold, but improved following RCH and RDH. Sublethal cold exposure reduced expression of four accessory gland proteins, while expression remained high in males exposed to RCH. Though rapid hardening may be cryptic in males, this study shows that it can be revealed by pre- and post-copulatory interactions with females.


title: Donor-derived vasculature is required to support neocortical cell grafts after stroke

abstract: Neural precursor cells (NPCs) transplanted into the adult neocortex generate neurons that synaptically integrate with host neurons, supporting the possibility of achieving functional tissue repair. However, poor survival of transplanted NPCs greatly limits efficient engraftment. Here, we test the hypothesis that combining blood vessel-forming vascular cells with neuronal precursors improves engraftment. By transplanting mixed embryonic neocortical cells into adult mice with neocortical strokes, we show that transplant-derived neurons synapse with appropriate targets while donor vascular cells form vessels that fuse with the host vasculature to perfuse blood within the graft. Although all grafts became vascularized, larger grafts had greater contributions of donor-derived vessels that increased as a function of their distance from the host-graft border. Moreover, excluding vascular cells from the donor cell population strictly limited graft size. Thus, inclusion of vessel-forming vascular cells with NPCs is required for more efficient engraftment and ultimately for tissue repair.


title: Somatosensory processing deficits and altered cortico-hippocampal connectivity in Shank3b-/- mice

abstract:
Abnormal tactile response is considered an integral feature of Autism Spectrum Disorders (ASDs), and hypo-responsiveness to tactile stimuli is often associated with the severity of ASDs core symptoms. Patients with Phelan-McDermid syndrome (PMS), caused by mutations in the SHANK3 gene, show ASD-like symptoms associated with aberrant tactile responses. However, the neural underpinnings of these somatosensory abnormalities are still poorly understood. Here we investigated, in Shank3b-/- adult mice, the neural substrates of whisker-guided behaviors, a key component of rodents interaction with the surrounding environment. To this aim, we assessed whisker-dependent behaviors in Shank3b-/- adult mice and age-matched controls, using the textured novel object recognition (tNORT) and whisker nuisance (WN) test. Shank3b-/- mice showed deficits in whisker-dependent texture discrimination in tNORT and behavioral hypo-responsiveness to repetitive whisker stimulation in WN. Notably, sensory hypo-responsiveness was accompanied by a significantly reduced activation of the primary somatosensory cortex (S1) and hippocampus, as measured by c-fos mRNA in situ hybridization, a proxy of neuronal activity following whisker stimulation. Moreover, resting-state fMRI showed a significantly reduced S1-hippocampal connectivity in Shank3b mutant mice. Together, these findings suggest that impaired crosstalk between hippocampus and S1 might underlie Shank3b-/- hypo-reactivity to whisker-dependent cues, highlighting a potentially generalizable form of dysfunctional somatosensory processing in ASD.

Significance StatementPatients with Phelan-McDermid syndrome, a syndromic form of ASD caused by mutation of the SHANK3 gene, often show aberrant responses to touch. However, the neural basis of atypical sensory responses in ASD remains undetermined. Here we used Shank3 deficient mice to investigate the neural substrates of behavioral responses to repetitive stimulation of the whiskers, a highly developed sensory organ in mice. We found that mice lacking the Shank3 gene are hypo-responsive to repetitive whisker stimulation. This trait was associated with reduced engagement and connectivity between the primary somatosensory cortex and hippocampus. These results suggest that dysfunctional cortico-hippocampal coupling may underlie somatosensory processing deficits in SHANK3 mutation carriers and related syndromic forms of ASD.


title: Gut microbial structural variations as determinants of human bile acid metabolism

abstract: Bile acids (BAs) facilitate intestinal fat absorption and act as important signaling molecules in host{square}gut microbiota crosstalk. BA-metabolizing pathways in the microbial community have been identified, but how the highly variable genomes of gut bacteria interact with host BA metabolism remains largely unknown. We characterized 8,282 structural variants (SVs) of 55 bacterial species in the gut microbiomes of 1,437 individuals from two Dutch cohorts and performed a systematic association study with 39 plasma BA parameters. Both variations in SV-based continuous genetic makeup and discrete subspecies showed correlations with BA metabolism. Metagenome-wide association analysis identified 797 replicable associations between bacterial SVs and BAs and SV regulators that mediate the effects of lifestyle factors on BA metabolism. This is the first large-scale microbial genetic association analysis to demonstrate the impact of bacterial SVs on human BA composition, and highlights the potential of targeting gut microbiota to regulate BA metabolism through lifestyle intervention.


title: Highly social pinyon jays, but not less social Clark's nutcrackers, modify their food-storing behaviour when observed by a heterospecific

abstract: Behavioural flexibility can be described as the ability to use information and generalise it across contexts. Social living is thought to favour behavioural flexibility. We used a food-storing (caching) paradigm, during which individuals either ate or cached food under different conditions, to investigate whether they could flexibly adjust their caching behaviour when observed by conspecifics and heterospecifics. We examined the location and number of caches made by two corvid species differing in sociality, highly social pinyon jays (Gymnorhinus cyanocephalus) and less social Clarks nutcrackers (Nucifraga columbiana). Although pinyon jays cached a similar amount of food across conditions, they allocated more caches to areas less accessible to the observer when the observer spent more time close to the caching locations. Nutcrackers, however, reduced the number of seeds cached when observed by another nutcracker in comparison to when they cached alone, but did not significantly change their caching behaviour when observed by a pinyon jay. The differences in cache protection strategies, and the social cues (e.g., presence and behaviour of an observing bird) that elicit them, may be explained by the species social organisation. Overall, our results provide insight into understanding how pressures associated with the social environment may influence foraging behaviours.


title: Collagen polarization provides a structural memory for the elongation of epithelial anlage.

abstract: Epithelial networks are commonly generated by processes where multicellular aggregates elongate and branch. Here we focus on understanding cellular mechanisms for elongation, using an organotypic culture system as a model of mammary epithelial anlage. Isotropic cell aggregates broke symmetry and slowly elongated when transplanted into collagen 1 gels. The elongating regions of aggregates displayed enhanced cell proliferation that was necessary for elongation to occur. Strikingly, this loco-regional increase in cell proliferation occurred where collagen 1 fibrils reorganized into bundles which were polarized with the elongating aggregates. Applying external stretch as a cell-independent way to reorganize the ECM, we found that collagen polarization stimulated regional cell proliferation to precipitate symmetry-breaking and elongation. This required {beta}1-integrin and ERK signaling. We propose that collagen polarization supports epithelial anlagen elongation by stimulating loco-regional cell proliferation. This could provide a long-lasting structural memory of the initial axis that is generated when anlage break symmetry.


title: Collagen polarization promotes epithelial elongation by stimulating locoregional cell proliferation.


title: Novel newt regeneration genes regulate Wingless signaling to restore patterning in Drosophila eye

abstract: A fundamental process of regeneration, which varies among animals, recruits conserved signaling pathways to restore missing parts. Only a few animals like newts can repeatedly regenerate lost body parts throughout their lifespan that can be attributed to strategic regulation of conserved signaling pathways by newts regeneration tool-kit genes. Here we report use of genetically tractable Drosophila eye model to demonstrate the regeneration potential of a group of unique protein(s) from newt (Notophthalmus viridescens), which when ectopically expressed can significantly rescue missing photoreceptor cells in a Drosophila eye mutant. These newt proteins with signal peptides motifs exhibit non-cell-autonomous rescue properties and their regeneration potential even extends into later stages of fly development. Ectopic expression of these newt genes can rescue eye mutant phenotype by promoting cell proliferation and blocking cell death. These novel newt genes downregulate evolutionarily conserved Wingless (Wg)/Wnt signaling pathway to promote rescue. Modulation of Wg/Wnt signaling levels by using antagonists or agonists of Wg/Wnt signaling pathway in eye mutant background where newt gene(s) is ectopically expressed suggests that Wg signaling acts downstream of newt genes. Our data highlights the regeneration potential of novel newt proteins that regulate conserved pathways to trigger a robust regeneration response in Drosophila model with weak regeneration capability.


title: Destabilization of β-cell FIT2 by saturated fatty acids contribute to ER stress and diabetes

abstract: Western type diets are linked to obesity and diabetes partly because of their high saturated fatty acid (SFA) content. We found that SFAs, but not unsaturated fatty acids (USFAs), reduced the number of lipid droplets (LDs) within pancreatic {beta}-cells. Mechanistically, SFAs but not USFAs disabled LD biogenesis by inducing palmitoylation and subsequent ERAD-C mediated degradation of LD formation protein, Fat storage-Inducing Transmembrane protein 2 (FIT2). Targeted ablation of FIT2 reduced {beta}-cell LD numbers, lowered {beta}-cell ATP levels, reduced Ca2+ signaling, downregulated {beta}-cell transcription factors (RNA sequencing analysis), and exacerbated diet-induced diabetes in mice. Subsequent mass spectrometry studies revealed increased C16:0 ceramide accumulation in islets of mice lacking {beta}-cell FIT2 under lipotoxic conditions. Inhibition of ceramide synthases ameliorated the enhanced ER stress. Overexpression of FIT2 increased number of intracellular LDs and rescued SFA-induced ER-stress and apoptosis thereby highlighting the protective role of FIT2 and LDs against {beta}-cell lipotoxicity and diet-induced diabetes.

category: biochemistry


title: A novel function for Rab proteins during maturation of secretory granules

abstract: Regulated exocytosis is an essential process whereby professional secretory cells synthesize and secrete specific cargo proteins in a stimulus-dependent manner. Cargo-containing secretory granules are synthesized in the trans-Golgi Network (TGN); after budding from the TGN, granules undergo many modifications, including a dramatic increase in size. These changes occur during a poorly understood process called secretory granule maturation. Here we leverage the professional secretory cells of the Drosophila larval salivary glands as a model system to characterize a novel and unexpected role for Rab GTPases during secretory granule maturation. We find that secretory granules in the larval salivary glands increase in size ~300-fold between biogenesis and release, and loss of Rab1 or Rab11 dramatically reduces granule size. Surprisingly, we find that Rab1 and Rab11 protein localize to secretory granule membranes. Rab11 associates with granule membranes throughout the maturation process, and Rab11 is required for recruitment of Rab1. In turn, Rab1 associates specifically with immature secretory granules and drives granule growth. In addition to their roles in granule growth, both Rab1 and Rab11 appear to have additional roles during exocytosis; Rab11 function is necessary for exocytosis, while the presence of Rab1 on immature granules may prevent precocious exocytosis. Overall, these results highlight a new and unexpected role for Rab GTPases in secretory granule maturation.


title: Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration

abstract: Retinal Ganglion Cells (RGCs) lose their ability to grow axons during development. Adult RGCs thus fail to regenerate their axons after injury, leading to vision loss. To uncover mechanisms that promote RGC axon regeneration, we identified transcription factors (TF) and chromatin accessible sites enriched in embryonic RGCs (high axon growth capacity) compared to postnatal RGC (low axon growth capacity). Developmental stage-specific gene expression changes correlated with changes in promoter chromatin accessibility. Binding motifs for TFs such as CREB, CTCF, JUN and YY1 were enriched in the differentially opened regions of the chromatin in embryonic RGCs and proteomic analysis confirmed their expression in RGC nuclei. The CREB/ATF binding motif was widespread at the open chromatin region of known pro-regenerative TFs, supporting a role of CREB in regulating axon growth. Consistently, overexpression of CREB fused to the VP64 transactivation domain in RGCs promoted axon regeneration after optic nerve injury. Our study provides a map of the chromatin accessibility during RGC development and highlights that TF associated with developmental axon growth can stimulate axon regeneration in mature RGC.


title: Emergence of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Co-harbouring a blaNDM-1-carrying Virulent Plasmid and a blaKPC-2-carrying Plasmid in an Egyptian Hospital

abstract:
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and the analysis of the plasmids associated with CR-hypervirulent-KP (CR-HvKP) in Egypt are not presented. Therefore, we attempt to decipher the plasmids sequences, which are responsible for transferring the determinants of carbapenem-resistance, particularly the blaNDM-1 and blaKPC-2. Out of 34 K. pneumoniae isolates collected from two tertiary hospitals in Egypt, 31 were CRKP. Whole-genome sequencing revealed that our isolates were related to 13 different sequence types (STs). The most prevalent ST was ST101, followed by ST383, and ST11. Among the CRKP isolates, one isolate named EBSI036 has been reassessed using Nanopore sequencing. Genetic environment analysis showed that EBSI036 carried 20 antibiotic resistance genes and was identified as CR-HvKP strain, it harboured four plasmids, namely; pEBSI036-1-NDM-VIR, pEBSI036-2-KPC, pEBSI036-3, and pEBSI036-4. The two carbapenemase genes, blaNDM-1 and blaKPC-2, were located on plasmids pEBSI036-1-NDM-VIR and pEBSI036-2-KPC, respectively. The IncFIB:IncHI1B hybrid plasmid pEBSI036-1-NDM-VIR also carried some virulence factors, including regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD, iutA). Thus, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. We reported for the first time a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient from the ICU in a tertiary-care hospital in Egypt, which showed the cohabitation of a novel hybrid plasmid coharbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid.

IMPORTANCECRKP had been registered in the critical priority tier by the World Health Organization and became a significant menace to public health. Therefore, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. Herein, we reported for the first time (to the best of our knowledge) a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient in a tertiary-care hospital from the ICU in Egypt, which showed the cohabitation of a novel hybrid plasmid co-harbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid. Herein, the high rate of CRKP might be due to the continuous usage of carbapenems as empirical therapy, besides the failure to implement an antibiotic stewardship program in Egyptian hospitals. Thus, this study serves to alert the contagious disease clinicians to the presence of hypervirulence in CRKP isolates in Egyptian hospitals.


title: Photochromic fluorophores enable imaging of lowly-expressed proteins in the autofluorescent fungus Candida albicans

abstract:
Fluorescence microscopy is a standard research tool in many fields, though collecting reliable images can be difficult in systems characterized by low expressions levels and/or high background fluorescence. We present the combination of a photochromic fluorescent protein and stochastic optical fluctuation imaging (SOFI) to deliver suppression of the background fluorescence. This strategy makes it possible to resolve lowly- or endogenously-expressed proteins, as we demonstrate for Gcn5, a histone acetyltransferase required for complete virulence, and Erg11, the target of the azole antifungals agents in the fungal pathogen C. albicans. We expect that our method can be readily used for sensitive fluorescence measurements in systems characterized by a high background fluorescence.

ImportanceUnderstanding the spatial and temporal organization of proteins-of-interest is key to unravel cellular processes and identify novel possible antifungal targets. Only a few therapeutic targets have been discovered in Candida albicans and resistance mechanisms against these therapeutic agents is rapidly acquired. Fluorescence microscopy is a valuable tool to investigate molecular processes and assess the localization of possible antifungal targets. Unfortunately, fluorescence microscopy of C. albicans suffers from extensive autofluorescence. In this work we present the use of a photochromic fluorescent protein and stochastic optical fluctuation imaging to enable imaging of lowly-expressed proteins in C. albicans through the suppression of autofluorescence. This method can be applied in C. albicans research or adapted for other fungal systems allowing the visualization of intricate processes.


title: Towards 3D-Bioprinting of an Endocrine Pancreas: A Building-Block Concept for Bioartificial Insulin-Secreting Tissue

abstract:
Background & Aims3D-Bioprinting of an endocrine pancreas is a promising future curative treatment for selected patients with insulin secretion deficiency. In this study we present an end-to-end integrative, scalable concept extending from the molecular to the macroscopic level.

MethodsA hybrid scaffold device was manufactured by 3D-(bio)printing. INS-1 cells with/without endothelial cells were bioprinted in gelatin methacrylate blend hydrogel. Polycaprolactone was 3D-printed and heparin-functionalized as structural scaffold component. In vitro evaluation was performed by viability and growth assays, total mRNA sequencing, and glucose-stimulated insulin secretion. In vivo, xenotransplantation to fertilized chicken eggs was used to investigate vascularization and function, and finite element analysis modeling served to detect boundary conditions and applicability for human islets of Langerhans.

ResultsInsulin-secreting pseudoislets were formed and resulted in a viable and proliferative experimental model. Transcriptomics revealed upregulation of proliferative and {beta}-cell-specific signaling cascades, downregulation of apoptotic pathways, and overexpression of extracellular matrix proteins and VEGF induced by pseudoislet formation and 3D culture. Co-culture with human endothelial cells created a natural cellular niche resulting in enhanced insulin response after glucose stimulation. Survival and function of the pseudoislets after explantation and extensive scaffold vascularization of both the hydrogel and heparinized polycaprolactone components were demonstrated in ovo. Computer simulations of oxygen, glucose, and insulin flows were used to evaluate scaffold architectures and Langerhans islets at a future transplantation site along neurovascular structures.

ConclusionA defined end-to-end process for multidisciplinary bioconvergence research on a bioartificial endocrine pancreas was developed. A modular, patient-specific device architecture is proposed for future research studies.


title: Transcriptomic analysis of loss of Gli1 in neural stem cells responding to demyelination in the mouse brain

abstract: In the adult mammalian brain, Gli1 expressing neural stem cells reside in the subventricular zone and their progeny are recruited to sites of demyelination in the white matter where they generate new oligodendrocytes, the myelin forming cells. Remarkably, genetic loss or pharmacologic inhibition of Gli1 enhances the efficacy of remyelination by these neural stem cells. To understand the molecular mechanisms involved, we performed a transcriptomic analysis of this Gli1-pool of neural stem cells. We compared murine NSCs with either intact or deficient Gli1 expression from adult mice on a control diet or on a cuprizone diet which induces widespread demyelination. These data will be a valuable resource for identifying therapeutic targets for enhancing remyelination in demyelinating diseases like multiple sclerosis.


title: Kinetic pathway of ATP-induced DNA interactions of ParA2, a protein essential for segregation of Vibrio cholerae chromosome 2

abstract: Vibrio cholerae chromosome 2 (Chr2) requires its own ParABS system for segregation. Without it, V. cholerae becomes nonviable and loses pathogenicity. ParA2 of Chr2 is a Walker-type ATPase that is the main driver of Chr2 segregation. Most of our understanding of ParA function comes from studying plasmid partition systems. How ParA provides the motive force in segregation of chromosomes, which are much larger than plasmids, is less understood and different models have been proposed. Here we analyzed in vivo behavior and kinetic properties of ParA2 using cell imaging, biochemical and biophysical approaches. ParA2 formed an asymmetric gradient in the cell that localized dynamically in the cell cycle. We found that ParA2 dimers bind ATP and undergo a slow conformational change to an active DNA-binding state, similar to P1 ParA. The presence of DNA catalyzes ParA2 conformational change to allow cooperative binding of active ParA2 dimers to form higher-order oligomers on DNA. Nucleotide exchange rates were also slow, thus providing a control of ParA2 recruitment and dynamic localizations. Although highly conserved in biochemical properties, ParA2 showed faster overall ATP cycling and DNA-rebinding rates than plasmid ParAs, suggesting that this could be shared kinetic features among chromosomal ParAs to regulate the transport of a much larger DNA cargo.


title: Dynamic Consequences of Specificity within the Cytidine Repressor DNA-Binding Domain

abstract: The E. coli cytidine repressor (CytR) is a member of the LacR family of bacterial repressors that regulates nine operons with distinct spacing and orientations of recognition sites. Understanding the structural features of the CytR DNA-binding domain (DBD) when bound to DNA is critical to understanding differential mechanisms of gene regulation. We previously reported the structure of the CytR DBD monomer bound specifically to half-site DNA and found that the DBD exists as a three-helix bundle containing a canonical helix-turn-helix motif, similar to other proteins that interact with DNA [Moody, et al (2011), Biochemistry 50:6622-32]. We also studied the free state of the monomer and found that since NMR spectra show it populates up to four distinct conformations, the free state exists as an intrinsically disordered protein (IDP). Here, we present further analysis of the DBD structure and dynamics in the context of full-site operator or nonspecific DNA. DBDs bound to full-site DNA show one set of NMR signals, consistent with fast exchange between the two binding sites. When bound to full-length DNA, we observed only slight changes in structure compared to the monomer structure and no folding of the hinge helix. Notably, the CytR DBD behaves quite differently when bound to nonspecific DNA compared to LacR. A dearth of NOEs and complete lack of protection from hydrogen exchange are consistent with the protein populating a flexible, molten state when associated with DNA nonspecifically, similar to fuzzy complexes. The CytR DBD structure is significantly more stable when bound specifically to the udp half-site substrate. For CytR, the transition from nonspecific association to specific recognition results in substantial changes in protein mobility that are coupled to structural rearrangements. These effects are more pronounced in the CytR DBD compared to other LacR family members.

category: biophysics


title: Considerations for MESF-bead based assignment of absolute fluorescence values to nanoparticles and extracellular vesicles by flow cytometry

abstract: Flow cytometry is a promising technique to characterize nanoparticles (NPs) and extracellular vesicles (EVs). However, the majority of reported experiments, use arbitrary units to indicate fluorescence intensity. This hampers comparison of results from different laboratories and different platforms. We investigated the advised use of calibrated molecules of equivalent soluble fluorophores (MESF)-beads for assignment of absolute fluorescence to NPs and EVs. Firstly, we evaluated the use of two different FITC MESF bead sets as calibrators on three different flow cytometry platforms (BD Influx, CytoFLEX LX and SORP BD FACSCelesta). Secondly, NPs and biological 4T1 mammary carcinoma-EVs were analyzed using the BD Influx and their fluorescence signals calibrated by using different sets of FITC and PE MESF beads. Although fluorescence calibration, using bright calibrators designed for cellular flow cytometry, makes inter-platform comparison possible for fluorescently labeled cells and brightly labeled particles, but the uncertainty of the currently available calibrators, which are far out of the fluorescence range of the sub-micron particles, hampers a reliable assignment of absolute MESF numbers based on extrapolation into the dim fluorescence range. Our results illustrate the need for calibration materials specifically designed for NPs and EVs to enable a reliable assignment of absolute fluorescence values in the lower fluorescent ranges.


title: Multi-scale brain simulation with integrated positron emission tomography yields hidden local field potential activity that augments machine-learning classification of Alzheimer's disease

abstract:
INTRODUCTIONComputational brain network modeling using The Virtual Brain (TVB) simulation platform acts synergistically with machine learning and multi-modal neuroimaging to reveal mechanisms and improve diagnostics in Alzheimers disease.

METHODSWe enhance large-scale whole-brain simulation in TVB with a cause-and-effect model linking local Amyloid {beta} PET with altered excitability. We use PET and MRI data from 33 participants of Alzheimers Disease Neuroimaging Initiative (ADNI3) combined with frequency compositions of TVB-simulated local field potentials (LFP) for machine-learning classification.

RESULTSThe combination of empirical neuroimaging features and simulated LFPs significantly outperformed the classification accuracy of empirical data alone by about 10% (weighted F1-score empirical 64.34% vs. combined 74.28%). Informative features showed high biological plausibility regarding the Alzheimers-typical spatial distribution.

DISCUSSIONThe cause-and-effect implementation of local hyperexcitation caused by Amyloid {beta} can improve the machine-learning-driven classification of Alzheimers and demonstrates TVBs ability to decode information in empirical data employing connectivity-based brain simulation.

RESEARCH IN CONTEXTO_LISYSTEMATIC REVIEW. Machine-learning has been proven to augment diagnostics of dementia in several ways. Imaging-based approaches enable early diagnostic predictions. However, individual projections of long-term outcome as well as differential diagnosis remain difficult, as the mechanisms behind the used classifying features often remain unclear. Mechanistic whole-brain models in synergy with powerful machine learning aim to close this gap.
C_LIO_LIINTERPRETATION. Our work demonstrates that multi-scale brain simulations considering Amyloid {beta} distributions and cause-and-effect regulatory cascades reveal hidden electrophysiological processes that are not readily accessible through measurements in humans. We demonstrate that these simulation-inferred features hold the potential to improve diagnostic classification of Alzheimers disease.
C_LIO_LIFUTURE DIRECTIONS. The simulation-based classification model needs to be tested for clinical usability in a larger cohort with an independent test set, either with another imaging database or a prospective study to assess its capability for long-term disease trajectories.
C_LI


title: Brain simulation augments machine-learning-based classification of dementia


title: Delivering on Biden's 2030 conservation commitment

abstract: On January 27, 2021, President Biden signed an executive order, Tackling the Climate Crisis at Home and Abroad, committing the United States to various goals within his campaigns major climate policy, the Biden Plan for a Clean Energy Revolution and Environmental Justice. Included in this executive order is a commitment to "conserving at least 30 percent of [the United States] lands and oceans by 2030." This ambitious conservation target signals a promising direction for biodiversity in the United States. However, while the executive order outlines several goals for climate mitigation, the  30x30 target remains vague in its objectives, actions, and implementation strategies for protecting biodiversity. Biodiversity urgently needs effective conservation action, but it remains unclear where and what this 30% target will be applied to. Achieving different climate and biodiversity objectives will require different strategies and, in combination with the associated costs of implementation, will lead to different priority areas for conservation actions. Here, we illustrate what the 30% target could look like across four objectives reflective of the ambitious goals outlined in the executive order. We compile several variations of terrestrial protected area networks guided by these different objectives and examine the trade-offs in costs, ecosystem representation, and climate mitigation potential between each. We find little congruence in priority areas across objectives, emphasizing just how crucial it will be for the Biden administration to develop clear objectives and establish appropriate performance metrics from the outset to maximize both conservation and climate outcomes in support of the 30x30 target. We discuss important considerations that must guide the administrations conservation strategies in order to ensure meaningful conservation outcomes can be achieved over the next decade.


title: Origin and fate of supergenes in Atlantic cod

abstract: Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here, we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate that chromosomal inversions underlie all four supergenes, and show that they originated at different times between 0.40 and 1.66 million years ago. While we found no evidence for a role of introgression in the origin of the four supergenes, we reveal gene flux between supergene haplotypes with derived and ancestral arrangements, occurring both through gene conversion and double crossover. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the purging of introduced genetic variation.


title: Supergenes origin and maintenance in Atlantic cod


title: CORO2A, AN EXPRESSION QUANTITATIVE TRAIT GENE UNDERLYING ESTQ1, CONTROLS UTERINE RESPONSIVENESS TO ESTRADIOL

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe response of the uterus to 17{beta}-estradiol (E2) is genetically controlled, with marked variation observed depending on the mouse strain studied. Previous studies from our laboratory using high (C57BL6/J; B6) and low uterine responders (C3H/HeJ; C3H) to E2 led to the identification of Estq1-Estq5, five quantitative trait loci (QTL) controlling phenotypic variation in uterine growth and eosinophilic leukocyte infiltration. Transcriptional profiling subsequently identified coronin actin binding protein 2A (Coro2a) as a candidate for an expression quantitative trait gene (eQTG) underlying Estq1. Here we show that like mRNA expression, allele specific expression of CORO2A in both the uterine epithelium and stroma similarly co-segregates with uterine responsiveness. Utilizing B6.C3H congenic mice carrying the Coro2aC3H allele, we confirm the genetic linkage between Coro2a and Estq1. Lastly, we show that B6-Coro2a-/- and B6-Coro2aB6/- mice phenocopy uterine responsiveness of mice carrying the Coro2aC3H/C3H and Coro2aB6/C3H alleles respectively, consistent with a haploinsufficiency model of genetic control. Together, these results identify Coro2a as the eQTG underlying Estq1, and establish a critical role for Coro2a in E2-regulated responses.


title: Confirmation bias optimizes reward learning

abstract: Confirmation bias--the tendency to overweight information that matches prior beliefs or choices--has been shown to manifest even in simple reinforcement learning. In line with recent work, we find that participants learned significantly more from choice-confirming outcomes in a reward-learning task. What is less clear is whether asymmetric learning rates somehow benefit the learner. Here, we combine data from human participants and artificial agents to examine how confirmation-biased learning might improve performance by counteracting decisional and environmental noise. We evaluate one potential mechanism for such noise reduction: visual attention--a demonstrated driver of both value-based choice and predictive learning. Surprisingly, visual attention showed the opposite pattern to confirmation bias, as participants were most likely to fixate on "missed opportunities", slightly dampening the effects of the confirmation bias we observed. Several million simulated experiments with artificial agents showed this bias to be a reward-maximizing strategy compared to several alternatives, but only if disconfirming feedback is not completely ignored--a condition that visual attention may help to enforce.


title: Male attention allocation depends on social context

abstract:
Attention, although limited, is a mechanism used to filter large amounts of information and determine what stimuli are most relevant at a particular moment. In dynamic social environments, multiple individuals may play a pivotal role in any given interaction where a males attention may be divided between a rival, a current mate, and/or future potential mates. Here, we investigated impacts of the social environment on attention allocation in male sailfin mollies, Poecilia latipinna, which are a part of a sexual-unisexual mating system with the Amazon molly, Poecilia formosa. We asked: 1) Does the species of female influence the amount of attention a male allocates to her? And 2) Is a males attention towards his mate influenced by different social partners? Males direct more attention toward a stimulus female when she was a conspecific. We also show that males perceive a larger male as a more relevant stimulus to pay attention to than a smaller male, and a conspecific female as a more relevant stimulus compared to a heterospecific female. Our results show differential allocation of attention is dependent upon multiple components of the social environment in which an individual interacts.

SignificanceThis study investigates how attention is allocated in males when presented with social distractions. Assuming that attentional capacity is finite, males may face a tradeoff between different cognitive-demanding stimuli, such as rival males and potential future mates, when mating. Here, we show that male attention allocation in both intra- and intersexual interactions is multifaceted and context dependent. This suggests that individuals within the social environment vary in how meaningful (i.e., able to capture attention) they are to males during mating encounters. Understanding how social partners can cause a shift of attention away from a mating opportunity is essential to understanding the influence of the social context on sexual selection.