title: A microRNA program controls the transition of cardiomyocyte hyperplasia to hypertrophy and stimulates mammalian cardiac regeneration

abstract: Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b[~]25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b[~]25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b[~]25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b[~]25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b[~]25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.


title: Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells

abstract: SARS-Cov-2 infected cells fused with the ACE2-positive neighboring cells forming syncytia. However, the effect of syncytia in disease development is largely unknown. We established an in vitro cell-cell fusion system and used it to mimic the fusion of SARS-CoV-2 infected cells with ACE2-expressing cells to form syncytia. We found that Caspase-9 was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9, but it triggered GSDME-dependent pyroptosis rather than apoptosis. What is more, single cell RNA-sequencing data showed that both ACE2 and GSDME were expression in alveolar type 2 cells in human lung. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host cells and ACE2-positive cells, which indicated that lytic death of syncytia may contribute to the excessive inflammatory responses in severe COVID-19 patients.

category: cell biology


title: The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium

abstract:
RationaleAsthma is associated with chronic changes in the airway epithelium, a key target of SARS-CoV-2. Many epithelial changes are driven by the type 2 cytokine IL-13, but the effects of IL-13 on SARS-CoV-2 infection are unknown.

ObjectivesWe sought to discover how IL-13 and other cytokines affect expression of genes encoding SARS-CoV-2-associated host proteins in human bronchial epithelial cells (HBECs) and determine whether IL-13 stimulation alters susceptibility to SARS-CoV-2 infection.

MethodsWe used bulk and single cell RNA-seq to identify cytokine-induced changes in SARS-CoV-2-associated gene expression in HBECs. We related these to gene expression changes in airway epithelium from individuals with mild-moderate asthma and chronic obstructive pulmonary disease (COPD). We analyzed effects of IL-13 on SARS-CoV-2 infection of HBECs.

Measurements and Main ResultsTranscripts encoding 332 of 342 (97%) SARS-CoV-2-associated proteins were detected in HBECs ([≥]1 RPM in 50% samples). 41 (12%) of these mRNAs were regulated by IL-13 (>1.5-fold change, FDR < 0.05). Many IL-13-regulated SARS-CoV-2-associated genes were also altered in type 2 high asthma and COPD. IL-13 pretreatment reduced viral RNA recovered from SARS-CoV-2 infected cells and decreased dsRNA, a marker of viral replication, to below the limit of detection in our assay. Mucus also inhibited viral infection.

ConclusionsIL-13 markedly reduces susceptibility of HBECs to SARS-CoV-2 infection through mechanisms that likely differ from those activated by type I interferons. Our findings may help explain reports of relatively low prevalence of asthma in patients diagnosed with COVID-19 and could lead to new strategies for reducing SARS-CoV-2 infection.


title: Mechanically Sensitive HSF1 is a Key Regulator of Left-Right Symmetry Breaking in Zebrafish Embryos

abstract: The left-right symmetry breaking of vertebrate embryos requires fluid flow (called nodal flow in zebrafish). However, the molecular mechanisms that mediate the asymmetric gene expression regulation under nodal flow remain elusive. In this paper, we report that heat shock factor 1 (HSF1) is asymmetrically activated in the Kuppfers vesicle at the early stage of zebrafish embryos in the presence of nodal flow. Deficiency in HSF1 expression caused a significant situs inversus and disrupted gene expression asymmetry of nodal signaling proteins in zebrafish embryos. Further studies demonstrated that HSF1 could be immediately activated by fluid shear stress. The mechanical sensation ability of HSF1 is conserved in a variety of mechanical stimuli in different cell types. Moreover, cilia and the Ca2+-Akt signaling axis are essential for the activation of HSF1 under mechanical stress in vitro and in vivo. Considering the conserved expression of HSF1 in organisms, these findings unveil a fundamental mechanism of gene expression regulation triggered by mechanical clues during embryonic development and other physiological and pathological transformations.

category: developmental biology


title: Positional and Compositional Analysis of Saturated, Monounsaturated and Polyunsaturated Fatty acids in Human Adipose Tissue Triglyceride by 13C NMR

abstract: Objectives and new findings, ends with short conclusion, no referencesThe synthesis and turnover of triglyceride in adipose tissue involves enzymes with preferences for specific fatty acid classes and/or regioselectivity with regard to the fatty acid position within the glycerol moiety. The focus of the present study was to characterize both the fatty acid composition and their positional distribution in triglycerides of biopsied human subcutaneous adipose tissue using 13C NMR spectroscopy. The triglyceride sn2 position was significantly more enriched with monounsaturated fatty acids compared to the sn1,3 sites, while saturated fatty acids abundance was significantly lower in the sn2 position compared to that of sn1,3. Furthermore, the analysis revealed significant positive correlations between the total fraction of palmitoleic acid with both BMI and HOMA-IR scores. Additionally, we established that 13C NMR chemical shifts for {omega} -3 signals, centered at 31.9 ppm, provided superior resolution of the most abundant FA species, including palmitoleate, compared to the {omega} -2 signals that were used previously. 13C NMR spectroscopy reveals for the first time a highly non-homogenous distribution of FA in the glycerol sites of human adipose tissue triglyceride and that these distributions are correlated with different phenotypes such as BMI and insulin resistance.

category: biochemistry


title: The plant immune receptors NRG1.1 and ADR1 are calcium influx channels

abstract:
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) regulate immunity and cell death. RPW8 domain-containing "helper" NLRs (RNLs) are required by many "sensor" NLRs. Our crystal structure of the RNL N REQUIREMENT GENE 1.1 (NRG1.1) N-terminal signaling domain resembled that of the resting state plant resistosome-forming HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) and the animal MIXED-LINEAGE KINASE-LIKE (MLKL) cation channel. Active NRG1.1 oligomerized, was enriched in plasma membrane puncta and conferred cytoplasmic Ca2+ influx in plant and human HeLa cells. NRG1.1-dependent Ca2+ influx and cell death were sensitive to Ca2+ channel blockers. Ca2+ influx and cell death mediated by NRG1.1 and ACTIVATED DISEASE RESISTANCE 1 (ADR1), another RNL, required conserved negatively charged N-terminal residues. Thus, RNLs apparently form influx channels to directly regulate cytoplasmic [Ca2+] and consequent cell death.

One Sentence SummaryA specific class of plant immune receptors function as calcium-permeable channels upon activation to induce cell death.

category: plant biology


title: Exploring the interaction network of a synthetic gut bacterial community

abstract: A key challenge in microbiome research is to predict functionality from microbial community composition. As central microbiota functions are determined by bacterial community networks it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments, as well as in community batch culture. Metabolomics analysis of spent culture supernatant of individual strains in combination with genome-informed pathway reconstruction provided insights into the metabolic potential of the individual community members. Thereby, we could show that the OMM12 interaction network is shaped by both, exploitative and interference competition in vitro. In particular, Enterococcus faecalis KB1 was identified as important driver of community composition by affecting the abundance of several other consortium members. Together, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network, which serves as knowledge base for future mechanistic studies.

category: microbiology


title: A minimal rDNA array replicates early, delays genome replication, and uncouples anaphase entry from S phase completion

abstract: Eukaryotes maintain hundreds of copies of ribosomal DNA (rDNA), many more than required for ribosome biogenesis, suggesting a yet undefined role for large rDNA arrays outside of ribosomal RNA synthesis. We demonstrate that reducing the Saccharomyces cerevisiae rDNA array to 35 copies, which is sufficient for ribosome function, shifts rDNA from being the latest replicating region in the genome to one of the earliest. This change in replication timing results in delayed genome-wide replication and classic replication defects. We present evidence that the requirement for rDNA to replicate late, which is conserved among eukaryotes, also coordinates the completion of genome replication with anaphase entry through the proper sequestration of the mitotic exit regulator Cdc14p in the rDNA-containing nucleolus. Our findings suggest that, instead of being a passive repetitive element, the large late-replicating rDNA array plays an active role in genome replication and cell cycle control.

category: molecular biology


title: Coordination of genome replication and anaphase entry by rDNA copy number in S. cerevisiae


title: Regulation of DNA (de)methylation positively impacts seed germination during seed development under heat stress

abstract:
Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling and the acquisition of germination capacity, desiccation tolerance, longevity and dormancy. Heat stress can negatively impact these processes and upon the increasing of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression and methylation on three stages of seed development. Notably, Arabidopsis Col-0 plants under heat stress presented a decrease in germination capacity and also a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms, including the activation of ABA pathway. By analyzing candidate epigenetic marks using mutants physiological assays, we observed that the lack of DNA demethylation by ROS1 gene impaired seed germination by affecting germination-related genes expression. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in promoters and gene sequences of germination-related genes. To conclude, our results indicate that DNA (de)methylation could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress.

Graphic Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: CINS: Cell Interaction Network inference from Single cell expression data

abstract: Studies comparing single cell RNA-Seq (scRNA-Seq) data between conditions mainly focus on differences in the proportion of cell types or on differentially expressed genes. In many cases these differences are driven by changes in cell interactions which are challenging to infer without spatial information. To determine cell-cell interactions that differ between conditions we developed the Cell Interaction Network Inference (CINS) pipeline. CINS combines Bayesian network analysis with regression-based modeling to identify differential cell type interactions and the proteins that underlie them. We tested CINS on a disease case control and on an aging human dataset. In both cases CINS correctly identifies cell type interactions and the ligands involved in these interactions. We performed additional mouse aging scRNA-Seq experiments which further support the interactions identified by CINS.

category: bioinformatics


title: Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and patterns of mutation accumulation

abstract: After the main out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today1,2. Here we investigate the size distribution of these fragments in non-African genomes3. We find consistent differences in fragment length distributions across Eurasia with 11% longer fragments in East Asians than in West Eurasians. By comparing extant populations and ancient samples, we show that these differences are due to a different rate of decay in length by recombination since the Neanderthal admixture. In line with this, we observe a strong correlation between the average fragment length and the accumulation of derived mutations, similar to what is expected by changing the ages at reproduction as estimated from trio studies4. Altogether, our results suggest consistent differences in the generation interval across Eurasia, by up to 20% (e.g. 25 versus 30 years), over the past 40,000 years. We use sex-specific accumulations of derived alleles to infer how these changes in generation intervals between geographical regions could have been mainly driven by shifts in either male or female age of reproduction, or both. We also find that previously reported variation in the mutational spectrum5 may be largely explained by changes to the generation interval and not by changes to the underlying mutational mechanism. We conclude that Neanderthal fragment lengths provide unique insight into differences of a key demographic parameter among human populations over the recent history.

category: evolutionary biology


title: Nothing in evolution makes sense except in the light of parasites

abstract: Parasitism emerges readily in models and laboratory experiments of RNA world and would lead to extinction unless prevented by compartmentalisation or spatial patterning. Modelling replication as an active computational process opens up many degrees of freedom that are exploited to meet environmental challenges, and to modify the evolutionary process itself. Here we use automata chemistry models and spatial RNA world models to study the emergence of parasitism and the complexity that evolves in response. The system is initialised with a hand-designed replicator that copies other replicators with a small chance of point mutation. Almost immediately, short parasites arise; these are copied more quickly, and so have an evolutionary advantage. The replicators also become shorter, and so are replicated faster; they evolve a mechanism to slow down replication, which reduces the difference of replication rate of replicators and parasites. They also evolve explicit mechanisms to discriminate copies of self from parasites; these mechanisms become increasingly complex. New parasite species continually arise from mutated replicators, rather than from evolving parasite lineages. Evolution itself evolves, eg by effectively increasing point mutation rates, and by generating novel emergent mutational operators. Thus, parasitism drives the evolution of complex replicators and complex ecosystems.


title: Nothing in evolution makes sense except in the light of parasitism: evolution of complex replication strategies


title: Stratified Random Sampling Methodology for Observing Community Mask Use within Indoor Settings: Results from Louisville, Kentucky during the COVID-19 Pandemic

abstract: Wearing a facial mask can limit COVID-19 transmission. Measurements of communities mask use behavior have mostly relied on self-report. This studys objective was to devise a method for measuring the prevalence of mask-wearing and proper mask use in indoor public areas without relying on self-report. A stratified random sample of retail trade stores (public areas) in Louisville, Kentucky, USA, was selected and targeted for observation by trained surveyors during December 14-20, 2020. The stratification allowed for investigating mask use behavior by city district, retail trade group, and public area size. The average mask use prevalence among observed visitors of the 382 visited public areas was 96%, while the average prevalence of proper use was 86%. In 17% of the public areas, at least one unmasked visitor was among the observed visitors; in 48%, at least one improperly masked visitor was observed. The average mask use among staff was 92%, but unmasked staff were observed in fewer public areas, as an unmasked staff member was observed in 11% of the visited public areas. The average prevalence of proper make use among staff was 87%, similar to the average among visitors. However, the percentage of public areas where at least one improperly masked staff was observed was 33. Significant disparities in mask use and its proper use were observed among both visitors and staff by public area size, retail trade type, and geographical area. Observing unmasked and incorrectly masked visitors was more common in small (less than 1500 square feet) public areas than larger ones, also in food and grocery stores than other retail stores. Also, the majority of the observed unmasked persons were male and middle age adults.

category: scientific communication and education


title: Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen

abstract:
BackgroundSince the beginning of the COVID-19 outbreak, many pharmaceutical companies were racing to develop a safe and effective COVID-19 vaccine. Simultaneously, rumors and misinformation about COVID-19 were and still widely spreading. Therefore, this study aimed to investigate the prevalence of COVID-19 misinformation among the Yemeni population and its association with vaccine acceptance and perceptions.

MethodsA cross-sectional online survey was conducted in four major cities in Yemen. The constructed questionnaire consisted of four main sections (sociodemographic data, misinformation, perceptions (perceived susceptibility, severity and worry), and vaccination acceptance evaluation). Subject recruitment and data collection were conducted online utilizing social websites and using the snowball sampling technique. Descriptive and inferential analyses were performed using SPSS version 27.

ResultsThe total number of respondents was 484. Over 60% of them were male and had a university education, more than half had less than 100$ monthly income and were Khat chewers, while only 18% were smokers. Misinformation prevalence ranged from 8.9% to 38.9%, depending on the statement being asked. Men, university education, higher income, employment, and living in urban areas were associated with a lower misinformation level (p <0.05). Statistically significant association (p <0.05) between university education, living in urban areas, and being employed with perceived susceptibility were observed. The acceptance rate was 61.2% for free vaccines, but it decreased to 43% if they had to purchase it. Females, respondents with lower monthly income, and those who believed that pharmaceutical companies made the virus for financial gains were more likely to reject the vaccination (p <0.05).

ConclusionThe study revealed that the acceptance rate to take a vaccine was suboptimal and significantly affected by gender, misinformation, cost, and income. Furthermore, being female, Nonuniversity educated, low-income, and living in rural areas were associated with higher susceptibility to misinformation about COVID-19. These findings show a clear link between misinformation susceptibility and willingness to vaccinate. Focused awareness campaigns to decrease misinformation and emphasize the vaccinations safety and efficacy might be fundamental before initiating any mass vaccination in Yemen.


title: A functional logic for neurotransmitter co-release in the cholinergic forebrain pathway

abstract: The forebrain cholinergic system has recently been shown to co-release both acetylcholine and GABA. We have discovered that such co-release by cholinergic inputs to the claustrum differentially affects neurons that project to cortical versus subcortical targets. The resulting changes in neuronal gain toggles network efficiency and discriminability of output between two different projection subcircuits. Our results provide a potential logic for neurotransmitter co-release in cholinergic systems.

category: neuroscience


title: A simple and robust method for automating analysis of naïve and regenerating peripheral nerves

abstract:
BackgroundManual axon histomorphometry (AH) is time- and resource-intensive, which has inspired many attempts at automation. However, there has been little investigation on implementation of automated programs for widespread use. Ideally such a program should be able to perform AH across imaging modalities and nerve states. AxonDeepSeg (ADS) is an open source deep learning program that has previously been validated in electron microscopy. We evaluated the robustness of ADS for peripheral nerve axonal histomorphometry in light micrographs prepared using two different methods.

MethodsAxon histomorphometry using ADS and manual analysis (gold-standard) was performed on light micrographs of naive or regenerating rat median nerve cross-sections prepared with either toluidine-resin or osmium-paraffin embedding protocols. The parameters of interest included axon count, axon diameter, myelin thickness, and g-ratio.

ResultsManual and automatic ADS axon counts demonstrated good agreement in naive nerves and moderate agreement on regenerating nerves. There were small but consistent differences in measured axon diameter, myelin thickness and g-ratio; however, absolute differences were small. Both methods appropriately identified differences between naive and regenerating nerves. ADS was faster than manual axon analysis.

ConclusionsWithout any algorithm retraining, ADS was able to appropriately identify critical differences between naive and regenerating nerves and work with different sample preparation methods of peripheral nerve light micrographs. While there were differences between absolute values between manual and ADS, ADS performed consistently and required much less time. ADS is an accessible and robust tool for AH that can provide consistent analysis across protocols and nerve states.


title: Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation

abstract:
ObjectiveAdult cartilage has limited repair capacity. MRL/MpJ mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and nonhealer mice and to evaluate microbiome transplantation as a novel regenerative therapy.

MethodsWe transplanted C57BL/6J mice with MRL/MpJ cecal contents in mice at weaning and as adults (n=57) and measured earhole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n=25) and B6-transplanted MRL (n=20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n=58), cecal microbiomes were profiled by 16S sequencing and compared to earhole closure rates. Microbial metagenomes were imputed using PICRUSt.

ResultsTransplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved earhole closure rates. Transplantation prior to ear punch was associated with the greatest earhole closure. Offspring of transplanted mice healed better than controls. Several microbiome clades were correlated with healing, including Firmicutes, Lactobacillales, and Verrucomicrobia. Gram-negative organisms were reduced. Females of all groups tended to heal better than males, female microbiota resembled MRL mice.

ConclusionIn this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to nonhealer mice via microbiome transplantation. We identified several microbiome clades associated with healing. Future studies should evaluate the mechanisms underlying these findings and confirm our results in murine OA.


title: Intrinsic Gating Behavior of Voltage-Gated Sodium Channels Predetermines Regulation by Auxiliary β-subunits

abstract: Voltage-gated sodium (Nav) channels mediate rapid millisecond electrical signaling in excitable cells. Auxiliary subunits, {beta}1-{beta}4, are thought to regulate Nav channel function through covalent and/or polar interactions with the channel s voltage-sensing domains. How these interactions translate into the diverse and variable regulatory effects of {beta}-subunits remains unclear. Here, we find that the intrinsic movement order of the voltage-sensing domains during channel gating is unexpectedly variable across Nav channel isoforms. This movement order dictates the channel s propensity for closed-state inactivation, which in turn modulates the actions of {beta}1 and {beta}3. We show that the differential regulation of skeletal muscle, cardiac, and neuronal Nav channels is explained by their variable levels of closed-state inactivation. Together, this study provides a unified mechanism for the regulation of all Nav channel isoforms by {beta}1 and {beta}3, which explains how the fixed structural interactions of auxiliary subunits can paradoxically exert variable effects on channel function.

category: biophysics


title: A precise and general FRET-based method for monitoring structural transitions in protein self-organization

abstract: Proteins assemble into a tremendous variety of dynamic and functional structures. Sensitive measurements directly in cells with a high spatiotemporal resolution are needed to distinguish these different assemblies. Here, we demonstrate precise and continuous monitoring of cytoplasmic protein self-assemblies and their structural transitions. Intermolecular FRET with both the donor and acceptor protein at the same target protein provides high sensitivity while retaining the advantage of straightforward ratiometric imaging. We measure different assembly structures, transient intermediate states kinetics, and assembly formation resolved in space and time. Specifically, the method recapitulates that i) the mutant Huntingtin exon1 (mHttex1) protein first forms low-FRET and presumably less ordered assemblies in yeast and human cells, which develop into high-FRET aggregates, ii) the chaperone DNAJB6b prevents low-FRET mHttex1 assemblies, yet coassembles with mHttex1 aggregates, and iii) FUS condensates have mutation-dependent nanoscopic structures. FACS measurements allow assembly measurement in a high-throughput manner crucial for screening efforts, while fluorescence microscopy provides spatiotemporally-resolved measurements on the single-condensate level during a cells lifetime to assess the biological consequences. Implementation in other native or non-native proteins could provide insight into many studies involving protein condensation or aggregation.


title: Frequent PIK3CA mutations in eutopic endometrium of patients with ovarian clear cell carcinoma

abstract: Recent studies have reported cancer-associated mutations in normal endometrium. Mutations in eutopic endometrium may lead to endometriosis and endometriosis-associated ovarian cancer. We investigated PIK3CA mutations (PIK3CAm) for three hotspots (E542K, E545K, H1047R) in eutopic endometrium in patients with ovarian cancer and endometriosis from formalin-fixed paraffin-embedded specimens by laser-capture microdissection and droplet digital PCR. The presence of PIK3CAm in eutopic endometrial glands with mutant allele frequency [≥]15% were as follows: ovarian clear cell carcinoma (OCCC) with PIK3CAm in tumors, 20/300 hotspots in 11/14 cases; OCCC without PIK3CAm, 42/78 hotspots in 11/12 cases; high-grade serous ovarian carcinoma, 8/45 hotspots in 3/5 cases; and endometriotic cysts, 5/63 hotspots in 5/6 cases. These rates were more frequent than in non-cancer non-endometriosis controls (7/309 hotspots in 5/17 cases). In OCCC without PIK3CAm, 7/12 (58%) cases showed multiple hotspot mutations in the same eutopic endometrial glands. In 3/54 (5.6%) cases, PIK3CAm was found in eutopic endometrial stroma. Multi-sampling of the OCCC tumors with PIK3CAm showed intratumor heterogeneity in three of eight cases. In two cases, PIK3CAm was detected in the stromal component of the tumor. Homogenous PIK3CAm in the epithelial component of the tumor matched the mutation in eutopic endometrial glands in only one case. Eutopic endometrial glands in ovarian cancer and endometriosis show high frequency of PIK3CAm that is not consistent with tumors, and multiple hotspot mutations are often found in the same glands. Our results suggest that most PIK3CAm in eutopic endometrial glands are passenger rather than driver mutations.

category: cancer biology


title: Rab11-dependent recycling of calcium channels is mediated by auxiliary subunit α2δ-1 but not α2δ-3

abstract:
N-type voltage-gated calcium channels (CaV2.2) are predominantly expressed at presynaptic terminals, and their function is regulated by auxiliary 2{delta} and {beta} subunits. All four mammalian 2{delta} subunits enhance calcium currents through CaV1 and CaV2 channels, and this increase is attributed, in part, to increased CaV expression at the plasma membrane. In the present study we provide evidence that 2{delta}-1, like 2{delta}-2, is recycled to the plasma membrane through a Rab11a-dependent endosomal recycling pathway. Using a dominant-negative Rab11a mutant, Rab11a(S25N), we show that 2{delta}-1 increases plasma membrane CaV2.2 expression by increasing the rate and extent of net forward CaV2.2 trafficking in a Rab11a-dependent manner. Dominant-negative Rab11a also reduces the ability of 2{delta}-1 to increase CaV2.2 expression on the cell-surface of hippocampal neurites. In contrast, 2{delta}-3 does not enhance rapid forward CaV2.2 trafficking, regardless of whether Rab11a(S25N) is present. In addition, whole-cell CaV2.2 currents are reduced by co-expression of Rab11a(S25N) in the presence of 2{delta}-1, but not 2{delta}-3. Taken together these data suggest that 2{delta} subtypes participate in distinct trafficking pathways which in turn influence the localisation and function of CaV2.2.

Summary statementThe calcium channel auxiliary subunit 2{delta}-1 but not 2{delta}-3 participates in Rab11a-dependent recycling, which in turn influences the localisation and function of CaV2.2.


title: Metabolomics of aging in primary fibroblasts from small and large breed dogs

abstract: Among several animal groups (eutherian mammals, birds, reptiles) lifespan positively correlates with body mass over several orders of magnitude. Contradicting this pattern are domesticated dogs, with small dog breeds exhibiting significantly longer lifespans than large dog breeds. The underlying mechanisms of differing aging rates across body masses are unclear, but it is generally agreed that metabolism is a significant regulator of the aging process. Herein, we performed a targeted metabolomics analysis on primary fibroblasts isolated from small and large breed young and old dogs. Regardless of size, older dogs exhibited lower glutathione and ATP, consistent with a role for oxidative stress and bioenergetic decline in aging. Furthermore, several size-specific metabolic patterns were observed with aging, including: (i) An apparent defect in the lower half of glycolysis in large old dogs at the level of pyruvate kinase. (ii) Increased glutamine anaplerosis into the TCA cycle in large old dogs. (iii) A potential defect in co-enzyme A biosynthesis in large old dogs. (iv) Low nucleotide levels in small young dogs that corrected with age. (v) An age dependent increase in carnitine in small dogs that was absent in large dogs. Overall, these data support the hypothesis that alterations in metabolism may underlie the different lifespans of small versus large breed dogs, and further work in this area may afford potential therapeutic strategies to improve the lifespan of large dogs.


title: Modulating the voltage sensor of a cardiac potassium channel shows antiarrhythmic effects

abstract:
Cardiac arrhythmias are the most common cause of sudden cardiac death worldwide. Lengthening the ventricular action potential duration (APD) either congenitally or via pathologic or pharmacologic means, predisposes to a life-threatening ventricular arrhythmia, Torsade de Pointes. IKs, a slowly activating K+ current plays a role in action potential repolarization. In this study, we screened a chemical library in silico by docking compounds to the voltage sensing domain (VSD) of the IKs channel. Here we show that C28 specifically shifted IKs VSD activation in ventricle to more negative voltages and reversed drug-induced lengthening of APD. At the same dosage, C28 did not cause significant changes of the normal APD in either ventricle or atrium. This study provides evidence in support of a computational prediction of IKs VSD activation as a potential therapeutic approach for all forms of APD prolongation. This outcome could expand the therapeutic efficacy of a myriad of currently approved drugs that may trigger arrhythmias.

Significance statementC28, identified by in silico screening, specifically facilitated voltage dependent activation of a cardiac potassium ion channel, IKs. C28 reversed drug-induced prolongation of action potentials, but minimally affected the normal action potential at the same dosage. This outcome supports a computational prediction of modulating IKs activation as a potential therapy for all forms of action potential prolongation, and could expand therapeutic efficacy of many currently approved drugs that may trigger arrhythmias.


title: Self-contained and modular structured illumination microscope

abstract: We present a modular implementation of structured illumination microscopy (SIM) that is fast, largely self-contained and that can be added onto existing fluorescence microscopes. Our instrument, which we call HIT-SIM, can theoretically deliver well over 50 super-resolved images per second and is readily compatible with existing acquisition software packages. We provide a full technical package consisting of schematics, a list of components and an alignment scheme that provides detailed specifications and assembly instructions. We illustrate the performance of the instrument by imaging optically large samples containing sequence-specifically stained DNA fragments.


title: Using optogenetics to link myosin patterns to contractile cell behaviors during convergent extension

abstract:
Distinct spatiotemporal patterns of actomyosin contractility are often associated with particular epithelial tissue shape changes during development. For example, a planar polarized pattern of myosin II localization regulated by Rho1 signaling during Drosophila body axis elongation is thought to drive the cell behaviors that contribute to convergent extension. However, it is not well understood how specific aspects of a myosin localization pattern influence the multiple cell behaviors--including cell intercalation, cell shape changes, and apical cell area fluctuations--that simultaneously occur within a tissue during morphogenesis. Here, we use optogenetic activation (optoGEF) and deactivation (optoGAP) of Rho1 signaling to perturb the myosin pattern in the germband epithelium during Drosophila axis elongation and analyze the effects on contractile cell behaviors within the tissue. We find that uniform photoactivation of optoGEF or optoGAP is sufficient to rapidly override the endogenous myosin pattern, abolishing myosin planar polarity and reducing cell intercalation and convergent extension. However, these two perturbations have distinct effects on junctional and medial myosin localization, apical cell area fluctuations, and cell packings within the germband. Activation of Rho1 signaling in optoGEF embryos increases myosin accumulation in the medial-apical domain of germband cells, leading to increased amplitudes of apical cell area fluctuations. This enhanced contractility is translated into heterogeneous reductions in apical cell areas across the tissue, disrupting cellular packings within the germband. Conversely, inactivation of Rho1 signaling in optoGAP embryos decreases both medial and junctional myosin accumulation, leading to a dramatic reduction in cell area fluctuations. These results demonstrate that the level of Rho1 activity and the balance between junctional and medial myosin regulate apical cell area fluctuations and cellular packings in the germband, which have been proposed to influence the biophysics of cell rearrangements and tissue fluidity.

STATEMENT OF SIGNIFICANCETissues are shaped by forces produced by dynamic patterns of actomyosin contractility. However, the mechanisms underlying these myosin patterns and their translation into cell behavior and tissue-level movements are not understood. Here, we show that optogenetic tools designed to control upstream regulators of myosin II can be used to rapidly manipulate myosin patterns and analyze the effects on cell behaviors during tissue morphogenesis. Combining optogenetics with live imaging in the developing fruit fly embryo, we show that acute perturbations to upstream myosin regulators are sufficient to rapidly perturb existing myosin patterns and alter cell movements and shapes during axis elongation, resulting in abnormalities in embryo shape. These results directly link myosin contractility patterns to cell behaviors that shape tissues, providing new insights into the mechanisms that generate functional tissues.


title: Cell Type Assignments for Spatial Transcriptomics Data

abstract:
MotivationRecent advancements in fluorescence in situ hybridization (FISH) techniques enable them to concurrently obtain information on the location and gene expression of single cells. A key question in the initial analysis of such spatial transcriptomics data is the assignment of cell types. To date, most studies used methods that only rely on the expression levels of the genes in each cell for such assignments. To fully utilize the data and to improve the ability to identify novel sub-types we developed a new method, FICT, which combines both expression and neighborhood information when assigning cell types.

ResultsFICT optimizes a probabilistic function that we formalize and for which we provide learning and inference algorithms. We used FICT to analyze both simulated and several real spatial transcriptomics data. As we show, FICT can accurately identify cell types and sub-types improving on expression only methods and other methods proposed for clustering spatial transcriptomics data. Some of the spatial sub-types identified by FICT provide novel hypotheses about the new functions for excitatory and inhibitory neurons.

AvailabilityFICT is available at: https://github.com/haotianteng/FICT

Contactzivbj@andrew.cmu.edu


title: Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness

abstract: Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements is rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter-enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny or contacts with target genes, is significantly associated with gene expression evolution.


title: Sensory and cognitive factors affecting multi-digit touch: a perceptual and modeling study

abstract:
Whilst everyday interactions with objects often involve multiple tactile contacts, integration of tactile signals remains poorly understood. Here we characterise the integration process of tactile motion on multiple fingerpads. Across four experiments, participants averaged the direction of two simultaneous tactile motion trajectories delivered to different fingerpads. Averaging performance differed between within- and between-hands in terms of sensitivity and precision but was unaffected by somatotopic proximity between stimulated fingers. The sensitivity to the average direction was influenced by the discrepancy between individual motion signals, but only for within-hand conditions. This was explained by a model, in which the  virtually leading finger received a higher perceptual weighting. Precision was greater in between-hand compared to within-hand conditions. While biased weighting accounted for differences in sensitivity, it was not sufficient to explain the difference in precision, implying additional sensory limitations during within-hand integration. We suggest that unimanual integration is limited and thus exploits a  natural cognitive prior involving a single object moving relative to the hand to maximise information gain.

Author summaryTactile stimulation is always on. Yet little is known about how the brain combines widespread tactile inputs for perception. Most tactile studies emphasize a single point of tactile stimulation (e.g., location or intensity of a static stimulus) and minimal units of tactile perception (e.g., acuity or selectivity). However, our daily interactions with the world involve encoding spatially and temporally extended tactile signals. Perceiving tactile objects and events as coherent entities requires the somatosensory system to aggregate tactile afferent signals across separate skin regions (i.e., separate digits). Across four experiments we asked participants to average direction of two tactile motion trajectories delivered simultaneously to two different fingerpads, either on the same, or on different hands. Our results show strong integration between multiple tactile inputs, but subject to limitations for inputs delivered within a hand. Our model suggests that tactile inputs are weighted according to an integrative model of hand-object interaction that operates within-hands on purely geometric information to prioritise  novel information from a  virtually leading finger (VLF).


title: Different underlying mechanisms for high and low arousal in probabilistic learning in humans

abstract: Humans are uniquely capable of adapting to highly changing environments by updating relevant information and adjusting ongoing behaviour accordingly. Here we show how this ability --termed cognitive flexibility-- is differentially modulated by high and low arousal fluctuations. We implemented a probabilistic reversal learning paradigm in healthy participants as they transitioned towards sleep or physical extenuation. The results revealed, in line with our pre-registered hypotheses, that low arousal leads to diminished behavioural performance through increased decision volatility, while performance decline under high arousal was attributed to increased perseverative behaviour. These findings provide evidence for distinct patterns of maladaptive decision-making on each side of the arousal inverted u-shaped curve, differentially affecting participants ability to generate stable evidence-based strategies, and introduces wake-sleep and physical exercise transitions as complementary experimental models for investigating neural and cognitive dynamics.


title: Underlying environmental factors and geomagnetic fields linked to 45 pilot whales Globicephala macrorhynchus stranding in Modung white beach, Indonesian coast on 19th February 2021

abstract: The reason whale and dolphin stranding is not fully understood and it is not linked to a standalone variable. Theories assume intertwined factors including sickness, underwater noise, navigational error, geographical features, the presence of predators, poisoning from pollution or algal blooms, geomagnetic field, and extreme weather are responsible to whale stranding. On 19th February 2021, a pod consists of 45 pilot whales Globicephala macrorhynchus was stranded in a remote 7050 m2 Modung white beach of Indonesian coast. This paper aims to assess the environmental factors that may be can explain and link to this stranding cases. Those factors include bathymetry, plankton cell density measured using MODIS, water sediment load measured using Sentinel 2 Bands 4,3,1, vessel traffic, precipitation (inch) and thunder (CAPE index J/kg), water salinity and temperature, and geomagnetic field (nT). The results show the water near stranding sites were shallow, has sediment load, high plankton density, warmer, receiving torrential rain prior stranding, having weak geomagnetic field and high total magnetic field change/year. The combination of those environmental covariates may influence the behavior, navigation, and echolocation of the said stranded pilot whale.

category: ecology


title: Multilamellar mesoporous silica nanoparticles using a cationic co-surfactant dual-templating method.

abstract: The utility of mesoporous silica nanoparticles (MSNs) has been repeatedly proven in a wide range of biomedical applications. The general morphology of these particles is easily modifiable by various post-grafting possibilities and adjustments within the surfactant-based template. The synthesis of multilamellar vesicular silica nanoparticles has led to the discovery of beneficial attributes regarding said particles. Depending on the synthesis process, various parameters are affected including packaging capacity, stability, drug adsorption and release. This research focused on synthesis and characterization of multilamellar MSNs using a cationic-cationic co-surfactant templating route testing various ratios of cetyltrimethylammonium bromide (CTAB) and didodecyldimethylammonium bromide (DDAB). TEM imaging showed clear differences in size and morphology between the different samples, and was further characterized by BET and BJH analysis. All multilamellar nanoparticles did exhibit a similar pore size distribution and overall gradual release of drug contents. However, the degree of drug adsorption and overtime drug release was clearly influenced by the number of layers of the MSNs, proving the utility of adjusting the template. Further experiments could be conducted to validate the utility of beta-cyclodextrin as a template regulator and to investigate both biocompatibility and biodegradability of the multilamellar MSNs.

category: bioengineering


title: Development of a label-free microfluidic impedimetric immunoassay for anti-SPAG16 antibody.

abstract:
A recently found biomarker regarding multiple sclerosis, namely the anti-SPAG16 antibody (Ab), could be a potential way for early detection, prognosis and diagnosis of said autoimmune disease. Merging electrochemical analysis with a microfluidic system is a novel approach, which avoids the use of labelling steps as seen in traditional ELISA immunoassays. In this study, aluminium interdigitated electrodes on polystyrene-coated PET foils were implemented in a microfluidic flow cell to bind and detect SPAG16 Abs by impedimetric measurements. The coated PET foils showed a clear affinity for the fusion protein SPAG16-THIO and thioredoxin (THIO). Determining sensitivity and specificity of antibody-antigen binding using a microfluidic ELISA immunoassay has revealed the test to be unreliable by showing no linear pattern of a dilution series of the standard and producing skewed inconsistent results. The impedimetric analysis showed opposite results of what one would expect. The systems efficiency is in need to be revised and optimised before undergoing actual diagnostic tests. Further advancement could be done by reducing leakage, securing a more stable entrance for injection and circumventing the occurence of air bubbles in the wells.

SAMENVATTINGMultiple sclerosis (MS) is een auto-immune ziekte, gekenmerkt door inflammatie van het centraal zenuwstelsel en demyelinisatie van axonen. Een recent gevonden proteine, namelijk het anti-SPAG16 antilichaam, is bewezen een biomerker te zijn voor MS. Met behulp van een elektrochemisch analytisch systeem gecombineerd met microfluidica zou men anti-SPAG16 antilichamen kunnen opsporen voor vroegtijdige detectie, prognose en diagnose. Het grote voordeel tegenover traditionele ELISA testen is het elimineren van labelling stappen waardoor de immunoassay goedkoper en gebruiksvriendelijk wordt. In deze studie werden overlappende aluminium elektrodes op polystyreen-gecoate PET-plaatjes geimplementeerd in een microfluidische flow cell voor binding en detectie van anti-SPAG16 antilichamen door middel van impedimetrische metingen. De gecoate PET-plaatjes vertonen een duidelijke affiniteit voor 0,1 g/ml SPAG16 en THIO. Het bepalen van sensitiviteit en specificiteit van antilichaam-antigen binding, gebruikmakende van een ELISA immunoassays, gaf aan dat de test onbetrouwbaar is doordat geen duidelijk patroon voor standaardoplossingen zichtbaar was en resultaten vertekend en inconsistent bleken te zijn. De impedimetrische analyse vertoonde tevens onbetrouwbare resultaten, waarbij een omgekeerd effect werd geobserveerd van wat er in theorie zou moeten gebeuren. De efficientie van het systeem moet herzien en geoptimaliseerd worden voordat men het voor diagnostische testen kan gebruiken. Verdere vorderingen zouden gerealiseerd kunnen worden door lekkages te reduceren, steviger bevestigen van de PDMS-ingang en de ontwikkeling van luchtbellen in de wells te vermijden.


title: Pipeline to detect the relationship between transposable elements and adjacent genes in host genome

abstract: AO_SCPLOWBSTRACTC_SCPLOWUnderstanding the relationship between transposable elements (TEs) and their closest positional genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of their transcriptional activity. A comprehensive knowledge of structural organization between transposable elements and neighboring genes is important to study TE functional role in gene regulation. We implemented a pipeline to display the relationship between the distribution of TEs and adjacent genes in host genomes. Our tool is freely available here: https://github.com/marieBvr/TEs_genes_relationship_pipeline.


title: Pipeline to detect the positional relationship between transposable elements and adjacent genes in host genome


title: Pipeline to detect the positional and directional relationship between transposable elements and adjacent genes in host genome


title: A pipeline to detect the relationship between transposable elements and adjacent genes in host genomes


title: Scaling concepts in 'omics: nuclear lamin-B scales with tumor growth and predicts poor prognosis, whereas fibrosis can be pro-survival

abstract:
Spatiotemporal relationships between genes expressed in tissues likely reflect physicochemical principles that range from stoichiometric interactions to co-organized fractals with characteristic scaling. For key structural factors within the nucleus and extracellular matrix (ECM), gene-gene power laws are found to be characteristic across several tumor types in The Cancer Genome Atlas (TCGA) and across single-cell RNA-seq data. The nuclear filament LMNB1 scales with many tumor-elevated proliferation genes that predict poor survival in liver cancer, and cell line experiments show LMNB1 regulates cancer cell cycle. Also high in the liver, lung, and breast tumors studied here are the main fibrosis-associated collagens, COL1A1 and COL1A2, that scale stoichiometrically with each other and super-stoichiometrically with a pan-cancer fibrosis gene set. However, high fibrosis predicts prolonged survival of patients undergoing therapy and does not correlate with LMNB1. Single-cell RNA-seq data also reveal scaling consistent with the pan-cancer power laws obtained from bulk tissue, allowing new power law relations to be predicted. Lastly, although noisy data frustrate weak scaling, concepts such as stoichiometric scaling highlight a simple, internal consistency check to qualify expression data.

ClassificationApplied Physical Sciences (major) and Cell Biology (minor)

Significance StatementNon-linear scaling analyses pervade polymer physics and chemistry and conceivably provide new insight into polymeric assemblies of genes expressed in tissues as well as co-regulated gene sets. Fractal scaling and stoichiometric scaling are among the gene-gene power law results identified here for key structural polymers in nuclei or extracellular matrix in human cancer data. Among nuclear envelope factors that might scale with DNA mass, only one nuclear filament scales with tumor proliferation and predicts poor survival in some cancer types. Collagen-1 scales with fibrosis and also tends to increase in multiple tumor types, but patients in therapy surprisingly survive longest with the highest levels of fibrosis, consistent with a therapeutic response.


title: A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat

abstract: Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys a suite of effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Nine effector - host susceptibility gene interactions have been reported in this pathosystem, presumed to be governed by unique pathogen effectors. This study presents the characterization of the SnTox267 necrotrophic effector that hijacks two separate host pathways to cause necrosis. An association mapping approach identified SnTox267 and the generation of gene-disrupted mutants and gain-of-function transformants confirmed its role in Snn2-, Snn6-, and Snn7-mediated necrosis. The Snn2 and Snn6 host susceptibility genes were complementary, and together they functioned cooperatively to elicit SnTox267-induced necrosis in the same light-dependent PCD pathway. Additionally, we showed that SnTox267 targeted Snn7, resulting in light-independent necrosis. Therefore, SnTox267 co-opts two distinct host pathways to elicit PCD. SnTox267 sequence comparison among a natural population of 197 North American P. nodorum isolates revealed 20 protein isoforms conferring variable levels of virulence, indicating continuing selection pressure on this gene. Protein isoform prevalence among discrete populations indicated that SnTox267 has likely evolved in response to local selection pressures and has diversified more rapidly in the Upper Midwest. Deletion of SnTox267 resulted in the upregulation of the unrelated effector genes SnToxA, SnTox1, and SnTox3, providing evidence for a complex genetic compensation mechanism. These results illustrate a novel evolutionary path by which a necrotrophic fungal pathogen uses a single proteinaceous effector to hijack two host pathways to induce cell death.

category: pathology


title: Screening of different cytotoxicity methods for the assessment of ENDS toxicity relative tobacco cigarettes

abstract: Electronic Nicotine Delivery Systems (ENDS), i.e., electronic cigarettes (e-cigs) and Tobacco Heating Products (THPs), are rapidly growing in popularity. The marketing of these products is regulated by specific rules in the European Union and in the US, which permit their legal sales. Nonetheless, comprehensive quality and safety requirements for regulatory purposes are still under development. Cytotoxicity studies are an important initial step in appraising the potential toxicity of ENDS. The aim of the present study was to screen a battery of different in vitro cytotoxicity methods for the assessment of toxicity induced by ENDS. We evaluated different cytotoxicity assays, including neutral red uptake (NRU), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), Annexin V apoptosis, High Content Screening (HCS) assays and Real Time Cell Analysis (RTCA), to compare two e-cigs (Vype ePen 3 and Vype eStick Maxx) and two THPs (IQOS and GLO) with the 1R6F reference tobacco cigarette. Human bronchial epithelial cells (H292) were exposed to 1R6F smoke (5 puffs by HCI regime), ePen vapor (10 puffs by modified HCI regime), eStick vapor (25 puffs by CRM81 regime), IQOS vapor (7 puffs by HCI regime) and GLO vapor (8 puffs by HCI regime) at air-liquid interface. All tests showed reduced cell viability following 1R6F smoke exposure and slight or no reduction with ENDS at 24 hours compared to controls. In addition, Annexin V and RTCA exhibited a further significant reduction in cell viability following 1R6F exposure compared with other assays. Furthermore, Annexin V allowed to discriminate viable cells from those in early/late apoptosis. Finally, RTCA and HCS being time-resolved analyses allowed also to determine the kinetic dependency parameter for toxicity of smoke/vapor chemicals on cell viability. In conclusion, NRU assay may be considered a suitable test, especially when combined with a time-resolved test, for assessing the kinetic of cytotoxicity induced by these products.

category: pharmacology and toxicology


title: Withaferin A promotes white adipose browning and prevents obesity through sympathetic nerve-activated Prdm16-FATP1 axis

abstract: The increasing prevalence of obesity has resulted in demands for the development of new effective strategies for obesity treatment. The Withaferin A (WA) shows a great potential for prevention of obesity by sensitizing leptin signaling in the hypothalamus. However, the mechanism underlying the weight- and adiposity-reducing effects of WA remains to be elucidated. Here, we report that WA treatment induced white adipose tissue (WAT) browning, elevated energy expenditure (EE), decreased respiratory exchange ratio (RER), and prevented high-fat diet (HFD)-induced obesity. The sympathetic chemical denervation dampened the WAT browning and also impeded the reduction of adiposity in WA-treated mice. WA markedly up-regulated the levels of Prdm16 and FATP1 (Slc27a1) in the inguinal WAT (iWAT), and this was blocked by sympathetic denervation. Prdm16 or FATP1 knockdown in iWAT abrogated the WAT browning-inducing effects of WA, and restored the weight gain and the adiposity in WA-treated mice. Together, these findings suggest that WA induces WAT browning through the sympathetic nerve-adipose axis; and the adipocytic Prdm16-FATP1 pathway mediates the promotive effects of WA on white adipose browning.

category: physiology


title: Visual object categorization in infancy

abstract: Humans make sense of the world by organizing things into categories. When and how does this process begin? We investigated whether real-world object categories that spontaneously emerge in the first months of life match categorical representations of objects in the human visual cortex. Taking infants looking times as a measure of similarity, we defined a representational space where each object was defined in relation to others of the same or different categories. This space was compared with hypothesis-based and fMRI-based models of visual-object categorization in the adults visual cortex. Analyses across different age groups revealed an incremental process with two milestones. Between 4 and 10 months, visual exploration guided by saliency gives way to an organization according to the animate-inanimate distinction. Between 10 and 19 months, a category spurt leads towards a mature organization. We propose that these changes underlie the coupling between seeing and thinking in the developing mind.


title: Unsupervised learning of haptic material properties

abstract: When touching the surface of an object, its spatial structure translates into a vibration on the skin. The perceptual system evolved to translate this pattern into a representation that allows to distinguish between different materials. Here we show that perceptual haptic representation of materials emerges from efficient encoding of vibratory patterns elicited by the interaction with materials. We trained a deep neural network with unsupervised learning (Autoencoder) to reconstruct vibratory patterns elicited by human haptic exploration of different materials. The learned compressed representation (i.e. latent space) allows for classification of material categories (i.e. plastic, stone, wood, fabric, leather/wool, paper, and metal). More importantly, distances between these categories in the latent space resemble perceptual distances, suggesting a similar coding. We could further show, that the temporal tuning of the emergent latent dimensions is similar to properties of human tactile receptors.


title: Dissociable oscillatory networks support gain and loss processing in human orbitofrontal cortex

abstract: Human neuroimaging and animal studies have linked neural activity in orbitofrontal cortex (OFC) to valuation of positive and negative outcomes. Additional evidence shows that neural oscillations, representing the coordinated activity of neuronal ensembles, support information processing in both animal and human prefrontal regions. However, the role of OFC neural oscillations in reward-processing in humans remains unknown, partly due to the difficulty of recording oscillatory neural activity from deep brain regions. Here, we examined the role of OFC neural oscillations (<30Hz) in reward processing by combining intracranial OFC recordings with a gambling task in which patients made economic decisions under uncertainty. Our results show that power in different oscillatory bands are associated with distinct components of reward evaluation. Specifically, we observed a double dissociation, with a selective theta band oscillation increase in response to monetary gains and a beta band increase in response to losses. These effects were interleaved across OFC in overlapping networks and were accompanied by increases in oscillatory coherence between OFC electrode sites in theta and beta band during gain and loss processing, respectively. These results provide evidence that gain and loss processing in human OFC are supported by distinct low-frequency oscillations in networks, and provide evidence that participating neuronal ensembles are organized functionally through oscillatory coherence, rather than local anatomical segregation.


title: Experimental increases in temperature mean and variance alter reproductive behaviors in the dung beetle 	Phanaeus vindex

abstract: Temperature profoundly impacts insect development, but plasticity of reproductive behaviors may mediate the impacts of temperature change on earlier life stages. Few studies have examined the potential for behavioral plasticity of adults to buffer developing offspring from warmer, more variable temperatures associated with climate change. We used a field manipulation to examine whether the dung beetle Phanaeus vindex alters breeding behaviors in response to climate change and whether adult behavioral shifts protect offspring from temperature increases. Dung beetles lay eggs inside brood balls made of dung that are buried underground for the entirety of offspring development. Depth of the brood ball impacts the temperatures offspring experience with consequences for beetle development. We placed females in either control or greenhouse treatments that simultaneously increased temperature mean and variance. We found that females produced smaller brood balls but buried them deeper in the greenhouse treatment, suggesting burial depth may come at a cost to brood ball size, which can impact offspring nutrition. Despite being buried deeper, brood balls from the greenhouse treatment experienced warmer mean temperatures but similar amplitudes of temperature fluctuation relative to the controls. Our findings suggest adult behaviors may buffer offspring from increased temperature variation due to climate change.


title: Evolution of thermal physiology alters predicted species distributions under climate change

abstract: Species distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine stickleback (Gasterosteus aculeatus). Using these data, we created geographic range projections using a mechanistic niche area approach under two climate change scenarios. Under both scenarios, trait data was either static ( no evolution models), allowed to evolve at observed evolutionary rates ( evolution models), or allowed to evolve at a rate of evolution scaled by the trait variance that is explained by quantitative trait loci (QTL;  scaled evolution models). We show that incorporating these traits and their evolution substantially altered the projected ranges for a widespread panmictic marine population, with over 7-fold increases in area under climate change projections when traits are allowed to evolve. Evolution-informed SDMs should improve the precision of forecasting range dynamics under climate change, and aid in their application to management and the protection of biodiversity.


title: Evolution of thermal physiology alters projected species distributions under climate change


title: Evolution of thermal physiology alters the projected range of threespine stickleback under climate change


title: Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

abstract: With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10x coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.


title: Bone Mineral Density modelled as a Random Field: a Feasibility Study on Pelvic Bone

abstract:
Background and ObjectiveCapturing the population variability of bone properties is of paramount importance to biomedical engineering. The aim of the present paper is to describe variability and correlations in bone mineral density with a spatial random field inferred from routine computed tomography data.

MethodsRandom fields were simulated by transforming pairwise uncorrelated Gaussian random variables into correlated variables through the spectral decomposition of an age-detrended correlation matrix. The validity of the random field model was demonstrated in the spatiotemporal analysis of bone mineral density. The similarity between the computed tomography samples and those generated via random fields was analyzed with the energy distance metric.

ResultsThe random field of bone mineral density was found to be approximately Gaussian/slightly left-skewed/strongly right-skewed at various locations. However, average bone density could be simulated well with the proposed Gaussian random field for which the energy distance, i.e., a measure that quantifies discrepancies between two distribution functions, is convergent with respect to the number of correlation eigenpairs.

ConclusionsThe proposed random field model allows the enhancement of computational biomechanical models with variability in bone mineral density, which could increase the usability of the model and provides a step forward in in-silico medicine.


title: Bone mineral density modeling via random field: normality, stationarity, sex and age dependence


title: A systematic analysis of metabolic pathways in the human gut microbiota

abstract: The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here, we systematically profile primary metabolic genes from the gut microbiome, identifying 19,885 gene clusters in 4,240 high-quality microbial genomes. We find marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 subjects from a Dutch population-based cohort shows that the level of 14 microbiome-derived metabolites in plasma is almost completely uncorrelated with the metagenomic abundance of the corresponding biosynthetic genes, revealing a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.


title: FrozenChicken: Promoting the meta-analysis of chicken microarray data

abstract: The FrozenChicken RData package, contains the frozen vectors for the commercially available (in situ oligonucleotide) Affymetrix Chicken Genome Array (GEO platform id GPL3213). This package will promote, simplify, and ease the meta-analysis of chicken microarray data by the research community studying vertebrate development using the chick model organism. The package is freely available in https://github.com/iduarte/FrozenChicken. (*Equal contribution.)


title: A Mixed-Modeling Framework for Whole-Brain Dynamic Network Analysis

abstract: The emerging area of dynamic brain network analysis has gained considerable attraction in recent years. While current tools have proven useful in providing insight into dynamic patterns of brain networks, development of multivariate statistical frameworks that allow for examining the associations between phenotypic traits and dynamic patterns of system-level properties of the brain, and drawing statistical inference about such associations, has largely lagged behind. To address this need we developed a mixed-modeling framework that allows for assessing the relationship between any desired phenotype and dynamic patterns of whole-brain connectivity and topology. Unlike current tools which largely use data-driven methods, our model-based method enables aligning neuroscientific hypotheses with the analytic approach. We demonstrate the utility of this model in identifying the relationship between fluid intelligence and dynamic brain networks using resting-state fMRI (rfMRI) data from 200 subjects in the Human Connectome Project (HCP) study. To our knowledge, this approach provides the first model-based statistical method for examining dynamic patterns of system-level properties of the brain and their relationships to phenotypic traits.


title: Early functional and cognitive declines measured by auditory evoked cortical potentials in Alzheimer's disease mice

abstract: Alzheimers disease (AD) is characterized with a progressive loss of memory and cognitive decline. However, assessment of AD-associated functional and cognitive changes is still a big challenge. Auditory evoked cortical potential (AECP) is an event-related potential reflecting not only neural activation in the auditory cortex but also cognitive activity in the brain. In this study, we used the subdermal needle electrodes with the same electrode setting as the auditory brainstem response (ABR) recording and recorded AECP in normal aging CBA/CaJ mice and APP/PS1 AD mice. AECP in mice usually appeared three positive peaks, i.e., P1, P2, and P3, and three corresponding negative peaks N1, N2, and N3. In normal aging CBA mice, the early sensory peaks P1, N1, and P2 were reduced as age increased, whereas the later cognitive peaks N2, P3, and N3 were increased or had no changes with aging. Moreover, the latency of P1 peak was increased as age increased, although the latencies of later peaks had significant reduction with aging. In AD mice, peak P1 was significantly reduced in comparison with wild-type (WT) littermates at young ages, proceeding AD phenotype presentation. In particular, the later cognitive peak P3 was diminished after 3 months old, different from normal aging effect. However, the latencies of AECP peaks in AD mice generally had no significant delay or changes with aging. Finally, consistent with AECP changes, the accumulation of amyloid precursor protein (APP) at the auditory cortex was visible in AD mice as early as 2 months old. These data suggest that AECP could serve as an early, noninvasive, and objective biomarker for detecting AD and AD-related dementia.


title: Immunity-longevity tradeoff neurally controlled by GABAergic transcription factor PITX1/UNC-30

abstract: A body of evidence indicates that metazoan immune and aging pathways are largely interconnected, but the mechanisms involved in their homeostatic control remain unclear. In this study, we found that the PITX (paired like homeodomain) transcription factor UNC-30 controls the tradeoff between immunity and longevity from the nervous system in Caenorhabditis elegans. PITX/UNC-30 functional loss enhanced immunity in a GATA/ELT-2- and p38 MAPK/PMK-1-dependent manner and reduced longevity by activating MXD/MDL-1 and the C2H2-type zinc finger transcription factor PQM-1. The immune inhibitory and longevity stimulatory functions of PITX/UNC-30 required the sensory neuron ASG and a neurotransmitter signaling pathway controlled by NPR-1, which is a G protein-coupled receptor related to mammalian neuropeptide Y receptors. Our findings uncovered a suppressive role of GABAergic signaling in the neural control of a biological tradeoff where energy is allocated towards immunity at the expense of longevity.

category: immunology


title: Kasugamycin is a novel chitinase 1 inhibitor with strong antifibrotic effects on pulmonary fibrosis

abstract:
RationalePulmonary fibrosis is a devastating lung disease with few therapeutic options. Chitinase 1 (CHIT1), an 18 glycosyl hydrolase family member, contributes to the pathogenesis of pulmonary fibrosis through regulation of Transforming Growth Factor (TGF)-{beta} signaling and effector function. Therefore, CHIT1 is a potential therapeutic target of pulmonary fibrosis.

ObjectivesThis study aimed to identify and characterize a druggable CHIT1 inhibitor with strong antifibrotic activity and minimal toxicity for therapeutic application to pulmonary fibrosis.

MethodsExtensive screening of small molecule libraries identified the aminoglycoside antibiotic Kasugamycin as a potent CHIT1 inhibitor.

Measurements and Main ResultsElevated levels of CHIT1 were detected in the lungs of patients with pulmonary fibrosis. In vivo bleomycin- and TGF-{beta}-stimulated murine models of pulmonary fibrosis, Kasugamycin showed impressive anti-fibrotic effects in both preventive and therapeutic conditions. In vitro studies also demonstrated that Kasugamycin inhibits fibrotic macrophage activation, fibroblast proliferation and myofibroblast transformation. Null mutation of transforming growth factor beta associated protein 1 (TGFBRAP1), a recently identified CHIT1 interacting signaling molecule, phenocopied antifibrotic effects of Kasugamycin in in vivo lungs and in vitro fibroblasts responses. Kasugamycin inhibits physical association between CHIT1 and TGFBRAP1, suggesting that antifibrotic effect of Kasugamycin is mediated through regulation of TGFBRAP1, at least in part.

ConclusionsThese studies demonstrate that Kasugamycin is a novel CHIT1 inhibitor with strong antifibrotic effect that can be further developed as an effective and safe therapeutic drug for pulmonary fibrosis.


title: AIM-CICs: automatic identification method for Cell-in-cell structures based on convolutional neural network

abstract: Whereas biochemical markers are available for most types of cell death, current studies on non-autonomous cell death by entosis relays strictly on the identification of cell-in-cell structure (CICs), a unique morphological readout that can only be quantified manually at present. Moreover, the manual CICs quantification is generally over-simplified as CICs counts, which represents a major hurdle against profound mechanistic investigations. In this study, we take advantage of artificial intelligence (AI) technology to develop an automatic identification method for CICs (AIM-CICs), which performs comprehensive CICs analysis in an automated and efficient way. The AIM-CICs, developed on the algorithm of convolutional neural network (CNN), can not only differentiate between CICs and non-CICs (AUC > 0.99), but also accurately categorize CICs into five subclasses based on CICs stages and cell number involved (AUC > 0.97 for all subclasses). The application of AIM-CICs would systemically fuel researches on CICs-mediated cell death such as high-throughput screening.

category: cell biology


title: Quantitative mapping of dense microtubule arrays in mammalian neurons

abstract: The neuronal microtubule cytoskeleton underlies the polarization and proper functioning of neurons, amongst others by providing tracks for motor proteins that drive intracellular transport. Different subsets of neuronal microtubules, varying in composition, stability and motor preference, are known to exist, but the high density of microtubules has so far precluded mapping their relative abundance and three-dimensional organization. Here we use different super-resolution techniques (STED, Expansion Microscopy) to explore the nanoscale organization of the neuronal microtubule network. This revealed that in dendrites stable, acetylated microtubules are enriched in the core of the dendritic shaft, while dynamic, tyrosinated microtubules enrich near the plasma membrane, thus forming a shell around the stable microtubules. Moreover, using a novel analysis pipeline we quantified the absolute number of acetylated and tyrosinated microtubules within dendrites and found that they account for 65-75% and [~]20-30% of all microtubules, respectively, leaving only few microtubules that do not fall in either category. Because these different microtubule subtypes facilitate different motor proteins, these novel insights help to understand the spatial regulation of intracellular transport.


title: The impact of invader number on whole community invasions in biomethane-producing communities

abstract: Microbes can invade as whole communities, but the ecology of whole community invasions are poorly understood. Here, we investigate how invader frequency affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of initial invader frequency, which varied between 0.01 and 10%. Invasion resulted in enhanced biogas production (to the level of the pure invading community), but only when invader frequency was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower number of invading taxa (but not individuals) at lower initial invader frequencies, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings.


title: Physiological and transcriptomic variability indicative of differences in key functions within a single coral colony

abstract: Polyps in different locations on individual stony coral colonies experience variation in numerous environmental conditions including flow and light, potentially leading to transcriptional and physiological differences across the colony. Here, we describe high-resolution physiological measurements and differential gene expression from multiple locations within a single colony of Stylophora pistillata, aiming to relate these to environmental gradients across the coral colony. We observed broad transcriptional responses in both the host and photosymbiont in response to height above the substrate, cardinal direction, and, most strongly, location along the branch axis. Specifically, several key physiological processes in the host appear more active toward branch tips including several metabolic pathways, toxin production for prey capture or defense, and biomolecular mechanisms of biomineralization. Further, the increase in gene expression related to these processes toward branch tips is conserved between S. pistillata and Acropora spp. The photosymbiont appears to respond transcriptionally to relative light intensity along the branch and due to cardinal direction. These differential responses were observed across the colony despite its genetic homogeneity and likely inter-polyp communication. While not a classical division of labor, each part of the colony appears to have distinct functional roles related to polyps differential exposure to environmental conditions.

category: genomics


title: A new parallel high-pressure packing system enables rapid multiplexed production of capillary columns

abstract:
Reversed-phase high performance liquid chromatography (HPLC) is the most commonly applied peptide separation technique in mass spectrometry (MS)-based proteomics. Particle-packed capillary columns are predominantly used in nano-flow HPLC systems. Despite being the broadly applied standard for many years capillary columns are still expensive and suffer from short lifetimes, particularly in combination with ultra-high-pressure chromatography systems. For this reason, and to achieve maximum performance, many laboratories produce their own in-house packed columns. This typically requires a considerable amount of time and trained personnel. Here, we present a new packing system for capillary columns enabling rapid, multiplexed column production with pressures reaching up to 3000 bar. Requiring only a conventional gas pressure supply and methanol as driving fluid, our system replaces the traditional setup of helium pressured packing bombs. By using 10x multiplexing, we have reduced the production time to just under 2 minutes for several 50 cm columns with 1.9 {micro}m particle size, speeding up the process of column production 40 to 800 times. We compare capillary columns with various inner diameters (ID) and length packed under different pressure conditions with our newly designed, broadly accessible high-pressure packing station.

One sentence summaryA newly constructed parallel high-pressure packing system enables the rapid multiplexed production of capillary columns.

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category: biochemistry


title: H3K36 methylation and DNA-binding are critical for Ioc4 recruitment and Isw1b remodeller function

abstract: The Isw1b chromatin-remodelling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeller. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promote the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodelling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.


title: H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeller function


title: Targeted replacement of full-length CFTR in human airway stem cells by CRISPR/Cas9 for pan-mutation correction in the endogenous locus

abstract: Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, there are many other pathogenic mutations throughout the CF gene. An autologous airway stem cell therapy in which the CFTR cDNA is precisely inserted into the CFTR locus may enable the development of a durable cure for almost all CF patients, irrespective of the causal mutation. Here, we use CRISPR/Cas9 and two adeno-associated viruses (AAV) carrying the two halves of the CFTR cDNA to sequentially insert the full CFTR cDNA along with a truncated CD19 (tCD19) enrichment tag in upper airway basal stem cells (UABCs) and human bronchial basal stem cells (HBECs). The modified cells were enriched to obtain 60-80% tCD19+ UABCs and HBECs from 11 different CF donors with a variety of mutations. Differentiated epithelial monolayers cultured at air-liquid interface showed restored CFTR function that was >70% of the CFTR function in non-CF controls. Thus, our study enables the development of a therapy for almost all CF patients, including patients who cannot be treated using recently approved modulator therapies.


title: Description and analysis of glycosidic residues in the largest open natural products database

abstract: Natural products (NP), biomolecules produced by living organisms, inspire the pharmaceutical industry and research due to their structural characteristics and the substituents from which they derive their activities. Glycosidic residues are frequently present in NP structures and have particular pharmacokinetic and pharmacodynamic importance as they improve their solubility and are often involved in molecular transport, target specificity, ligand-target interactions and receptor binding. The COlleCtion of Open Natural prodUcTs (COCONUT) is currently the largest open database of NP and therefore a suitable starting point for the detection and analysis of the diversity of glycosidic residues in NP. In this work, we report and describe the presence of circular, linear, terminal and non-terminal glycosidic units in NP, together with their importance in drug discovery.


title: Decisive Role of Polymer-BSA Interactions in Biofilm Substrates on Philicity and EPS Composition

abstract: Formation of extracellular polymeric substances (EPS) is a crucial step for bacterial biofilm growth. Dependence of EPS composition on the growth substrate and the conditioning of the latter is thus of primary importance. Here, we present results of studies on the growth of biofilms of two different strains each, of the Gram negative bacteria Escherichia coli and Klebsiella pneumoniae, on four polymers used commonly in indwelling medical devices - Polyethene, Polypropylene, Polycarbonate, and Polytetrafluoroethylene immersed in Bovine Serum Albumin (BSA) for 24 hrs. The polymer substrates are studied before and after immersing in BSA for 9 hrs and 24 hrs, using contact angle measurement (CAM) and Field Emission Scanning Electron Microscopy (FE-SEM) to extract, respectively, the  philicity (defined as{phi} {equiv} sin ({theta}-90{degrees}), where{theta} is contact angle of the liquid on the solid at a particular temperature and ambient pressure) and spatial Hirsch parameter H (defined from the relation, F(r) ~ r2H, where F(r) is the mean squared density fluctuation at the sample surface). H =, <0.5 or >0.5 signifies no correlation, anti-correlation, and correlation, respectively. The substrates are seen to transform from large hydrophobicity to near amphiphilicity with the formation of BSA conditioning surface layer, and the H-values distinguish the length scales of ~ 100 nm, 500 nm, and 2000 nm, with the anti-correlation increasing with length scale. Biofilms grown on the BSA-covered surfaces are studied with CAM, FE-SEM, Fourier Transform Infrared (FTIR) and Surface Enhanced Raman Spectroscopy (SERS). Most notably, the{phi} -values are independent of the bacterial species and strain but dependent on the polymer, as is also shown strikingly by both types of spectra, while H-values show some bacterial variation. Thus, the EPS composition and consequently the wetting properties of the corresponding bacterial biofilms seems to be decided by the interaction of the conditioning BSA layer with a specific polymer used as the growth substrate.


title: Negative DNA supercoiling tunes protein-mediated looping

abstract: Protein-mediated DNA looping is fundamental to gene regulation and such loops occur stochastically in purified systems. Additional proteins increase the probability of looping, but these probabilities maintain a broad distribution. For example, the probability of lac repressor-mediated looping in individual molecules ranged 0-100%, and individual molecules exhibited representative behavior only in observations lasting an hour or more. Titrating with HU protein progressively compacted the DNA without narrowing the 0-100% distribution. Increased negative supercoiling produced an ensemble of molecules in which all individual molecules more closely resembled the average. Furthermore, in only twelve minutes of observation, well within the doubling time of the bacterium, most molecules exhibited the looping probability of the ensemble. DNA supercoiling, an inherent feature of all genomes, appears to impose time-constrained, emergent behavior on otherwise random molecular activity.


title: Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time


title: Activity-induced fluidization of arrested coalescence in fusion of cellular aggregates

abstract: At long time scales, tissue spheroids may flow or appear solid depending on their capacity to reorganize their internal structure. Understanding the relationship between intrinsic mechanical properties at the single cell level, and the tissue spheroids dynamics at the long-time scale is key for artificial tissue constructs, which are assembled from multiple tissue spheroids that over time fuse to form coherent structures. The dynamics of this fusion process are frequently analyzed in the framework of liquid theory, wherein the time scale of coalescence of two droplets is governed by its radius, viscosity and surface tension. In this work, we extend this framework to glassy or jammed cell behavior which can be observed in spheroid fusion. Using simulations of an individual-cell based model, we demonstrate how the spheroid fusion process can be steered from liquid to arrested by varying active cell motility and repulsive energy as established by cortical tension. The divergence of visco-elastic relaxation times indicates glassy relaxation near the transition towards arrested coalescence. Finally, we investigate the role of cell growth in spheroid fusion dynamics. We show that the presence of cell division introduces plasticity in the material and thereby increases coalescence during fusion.


title: Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants

abstract:
The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 g/mL; IC80 < 0.0006 to 0.0251 g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs.

One Sentence SummaryUltrapotent antibodies from convalescent donors neutralize and mitigate resistance of SARS-CoV-2 variants of concern.


title: Graphene oxide/silver nanoparticle ink formulations rapidly inhibit influenza A virus and OC43 coronavirus infection in vitro

abstract:
Respiratory tract infections present a significant risk to the human population, both through seasonal circulation and novel introductions with pandemic potential. There is a strong need for antiviral compounds with broad antimicrobial activity that can be coated onto filtration systems and personal protective equipment to augment their ability to remove infectious particles from the environment. Graphene oxide and silver nanoparticles are both materials with documented antimicrobial properties. Here, we tested the in vitro antiviral properties of several graphene oxide-silver nanoparticle composite materials, which were prepared through three different methods: reduction with silver salt, direct addition of silver nanospheres, and direct addition of silver nanospheres to thiolized graphene. These materials were tested over short time scales for their antiviral activity against two enveloped RNA viruses, influenza A virus and OC43 coronavirus, by performing viral plaque assays after exposure of the viruses to each material. It was found that the graphene oxide - silver nanoparticle materials generated by direct addition of the silver nanospheres were able to completely inhibit plaque formation by both viruses within one minute of exposure. Materials generated by the other two methods had varying levels of efficacy against influenza A virus. These studies indicate that graphene oxide-silver nanoparticle composite materials can rapidly neutralize RNA viruses and demonstrate their potential for use in a wide range of applications.

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category: microbiology