bluuebunny/crossref_metadata_2025 huggingface dataset:
Making sense of virus size and the tradeoffs shaping viral fitness
Authors: Edwards Kyle F. , Steward Grieg F. , Schvarcz Christopher R.
Published: April 2020

Viruses span an impressive size range, with genome length varying more than a thousandfold and capsid volume nearly a millionfold. Physical constraints suggest that smaller viruses may have multiple fitness advantages, because a greater number of viral offspring can be created from limited host resources, and because smaller particles diffuse to encounter new hosts more rapidly. At the same time, a larger genome size allows for numerous additional functions that may increase fitness, such as better control of replication, transcription, translation, and host metabolism, and neutralization of host defenses. However, it is unclear whether important viral traits correlate with size, and whether this causes size to vary among host types or environmental contexts. Here we focus on viruses of aquatic unicellular organisms, which exhibit the greatest known range of virus size. We develop and synthesize theory, and analyze data where available, to consider how size affects the primary components of viral fitness. We suggest that the costs of larger size (lower burst size and diffusivity) are mitigated by the role of a larger genome in increasing infection efficiency, broadening host range, and potentially increasing attachment success and decreasing decay rate. These countervailing selective pressures may explain why such a breadth of sizes exist and can even coexist when infecting the same host populations. We argue that oligotrophic environments may be particularly enriched in unusually large or “giant” viruses, because environments with diverse, resource-limited phagotrophic eukaryotes at persistently low concentrations may select for broader host range, better control of host metabolism, lower decay rate, and a physical size that mimics bacterial prey. Finally, we describe areas where further research is needed to understand the ecology and evolution of viral size diversity.
An updated and extended atlas for corresponding brain activation during task and rest
Authors: Tahedl Marlene , Schwarzbach Jens V.
Published: April 2020

The complexity of our actions and thinking is likely reflected in functional brain networks. Independent component analysis (ICA) is a popular data-driven method to compute group differences between such networks. To aid interpretation of functional network analyses, Smith and colleagues proposed a template of ten functional networks identified in 36 healthy participants. They labeled them those components according to their similarity with statistical parameter maps from a metaanalysis of task-based functional magnetic resonance imaging studies (Smith et al., 2009). However, those original templates show substantial distortion with respect to what up-to date correction methods can achieve, such that trying to capture relevant effects within several cortical regions, especially the sensorimotor and orbitofrontal cortices, as well as the cerebellum may yield suboptimal results. Here, we provide a technical update and extension to the original templates. Using correlation analyses, we identified the best matching maps of each of the original ten templates to ICA maps from the Human Connectome Project (HCP). The HCP provides group-parcellations of a large dataset (n = 1003) with high-quality data. This approach yields a better fit of spatial component maps with anatomical borders and gray-/white-matter-boundaries. Additionally, we provide a version of the updated templates in CIFTI file-format, an emerging format in the neuroimaging community that combines surface-based data with subcortical/cerebellar data in volumetric space. The two formats we provide here offer an improvement on the templates by Smith et al., which should enhance sensitivity and interpretability of future research that compares functional networks between groups.
Visualization of spatial gene expression in plants by modified RNAscope fluorescentin situhybridization
Authors: Solanki Shyam , Ameen Gazala , Zhao Jin , Flaten Jordan , Borowicz Pawel , Brueggeman Robert
Published: April 2020

In situanalysis of biomarkers such as DNA, RNA and proteins are important for research and diagnostic purposes. At the RNA level, plant gene expression studies rely on qPCR, RNAseq and probe-basedinsituhybridization (ISH). However, for ISH experiments poor stability of RNA and RNA based probes commonly results in poor detection or poor reproducibility. Recently, the development and availability of the RNAscope RNA-ISH method addressed these problems by novel signal amplification and background suppression. This method is capable of simultaneous detection of multiple target RNAs down to the single molecule level in individual cells, allowing researchers to study spatio-temporal patterning of gene expression. However, this method has not been optimized thus poorly utilized for plant specific gene expression studies which would allow for fluorescent multiplex detection. Here we provide a step-by-step method for sample collection and pretreatment optimization to perform the RNAscope assay in the leaf tissues of model monocot plant barley. We have shown the ubiquitousHvGAPHand predominantly stomatal guard cell expressedRpg1expression pattern in barley leaf sections and described the improve RNAcope methodology suitable for plant tissues using confocal laser microscope. By addressing the problems in the sample collection and incorporating additional sample backing steps we have significantly reduced the section detachment and experiment failure problems. Further, by reducing the time of protease treatment, we minimized the sample disintegration due to over digestion of barley tissues. Thus, we optimized the RNAscope detection method in plants to visualize the spatial expression and semi-quantification of target RNAs which can be employed in other plants such as the widely utilized model dicot plant Arabidopsis.
Modeling the Degradation Effects of Autophagosome Tethering Compounds (ATTEC)
Authors: Zhang Hang , An Ping , Fei Yiyan , Lu Boxun
Published: April 2020

Autophagy is a powerful protein degradation pathway with limited specificity. Our recent study proposed and demonstrated a potential strategy to harness autophagy to selectively degrade a specific pathogenic protein using autophagosome tethering compounds (ATTEC). ATTEC interact with both the target protein and the autophagosome protein LC3, and thus tether the target protein to the autophagosomes for subsequent degradation. The concentration-dependent curve of the target protein is U-shaped, but there has been lack of both kinetic and steady-state modeling of the degradation effects of ATTEC. Here we established a simplified model describing the kinetics and steady-state level of target protein, and characterized how compounds’ properties, especially binding affinities to LC3 and to the target protein, may influence their degradation effects.
Hyperactive end joining repair mediates resistance to DNA damaging therapy in p53-deficient cells
Authors: Kumar Rashmi J. , Chao Hui Xiao , Roberts Victoria R. , Sullivan Aurora R. , Shah Sonam J. , Simpson Dennis A. , Feng Wanjuan , Wozny Anne-Sophie , Kumar Sunil , Purvis Jeremy E. , Gupta Gaorav P.
Published: April 2020

TP53mutations in cancer are associated with poor patient outcomes and resistance to DNA damaging therapies1–3. However, the mechanisms underlying treatment resistance in p53-deficient cells remain poorly characterized. Here, we show that p53-deficient cells exhibit hyperactive repair of therapy-induced DNA double strand breaks (DSBs), which is suppressed by inhibition of DNA-dependent protein kinase (DNA-PK). Single-cell analyses of DSB repair kinetics and cell cycle state transitions reveal an essential role for DNA-PK in suppressing S phase DNA damage and mitotic catastrophe in p53-deficient cells. Yet, a subset of p53-deficient cells exhibit intrinsic resistance to therapeutic DSBs due to a repair pathway that is not sensitive to DNA-PK inhibition. We show that p53 deficiency induces overexpression of DNA Polymerase Theta (Pol θ), which mediates an alternative end-joining repair pathway that becomes hyperactivated by DNA-PK inhibition4. Combined inhibition of DNA-PK and Pol θ restores therapeutic DNA damage sensitivity in p53-deficient cells. Thus, our study identifies two targetable DSB end joining pathways that can be suppressed as a strategy to overcome resistance to DNA-damaging therapies in p53-deficient cancers.
The Effectiveness of Targeted Quarantine for Minimising Impact of COVID-19
Authors: Jamieson-Lane Alastair , Cytrnbaum Eric
Published: April 2020

We model the extent to which age targeted quarantine can be used to reduce ICU admissions caused by novel coronavirus COVID-19. Using demographic data from New Zealand, we demonstrate that lowering the age threshold for quarantine to 50 years of age reduces ICU admissions drastically, and show that for sufficiently strict isolation protocols, isolating one third of the countries population for a total of 6 months is sufficient to avoid overwhelming ICU capacity throughout the entire course of the epidemic. Similar results are expected to hold for other countries, though some minor adaption will be required based on local age demographics and hospital facilities.
A Deep Learning Algorithm for Automated Cardiac Murmur Detection Via a Digital Stethoscope Platform
Authors: Chorba John S. , Shapiro Avi M. , Le Le , Maidens John , Prince John , Pham Steve , Kanzawa Mia M. , Barbosa Daniel N. , White Brent E. , Paek Jason , Fuller Sophie G. , Stalker Grant W. , Bravo Sara A. , Jean Dina , Venkatraman Subramaniam , McCarthy Patrick M. , Thomas James D.
Published: April 2020

Background

There is variability among clinicians in their ability to detect murmurs during cardiac auscultation and identify the underlying pathology. Deep learning approaches have shown promise in medicine by transforming collected data into clinically significant information.

Objective

The objective of this research is to assess the performance of a deep learning algorithm to detect murmurs and clinically significant valvular heart disease using recordings from a commercial digital stethoscope platform.

Methods

Using over 34 hours of previously acquired and annotated heart sound recordings, we trained a deep neural network to detect murmurs. To test the algorithm, we enrolled 373 patients in a clinical study and collected recordings at the four primary auscultation locations. Ground truth was established using patient echocardiograms and annotations by three expert cardiologists.

Results

Algorithm performance for detecting murmurs has sensitivity and specificity of 76.3% and 91.4%, respectively. By omitting softer murmurs, those with grade 1, sensitivity increases to 90.0%. The algorithm detects moderate-to-severe or greater aortic stenosis with sensitivity of 97.5% and specificity of 77.7% and detects moderate-to-severe or greater mitral regurgitation with sensitivity of 64.0% and specificity of 90.5%.

Conclusion

The deep learning algorithm’s ability to detect murmurs and clinically significant aortic stenosis and mitral regurgitation is comparable to expert cardiologists. The research findings attest to the reliability and utility of such algorithms as front-line clinical support tools to aid clinicians in screening for cardiac murmurs caused by valvular heart disease.
Screening for dementia: Q* index as a global measure of test accuracy revisited
Authors: Larner Andrew J
Published: April 2020

Receiver operating characteristic (ROC) curves intersect the downward diagonal through ROC space at a point, the Q* index, where by definition sensitivity and specificity are equal. Aside from its use in meta-analysis, Q* index has also been suggested as a possible global parameter summarising test accuracy of cognitive screening instruments and as a definition for optimal test cut-off. Area under the ROC curve (AUC ROC) is a recognised measure of test accuracy. This study compared different methods for determining Q* index (both graphical and calculation from diagnostic odds ratio) and AUC ROC (integration and calculation from diagnostic odds ratio) using the dataset of a prospective screening test accuracy study of the Mini-Addenbrooke’s Cognitive Examination. The different methods did not agree. DOR-based calculations gave a very sensitive cut-off but with poorer global metrics than the graphical method. DOR-based calculations are not recommended for defining optimal test cut-off or test accuracy.
KMT2D links TGF-β Signalling to Non-Canonical Activin Pathway and Regulates Pancreatic Cancer Cell Plasticity
Authors: Lu Shuang , Kim Hong Sun , Cao Yubo , Bedi Karan , Chain Krista , Zhao Lili , Narayanan Ishwarya Venkata , Yi Zhujun , Yang Jing , Gu Yumei , Paulsen Michelle T. , Ljungman Mats , Jeyarajan Sivakumar , Thomas Dafydd , Dou Yali , Crawford Howard , di Magliano Marina Pasca , Shi Jiaqi
Published: April 2020

Although KMT2D, also known as MLL2, is known to play an essential role in development, differentiation, and tumor suppression, its role in pancreatic cancer development is not well understood. Here, we discovered a novel signaling axis mediated by KMT2D, which links TGF-β to the activin A pathway. We found that TGF-β upregulates a microRNA, miR-147b, which in turn leads to post-transcriptional silencing of KMT2D. Loss of KMT2D induces the expression and secretion of activin A, which activates a non-canonical p38 MAPK-mediated pathway to modulate cancer cell plasticity, promote a mesenchymal phenotype, and enhance tumor invasion and metastasis in mice. We observed a decreased KMT2D expression in human primary and metastatic pancreatic cancer. Furthermore, inhibition or knockdown of activin A reversed the pro-tumoral role of KMT2D. These findings reveal a tumor-suppressive role of KMT2D and identify miR-147b and activin A as novel therapeutic targets in pancreatic cancer.
Inhibition of PTEN activity promotes IB4-positive sensory neuronal axon growth
Authors: Zhou Li-Yu , Han Feng , Qi Shi-Bin , Ma Jin-Jin , Ma Yan-Xia , Zhang Hong-Cheng , Xie Ji-Le , Fu Xin-Ya , Chen Jian-Quan , Li Bin , Yang Hui-Lin , Zhou Feng , Saijilafu
Published: April 2020

Traumatic nerve injuries have become a common clinical problem, and axon regeneration is a critical process in the successful functional recovery of the injured nervous system. In this study, we found that peripheral axotomy reduce total PTEN expression in adult sensory neurons, however, it did not alter the expression level of PTEN in IB4-positive sensory neurons. Additionally, our results indicate that the artificial inhibition of PTEN markedly promotes adult sensory axon regeneration, including IB4-positive neuronal axon growth. Thus, our results provide strong evidence that PTEN is a prominent repressor of adult sensory axon regeneration, especially in IB4-positive neurons.
Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance
Authors: Chakravarthy Ankur , Reddin Ian , Henderson Stephen , Dong Cindy , Kirkwood Nerissa , Jeyakumar Maxmilan , Rodriguez Daniela Rothschild , Martinez Natalia Gonzalez , McDermott Jacqueline , Su Xiaoping , Egawa Nagayasau , Fjeldbo Christina S , Skingen Vilde Eide , Halle Mari Kyllesø , Krakstad Camilla , Soleiman Afschin , Sprung Susanne , Ellis Peter , Wass Mark , Michaelis Martin , Lyng Heidi , Fiegl Heidi , Salvesen Helga , Thomas Gareth , Doorbar John , Chester Kerry , Feber Andrew , Fenton Tim R
Published: April 2020

Human papillomavirus (HPV)-associated cervical cancer represents one of the leading causes of cancer death worldwide. Although low-middle income countries are disproportionately affected, our knowledge of the disease predominantly originates from populations in high-income countries. Using the largest multi-omic analysis of cervical squamous cell carcinoma (CSCC) to date, totalling 643 tumours and representing patient populations from the USA, Europe and Sub-Saharan Africa, we identify two CSCC subtypes (C1 and C2) with differing prognosis. C1 tumours are largely HPV16-driven, display increased cytotoxic T-lymphocyte infiltration and frequently harbourPIK3CAandEP300mutations. C2 tumours are associated with shorter overall survival, are frequently driven by HPVs from the HPV18-containing alpha-7 clade, harbour alterations in the Hippo signalling pathway and increased expression of immune checkpoint genes,B7-H3(also known asCD276) andNT5E(also known asCD73) andPD-L2(also known asPDCD1LG2). In conclusion, we identify two novel, therapy-relevant CSCC subtypes that share the same defining characteristics across three geographically diverse cohorts.
Monocyte-derived Prostaglandin E2 inhibits antigen-specific cutaneous immunity during ageing
Authors: Chambers Emma S , Vukmanovic-Stejic Milica , Shih Barbara B , Trahair Hugh , Subramanian Priya , Devine Oliver P , Glanville James , Gilroy Derek , Rustin Malcom , Freeman Tom C , Mabbot Neil A , Akbar Arne N
Published: April 2020

Ageing results in a decline in immune function. We showed previously that healthy older humans (>65 years old) have reduced antigen-specific cutaneous immunity to varicella zoster virus (VZV) antigen challenge. This was associated with p38 MAP kinase driven inflammation that was induced by mild tissue injury caused by the injection of the antigen itself. Here we show that non-specific injury induced by injection of air or saline into the skin of older adults recruits CCR2+CD14+monocytes by CCL2 produced by senescent fibroblasts. These monocytes reduced TRMproliferation via secretion of prostaglandin E2 (PGE2). Pre-treatment with a p38-MAPK inhibitor (Losmapimod) in older adultsin vivosignificantly decreased CCL2 expression, recruitment of monocyte into the skin, COX2 expression and PGE2production. This enhanced the VZV response in the skin. Therefore, local inflammation arising from interaction between senescent cells and monocytes leads to immune decline in the skin during ageing, a process that can be reversed.

Inflammation resulting from tissue injury blocks antigen-specific cutaneous immunity during ageing. Monocytes recruited to the skin inhibit TRMfunction through COX2-derived prostaglandin E2production. Blocking inflammation and resulting prostaglandin E2production with a p38-MAP kinase inhibitor significantly enhances cutaneous antigen-specific responses.
Reactivation of atrium genes is a primer for heart infarction or regeneration
Authors: Zhen Yisong
Published: April 2020

The inability of the adult heart to repair or regenerate is manifested in prevalent morbidity and mortality related to myocardial infarction and heart failure. However, the cue to the reactivation of cardiomyocyte proliferation in the adult remains largely unknown. In the present study, three independent datasets were explored using bioinformatics analysis methods to solve the problem. Our results revealed that atrium genes were upregulated in response to the injury, which indicates the possible cell type withdraw and reinitiation of proliferation capability. Our findings might provide an alternative viewpoint on the cardiomyocyte regeneration or myocardial infarction.
AutoGenome V2: New Multimodal Approach Developed for Multi-Omics Research
Authors: Xu Chi , Liu Denghui , Zhang Lei , Xu Zhimeng , He Wenjun , Wang Deyong , Zheng Mingyue , Qiao Nan
Published: April 2020

Deep learning is very promising in solving problems in omics research, such as genomics, epigenomics, proteomics, and metabolics. The design of neural network architecture is very important in modeling omics data against different scientific problems. Residual fully-connected neural network (RFCN) was proposed to provide better neural network architectures for modeling omics data. The next challenge for omics research is how to integrate informations from different omics data using deep learning, so that information from different molecular system levels could be combined to predict the target. In this paper, we present a novel multimodal approach that could efficiently integrate information from different omics data and achieve better accuracy than previous approaches. We evaluate our method in four different tasks: drug repositioning, target gene prediction, breast cancer subtyping and cancer type prediction, and all the four tasks achieved state of art performances. The multimodal approach is implemented in AutoGenome V2 and is also powered with all the previous AutoML convenience to facilitate biomedical researchers.
Attractiveness in the eyes: A possibility of positive loop between transient pupil constriction and facial attraction
Authors: Liao Hsin-I , Kashino Makio , Shimojo Shinsuke
Published: April 2020

Contrary to the long-held belief of a close linkage between pupil dilation and attractiveness, we found an early and transient pupil constriction response when participants viewed an attractive face (and the effect of luminance/contrast is controlled). While human participants were making an attractiveness judgment on faces, their pupil constricted more for the more attractive (as-to-be-rated) faces. Further experiments showed that the effect of pupil constriction to attractiveness judgment extended to intrinsically aesthetic visual objects such as natural scene images (as well as faces) but not to line-drawing geometric figures. When participants were asked to judge the roundness of faces, pupil constriction still correlated with their attractiveness but not the roundness rating score, indicating the automaticity of the pupil constriction to attractiveness. When pupillary responses were manipulated implicitly by relative background luminance changes (from the pre-stimulus screen), the facial attractiveness ratings were in accordance with the amount of pupil constriction, which could not be explained solely by simultaneous or sequential luminance contrast. The overall results suggest that pupil constriction not only reflects but, as a part of self-monitoring and attribution mechanisms, also possibly contributes facial attractiveness implicitly.
Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs
Authors: Shen Zeyang , Li Rick Z. , Prohaska Thomas A. , Hoeksema Marten A. , Spann Nathan J. , Tao Jenhan , Fonseca Gregory J. , Le Thomas , Stolze Lindsey , Sakai Mashito , Romanoski Casey E. , Glass Christopher K.
Published: April 2020

Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Prior studies showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of TF spacing alterations resulting from naturally occurring insertions and deletions (InDels) has not been systematically analyzed. To address this question, we first characterized the genome-wide spacing relationships of 75 TFs in K562 cells as determined by ChIP-sequencing. We found a dominant pattern of a relaxed range of spacing between collaborative factors, including 46 TFs exclusively exhibiting relaxed spacing with their binding partners. Next, we exploited millions of InDels provided by genetically diverse mouse strains and human individuals to investigate the effects of altered spacing on TF binding and local histone acetylation. Spacing alterations resulting from naturally occurring InDels are generally tolerated in comparison to genetic variants directly affecting TF binding sites. A remarkable range of tolerance was further established for PU.1 and C/EBPβ, which exhibit relaxed spacing, by introducing synthetic spacing alterations ranging from 5-bp increase to >30-bp decrease using CRISPR/Cas9 mutagenesis. These findings provide implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation.
Diabetes induced decreases in PKA signaling in cardiomyocytes: the role of insulin
Authors: Eyster Craig A. , Matsuzaki Satoshi , Giorgione Jennifer R. , Humphries Kenneth M.
Published: April 2020

The cAMP-dependent protein kinase (PKA) signaling pathway is the primary means by which the heart regulates moment-to-moment changes in contractility and metabolism. We have previously found that PKA signaling is dysfunctional in the diabetic heart, yet the underlying mechanisms are not fully understood. The objective of this study was to determine if decreased insulin signaling contributes to a dysfunctional PKA response. To do so, we isolated adult cardiomyocytes (ACMs) from wild type and Akita type 1 diabetic mice. ACMs were cultured in the presence or absence of insulin and PKA signaling was visualized by immunofluorescence microscopy using an antibody that recognizes proteins specifically phosphorylated by PKA. We found significant decreases in proteins phosphorylated by PKA in wild type ACMs cultured in the absence of insulin. Akita ACMs also had decreased PKA signaling in the absence of insulin and this was not rescued by insulin. The decrease in PKA signaling was observed regardless of whether the kinase was stimulated with a beta-agonist, a cell-permeable cAMP analog, or with phosphodiesterase inhibitors. PKA content was unaffected, suggesting that the decrease in PKA signaling may be occurring by the loss of specific PKA substrates. Phospho-specific antibodies were therefore used to discern which potential substrates may be sensitive to the loss of insulin. Contractile proteins were phosphorylated similarly in wild type and Akita ACMs regardless of insulin. However, phosphorylation of the glycolytic regulator, PFK-2, was significantly decreased in an insulin-dependent manner in wild type ACMs and in an insulin-independent manner in Akita ACMs. These results demonstrate a defect in PKA activation in the diabetic heart, mediated in part by deficient insulin signaling, that results in an abnormal activation of a primary metabolic regulator.
Neuronal adenosine A2Areceptors signal ergogenic effects of caffeine
Authors: Aguiar Aderbal S , Speck Ana Elisa , Canas Paula M. , Cunha Rodrigo A.
Published: April 2020

Ergogenic aid is a substance or method used for enhancing exercise and sports performance. Caffeine is the most used ergogenic aid for athletes, but the mechanisms are still unknown. Forty-two adult female (19±0.6 g) and 40 male mice (24±0.4 g) from a global and forebrain A2AR knockout and colony (FMUC, University of Coimbra) underwent an open field and ergospirometry exercise test. Caffeine (15 mg/kg, i.p.) and SCH 58261 (1 mg/kg, i.p.) were administered 15 minutes before the animals ran to exhaustion. We also evaluate the estrous cycle and infrared temperature (rest and recovery). Caffeine was psychostimulant in wild type females and males, but we observed this expected effect of SCH-58261 only in males. Caffeine and SCH-58261 were also ergogenic for wild type animals, that is, they increased running power and maximal O2consumption (O2max). The psychostimulant and ergogenic effects of caffeine and SCH-58261 disappeared in A2AR knockout females (global) and males (forebrain). The estrous cycle did not influence any evaluated parameters, as well as exercise-induced hyperthermia was similar between savages and knockouts. Our results suggest that the neuronal A2AR receptors signal the ergogenic effects of caffeine in female and male mice.
Evaluating features of scientific conferences: A call for improvements
Authors: Sarabipour Sarvenaz , Khan Aziz , Seah Samantha , Mwakilili Aneth D. , Mumoki Fiona N. , Sáez Pablo J. , Schwessinger Benjamin , Debat Humberto J. , Mestrovic Tomislav
Published: April 2020

Scientific conferences provide valuable opportunities for researchers across career stages and disciplines to present their latest work, and to network with their peers. These meetings have largely been held in-person with rapid proliferation in the number of meetings and attendees. Yet the format and quality of their organization lag behind what is possible and as a result, the current experience of attending conferences in many disciplines remains unchanged in many respects. We created a database of 270 national and international academic conferences held in-person during 2018-2019 in various disciplines and examined them for their features, costs and impact on the community. We found that many meetings could still be improved significantly in terms of diversity, inclusivity, promoting early career researcher (ECR) networking and career development, venue accessibility, and importantly, reducing the meetings’ carbon footprint. It is important to accelerate and mandate efforts to improve conferences so that researchers in all disciplines, in particular ECRs, consistently benefit from scientific gatherings, for years to come. We discuss a combination of approaches and recommendations to make conferences more modern, effective, equitable and intellectually productive for the research community and environmentally sustainable for our planet.

“They always say time changes things, but you actually have to change them yourself.”

— Andy Warhol
Alternative splicing is a developmental switch for hTERT expression
Authors: Penev Alex , Bazley Andrew , Shen Michael , Boeke Jef D. , Savage Sharon A. , Sfeir Agnel
Published: April 2020

High telomerase activity is restricted to the blastocyst stage of embryonic development when telomere length is reset, and is characteristic of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). However, the pathways involved in telomerase regulation as a function of pluripotency remain unknown. To explore hTERT transcriptional control, we compare genome-wide interactions (4C-seq) and chromatin accessibility (ATAC-seq) between human ESCs and epithelial cells and identify several putative hTERTcis-regulatory elements. CRISPR/Cas9-mediated deletion of candidate elements in ESCs reduces the levels of hTERT mRNA but does not abolish telomerase expression, thus implicating post-transcriptional processes in telomerase regulation. In agreement with this hypothesis, we find an hTERT splice variant lacking exon-2 and prone to degradation, to be enriched in differentiated cells but absent from ESCs. In addition, we show that forced retention of exon-2 prevents telomerase silencing during differentiation. Lastly, we highlight a role for the splicing co-factor SON in hTERT exon-2 inclusion and identify a SON mutation in a Dyskeratosis congenita patient with short telomeres and decreased telomerase activity. Altogether, our data uncover a novel alternative splice switch that is critical for telomerase activity during development.
Coordinated postnatal maturation of striatal cholinergic interneurons and dopamine release dynamics in mice
Authors: McGuirt Avery , Lieberman Ori , Post Michael , Pigulevskiy Irena , Sulzer David
Published: April 2020

Dynamic changes in motor abilities and motivated behaviors occur during the juvenile and adolescent periods. The striatum is a subcortical nucleus critical for action selection, motor learning and reward processing. Its tonically active cholinergic interneuron (ChI) is an integral regulator of the synaptic activity of other striatal neurons, as well as afferent axonal projections of midbrain dopamine neurons. Thalamic and dopaminergic inputs initiate pauses in ChI firing following salient sensory cues that are extended for several hundred milliseconds by intrinsic regenerative currents. Here, we characterize the electrophysiological and morphological features of ChIs during mouse postnatal development. We demonstrate that ChI spontaneous activity increases with age while the duration of the pause in firing induced by depolarizing inputs decreases during postnatal development. Maturation of ChI activity is driven by two distinct physiological changes: decreased amplitude of the afterhypolarization between P14 and P18 and and increased Ih conductance between the late postnatal period and adulthood. Finally, we uncover postnatal changes in dopamine release properties that are mediated by cholinergic signalling. At P10, striatal dopamine release is diminished compared to the adult, but our data show efficient summation of dopamine relase evoked by multiple grouped stimuli that subsides by P28. Blockade of nictonic acetylcholine receptors enhances release summation in mice older than P28 but has little effect at P10. These data demonstrate a physiological maturation of ChI activity and indicate a reciprocal interaction between the postnatal maturation of striatal ChI and dopamine neurotransmission.

Significance Statement

Motor skills and motivated behavior regimes develop rapidly during the postnatal period. The functional development of the striatal cholinergic interneuron (ChI), which contributes to these behaviors in adulthood, remains unexplored. In this study, we tracked the ontogeny of spontaneous ChI activity and cellular morphology, as well as the developmental trajectory of ion conductances characteristic to this population. We further report a developmental link between ChI activity and dopamine release, revealing a change in the frequency-dependence of dopamine release during the early postnatal period that is mediated by cholinergic signaling. This study provides evidence that striatal microcircuits are dynamic during the postnatal period and that they undergo coordinated maturation.
An influenza A hemagglutinin small-molecule fusion inhibitor identified by a new high-throughput fluorescence polarization screen
Authors: Yao Yao , Kadam Rameshwar U. , Lee Chang-Chun David , Woehl Jordan L. , Wu Nicholas C. , Zhu Xueyong , Kitamura Seiya , Wilson Ian A. , Wolan Dennis W.
Published: April 2020

Influenza hemagglutinin (HA) glycoprotein is the primary surface antigen targeted by the host immune response and a focus for development of novel vaccines, broadly neutralizing antibodies (bnAbs) and therapeutics. HA enables viral entry into host cells via receptor binding and membrane fusion and is a validated target for drug discovery. However, to date, only a very few bona fide small molecules have been reported against the HA. To identity new antiviral lead candidates against the highly conserved fusion machinery in the HA stem, we synthesized a fluorescence-polarization probe based on a recently described neutralizing cyclic peptide P7 derived from the complementarity-determining region loops of human bnAbs FI6v3 and CR9114 against the HA stem. We then designed a robust binding assay compatible with high-throughput screening to identify molecules with low μM to nM affinity to influenza A group 1 HAs. Our simple, low-cost, and efficient in vitro assay was used to screen H1/Puerto Rico/8/1934 HA trimer against approximately 72,000 compounds. The crystal structure of H1/Puerto Rico/8/1934 HA in complex with our best hit compound F0045(S) confirmed that it binds to pockets in the HA stem similar to bnAbs FI6v3 and CR9114, cyclic peptide P7, and small molecule inhibitor JNJ4796. F0045 is enantioselective against a panel of group 1 HAs and F0045(S) exhibits in vitro neutralization activity against multiple H1N1 and H5N1 strains. Our assay, compound characterization, and small-molecule candidate should further stimulate the discovery and development of new compounds with unique chemical scaffolds and enhanced influenza antiviral capabilities.

Influenza hemagglutinin (HA) glycoprotein enables viral entry into host cells and is the main target for antibodies in our immune system. While HA has now been established as a validated target for drug discovery, no FDA-approved small molecules are available that specifically prevent HA from binding host receptors or inhibit its membrane fusion activity and thus prevent infection. We therefore designed a fluorescence polarization probe to enable rapid identification of small molecules that bind to the stem fusion machinery of group 1 HAs. Application of our assay yielded a small molecule to the influenza A group 1 HA stem with antiviral efficacy.
A resource for exploring the understudied human kinome for research and therapeutic opportunities
Authors: Moret Nienke , Liu Changchang , Gyori Benjamin M. , Bachman John A. , Steppi Albert , Hug Clemens , Taujale Rahil , Huang Liang-Chin , Berginski Matthew E. , Gomez Shawn M. , Kannan Natarajan , Sorger Peter K.
Published: April 2020

The functions of protein kinases have been widely studied and over 60 kinase inhibitors are FDA-approved drugs. Membership in the human kinome is nonetheless subject to multiple overlapping and inconsistent definitions and is unevenly studied, complicating functional genomics and chemical genetics. We describe objective criteria for refining the definition of the human kinome to comprise an extended set of 710 kinase domains and a more narrowly curated set of 557 protein kinase like (PKL) domains. An online tool (www.kinome.org)makes it possible to sort these sets on multiple structural and functional criteria. Focusing on the least studied one-third of the kinome we find that many proteins are differentially expressed, essential in multiple cell lines, and mutated in the Cancer Genome Atlas. We show that some understudied kinases are high affinity off-targets of clinical-grade compounds and approved drugs and we describe an optimized small molecule library making use of this information for selective kinome perturbation. We conclude that the understudied kinome contains physiologically important proteins, including possible targets for future drug discovery campaigns.
Cre-mediated deletion of SMARCA5 disrupts pluripotency in mouse embryonic stem cells
Authors: Cook David P. , Vanderhyden Barbara C.
Published: April 2020

In embryonic stem cells (ESCs), the SWI/SNF, CHD, and INO80 families of ATP-dependent chromatin remodellers have been implicated in maintaining pluripotency-associated gene expression. At the time of this study, the importance of ISWI family remodellers had yet to be defined, and we had sought to assess their involvement. During this time, Barisicet al. (Nature, 2019) elegantly demonstrated that the ISWI homologue SNF2H (Smarca5) is important for nucleosomal periodicity, the binding of select transcription factors, and proper differentiation of mouse ESCs. While we do not dispute their findings to any extent, our experiments have led to slightly different conclusions, and we have chosen to use this platform to share our results.

Here, we explore the importance of SNF2H by deriving a conditional knockout mouse ESC line and observing the consequences of SNF2H depletion on the pluripotent state. Cre-mediated deletion ofSnf2hdisrupts hallmark characteristics of pluripotency, resulting in distinct morphological changes; reduced expression of the master transcription factorsOct4,Sox2, andNanog; and reduced alkaline phosphatase activity. To understand the mechanisms of SNF2H-mediated regulation, we mapped SNF2H-bound nucleosomes genome-wide. SNF2H is broadly distributed across the genome but is preferentially enriched at active regulatory regions and transcription factor binding sites.
In vivoselection for formate dehydrogenases with high efficiency and specificity towards NADP+
Authors: Ramirez Liliana Calzadiaz , Calvó-Tusell Carla , Stoffel Gabriele M. M. , Lindner Steffen N. , Osuna Sílvia , Erb Tobias J. , Garcia-Borràs Marc , Bar-Even Arren , Acevedo-Rocha Carlos G.
Published: April 2020

Efficient regeneration of cofactors is vital for the establishment of continuous biocatalytic processes. Formate is an ideal electron donor for cofactor regeneration due to its general availability, low reduction potential, and benign byproduct (CO2). However, formate dehydrogenases (FDHs) are usual specific to NAD+, such that NADPH regeneration with formate is challenging. Previous studies reported naturally occurring FDHs or engineered FDHs that accept NADP+, but these enzymes show low kinetic efficiencies and specificities. Here, we harness the power of natural selection to engineer FDH variants to simultaneously optimize three properties: kinetic efficiency with NADP+, specificity towards NADP+, and affinity towards formate. By simultaneously mutating multiple residues of FDH fromPseudomonas sp.101, which exhibits no initial activity towards NADP+, we generate a library of >106variants. We introduce this library into anE. colistrain that cannot produce NADPH. By selecting for growth with formate as sole NADPH source, we isolate several enzyme variants that support efficient NADPH regeneration. We find that the kinetically superior enzyme variant, harboring five mutations, has 5-fold higher efficiency and 13-fold higher specificity than the best enzyme previously engineered, while retaining high affinity towards formate. By using molecular dynamics simulations, we reveal the contribution of each mutation to the superior kinetics of this variant. We further determine how non-additive epistatic effects improve multiple parameters simultaneously. Our work demonstrates the capacity ofin vivoselection to identify superior enzyme variants carrying multiple mutations which would be almost impossible to find using conventional screening methods.
Conserved and Divergent Modulation of Calcification in Atherosclerosis and Aortic Valve Disease by Tissue Extracellular Vesicles
Authors: Blaser Mark C. , Buffolo Fabrizio , Halu Arda , Schlotter Florian , Higashi Hideyuki , Pantano Lorena , Saddic Louis A. , Atkins Samantha K. , Rogers Maximillian A. , Pham Tan , Shvartz Eugenia , Sukhova Galina K , Monticone Silvia , Camussi Giovanni , Body Simon C. , Muehlschlegel Jochen D. , Singh Sasha A. , Aikawa Masanori , Aikawa Elena
Published: April 2020

Background

Fewer than 50% of patients develop calcification of both atherosclerotic plaques and aortic valves, implying differential pathogenesis. While circulating extracellular vesicles (EVs) act as biomarkers of cardiovascular diseases, tissue-entrapped EVs associate with early mineralization, but their contents, function, and contributions to disease remain unknown.

Results

Global proteomics of human carotid artery endarterectomies and calcified aortic valves from a total of 27 donors/patients revealed significant over-representation of proteins with vesicle-associated pathways/ontologies common to both diseases. We exploited enzymatic digestion, serial (ultra)centrifugation and OptiPrep density-gradient separation to isolate EV populations from diseased arteries and valves. Mass spectrometry found 22 EV marker proteins to be highly enriched in the four least-dense OptiPrep fractions while extracellular matrix proteins predominated in denser fractions, as confirmed by CD63 immunogold electron microscopy and nanoparticle tracking analysis. Proteomics and miRNA-sequencing of OptiPrep-enriched tissue EVs quantified 1,104 proteins and 123 miR cargoes linked to 5,182 target genes. Pathway networks of proteins and miR targets common to artery and valve tissue EVs revealed a shared regulation of Rho GTPase and MAPK intracellular signaling cascades. 179 proteins and 5 miRs were significantly altered between artery and valve EVs; multi-omics integration determined that EVs differentially modulated cellular contraction and p53-mediated transcriptional regulation in diseased vascular vs. valvular tissue.

Conclusions

Our findings delineate a strategy to isolate, purify, and study protein and RNA cargoes from EVs entrapped in fibrocalcific tissues. Multi-omics and network approaches implicated tissue-resident EVs in human cardiovascular disease.
Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation
Authors: Georgolopoulos Grigorios , Psatha Nikoletta , Iwata Mineo , Nishida Andrew , Som Tannishtha , Yiangou Minas , Stamatoyannopoulos John A. , Vierstra Jeff
Published: April 2020

Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. We performed dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) alongex vivohuman erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit pluripotency. Collectively, these data provide novel insights into the global regulatory landscape during hematopoiesis.
Computational analysis of lamin isoform interactions with nuclear pore complexes
Authors: Kittisopikul Mark , Shimi Takeshi , Tatli Meltem , Tran Joseph R. , Zheng Yixian , Medalia Ohad , Jaqaman Khuloud , Adam Stephen A. , Goldman Robert D.
Published: April 2020

Nuclear lamin isoforms form fibrous meshworks associated with nuclear pore complexes (NPCs). Using data sets prepared from sub-pixel and segmentation analyses of 3D-Structured Illumination Microscopy images of WT and lamin isoform knockout mouse embryo fibroblasts, we determined with high precision the spatial association of NPCs with specific lamin isoform fibers. These relationships are retained in the enlarged lamin meshworks ofLmna-/-andLmnb1-/-fibroblast nuclei. Cryo-ET observations reveal that the lamin filaments composing the fibers contact the nucleoplasmic ring of NPCs. Knockdown of the ring-associated nucleoporin ELYS induces NPC clusters that exclude lamin A/C fibers, but include LB1 and LB2 fibers. Knockdown of the nucleoporins TPR or NUP153 alter the arrangement of lamin fibers and NPCs. Evidence that the number of NPCs is regulated by specific lamin isoforms is presented. Overall the results demonstrate that lamin isoforms and nucleoporins act together to maintain the normal organization of lamin meshworks and NPCs within the nuclear envelope.
Size-dependent eco-evolutionary feedbacks in fisheries
Authors: Eric Edeline , Nicolas Loeuille
Published: April 2020

Abstract

Harvesting may drive body downsizing along with population declines and decreased harvesting yields. These changes are commonly construed as consequences of direct harvest selection, where small-bodied, early-reproducing individuals are immediately favoured. However, together with directly selecting against a large body size, harvesting and body downsizing alter many ecological features, such as competitive and trophic interactions, and thus also indirectly reshape natural selection acting back on body sizes through eco-evolutionary feedback loops (EEFLs). We sketch plausible scenarios of simple EEFLs in which one-dimensional, density-dependent natural selection acts either antagonistically or synergistically with direct harvest selection on body size. Antagonistic feedbacks favour body-size stasis but erode genetic variability and associated body-size evolvability, and may ultimately impair population persistence and recovery. In contrast, synergistic feedbacks drive fast evolution towards smaller body sizes and favour population resilience, but may have far-reaching bottom-up or top-down effects. We illustrate the further complexities resulting from multiple environmental feedbacks using a co-evolving predator-prey pair, in which case outcomes from EEFLs depend not only on population densities, but also on whether prey sit above or below the optimal predator/prey body-size ratio, and whether prey are more or less evolvable than their predators. EEFLs improve our ability to understand and predict nature’s response to harvesting, but their integration into the research agenda will require a full consideration of the effects and dynamics of natural selection.