Combinatorial Click Chemistry Labeling to Study Live Human Gut-Derived Microbiota Communities.

Gut bacteria were shown to exert pivotal effects on health and disease. However, mechanistic studies of gut bacterial communities are limited due to the lack of technologies for real-time studies on live bacteria. Here, we developed COMBInatorial cliCK-chemistry (COMBICK) labeling on human gut-derived bacteria, both aerobic and anaerobic strains, to enable dynamic tracing of live, heterogeneous bacterial communities on the strain level, including clinical isolates of the family.

Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes.

Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of opposite chronotypes. Growing evidence suggests that the late chronotype significantly impacts the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. Despite the vast potential of utilizing chronotype information for precision medicine, those factors that shape chronotypes remain poorly understood.

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources.

Observation of the Decrease of Larmor Tunneling Times with Lower Incident Energy.

How much time does a tunneling particle spend in a barrier? A Larmor clock, one proposal to answer this question, measures the interaction between the particle and the barrier region using an auxiliary degree of freedom of the particle to clock the dwell time inside the barrier. We report on precise Larmor time measurements of ultracold ^{87}Rb atoms tunneling through an optical barrier, which confirm longstanding predictions of tunneling times. We observe that atoms generally spend less time tunneling through higher barriers and that this time decreases for lower energy particles.

Integration of DNA damage responses with dynamic spatial genome organization.

The maintenance of genome stability and cellular homeostasis depends on the temporal and spatial coordination of successive events constituting the classical DNA damage response (DDR). Recent findings suggest close integration and coordination of DDR signaling with specific cellular processes. The mechanisms underlying such coordination remain unclear.

Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes.

R2TP is a highly conserved chaperone complex formed by two AAA+ ATPases, RUVBL1 and RUVBL2, that associate with PIH1D1 and RPAP3 proteins. R2TP acts in promoting macromolecular complex formation. Here, we establish the principles of R2TP assembly.

Excitonic and Valley-Polarization Signatures of Fractional Correlated Electronic Phases in a WSe_{2}/WS_{2} Moiré Superlattice.

We have measured the reflectance contrast, photoluminescence, and valley polarization of a WSe_{2}/WS_{2} heterobilayer moiré superlattice at gate-tunable charge density. We observe absorption modulation of three intralayer moiré excitons at filling factors ν=1/3 and 2/3. We also observe luminescence modulation of interlayer trions at around a dozen fractional filling factors, including ν=-3/2, 1/4, 1/3, 2/5, 2/3, 6/7, 5/3.

Design, Synthesis, and Characterization of 4-Aminoquinazolines as Potent Inhibitors of the G Protein-Coupled Receptor Kinase 6 (GRK6) for the Treatment of Multiple Myeloma.

Both previous and additional genetic knockdown studies reported herein implicate G protein-coupled receptor kinase 6 (GRK6) as a critical kinase required for the survival of multiple myeloma (MM) cells. Therefore, we sought to develop a small molecule GRK6 inhibitor as an MM therapeutic. From a focused library of known kinase inhibitors, we identified two hits with moderate biochemical potencies against GRK6.

"More Guts Than Brains?"-The Role of Gut Microbiota in Idiopathic Intracranial Hypertension.

Background: Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity.

Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors.

The ubiquitin-proteasome system (UPS) is a critical regulator of cellular protein levels and activity. It is, therefore, not surprising that its dysregulation is implicated in numerous human diseases, including many types of cancer. Moreover, since cancer cells exhibit increased rates of protein turnover, their heightened dependence on the UPS makes it an attractive target for inhibition via targeted therapeutics.

Simulating and Mitigating Crosstalk.

We describe an efficient and scalable framework for modeling crosstalk effects on quantum information processors. By applying optimal control techniques, we show how to tune-up arbitrary high-fidelity parallel operations on systems with substantial local and nonlocal crosstalk. As an example, we simulate a 2D square array of 100 superconducting transmon qubits.

An open-source platform to quantify subnuclear foci and protein colocalization in response to replication stress.

Nuclear reorganization, including the localization of proteins into discrete subnuclear foci, is a hallmark of the cellular response to DNA damage and replication stress. These foci are thought to represent transient environments or repair factories, in which the lesion is sequestered with molecules and co-factors that catalyze repair. For example, nuclear foci contain signaling proteins that recruit transducer proteins.

The gene affects social networks.

displays social behaviors including courtship, mating, aggression, and group foraging. Recent studies employed social network analyses (SNAs) to show that strains differ in their group behavior, suggesting that genes influence social network phenotypes. Aside from genes associated with sensory function, few studies address the genetic underpinnings of these networks.

Recent developments in engineering protein-protein interactions using phage display.

Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families.

A story of fibers and stress: Matrix-embedded signals for fibroblast activation in the skin.

Our skin is continuously exposed to mechanical challenge, including shear, stretch, and compression. The extracellular matrix of the dermis is perfectly suited to resist these challenges and maintain integrity of normal skin even upon large strains. Fibroblasts are the key cells that interpret mechanical and chemical cues in their environment to turnover matrix and maintain homeostasis in the skin of healthy adults.

Results from a Theory-Guided Survey to Support Breast Cancer Trial Participation: Barriers, Enablers, and What to Do about them.

Background: Ensuring adequate, informed, and timely participation in clinical trials is a multifactorial problem. We have previously developed a systematic, tailorable survey development approach that is informed by theory, can identify barriers and enablers to participation, and can suggest recruitment strategies to address these issues. In this study, we surveyed subscribers to the Canadian Breast Cancer Network (CBCN) in order to identify a comprehensive list of theory-informed barriers and enablers relevant to participation in a hypothetical breast cancer trial.

Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries.

Background: Public trust is central to the collection of genomic and health data and the sustainability of genomic research. To merit trust, those involved in collecting and sharing data need to demonstrate they are trustworthy. However, it is unclear what measures are most likely to demonstrate this.

The inflammatory speech of fibroblasts.

Activation of fibroblasts is a key event during normal tissue repair after injury and the dysregulated repair processes that result in organ fibrosis. To most researchers, fibroblasts are rather unremarkable spindle-shaped cells embedded in the fibrous collagen matrix of connective tissues and/or deemed useful to perform mechanistic studies with adherent cells in culture. For more than a century, fibroblasts escaped thorough classification due to the lack of specific markers and were treated as the leftovers after all other cells have been identified from a tissue sample.

Searching for pneumothorax in x-ray images using autoencoded deep features.

Fast diagnosis and treatment of pneumothorax, a collapsed or dropped lung, is crucial to avoid fatalities. Pneumothorax is typically detected on a chest X-ray image through visual inspection by experienced radiologists. However, the detection rate is quite low due to the complexity of visual inspection for small lung collapses.

Interphase microtubules in nuclear organization and genome maintenance.

Microtubules are major cytoskeletal components mediating fundamental cellular processes, including cell division. Recent evidence suggests that microtubules also regulate the nucleus during the cell cycle's interphase stage. Deciphering such roles of microtubules should uncover direct crosstalk between the nucleus and cytoplasm, impacting genome function and organismal health.

Constraints on the Time Variation of the Gravitational Constant Using Gravitational Wave Observations of Binary Neutron Stars.

We propose a method to constrain the variation of the gravitational constant G with cosmic time using gravitational wave (GW) observations of merging binary neutron stars. The method essentially relies on the fact that the maximum and minimum allowed masses of neutron stars at a particular cosmic epoch have a simple dependence on the value of G at that epoch. GWs carry an imprint of the value of G at the time of the merger.

Coagulase-negative staphylococci release a purine analog that inhibits Staphylococcus aureus virulence.

Coagulase-negative staphylococci and Staphylococcus aureus colonize similar niches in mammals and conceivably compete for space and nutrients. Here, we report that a coagulase-negative staphylococcus, Staphylococcus chromogenes ATCC43764, synthesizes and secretes 6-thioguanine (6-TG), a purine analog that suppresses S. aureus growth by inhibiting de novo purine biosynthesis.

Identification of bacteria-derived HLA-bound peptides in melanoma.

A variety of species of bacteria are known to colonize human tumours, proliferate within them and modulate immune function, which ultimately affects the survival of patients with cancer and their responses to treatment. However, it is not known whether antigens derived from intracellular bacteria are presented by the human leukocyte antigen class I and II (HLA-I and HLA-II, respectively) molecules of tumour cells, or whether such antigens elicit a tumour-infiltrating T cell immune response. Here we used 16S rRNA gene sequencing and HLA peptidomics to identify a peptide repertoire derived from intracellular bacteria that was presented on HLA-I and HLA-II molecules in melanoma tumours.

Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice.

Drug addiction develops due to brain-wide plasticity within neuronal ensembles, mediated by dynamic gene expression. Though the most common approach to identify such ensembles relies on immediate early gene expression, little is known of how the activity of these genes is linked to modified behavior observed following repeated drug exposure. To address this gap, we present a broad-to-specific approach, beginning with a comprehensive investigation of brain-wide cocaine-driven gene expression, through the description of dynamic spatial patterns of gene induction in subregions of the striatum, and finally address functionality of region-specific gene induction in the development of cocaine preference.