Transcription factor prediction using protein 3D secondary structures.

Motivation: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs.

Intrinsically disordered regions regulate RhlE RNA helicase functions in bacteria.

RNA helicases-central enzymes in RNA metabolism-often feature intrinsically disordered regions (IDRs) that enable phase separation and complex molecular interactions. In the bacterial pathogen Pseudomonas aeruginosa, the non-redundant RhlE1 and RhlE2 RNA helicases share a conserved REC catalytic core but differ in C-terminal IDRs. Here, we show how the IDR diversity defines RhlE RNA helicase specificity of function.

Polymerization of Physisorbed Molecular Monolayers via Overhanging Alkynyl Chains: Characterization of Polymerization Kinetics and Monolayer Durability.

Monolayers self-assembled by triphenyleneethynylene (TPE) compounds bearing two terminal alkynyl chains were polymerized by Glaser-Hay (G-H) alkyne coupling at the acetonitrile-HOPG interface. The alkynyl chains extend into the solution due to the monolayer's dense-packed morphology. Reacting substructures that have no morphology-determining roles is a potential strategy for preserving monolayer morphology throughout polymerization.

KaiC-like proteins contribute to stress resistance and biofilm formation in environmental Pseudomonas species.

KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologues of this protein are widespread among nonphotosynthetic bacteria, but the function, interaction network, and mechanism of action of these proteins are still largely unknown. Here, we focus on KaiC homologues found in environmental Pseudomonas species.

Mechanism of inhibition of bacterial RNA helicases by diazo dyes and implications for antimicrobial drug development.

RNA helicases represent attractive drug targets as their activity is linked to several human diseases and impacts microbial infectious processes. While some inhibitors of human RNA helicases demonstrated therapeutic potential as anticancer and antiviral drugs in preclinical trials, chemical inhibition of microbial RNA helicases is less investigated. Here, we address this matter by focusing on the RhlE proteobacterial group of RNA helicases.

Secret messaging with endogenous chemistry.

Data encoded in molecules offers opportunities for secret messaging and extreme information density. Here, we explore how the same chemical and physical dimensions used to encode molecular information can expose molecular messages to detection and manipulation. To address these vulnerabilities, we write data using an object's pre-existing surface chemistry in ways that are indistinguishable from the original substrate.

The DEAD-box RNA helicase RhlE2 is a global regulator of Pseudomonas aeruginosa lifestyle and pathogenesis.

RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The bacterial RhlE-like DEAD-box RNA helicases are among the least well studied of these enzymes. They are widespread especially among Proteobacteria, whose genomes often encode multiple homologs.

RSV and HMPV Infections in 3D Tissue Cultures: Mechanisms Involved in Virus-Host and Virus-Virus Interactions.

Respiratory viral infections constitute a global public health concern. Among prevalent respiratory viruses, two pneumoviruses can be life-threatening in high-risk populations. In young children, they constitute the first cause of hospitalization due to severe lower respiratory tract diseases.

Author Correction: Interferon-Dependent and Respiratory Virus-Specific Interference in Dual Infections of Airway Epithelia.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation.

Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions, it is important to understand their relative merits. In the present study, we evaluate the respective scattering cross sections of the two methods and simulate their ability to determine excited state molecular structures in light of currently existing XFEL and MeV source parameters.

Interferon-Dependent and Respiratory Virus-Specific Interference in Dual Infections of Airway Epithelia.

Many respiratory viruses cocirculate in the population and multiple infections are commonly reported. The clinical impact of coinfection is unclear and may vary depending on the viral couples involved. Using three-dimensional reconstituted human airway epithelia and clinical viral strains, we investigated the interaction between influenza virus (Flu), respiratory syncytial virus (RSV) and rhinovirus (RV).

Principles of Information Storage in Small-Molecule Mixtures.

Molecular data systems have the potential to store information at dramatically higher density than existing electronic media. Some of the first experimental demonstrations of this idea have used DNA, but nature also uses a wide diversity of smaller non-polymeric molecules to preserve, process, and transmit information. In this paper, we present a general framework for quantifying chemical memory, which is not limited to polymers and extends to mixtures of molecules of all types.

Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences.

RNA helicases are fundamental players in RNA metabolism: they remodel RNA secondary structures and arrange ribonucleoprotein complexes. While DExH-box RNA helicases function in ribosome biogenesis and splicing in eukaryotes, information is scarce about bacterial homologs. HrpB is the only bacterial DExH-box protein whose structure is solved.

Multicomponent molecular memory.

Multicomponent reactions enable the synthesis of large molecular libraries from relatively few inputs. This scalability has led to the broad adoption of these reactions by the pharmaceutical industry. Here, we employ the four-component Ugi reaction to demonstrate that multicomponent reactions can provide a basis for large-scale molecular data storage.

Encoding information in synthetic metabolomes.

Biomolecular information systems offer exciting potential advantages and opportunities to complement conventional semiconductor technologies. Much attention has been paid to information-encoding polymers, but small molecules also play important roles in biochemical information systems. Downstream from DNA, the metabolome is an information-rich molecular system with diverse chemical dimensions which could be harnessed for information storage and processing.

Spatially resolved standoff trace chemical sensing using backwards transient absorption spectroscopy.

A technique for the spatially resolved and molecule-specific detection of chemical vapors is presented. The chemical specificity arises from a transient absorption spectrum where an ultraviolet (UV) pulse excites the molecule to a Rydberg state, and a near-infrared (NIR) or visible probe pulse records a transient absorption spectrum. By recording the NIR pulse reflected off a random, distant object and measuring the elapsed time between the emission of the UV pulse and the absorption of a counter-propagating NIR pulse, the distance to the absorber is obtained.

No Dose Adjustment is Recommended for Digoxin, Warfarin, Atorvastatin or a Combination Oral Contraceptive When Coadministered with Dulaglutide.

Background: Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) for the treatment of type 2 diabetes mellitus are known to delay gastric emptying (GE). The potential effect of the GLP-1 RA dulaglutide on the pharmacokinetics (PK) of four orally administered drugs and on the pharmacodynamic (PD) effect of warfarin was investigated.

Methods: In four separate clinical pharmacology studies, digoxin, warfarin, atorvastatin and Ortho-Cyclen were orally administered to healthy subjects with and without a subcutaneous dose of dulaglutide 1.

A new real-time RT-PCR targeting VP4-VP2 to detect and quantify enterovirus D68 in respiratory samples.

Causing an international outbreak of respiratory disease, Enterovirus D68 quickly entered the closed circle of emerging viral pathogens of public health significance. As rapid and accurate detection of EV-D68 is essential for an efficient clinical management, we designed and validated a new highly efficient one-step quantitative rRT-PCR specific to EV-D68 VP4-VP2 region. With 100% specificity and 95.

Clinical Pharmacokinetics of Dulaglutide in Patients with Type 2 Diabetes: Analyses of Data from Clinical Trials.

Background And Objective: Dulaglutide is a long-acting glucagon-like peptide-1 receptor agonist administered as once-weekly subcutaneous injections for the treatment of type 2 diabetes (T2D). The clinical pharmacokinetics of dulaglutide were characterized in patients with T2D and healthy subjects.

Methods: The pharmacokinetics of dulaglutide were assessed throughout clinical development, including conventional pharmacokinetic analysis in clinical pharmacology studies and population pharmacokinetic analyses of data from combined phase 2 and phase 3 studies in patients with T2D.

Tamoxifen prevents apoptosis and follicle loss from cyclophosphamide in cultured rat ovaries.

Recent studies documented that the selective estrogen receptor modulator tamoxifen prevents follicle loss and promotes fertility following in vivo exposure of rodents to irradiation or ovotoxic cancer drugs, cyclophosphamide and doxorubicin. In an effort to characterize the ovarian-sparing mechanisms of tamoxifen in preantral follicle classes, cultured neonatal rat ovaries (Day 4, Sprague Dawley) were treated for 1-7 days with active metabolites of cyclophosphamide (i.e.

The zinc transporter Zip5 (Slc39a5) regulates intestinal zinc excretion and protects the pancreas against zinc toxicity.

Background: ZIP5 localizes to the baso-lateral membranes of intestinal enterocytes and pancreatic acinar cells and is internalized and degraded coordinately in these cell-types during periods of dietary zinc deficiency. These cell-types are thought to control zinc excretion from the body. The baso-lateral localization and zinc-regulation of ZIP5 in these cells are unique among the 14 members of the Slc39a family and suggest that ZIP5 plays a role in zinc excretion.

Clioquinol synergistically augments rescue by zinc supplementation in a mouse model of acrodermatitis enteropathica.

Background: Zinc deficiency due to poor nutrition or genetic mutations in zinc transporters is a global health problem and approaches to providing effective dietary zinc supplementation while avoiding potential toxic side effects are needed.

Methods/principal Findings: Conditional knockout of the intestinal zinc transporter Zip4 (Slc39a4) in mice creates a model of the lethal human genetic disease acrodermatitis enteropathica (AE). This knockout leads to acute zinc deficiency resulting in rapid weight loss, disrupted intestine integrity and eventually lethality, and therefore provides a model system in which to examine novel approaches to zinc supplementation.