The human microbiome encodes resistance to the antidiabetic drug acarbose.

The human microbiome encodes a large repertoire of biochemical enzymes and pathways, most of which remain uncharacterized. Here, using a metagenomics-based search strategy, we discovered that bacterial members of the human gut and oral microbiome encode enzymes that selectively phosphorylate a clinically used antidiabetic drug, acarbose1,2, resulting in its inactivation. Acarbose is an inhibitor of both human and bacterial α-glucosidases3, limiting the ability of the target organism to metabolize complex carbohydrates. Using biochemical assays, X-ray crystallography and metagenomic analyses, we show that microbiome-derived acarbose kinases are specific for acarbose, provide their harbouring organism with a protective advantage against the activity of acarbose, and are widespread in the microbiomes of western and non-western human populations. These results provide an example of widespread microbiome resistance to a non-antibiotic drug, and suggest that acarbose resistance has disseminated in the human microbiome as a defensive strategy against a potential endogenous producer of a closely related molecule.

Region-specific reversal of epidermal planar polarity in the rosette fancy mouse.

The planar cell polarity (PCP) pathway collectively orients cells with respect to a body axis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment across the skin. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that rosette hair follicles emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6, which alters a consensus site for N-linked glycosylation, inhibiting its membrane localization. Unexpectedly, the Fzd6 trafficking defect does not block asymmetric localization of the other PCP proteins. Rather, the normally uniform axis of PCP asymmetry rotates where the PCP-directed cell movements that orient follicles are reversed, suggesting the PCP axis rotates 180°. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce posterior whorls in the rosette fancy mouse.

New mouse models for high resolution and live imaging of planar cell polarity proteins in vivo.

The collective polarization of cellular structures and behaviors across a tissue plane is a near universal feature of epithelia known as planar cell polarity (PCP). This property is controlled by the core PCP pathway, which consists of highly conserved membrane-associated protein complexes that localize asymmetrically at cell junctions. Here, we introduce three new mouse models for investigating the localization and dynamics of transmembrane PCP proteins: Celsr1, Fz6 and Vangl2. Using the skin epidermis as a model, we characterize and verify the expression, localization and function of endogenously tagged Celsr1-3xGFP, Fz6-3xGFP and tdTomato-Vangl2 fusion proteins. Live imaging of Fz6-3xGFP in basal epidermal progenitors reveals that the polarity of the tissue is not fixed through time. Rather, asymmetry dynamically shifts during cell rearrangements and divisions, while global, average polarity of the tissue is preserved. We show using super-resolution STED imaging that Fz6-3xGFP and tdTomato-Vangl2 can be resolved, enabling us to observe their complex localization along junctions. We further explore PCP fusion protein localization in the trachea and neural tube, and discover new patterns of PCP expression and localization throughout the mouse embryo.

Food gels: principles, interaction mechanisms and its microstructure.

Food hydrogels are important materials having great scientific interest due to biocompatibility, safety and environment-friendly characteristics. In the food industry, hydrogels are widely used due to their three-dimensional crosslinked networks. Furthermore, they have attracted great attention due to their wide range of applications in the food industry, such as fat replacers, encapsulating agents, target delivery vehicles, and many more. In addition to basic and recent knowledge on food hydrogels, this review exclusively focuses on sensorial perceptions, nutritional significance, body interactions, network structures, mechanical properties, and potential hydrogel applications in food and food-based matrices. Additionally, this review highlights the structural design of hydrogels, which provide the forward-looking idea for future applications of food hydrogels (e.g., 3D or 4D printing).

Chronic obstructive pulmonary disease and lung cancer: inter-relationships.

PURPOSE OF REVIEW: Chronic obstructive pulmonary disease (COPD) is a well established risk factor for lung cancer. Newer studies reveal a myriad of other mechanisms, some proven and some putative, which may contribute to their association. RECENT FINDINGS: There is an ever-growing bundle of evidence that suggests a close association between persistent chronic inflammation and lung cancer. A few potential targets of genetic susceptibility locus for COPD and lung cancer have been suggested. Better characterization of immune dysregulation and identification of signaling pathways may assist the development of strategies to reduce risk of developing lung cancer in patients with COPD. Current lung cancer screening strategies may exclude some patients at high risk of having lung cancer. Prospective studies indicate that a screening criterion that includes variables reflecting the severity of COPD may increase the sensitivity of the screening program and reduce 'over-diagnosis bias' of indolent lung cancers. Examples of such variables include the emphysema score generated from computed tomography scans and diffusion capacity for carbon monoxide derived from lung function tests. SUMMARY: A better understanding of the inter-relationship between lung cancer pathogenesis and COPD has been described recently. Improving lung cancer screening strategies by incorporating markers of COPD severity has recently been proposed.

ISQuest: finding insertion sequences in prokaryotic sequence fragment data.

MOTIVATION: Insertion sequences (ISs) are transposable elements present in most bacterial and archaeal genomes that play an important role in genomic evolution. The increasing availability of sequenced prokaryotic genomes offers the opportunity to study ISs comprehensively, but development of efficient and accurate tools is required for discovery and annotation. Additionally, prokaryotic genomes are frequently deposited as incomplete, or draft stage because of the substantial cost and effort required to finish genome assembly projects. Development of methods to identify IS directly from raw sequence reads or draft genomes are therefore desirable. Software tools such as Optimized Annotation System for Insertion Sequences and IScan currently identify IS elements in completely assembled and annotated genomes; however, to our knowledge no methods have been developed to identify ISs from raw fragment data or partially assembled genomes. We have developed novel methods to solve this computationally challenging problem, and implemented these methods in the software package ISQuest. This software identifies bacterial ISs and their sequence elements-inverted and direct repeats-in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours, making it a valuable high-throughput tool for a global search of IS elements. We tested ISQuest on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and transposases annotated in GenBank with 80% sequence identity. CONTACT: abiswas@cs.odu.edu.

Management of Intrapleural Sepsis with Once Daily Use of Tissue Plasminogen Activator and Deoxyribonuclease.

BACKGROUND: Pleural infection remains a significant cause of morbidity, mortality, prolonged hospital stay, and increased healthcare costs, despite advances in therapy. Twice daily intrapleural tissue plasminogen activator (tPA)/deoxyribonuclease (DNase) initiated at the time of diagnosis has been shown to significantly improve radiological outcomes and decrease the need for surgery. OBJECTIVES: To analyze our experience with once daily tPA/DNase for intrapleural sepsis. METHODS: Data derived from consecutive patients with empyema and complicated parapneumonic effusion who received once daily intrapleural tPA/DNase between January 2012 and August 2014 were reviewed. Measured outcomes included treatment success at 30 days, volume of pleural fluid drained, improvement in radiographic pleural opacity, length of hospital stay, need for surgery, and adverse events. RESULTS: 55 consecutive patients (33 male; mean age ± SD, 54.6 ± 16.1 years) were treated with once daily intrapleural tPA/DNase for 3 days. The majority of the patients (n = 51; 92.7%) were successfully managed without the need for surgical intervention. The mean change in pleural opacity measured on chest radiograph at day 7 was -28.8 ±17.6%. The median amount of fluid drained was 2,195 ml. No serious adverse events requiring discontinuation of intrapleural medications were observed. The most common complication was pain requiring escalating doses of analgesics (n = 8; 15%). Compliance with the protocol was excellent. CONCLUSION: Early administration of once daily intrapleural tPA/DNase for 3 days is safe, effective, and represents a viable option for the management of empyema and complicated parapneumonic effusion.

Right heart failure in acute respiratory distress syndrome: An unappreciated albeit a potential target for intervention in the management of the disease.

Mortality from acute respiratory distress syndrome (ARDS) has gone down recently. In spite of this trend, the absolute numbers continue to be high even with improvements in ventilator strategies and a better understanding of fluid management with this disease. A possible reason for this could be an under-recognized involvement of the pulmonary vasculature and the right side of the heart in ARDS. The right heart is not designed to function under situations leading to acute elevations in afterload as seen in ARDS, and hence it decompensates. This brief review focuses on the magnitude of the problem, its detection in the intensive care unit, and recognizes the beneficial effect of prone-positioning on the pulmonary vasculature and right heart.

From ground to gut: Evaluating the human health risk of potentially toxic elements in soil, groundwater, and their uptake by Cocos nucifera in arsenic-contaminated environments.

This study aimed to gauge the toxicity of potentially toxic elements (PTEs) in coconut crops cultivated in arsenic-contaminated areas while offering a global perspective encompassing more than 100 impacted countries. The current investigation provides crucial insights into the assessment of PTEs pollution using the Bioaccumulation factor, Geo-accumulation index, Potential ecological risk index, Hazardous index, and Lifetime cancer risk (LCR) and highlights the potential human health risks posed by contaminated food, water, and soil. From 22 severely polluted sites in West Bengal, India, soil, groundwater (GW), and coconut water (CW) samples were collected, acidified, and digested using microwave digestion, for PTEs quantification using inductively coupled plasma-optical emission spectroscopy (ICP-OES). Results revealed that despite high concentrations of arsenic in soils (4.6 ± 3.4 mg kg-1), and GW (22.2 ± 150.9 µg L-1), CW (0.7 ± 3.1 µg L-1) levels were within permissible limits. Groups of PTEs with comparable sources and distributions were discovered through Principal Component Analysis (PCA). A speciation diagram was used to predict the prevalence of arsenic species in all three matrices. The Hazardous Index (HI < 1) indicated no probability of non-carcinogenic diseases for children and adults in all the compartments. However, exposure to GW and soil contaminated with Cr, As, and Cd by children (9.02 × 10-13 to 2.77 × 10-4) and adults (6.51 × 10-14 to 1.18 × 10-4) would increase their susceptibility to cancer (LCR >10-6). The study concluded that moderate lifetime consumption of CW is safe and has no significant impact on healthy individuals. Additionally, CW is a rich source of essential micronutrients such as Zn, Fe, Mn, and B. Overall, the findings of this study could help in developing appropriate strategies for reducing PTEs contamination and protecting human health.

Liver-specific Mettl14 deletion induces nuclear heterotypia and dysregulates RNA export machinery.

Modification of RNA with N 6 -methyladenosine (m 6 A) has gained attention in recent years as a general mechanism of gene regulation. In the liver, m 6 A, along with its associated machinery, has been studied as a potential biomarker of disease and cancer, with impacts on metabolism, cell cycle regulation, and pro-cancer state signaling. However these observational data have yet to be causally examined in vivo. For example, neither perturbation of the key m 6 A writers Mettl3 and Mettl14 , nor the m 6 A readers Ythdf1 and Ythdf2 have been thoroughly mechanistically characterized in vivo as they have been in vitro . To understand the functions of these machineries, we developed mouse models and found that deleting Mettl14 led to progressive liver injury characterized by nuclear heterotypia, with changes in mRNA splicing, processing and export leading to increases in mRNA surveillance and recycling.

Mechanical Behavior of Austenitic Steel under Multi-Axial Cyclic Loading.

Low-nickel austenitic steel is subjected to high-pressure torsion fatigue (HPTF) loading, where a constant axial compression is overlaid with a cyclic torsion. The focus of this work lies on investigating whether isotropic J2 plasticity or crystal plasticity can describe the mechanical behavior during HPTF loading, particularly focusing on the axial creep deformation seen in the experiment. The results indicate that a J2 plasticity model with an associated flow rule fails to describe the axial creep behavior. In contrast, a micromechanical model based on an empirical crystal plasticity law with kinematic hardening described by the Ohno-Wang rule can match the HPTF experiments quite accurately. Hence, our results confirm the versatility of crystal plasticity in combination with microstructural models to describe the mechanical behavior of materials under reversing multiaxial loading situations.

Structural features stabilized by divalent cation coordination within hepatitis E virus ORF1 are critical for viral replication.

Hepatitis E virus (HEV) is an RNA virus responsible for over 20 million infections annually. HEV's open reading frame (ORF)1 polyprotein is essential for genome replication, though it is unknown how the different subdomains function within a structural context. Our data show that ORF1 operates as a multifunctional protein, which is not subject to proteolytic processing. Supporting this model, scanning mutagenesis performed on the putative papain-like cysteine protease (pPCP) domain revealed six cysteines essential for viral replication. Our data are consistent with their role in divalent metal ion coordination, which governs local and interdomain interactions that are critical for the overall structure of ORF1; furthermore, the 'pPCP' domain can only rescue viral genome replication in trans when expressed in the context of the full-length ORF1 protein but not as an individual subdomain. Taken together, our work provides a comprehensive model of the structure and function of HEV ORF1.

Region-specific reversal of epidermal planar polarity in the fancy rosette mouse.

The planar cell polarity (PCP) pathway collectively orients thousands of cells with respect to a body axis to direct cellular behaviors that are essential for embryonic morphogenesis. Hair follicles of the murine epidermis provide a striking readout of PCP activity in their uniform alignment along the entire skin surface. Here, we characterize, from the molecular to tissue-scale, PCP establishment in the rosette fancy mouse, a natural variant with posterior-specific whorls in its fur, to understand how epidermal polarity is coordinated across the tissue. We find that embryonic hair follicles of rosette mutants emerge with reversed orientations specifically in the posterior region, creating a mirror image of epidermal polarity. The rosette trait is associated with a missense mutation in the core PCP gene Fzd6 , which alters a consensus site for N-linked glycosylation and inhibits its membrane localization. Unexpectedly, this defect in Fzd6 trafficking, observed across the entire dorsal epidermis, does not interfere with the ability of other core PCP proteins to localize asymmetrically. Rather, the normally uniform axis of PCP asymmetry is disrupted and rotated in the posterior region such that polarity is reflected on either side of a transition zone. The result is a reversal of polarized cell movements that orient nascent follicles, specifically in the posterior of the embryo. Collectively, our multiscale analysis of epidermal polarity reveals PCP patterning can be regionally decoupled to produce the unique posterior whorls of the fancy rosette mouse. Summary: Region-specific rotation of the Planar Cell Polarity axis reverses posterior hair follicles in the fancy rosette mouse.

Targeted viral adaptation generates a simian-tropic hepatitis B virus that infects marmoset cells.

Hepatitis B virus (HBV) only infects humans and chimpanzees, posing major challenges for modeling HBV infection and chronic viral hepatitis. The major barrier in establishing HBV infection in non-human primates lies at incompatibilities between HBV and simian orthologues of the HBV receptor, sodium taurocholate co-transporting polypeptide (NTCP). Through mutagenesis analysis and screening among NTCP orthologues from Old World monkeys, New World monkeys and prosimians, we determined key residues responsible for viral binding and internalization, respectively and identified marmosets as a suitable candidate for HBV infection. Primary marmoset hepatocytes and induced pluripotent stem cell-derived hepatocyte-like cells support HBV and more efficient woolly monkey HBV (WMHBV) infection. Adapted chimeric HBV genome harboring residues 1-48 of WMHBV preS1 generated here led to a more efficient infection than wild-type HBV in primary and stem cell derived marmoset hepatocytes. Collectively, our data demonstrate that minimal targeted simianization of HBV can break the species barrier in small NHPs, paving the path for an HBV primate model.

Micromechanical Modeling of AlSi10Mg Processed by Laser-Based Additive Manufacturing: From as-Built to Heat-Treated Microstructures.

The unique microstructure of the alloy AlSi10Mg produced by the laser-based powder bed fusion of metals (PBF-LB/M) provides high-strength and high-strain-hardening capabilities of the material. The microstructure and mechanical properties of 3D-printed, i.e., additively manufactured, AlSi10Mg are significantly altered by post-building heat-treatment processes applied in order to tailor the final properties of the parts. Using an accurate computational model to predict and improve the mechanical performance of 3D-printed samples considering their microstructural features can accelerate their employment in envisaged applications. The present study aims to investigate the correlation between microstructural features and the mechanical behavior of as-built, direct-aged, and T6 heat-treated samples of PBF-LB/M AlSi10Mg under tensile loading using experiment and microstructure-sensitive modeling approaches. Nanoindentation tests are used to calibrate the parameters of the constitutive models for the Al and Si-rich phases. The experimental investigations revealed that heat treatment significantly changes the sub-grain morphology of the Si-rich phase, and this can have a considerable effect on the mechanical behavior of the components. The effect of the modeling of the Si-rich phase in the representative volume elements on the prediction of mechanical behavior is investigated using the J2 plasticity model. The combination of the crystal plasticity model for Al and the J2 plasticity model for the Si-rich phase is used to predict the tensile properties of the as-built and heat-treated states. The predicted results are in good agreement with the experimental results. This approach can be used to understand the microstructure-property relationship of PBF-LB/M AlSi10Mg and eventually tailor heat treatment for PBF-LB/M AlSi10Mg based on the requirement of the application.

Generation and characterization of genetically and antigenically diverse infectious clones of dengue virus serotypes 1-4.

Dengue is caused by four genetically distinct viral serotypes, dengue virus (DENV) 1-4. Following transmission by Aedes mosquitoes, DENV can cause a broad spectrum of clinically apparent disease ranging from febrile illness to dengue hemorrhagic fever and dengue shock syndrome. Progress in the understanding of different dengue serotypes and their impacts on specific host-virus interactions has been hampered by the scarcity of tools that adequately reflect their antigenic and genetic diversity. To bridge this gap, we created and characterized infectious clones of DENV1-4 originating from South America, Africa, and Southeast Asia. Analysis of whole viral genome sequences of five DENV isolates from each of the four serotypes confirmed their broad genetic and antigenic diversity. Using a modified circular polymerase extension reaction (CPER), we generated de novo viruses from these isolates. The resultant clones replicated robustly in human and insect cells at levels similar to those of the parental strains. To investigate in vivo properties of these genetically diverse isolates, representative viruses from each DENV serotype were administered to NOD Rag1-/-, IL2rgnull Flk2-/- (NRGF) mice, engrafted with components of a human immune system. All DENV strains tested resulted in viremia in humanized mice and induced cellular and IgM immune responses. Collectively, we describe here a workflow for rapidly generating de novo infectious clones of DENV - and conceivably other RNA viruses. The infectious clones described here are a valuable resource for reverse genetic studies and for characterizing host responses to DENV in vitro and in vivo.