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UCGretina, a GEANT4 simulation of the GRETINA gamma-ray tracking array of highly-segmented high-purity germanium detectors is described. We have developed a model of the array, in particular of the Quad Module and the capsules, that gives good agreement between simulated and measured photopeak efficiencies over a broad range of gamma-ray energies and reproduces the shape of the measured Compton continuum. Both of these features are needed in order to accurately extract gamma-ray yields from spectra collected in in-beam gamma-ray spectroscopy measurements with beams traveling at v∕c≳0.3 at the National Superconducting Cyclotron Laboratory and the Facility for Rare Isotope Beams. In the process of developing the model, we determined that millimeter-scale layers of passive germanium surrounding the active volumes of the simulated crystals must be included in order to reproduce measured photopeak efficiencies. We adopted a simple model of effective passive layers and developed heuristic methods of determining passive-layer thicknesses by comparison of simulations and measurements for a single crystal and for the full array. Prospects for future development of the model are discussed.

In this paper, we provide a formalism for the characterization of tracking arrays with emphasis on the proper corrections required to extract their photopeak efficiencies and peak-to-total ratios. The methods are first applied to Gammasphere, a well characterized 4π array based on the principle of Compton suppression, and subsequently to GRETINA. The tracking efficiencies are then discussed and some guidelines as to what clustering angle to use in the tracking algorithm are presented. It was possible, using GEANT4 simulations, to scale the measured efficiencies up to the expected values for the full 4π implementation of GRETA.

Abstract Objectives Exoscopes represent a promising alternative to conventional binocular microscopes (OM) in otology offering potential advantages such as enhanced ergonomics and a more compact device design. While previous research has demonstrated the effectiveness of exoscopes in various surgical specialties, their objective assessment in the field of otology remains limited. Therefore, this investigation aims to assess task‐based efficiency associated with exoscopes in the field of otology by use of simulated surgical models. Methods A prospective cross‐over study design was used to compare an OM to an exoscope in otolaryngology residents and medical students. Participants performed five tasks on 3D‐printed ear models using both the exoscope and OM. Data collection included completion time, frequency of predefined errors, mental effort, and user experience. Subgroup analysis was performed based on level of experience. Results Fourteen students and fifteen residents participated. Participants completed four of five tasks faster with the OM and there was no difference in number of errors committed. When separated by surgical experience, residents performed four of five tasks faster using the OM while students completed one of five tasks faster with the OM. Students committed more errors with the exoscope for one task with no difference in errors for residents. There was no difference in perceived difficulty performing tasks with either visualization system. Exit survey results showed more favorable opinions of the OM among residents and more favorable opinions of the exoscope among students. Conclusions The exoscope permits successful performance in simulated otologic tasks. Task performance and user experience between operative microscopes and exoscopes differ based on level of surgical experience. Level of Evidence 2.

Abstract We present a microscopic many-body calculation of the nonlinear two-dimensional coherent spectroscopy (2DCS) of trion-polaritons and exciton-polaritons in charge-tunable transition-metal-dichalcogenides monolayers placed in an optical microcavity. The charge tunability leads to an electron gas with nonzero density that brings brightness to the trion — a polaron quasiparticle formed by an exciton with a nonzero residue bounded to the electron gas. As a result, a trion-polariton is created under strong light-matter coupling, as observed in the recent experiment by Sidler et al. [Nat. Phys. 13, 255 (2017)]. We analyze in detail the structure of trion-polaritons, by solving an extended Chevy ansatz for the trion quasiparticle wave-function. We confirm that the effective light-matter coupling for trion-polaritons is determined by the residue of the trion quasiparticle. The solution of the full many-body polaron states within Chevy ansatz enables us to microscopically calculate the nonlinear 2DCS spectrum of both trion-polaritons and exciton-polaritons. We predict the existence of three kinds of off-diagonal cross-peaks in the 2DCS spectrum, as an indication of the coherence among the different branches of trion-polaritons and exciton-polaritons. Due to the sensitivity of 2DCS spectrum to quasiparticle interactions, our work provides a good starting point to explore the strong nonlinearity exhibited by trion-polaritons in some recent exciton-polariton experiments.

Abstract High‐quality paleointensity data are essential for improving our understanding of the geomagnetic field; however, it is challenging to find materials that reliably record full vector magnetization going back in time. Here, we examine a new candidate material for paleointensity studies: clinkers, which are rocks that have been baked, metamorphosed, or melted by underlying coal seam fires. Previous studies conducted on clinkers suggest that they may be high‐fidelity magnetic field recorders. However, due to the inhomogeneity of clinker deposits and limited scope of previous studies, it is unknown under what conditions these conclusions hold true. To better assess this, we quantified the variation of magnetic properties within clinker deposits collected from the Powder River Basin, Montana, as a function of lithology, oxidation state, distance from the coal seam, and location. Our results indicate that the clinker products contain three main magnetic minerals: magnetite, hematite, and the rare ε‐Fe2O3. Clinker lithology was found to be the primary control on magnetic mineralogy, where strongly baked sediment and porcellanite are dominated by varying proportions of hematite, ε‐Fe2O3, and magnetite, and paralavas are dominated by low‐Ti magnetite. All clinker materials are thermally stable and likely experienced temperatures in excess of the magnetite Curie temperature. Grain size analysis indicates that the magnetic particles in all clinker materials are amenable to high‐quality paleointensity study. In total, our study confirms that clinkers should be reliable full vector paleomagnetic recorders.

Background As the most powerful T cell agonists known, superantigens (SAgs) have enormous potential for cancer immunotherapy. Their development has languished due to high incidence (60%–80%) of seroreactive neutralizing antibodies in humans and tumor necrosis factor-α (TNFα)-mediated cardiopulmonary toxicity. Such toxicity has narrowed their therapeutic index while neutralizing antibodies have nullified their therapeutic effects.Methods Female HLA-DQ8 (DQA*0301/DQB*0302) tg mice expressing the human major histocompatibility complex II (MHCII) HLA-DQ8 allele on a high proportion of PBL, spleen and lymph node cells were used. In the established tumor model, staphylococcal enterotoxin G and staphylococcal enterotoxin I (SEG/ SEI) (50 µg each) were injected on days 6 and 9 following tumor inoculation. Lymphoid, myeloid cells and tumor cell digests from tumor tissue were assayed using flow cytometry or quantitated using a cytometric bead array. Tumor density, necrotic and viable areas were quantitated using the ImageJ software.Results In a discovery-driven effort to address these problems we introduce a heretofore unrecognized binary complex comprizing SEG/SEI SAgs linked to the endogenous human MHCII HLA-DQ8 allele in humanized mice. By contrast to staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin B (SEB) deployed previously in clinical trials, SEG and SEI does not exhibit neutralizing antibodies in humans or TNFα-mediated toxicity in humanized HLA-DQ8 mice. In the latter model wherein SAg behavior is known to be ‘human-like’, SEG/SEI induced a powerful tumoricidal response and long-term survival against established melanoma in 82% of mice. Other SAgs deployed in the same model displayed toxic shock. Initially, HLA-DQ8 mediated melanoma antigen priming, after which SEG/SEI unleashed a broad CD4+ and CD8+ antitumor network marked by expansion of melanoma reactive T cells and interferon-γ (IFNy) in the tumor microenvironment (TME). SEG/SEI further initiated chemotactic recruitment of tumor reactive T cells to the TME converting the tumor from ‘cold’ to a ‘hot’. Long-term survivors displayed remarkable resistance to parental tumor rechallenge along with the appearance of tumor specific memory and tumor reactive T memory cells.Conclusions Collectively, these findings show for the first time that the SEG/SEI-(HLA-DQ8) empowers priming, expansion and recruitment of a population of tumor reactive T cells culminating in tumor specific memory and long-term survival devoid of toxicity. These properties distinguish SEG/SEI from other SAgs used previously in human tumor immunotherapy. Consolidation of these principles within the SEG/SEI-(HLA-DQ8) complex constitutes a conceptually new therapeutic weapon with compelling translational potential.

Emerging evidence suggests an associative link between gut dysbiosis, the autonomic nervous system (ANS) and the immune system in pathophysiology of neurogenic hypertension (HTN). However, the close interplay between these three systems presents us with difficulties in deciphering the cause-effect relationship in disease. The present study utilized beta 1 and 2 adrenergic receptor knock out (AdrB1tm1BkkAdrB2tm1Bkk/J KO) mice to isolate the effects of reduced overall sympathetic drive on gut microbiota and systemic immune system. We observed the following: (i) Diminished beta adrenergic signaling mainly reflects in shifts in the Firmicutes phyla, with a significant increase in abundance of largely beneficial Bacilli Lactobacillales in the KO mice; (ii) This was associated with increased colonic production of beneficial short chain fatty acids (SCFAs) butyrate, acetate and propionate, confirming functional microbiota shifts in the KO mice; (iii) Dampened systemic immune responses in the KO mice reflected in reduction on circulating CD4+.IL17+ T cells and increase in young neutrophils, both previously associated with shifts in the gut microbiota. Taken together, these observations demonstrate that reduced expression of beta adrenergic receptors may lead to beneficial shifts in the gut microbiota and dampened systemic immune responses. Considering the role of both in hypertension, this suggests that dietary intervention may be a viable option for manipulation of blood pressure via correcting gut dysbiosis.

Abstract Background Shigatoxigenic E. coli are a global and emerging health concern. Shiga toxin, Stx, is encoded on the genome of temperate, lambdoid Stx phages. Genes essential for phage maintenance and replication are encoded on approximately 50% of the genome, while most of the remaining genes are of unknown function nor is it known if these annotated hypothetical genes are even expressed. It is hypothesized that many of the latter have been maintained due to positive selection pressure, and that some, expressed in the lysogen host, have a role in pathogenicity. This study used Change Mediated Antigen Technology (CMAT)™ and 2D-PAGE, in combination with RT-qPCR, to identify Stx phage genes that are expressed in E. coli during the lysogenic cycle. Results Lysogen cultures propagated for 5-6 hours produced a high cell density with a low proportion of spontaneous prophage induction events. The expression of 26 phage genes was detected in these cultures by differential 2D-PAGE of expressed proteins and CMAT. Detailed analyses of 10 of these genes revealed that three were unequivocally expressed in the lysogen, two expressed from a known lysogenic cycle promoter and one uncoupled from the phage regulatory network. Conclusion Propagation of a lysogen culture in which no cells at all are undergoing spontaneous lysis is impossible. To overcome this, RT-qPCR was used to determine gene expression profiles associated with the growth phase of lysogens. This enabled the definitive identification of three lambdoid Stx phage genes that are expressed in the lysogen and seven that are expressed during lysis. Conservation of these genes in this phage genome, and other Stx phages where they have been identified as present, indicates their importance in the phage/lysogen life cycle, with possible implications for the biology and pathogenicity of the bacterial host.

Efficient genome engineering is critical to understand and use microbial functions. Despite recent development of tools such as CRISPR-Cas gene editing, efficient integration of exogenous DNA with well-characterized functions remains limited to model bacteria. Here, we describe serine recombinase-assisted genome engineering, or SAGE, an easy-to-use, highly efficient, and extensible technology that enables selection marker-free, site-specific genome integration of up to 10 DNA constructs, often with efficiency on par with or superior to replicating plasmids. SAGE uses no replicating plasmids and thus lacks the host range limitations of other genome engineering technologies. We demonstrate the value of SAGE by characterizing genome integration efficiency in five bacteria that span multiple taxonomy groups and biotechnology applications and by identifying more than 95 heterologous promoters in each host with consistent transcription across environmental and genetic contexts. We anticipate that SAGE will rapidly expand the number of industrial and environmental bacteria compatible with high-throughput genetics and synthetic biology.

Escherichia coli is the most studied and well understood microorganism, but research in this system can still be limited by available genetic tools, including the ability to rapidly integrate multiple DNA constructs efficiently into the chromosome. Site-specific, large serine-recombinases can be useful tools, catalyzing a single, unidirectional recombination event between 2 specific DNA sequences, attB and attP, without requiring host proteins for functionality. Using these recombinases, we have developed a system to integrate up to 12 genetic constructs sequentially and stably into in the E. coli chromosome. A cassette of attB sites was inserted into the chromosome and the corresponding recombinases were cloned onto temperature sensitive plasmids to mediate recombination between a non-replicating, attP -containing "cargo" plasmid and the corresponding attB site on the chromosome. The efficiency of DNA insertion into the E. coli chromosome was approximately 10 7 CFU/μg DNA for six of the recombinases when the competent cells already contained the recombinase-expressing plasmid and approximately 10 5 CFU/μg DNA or higher when the recombinase-expressing plasmid and "cargo" plasmid were co-transformed. The "cargo" plasmid contains ΦC31 recombination sites flanking the antibiotic gene, allowing for resistance markers to be removed and reused following transient expression of the ΦC31 recombinase. As an example of the utility of this system, eight DNA methyltransferases from Clostridium clariflavum 4-2a were inserted into the E. coli chromosome to methylate plasmid DNA for evasion of the C. clariflavum restriction systems, enabling the first demonstration of transformation of this cellulose-degrading species. IMPORTANCE More rapid genetic tools can help accelerate strain engineering, even in advanced hosts like Escherichia coli. Here, we adapt a suite of site-specific recombinases to enable simple, rapid, and highly efficient site-specific integration of heterologous DNA into the chromosome. This utility of this system was demonstrated by sequential insertion of eight DNA methyltransferases into the E. coli chromosome, allowing plasmid DNA to be protected from restriction in Clostridium clariflavum and enabling genetic transformation of this organism. This integration system should also be highly portable into non-model organisms.

The objective of this study was to test the hypothesis that targeting sclerostin would accelerate the progression of aortic valve stenosis. Sclerostin (mouse gene, Sost ) is a secreted glycoprotein that acts as a potent regulator of bone remodeling. Antibody therapy targeting sclerostin is approved for osteoporosis but results from a stage III clinical trial showed multiple off-target cardiovascular effects. Wild-type (WT, Sost +/+ ) and Sost -gene knockout-expression (Null, Sost -/- ) mice were generated and maintained to 12 mo of age on a high-cholesterol diet to induce aortic valve stenosis. Mice were examined by echocardiography, histology, and RNAseq. Immortalized valve interstitial cells were developed from each genotype for in vitro studies. Null mice developed a bone overgrowth phenotype, similar to patients with sclerosteosis. Surprisingly, however, WT mice developed hemodynamic signs of aortic valve stenosis, whereas Null mice were unchanged. WT mice had thicker aortic valve leaflets and higher amounts of α-smooth muscle actin, a marker myofibroblast activation and dystrophic calcification, with very little evidence of Runx2 expression, a marker of osteogenic calcification. RNAseq analysis of aortic roots indicated the HOX family of transcription factors was significantly upregulated in Null mice, and valve interstitial cells from Null animals were enriched with Hoxa1, Hoxb2, and Hoxd3 subtypes with downregulated Hoxa7. In addition, Null valve interstitial cells were shown to be less contractile than their WT counterparts. Contrary to our hypothesis, sclerostin targeting prevented hallmarks of aortic valve stenosis and indicates that targeted antibody treatments for osteoporosis may be beneficial for these patients regarding aortic stenosis. NEW & NOTEWORTHY We have found that genetic ablation of the Sost gene (protein: sclerostin) prevents aortic valve stenosis in aged, Western diet mice. This is a new role for sclerostin in the cardiovascular system. To the knowledge of the authors, this is one of the first studies directly manipulating sclerostin in a cardiovascular disease model and the first to specifically study the aortic valve. We also provide a potential new role for Hox genes in cardiovascular disease, noting pan- Hox upregulation in the aortic roots of sclerostin genetic knockouts. The role of Hox genes in postnatal cardiovascular health and disease is another burgeoning field of study to which this article contributes.

Circadian rhythms are maintained by a cell-autonomous, transcriptional-translational feedback loop known as the molecular clock. While previous research suggests a role of the molecular clock in regulating skeletal muscle structure and function, no mechanisms have connected the molecular clock to sarcomere filaments. Utilizing inducible, skeletal muscle specific, Bmal1 knockout (iMS Bmal1 -/- ) mice, we showed that knocking out skeletal muscle clock function alters titin isoform expression using RNAseq, liquid chromatography-mass spectrometry, and sodium dodecyl sulfate-vertical agarose gel electrophoresis. This alteration in titin's spring length resulted in sarcomere length heterogeneity. We demonstrate the direct link between altered titin splicing and sarcomere length in vitro using U7 snRNPs that truncate the region of titin altered in iMS Bmal1 -/- muscle. We identified a mechanism whereby the skeletal muscle clock regulates titin isoform expression through transcriptional regulation of Rbm20 , a potent splicing regulator of titin. Lastly, we used an environmental model of circadian rhythm disruption and identified significant downregulation of Rbm20 expression. Our findings demonstrate the importance of the skeletal muscle circadian clock in maintaining titin isoform through regulation of RBM20 expression. Because circadian rhythm disruption is a feature of many chronic diseases, our results highlight a novel pathway that could be targeted to maintain skeletal muscle structure and function in a range of pathologies., Competing Interests: LR, XZ, CD, JM, DH, CW, NW, HO, PD, SL, MP, EW, KE No competing interests declared, (© 2022, Riley et al.)

Pressure overload of the heart is characterized by concentric hypertrophy and interstitial fibrosis. Cardiac fibroblasts (CFs) in the ventricular wall become activated during injury and synthesize and compact the extracellular matrix, which causes interstitial fibrosis and stiffening of the ventricular heart walls. Talin1 (Tln1) and Talin2 (Tln2) are mechanosensitive proteins that participate in focal adhesion transmission of signals from the extracellular environment to the actin cytoskeleton of CFs. The aim of the present study was to determine whether the removal of Tln1 and Tln2 from CFs would reduce interstitial fibrosis and cardiac hypertrophy. Twelve-week-old male and female Tln2-null ( Tln2 -/- ) and Tln2-null, CF-specific Tln1 knockout ( Tln2 -/- ; Tln1 CF-/- ) mice were given angiotensin-II (ANG II) (1.5 mg/kg/day) or saline through osmotic pumps for 8 wk. Cardiomyocyte area and measures of heart thickness were increased in the male ANG II-infused Tln2 -/- ; Tln1 CF-/- mice, whereas there was no increase in interstitial fibrosis. Systolic blood pressure was increased in the female Tln2 -/- ; Tln1 CF-/- mice after ANG II infusion compared with the Tln2 -/- mice. However, there was no increase in cardiac hypertrophy in the Tln2 -/- ; Tln1 CF-/- mice, which was seen in the Tln2 -/- mice. Collectively, these data indicate that in male mice, the absence of Tln1 and Tln2 in CFs leads to cardiomyocyte hypertrophy in response to ANG II, whereas it results in a hypertrophy-resistant phenotype in female mice. These findings have important implications for the role of mechanosensitive proteins in CFs and their impact on cardiomyocyte function in the pathogenesis of hypertension and cardiac hypertrophy. NEW & NOTEWORTHY The role of talins has been previously studied in cardiomyocytes; however, these mechanotransductive proteins that are members of the focal adhesion complex have not been examined in cardiac fibroblasts previously. We hypothesized that loss of talins in cardiac fibroblasts would reduce interstitial fibrosis in the heart with a pressure overload model. However, we found that although loss of talins did not alter fibrosis, it did result in cardiomyocyte and ventricular hypertrophy.

Background: Myocardial infarction (MI) induces an intense injury response that ultimately generates a collagen-dominated scar. Although required to prevent ventricular rupture, the fibrotic process is often sustained in a manner detrimental to optimal recovery. Cardiac myofibroblasts are the cells tasked with depositing and remodeling collagen and are a prime target to limit the fibrotic process after MI. Serotonin 2B receptor (5-HT 2B ) signaling has been shown to be harmful in a variety of cardiopulmonary pathologies and could play an important role in mediating scar formation after MI., Methods: We used 2 pharmacological antagonists to explore the effect of 5-HT 2B inhibition on outcomes after MI and characterized the histological and microstructural changes involved in tissue remodeling. Inducible 5-HT 2B ablation driven by Tcf21 MCM and Postn MCM was used to evaluate resident cardiac fibroblast- and myofibroblast-specific contributions of 5-HT 2B , respectively. RNA sequencing was used to motivate subsequent in vitro analyses to explore cardiac fibroblast phenotype., Results: 5-HT 2B antagonism preserved cardiac structure and function by facilitating a less fibrotic scar, indicated by decreased scar thickness and decreased border zone area. 5-HT 2B antagonism resulted in collagen fiber redistribution to thinner collagen fibers that were more anisotropic, enhancing left ventricular contractility, whereas fibrotic tissue stiffness was decreased, limiting the hypertrophic response of uninjured cardiomyocytes. Using a tamoxifen-inducible Cre, we ablated 5-HT 2B from Tcf21 -lineage resident cardiac fibroblasts and saw similar improvements to the pharmacological approach. Tamoxifen-inducible Cre-mediated ablation of 5-HT 2B after onset of injury in Postn -lineage myofibroblasts also improved cardiac outcomes. RNA sequencing and subsequent in vitro analyses corroborate a decrease in fibroblast proliferation, migration, and remodeling capabilities through alterations in Dnajb4 expression and Src phosphorylation., Conclusions: Together, our findings illustrate that 5-HT 2B expression in either cardiac fibroblasts or activated myofibroblasts directly contributes to excessive scar formation, resulting in adverse remodeling and impaired cardiac function after MI.

Cardiac fibrosis represents an enormous health concern as it is prevalent in nearly every form of cardiovascular disease, the leading cause of death worldwide. Fibrosis is characterized by the activation of fibroblasts into myofibroblasts, a contractile cell type that secretes significant amounts of extracellular matrix components; however, the onset of this condition is also due to persistent inflammation and the cellular responses to a changing mechanical environment. In this review, we provide an overview of the pro-fibrotic, pro-inflammatory, and biomechanical mechanisms that lead to cardiac fibrosis in cardiovascular diseases. We then discuss cadherin-11, an intercellular adhesion protein present on both myofibroblasts and inflammatory cells, as a potential link for all three of the fibrotic mechanisms. Since experimentally blocking cadherin-11 dimerization prevents fibrotic diseases including cardiac fibrosis, understanding how this protein can be targeted for therapeutic use could lead to better treatments for patients with heart disease., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, "domestication" of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.

Here, we present the first complete genome assembly of the thermophilic bacterium Parageobacillus toebii DSM 14590 T The P. toebii DSM 14590 T genome consists of a 3,270,071-bp circular chromosome and a 52,989-bp native plasmid., (Copyright © 2020 Hatmaker et al.)

A major barrier to both metabolic engineering and fundamental biological studies is the lack of genetic tools in most microorganisms. One example is Clostridium thermocellum ATCC 27405 T , where genetic tools are not available to help validate decades of hypotheses. A significant barrier to DNA transformation is restriction-modification systems, which defend against foreign DNA methylated differently than the host. To determine the active restriction-modification systems in this strain, we performed complete methylome analysis via single-molecule, real-time sequencing to detect 6-methyladenine and 4-methylcytosine and the rarely used whole-genome bisulfite sequencing to detect 5-methylcytosine. Multiple active systems were identified, and corresponding DNA methyltransferases were expressed from the Escherichia coli chromosome to mimic the C. thermocellum methylome. Plasmid methylation was experimentally validated and successfully electroporated into C. thermocellum ATCC 27405. This combined approach enabled genetic modification of the C. thermocellum-type strain and acts as a blueprint for transformation of other non-model microorganisms.

Background: Skeletal muscle contributes to roughly 40% of lean body mass, and its loss contributes to morbidity and mortality in a variety of pathogenic conditions. Significant insights into muscle function have been made using cultured cells, in particular, the C2C12 myoblast line. However, differentiation of these cells in vitro typically yields immature myotubes relative to skeletal muscles in vivo. While many efforts have attempted to improve the maturity of cultured myotubes, including the use of bioengineered substrates, lack of molecular characterization has precluded their widespread implementation. This study characterizes morphological, molecular, and transcriptional features of C2C12 myotubes cultured on crosslinked, micropatterned gelatin substrates fabricated using previously established methods and compares them to myotubes grown on unpatterned gelatin or traditional plasticware., Methods: We used immunocytochemistry, SDS-PAGE, and RNAseq to characterize C2C12 myotubes grown on micropatterned gelatin hydrogels, unpatterned gelatin hydrogels, and typical cell culture substrates (i.e., plastic or collagen-coated glass) across a differentiation time course. The ability to form aligned sarcomeres and myofilament protein concentration was assessed. Additionally, the transcriptome was analyzed across the differentiation time course., Results: C2C12 myotubes grown on micropatterned gelatin hydrogels display an increased ability to form aligned sarcomeres as well as increased contractile protein content relative to myotubes cultured on unpatterned gelatin and plastic. Additionally, genes related to sarcomere formation and in vivo muscle maturation are upregulated in myotubes grown on micropatterned gelatin hydrogels relative to control myotubes., Conclusions: Our results suggest that growing C2C12 myotubes on micropatterned gelatin hydrogels accelerates sarcomere formation and yields a more fully matured myotube culture. Thus, the use of micropatterned hydrogels is a viable and simple approach to better model skeletal muscle biology in vitro.

Here, we report the complete genome sequences of two Megasphaera elsdenii strains, ATCC 25940 and NCIMB 702410. M. elsdenii is an anaerobic bacterium capable of producing butanoate and hexanoate and is a member of the Negativicutes.

Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively affect certain muscle groups. These observations suggest that factors intrinsic to muscle tissues influence their resistance to disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq to profile mRNA expression in skeletal, smooth, and cardiac muscle tissues from mice and rats. Our data set, MuscleDB, reveals extensive transcriptional diversity, with greater than 50% of transcripts differentially expressed among skeletal muscle tissues. We detect mRNA expression of hundreds of putative myokines that may underlie the endocrine functions of skeletal muscle. We identify candidate genes that may drive tissue specialization, including Smarca4 , Vegfa , and Myostatin . By demonstrating the intrinsic diversity of skeletal muscles, these data provide a resource for studying the mechanisms of tissue specialization., Competing Interests: ET, XZ, CH, LH, SL, JL, MW, LR, CD, MG, NL, MG, FA, KE, MH No competing interests declared, (© 2018, Terry et al.)

Chromosome abnormalities detected during cytogenetic investigations for B-cell malignancy offer prognostic information that can have wide ranging clinical impacts on patients. These impacts may include monitoring frequency, treatment type, and disease staging level. The use of the synthetic oligonucleotide DSP30 combined with interleukin 2 (IL2) has been described as an effective mitotic stimulant in B-cell disorders, not only in chronic lymphocytic leukemia (CLL) but also in a range of other B-cell malignancies. Here, we describe the comparison of two B-cell mitogens, lipopolysaccharide (LPS), and DSP30 combined with IL2 as mitogens in a range of common B-cell disorders excluding CLL. The results showed that DSP30/IL2 was an effective mitogen in mature B-cell disorders, revealing abnormal cytogenetic results in a range of B-cell malignancies. The abnormality rate increased when compared to the use of LPS to 64% (DSP30/IL2) from 14% (LPS). In a number of cases the disease burden was proportionally very low, less than 10% of white cells. In 37% of these cases, the DSP30 culture revealed abnormal results. Importantly, we also obtained abnormal conventional cytogenetics results in 3 bone marrow cases in which immunophenotyping showed an absence of an abnormal B-cell clone. In these cases, the cytogenetics results correlated with the provisional diagnosis and altered their staging level. The use of DSP30 and IL2 is recommended for use in many B-cell malignancies as an effective mitogen and their use has been shown to enable successful culture of the malignant clone, even at very low levels of disease., (© 2018 Wiley Periodicals, Inc.)

Muscles have evolved to power a wide variety of movements. A protein component critical to varying power generation is the myosin isoform present in the muscle. However, how functional variation in muscle arises from myosin structure is not well understood. We studied the influence of the converter, a myosin structural region at the junction of the lever arm and catalytic domain, using Drosophila because its single myosin heavy chain gene expresses five alternative converter versions (11a-e). We created five transgenic fly lines, each forced to express one of the converter versions in their indirect flight muscle (IFM) fibers. Electron microscopy showed that the converter exchanges did not alter muscle ultrastructure. The four lines expressing converter versions (11b-e) other than the native IFM 11a converter displayed decreased flight ability. IFM fibers expressing converters normally found in the adult stage muscles generated up to 2.8-fold more power and displayed up to 2.2-fold faster muscle kinetics than fibers with converters found in the embryonic and larval stage muscles. Small changes to stretch-activated force generation only played a minor role in altering power output of IFM. Muscle apparent rate constants, derived from sinusoidal analysis of the chimeric converter fibers, showed a strong positive correlation between optimal muscle oscillation frequency and myosin attachment kinetics to actin, and an inverse correlation with detachment related cross-bridge kinetics. This suggests the myosin converter alters at least two rate constants of the cross-bridge cycle with changes to attachment and power stroke related kinetics having the most influence on setting muscle oscillatory power kinetics., (Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

We report here the complete genome sequence of Streptococcus thermophilus DGCC 7710. S. thermophilus is widely used in industrial dairy production., (Copyright © 2018 Hatmaker et al.)

Purpose of Review: This review summarizes what has been learned about the interaction between skeletal muscle and bone from mouse models in which BMAL1, a core molecular clock protein has been deleted. Additionally, we highlight several genes which change following loss of BMAL1. The protein products from these genes are secreted from muscle and have a known effect on bone homeostasis., Recent Findings: Circadian rhythms have been implicated in regulating systems homeostasis through a series of transcriptional-translational feedback loops termed the molecular clock. Recently, skeletal muscle-specific disruption of the molecular clock has been shown to disrupt skeletal muscle metabolism. Additionally, loss of circadian rhythms only in adult muscle has an effect on other tissue systems including bone. Our finding that the expression of a subset of skeletal muscle-secreted proteins changes following BMAL1 knockout combined with the current knowledge of muscle-bone crosstalk suggests that skeletal muscle circadian rhythms are important for maintenance of musculoskeletal homeostasis. Future research on this topic may be important for understanding the role of the skeletal muscle molecular clock in a number of diseases such as sarcopenia and osteoporosis.

We report here on a case of ETV6-RUNX1 -positive B-cell acute lymphoblastic leukemia (B-ALL) that has acquired a BCR-ABL1 gene rearrangement as a subclonal change. The 19-year-old female patient presented with B symptoms, pancytopenia, and circulating blasts. The bone marrow aspirate was hypercellular and was infiltrated by an immature blast population that was confirmed as B-ALL by flow cytometry. Sequential fluorescent in situ hybridization was performed on the patient's leukemic cells, which were shown to contain both ETV6-RUNX1 and BCR-ABL1 gene rearrangements. The majority of nuclei (85%) showed only the ETV6-RUNX1 gene rearrangement; however, an additional 10% also showed a variant BCR-ABL1 gene rearrangement, indicating the ETV6-RUNX1 gene rearrangement was the primary change. A review of the literature has shown that acquisition of a BCR-ABL1 gene rearrangement as a secondary change in B-ALL is a very rare occurrence, and the effect it may have on prognosis is uncertain in the modern therapy age., Competing Interests: Conflict-of-interest disclosure: The authors declare no competing financial interests.

Key Points: The endogenous molecular clock in skeletal muscle is necessary for maintenance of phenotype and function. Loss of Bmal1 solely from adult skeletal muscle (iMSBmal1(-/-) ) results in reductions in specific tension, increased oxidative fibre type and increased muscle fibrosis with no change in feeding or activity. Disruption of the molecular clock in adult skeletal muscle is sufficient to induce changes in skeletal muscle similar to those seen in the Bmal1 knockout mouse (Bmal1(-/-) ), a model of advanced ageing. iMSBmal1(-/-) mice develop increased bone calcification and decreased joint collagen, which in combination with the functional changes in skeletal muscle results in altered gait. This study uncovers a fundamental role for the skeletal muscle clock in musculoskeletal homeostasis with potential implications for ageing., Abstract: Disruption of circadian rhythms in humans and rodents has implicated a fundamental role for circadian rhythms in ageing and the development of many chronic diseases including diabetes, cardiovascular disease, depression and cancer. The molecular clock mechanism underlies circadian rhythms and is defined by a transcription-translation feedback loop with Bmal1 encoding a core molecular clock transcription factor. Germline Bmal1 knockout (Bmal1 KO) mice have a shortened lifespan, show features of advanced ageing and exhibit significant weakness with decreased maximum specific tension at the whole muscle and single fibre levels. We tested the role of the molecular clock in adult skeletal muscle by generating mice that allow for the inducible skeletal muscle-specific deletion of Bmal1 (iMSBmal1). Here we show that disruption of the molecular clock, specifically in adult skeletal muscle, is associated with a muscle phenotype including reductions in specific tension, increased oxidative fibre type, and increased muscle fibrosis similar to that seen in the Bmal1 KO mouse. Remarkably, the phenotype observed in the iMSBmal1(-/-) mice was not limited to changes in muscle. Similar to the germline Bmal1 KO mice, we observed significant bone and cartilage changes throughout the body suggesting a role for the skeletal muscle molecular clock in both the skeletal muscle niche and the systemic milieu. This emerging area of circadian rhythms and the molecular clock in skeletal muscle holds the potential to provide significant insight into intrinsic mechanisms of the maintenance of muscle quality and function as well as identifying a novel crosstalk between skeletal muscle, cartilage and bone., (© 2015 The Authors. The Journal of Physiology © 2015 The Physiological Society.)

Consolidated bioprocessing (CBP) has the potential to reduce biofuel or biochemical production costs by processing cellulose hydrolysis and fermentation simultaneously without the addition of pre-manufactured cellulases. In particular, Clostridium thermocellum is a promising thermophilic CBP host because of its high cellulose decomposition rate. Here we report the engineering of C. thermocellum to produce isobutanol. Metabolic engineering for isobutanol production in C. thermocellum is hampered by enzyme toxicity during cloning, time-consuming pathway engineering procedures, and slow turnaround in production tests. In this work, we first cloned essential isobutanol pathway genes under different promoters to create various plasmid constructs in Escherichia coli. Then, these constructs were transformed and tested in C. thermocellum. Among these engineered strains, the best isobutanol producer was selected and the production conditions were optimized. We confirmed the expression of the overexpressed genes by their mRNA quantities. We also determined that both the native ketoisovalerate oxidoreductase (KOR) and the heterologous ketoisovalerate decarboxylase (KIVD) expressed were responsible for isobutanol production. We further found that the plasmid was integrated into the chromosome by single crossover. The resulting strain was stable without antibiotic selection pressure. This strain produced 5.4 g/L of isobutanol from cellulose in minimal medium at 50(o)C within 75 h, corresponding to 41% of theoretical yield., (Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.)

Background: Skeletal muscle is a major contributor to whole-body metabolism as it serves as a depot for both glucose and amino acids, and is a highly metabolically active tissue. Within skeletal muscle exists an intrinsic molecular clock mechanism that regulates the timing of physiological processes. A key function of the clock is to regulate the timing of metabolic processes to anticipate time of day changes in environmental conditions. The purpose of this study was to identify metabolic genes that are expressed in a circadian manner and determine if these genes are regulated downstream of the intrinsic molecular clock by assaying gene expression in an inducible skeletal muscle-specific Bmal1 knockout mouse model (iMS-Bmal1 (-/-) )., Methods: We used circadian statistics to analyze a publicly available, high-resolution time-course skeletal muscle expression dataset. Gene ontology analysis was utilized to identify enriched biological processes in the skeletal muscle circadian transcriptome. We generated a tamoxifen-inducible skeletal muscle-specific Bmal1 knockout mouse model and performed a time-course microarray experiment to identify gene expression changes downstream of the molecular clock. Wheel activity monitoring was used to assess circadian behavioral rhythms in iMS-Bmal1 (-/-) and control iMS-Bmal1 (+/+) mice., Results: The skeletal muscle circadian transcriptome was highly enriched for metabolic processes. Acrophase analysis of circadian metabolic genes revealed a temporal separation of genes involved in substrate utilization and storage over a 24-h period. A number of circadian metabolic genes were differentially expressed in the skeletal muscle of the iMS-Bmal1 (-/-) mice. The iMS-Bmal1 (-/-) mice displayed circadian behavioral rhythms indistinguishable from iMS-Bmal1 (+/+) mice. We also observed a gene signature indicative of a fast to slow fiber-type shift and a more oxidative skeletal muscle in the iMS-Bmal1 (-/-) model., Conclusions: These data provide evidence that the intrinsic molecular clock in skeletal muscle temporally regulates genes involved in the utilization and storage of substrates independent of circadian activity. Disruption of this mechanism caused by phase shifts (that is, social jetlag) or night eating may ultimately diminish skeletal muscle's ability to efficiently maintain metabolic homeostasis over a 24-h period.

A new technique to measure (p,n) charge-exchange reactions in inverse kinematics at intermediate energies on unstable isotopes was successfully developed and used to study the (56)Ni(p,n) reaction at 110 MeV/u. Gamow-Teller transition strengths from (56)Ni leading to (56)Cu were obtained and compared with shell-model predictions in the pf shell using the KB3G and GXPF1A interactions. The calculations with the GXPF1A interaction reproduce the experimental strength distribution much better than the calculations that employed the KB3G interaction, indicating deficiencies in the spin-orbit and proton-neutron residual potentials for the latter. The results are important for improving the description of electron-capture rates on nuclei in the iron region, which are important for modeling the late evolution of core-collapse and thermonuclear supernovae.

An alumina surface coating is demonstrated to improve electrochemical performance of MoO(3) nanoparticles as high capacity/high-volume expansion anodes for Li-ion batteries. Thin, conformal surface coatings were grown using atomic layer deposition (ALD) that relies on self-limiting surface reactions. ALD coatings were tested on both individual nanoparticles and prefabricated electrodes containing conductive additive and binder. The coated and non-coated materials were characterized using transmission electron microscopy, energy-dispersive X-ray spectroscopy, electrochemical impedance spectroscopy, and galvanostatic charge/discharge cycling. Importantly, increased stability and capacity retention was only observed when the fully fabricated electrode was coated. The alumina layer both improves the adhesion of the entire electrode, during volume expansion/contraction and protects the nanoparticle surfaces. Coating the entire electrode also allows for an important carbothermal reduction process that occurs during electrode pre-heat treatment. ALD is thus demonstrated as a novel and necessary method that may be employed to coat the tortuous network of a battery electrode.

Understanding the mechanisms that species use to succeed in new environments is vital to predicting the extent of invasive species impacts. Food quality is potentially important because it can affect population dynamics by affecting life history traits. The New Zealand mudsnail, Potamopyrgus antipodarum, is a worldwide invader. We examined how mudsnail growth rate and fecundity responded to the C:P ratio of algal food in laboratory conditions. Mudsnails fed low-P algae (C:P 1,119) grew more slowly, matured later, produced smaller offspring, and grew to a smaller adult size than snails reared on algae with high levels of P. A relatively small increase in algal C:P (203-270) significantly increased mudsnail age at maturity. We suggest that the relatively high body P requirements of mudsnails make them susceptible to allocation trade-offs between growth and reproduction under P-limited conditions. The elemental composition of algae varies greatly in nature, and over half of the rock biofilms in streams surveyed within the introduced range of mudsnails in the Greater Yellowstone Area had C:P ratios above which could potentially pose P limitation of life history traits. High growth rate and fecundity are common traits of many species that become invasive and are also associated with high-P demands. Therefore, fast-growing consumers with high P demands, such as mudsnails, are potentially more sensitive to P limitation suggesting that limitation of growth and reproduction by food quality is an important factor in understanding the resource demands of invasive species.

The first isolation of Bordetella petrii from a patient with chronic suppurative mastoiditis is reported. Molecular characterization of the isolate was performed by sequencing the small-subunit rRNA gene, the Bordetella outer-membrane protein A gene (ompA) and the RisA response regulator gene (risA). This is the first reported case of B. petrii causing suppurative mastoiditis and only the second documented case of a clinically significant B. petrii isolate.

The 9Be(32Ar, 31Ar)X reaction, leading to the 5/2+ ground state of a nucleus at the proton drip line, has a cross section of 10.4(13) mb at a beam energy of 65.1 MeV/nucleon. This translates into a spectroscopic factor that is only 24(3)% of that predicted by the many-body shell-model theory. We introduce refinements to the eikonal reaction theory used to extract the spectroscopic factor to clarify that this very strong reduction represents an effect of nuclear structure. We suggest that it reflects correlation effects linked to the high neutron separation energy (22.0 MeV) for this state., (Copyright 2004 The American Physical Society)

We measured the strength of the 0(+)(gs)-->2(+)(1) excitations in the radioactive mirror nuclei 32Ar and 32Si using the techniques of intermediate-energy Coulomb excitation for 32Ar and inelastic proton scattering in inverse kinematics for 32Si. The 32Ar measurement, taken together with previously existing Coulomb excitation data for 32Si, yields the isoscalar and isovector multipole matrix elements for the 0(+)(1)-->2(+)(1) transition between T = 2 states in the A = 32 system. The proton scattering measurement for 32Si, when combined with the Coulomb excitation data for this nucleus, yields a ratio of neutron and proton matrix elements, M(n)/M(p), for 32Si.