bluuebunny/crossref_metadata_2025 huggingface dataset:
Single Event Effect cross section calibration and application to quasi-monoenergetic and spallation facilities
Authors: Alía Rubén García , Bonaldo Stefano , Brugger Markus , Danzeca Salvatore , Ferrari Alfredo , Frost Christopher , Infantino Angelo , Iwamoto Yosuke , Mekki Julien , Theis Cris , Thornton Adam
Published: February 2018

We describe an approach to calibrate Single Event Effect (SEE)-based detectors in monoenergetic fields and apply the resulting semi-empiric responses to more general mixed-field cases in which a broad variety of particle species and energy spectra are present. The calibration of the response functions is based both on experimental proton (30–200 MeV) and neutron (5–300 MeV) data and considerations derived from Monte Carlo simulations using the FLUKA Monte Carlo code. The application environments include the quasi-monoenergetic neutrons at RCNP, the atmospheric-like VESUVIO spallation spectrum and the CHARM high-energy accelerator test facility. The agreement between the mixed-field response and that predicted through the mono-energetic calibration is within ±30% for the broad variety of cases considered and thus regarded as highly successful for mixed-field monitoring applications.
A Practical and Efficient Synthesis of (±)-Anatabine
Authors: Palmieri Alessandro , Rossi Federico , Ballini Roberto , Barboni Luciano , Allegrini Pietro
Published: February 2018

A new efficient synthesis of racemic anatabine is reported. The title target was obtained in an excellent overall yield of 70%, by a five-step synthesis, using cheap reagents and mild reaction conditions.
Smith–Lemli–Opitz Mutations in Unexplained Stillbirths
Authors: Reddy Uma , Saade George , Goldenberg Robert , Dudley Donald , Parker Corette , Thorsten Vanessa , Pinar Halit , Bukowski Radek , Hogue Carol , Silver Robert , Gibbins Karen
Published: February 2018

Objective Smith–Lemli–Opitz syndrome (SLOS) is an autosomal recessive syndrome caused by a defect in cholesterol biosynthesis with mutations in 7-dehydrocholesterol reductase (DHCR7). A total of 3% of Caucasians carry DHCR7 mutations, theoretically resulting in a homozygote frequency of 1/4000. However, SLOS occurs in only 1/20,000 to 60,000 live births. Our objective was to assess DHCR7 mutations in unexplained stillbirths.

Study Design Prospective, multicenter, population-based case–control study of all stillbirths and a representative sample of live births enrolled in five geographic areas. Cases with stillbirth due to obstetric complications, infection, or aneuploidy, and those with poor quality deoxyribonucleic acid (DNA) were excluded. DNA was extracted from placental tissue stored at –80°C, and exons 3 to 9 of the DCHR7 gene were amplified, purified, and subjected to bidirectional sequencing to identify mutations.

Results One-hundred forty four stillbirths were unexplained and had adequate DNA for analysis. Nine stillbirths of 139 (6.5%) had a single mutation in one allele in coding exons 3 to 9 of DHCR7 (Table 1). One case (0.7%) was a compound heterozygote for mutations in exons 3 to 9 of DHCR7; this fetus had no clinical or histologic features of SLOS.

Conclusion We detected SLOS mutations in only 0.7% of stillbirths. This does not support a strong association between unrecognized DHCR7 mutations and stillbirth.
Detecting Microsurgical Complications with ViOptix Tissue Oximetry in a Pediatric Myocutaneous Free Flap: Case Presentation and Literature Review
Authors: Kozusko Steven , Gbulie Uzoma
Published: February 2018

Background Microvascular compromise from arterial or venous occlusion is a common cause of free flap failure. The salvage rate following a microvascular compromise is dependent on detecting the problem early and intervening quickly.

Methods The ViOptix tissue oximeter measures tissue oxygen saturation using the near-infrared spectroscopy technology. The ViOptix device has an alarm capability to warn of potential compromise to tissue perfusion. The tissue oximetry readings are visible on the bedside monitor and are relayed to a webpage link, which is accessible on a personal computer or mobile device, allowing real-time monitoring. This article presents a case where real-time monitoring allowed almost immediate detection of inadvertent pedicle compromise allowing flap salvage by repositioning without surgical intervention.

Results In the case presented, the patient's nurse inadvertently positioned a pillow under the location of the vascular pedicle likely causing microvascular compression. The ViOptix reading dropped and for this reason the nurse contacted the Plastic Surgery team. The drop was confirmed remotely and the flap was urgently evaluated in person. Once the pillow was removed, the ViOptix readings normalized and Doppler signals strengthened in the flap.

Discussion While tissue oximetry monitoring does not by itself ensure flap survival, it provides critical information than conventional flap monitoring would allow giving the microsurgeon the opportunity to make a quicker decision. ViOptix tissue oximeters are able to detect vascular compromise even before conventional clinical symptoms are present. Alas in several cases by the time clinical symptoms develop the flap may be beyond salvage.
Theory of electromagnetic wave propagation in ferromagnetic Rashba conductor
Authors: Shibata Junya , Takeuchi Akihito , Kohno Hiroshi , Tatara Gen
Published: February 2018

We present a comprehensive study of various electromagnetic wave propagation phenomena in a ferromagnetic bulk Rashba conductor from the perspective of quantum mechanical transport. In this system, both the space inversion and time reversal symmetries are broken, as characterized by the Rashba field α and magnetization M, respectively. First, we present a general phenomenological analysis of electromagnetic wave propagation in media with broken space inversion and time reversal symmetries based on the dielectric tensor. The dependence of the dielectric tensor on the wave vector q and M is retained to first order. Then, we calculate the microscopic electromagnetic response of the current and spin of conduction electrons subjected to α and M, based on linear response theory and the Green's function method; the results are used to study the system optical properties. First, it is found that a large α enhances the anisotropic properties of the system and enlarges the frequency range in which the electromagnetic waves have hyperbolic dispersion surfaces and exhibit unusual propagations known as negative refraction and backward waves. Second, we consider the electromagnetic cross-correlation effects (direct and inverse Edelstein effects) on the wave propagation. These effects stem from the lack of space inversion symmetry and yield q-linear off-diagonal components in the dielectric tensor. This induces a Rashba-induced birefringence, in which the polarization vector rotates around the vector (α×q). In the presence of M, which breaks time reversal symmetry, there arises an anomalous Hall effect and the dielectric tensor acquires off-diagonal components linear in M. For α∥M, these components yield the Faraday effect for the Faraday configuration q∥M and the Cotton-Mouton effect for the Voigt configuration (q⊥M). When α and M are noncollinear, M- and q-induced optical phenomena are possible, which include nonreciprocal directional dichroism in the Voigt configuration. In these nonreciprocal optical phenomena, a “toroidal moment,” α×M, and a “quadrupole moment,” αiMj+Miαj, play central roles. These phenomena are strongly enhanced at the spin-split transition edge in the electron band.
Development of a golf‐specific load monitoring tool: Content validity and feasibility
Authors: Williams Scott B. , Gastin Paul B. , Saw Anna E. , Robertson Sam
Published: February 2018

Athletes often record details of their training and competitions, supported by information such as environmental conditions, travel, as well as how they felt. However, it is not known how prevalent these practices are in golfers, or how valuable this process is perceived. The purpose of this study was to develop a golf‐specific load monitoring tool (GLMT), and establish the content validity and feasibility of this tool amongst high‐level golfers. In the first phase of development, 21 experts were surveyed to determine the suitability of items for inclusion in the GLMT. Of the 36 items, 21 received >78% agreement, a requirement to establish content validity and for inclusion in the GLMT. Total duration was the preferred metric for golf‐specific activities, whilst rating of perceived exertion (RPE) was preferred for measuring physical training. In the second phase, feasibility of the tool was assessed by surveying 13 high‐level male golfers following 28‐days of daily GLMT use. All items included in the GLMT were deemed feasible to record, with all players participating in the feasibility study providing high to very high ratings. Golfers responded that they would consider using a load monitoring tool of this nature long term, provided it can be completed in less than five minutes per day.
In‐season changes in ventricular morphology and systolic function in adolescent female athletes
Authors: Watson Andrew M. , Coutinho Carol , Haraldsdottir Kristin , Brickson Stacey , Dunn Warren , Eldridge Marlowe
Published: February 2018

Purpose: To evaluate the influence of physical maturity on the changes in ventricular morphology and function with sport training in female youth athletes.

Methods: Thirty‐two female athletes (age 13–18 years) underwent height and weight measurement and 2‐D echocardiographic evaluation immediately prior to, and following, a 20‐week soccer season. Pre‐ and post‐season left ventricular end‐diastolic diameter (LVEDD), end‐diastolic volume (LVEDV), ejection fraction (LVEF), stroke volume (LVSV), mass (LVM), and posterior wall thickness (LVPWT), right ventricular end‐diastolic diameter (RVEDD), end‐diastolic area (RVEDA), and fractional area change (RVFAC), and interventricular septal thickness (IVST) were compared. In‐season change in each variable was compared across pre‐season hours of vigorous physical activity (0–1, 2–3, >3 hours).

Results: Significant increases were identified in LVEDV (51.3 ± 10.4 v 56.4 ± 9.6 ml/m2, p = 0.001) and RVEDA (10.5 ± 1.9 v 11.3 ± 2.5 cm2/m2, p = 0.040), but not LVEDD, LVM, LVPWT, LVSV, RVEDD, RVEDA, RVFAC, or IVST (p > 0.05 for all). In‐season changes in echocardiographic variables did not differ across hours of pre‐season vigorous physical activity (p > 0.05 for all).

Conclusion: Among female adolescent soccer players, in‐season training elicits changes in resting ventricular volume, but not wall thickness or systolic function. These adaptations do not appear to be influenced by pre‐season physical activity level.
Defusing inflammasomes
Authors: Sandstrom Andrew , Vance Russell E.
Published: February 2018

In this issue of JEM, Boucher et al. (https://doi.org/10.1084/jem.20172222) report isolation of active caspase-1 from macrophages after inflammasome activation. Surprisingly, they find that caspase-1 is quickly inactivated upon autoproteolytic processing.
Quantum return probability of a system of N non-interacting lattice fermions
Authors: Krapivsky P L , Luck J M , Mallick K
Published: February 2018

We consider N non-interacting fermions performing continuous-time quantum walks on a one-dimensional lattice. The system is launched from a most compact configuration where the fermions occupy neighboring sites. We calculate exactly the quantum return probability (sometimes referred to as the Loschmidt echo) of observing the very same compact state at a later time t. Remarkably, this probability depends on the parity of the fermion number—it decays as a power of time for even N, while for odd N it exhibits periodic oscillations modulated by a decaying power law. The exponent also slightly depends on the parity of N, and is roughly twice smaller than what it would be in the continuum limit. We also consider the same problem, and obtain similar results, in the presence of an impenetrable wall at the origin constraining the particles to remain on the positive half-line. We derive closed-form expressions for the amplitudes of the power-law decay of the return probability in all cases. The key point in the derivation is the use of Mehta integrals, which are limiting cases of the Selberg integral.
Long-read sequencing across theC9orf72‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease
Authors: Ebbert Mark T. W. , Farrugia Stefan , Sens Jonathon , Jansen-West Karen , Gendron Tania F. , Prudencio Mercedes , McLaughlin lan J. , Bowman Brett , Seetin Matthew , DeJesus-Hernandez Mariely , Jackson Jazmyne , Brown Patricia H , Dickson Dennis W. , van Blitterswijk Marka , Rademakers Rosa , Petrucelli Leonard , Fryer John D.
Published: February 2018

Background:Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like theC9orf72‘GGGGCC’ (G4C2) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences’ (PacBio) and Oxford Nanopore Technologies’ (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing G4C2repeat expansion. We also report the first long-read sequencing data characterizing theC9orf72G4C2repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9.

Results:Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinlON was a challenge for whole-genome sequencing; we were unable to attain reads covering the humanC9orf72repeat expansion using 15 flow cells. We obtained 8x coverage across theC9orf72locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained >800x coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual’s repeat region was >99% G4C2content, though we cannot rule out small interruptions.

Conclusions:Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies inC9orf72expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-G4C2content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.
Transcranial focused ultrasound neuromodulation of the human primary motor cortex
Authors: Legon Wynn , Bansal Priya , Tyshynsky Roman , Ai Leo , Mueller Jerel K.
Published: February 2018

Transcranial focused ultrasound is a form of non-invasive neuromodulation that uses acoustic energy to affect neuronal excitability. The effect of ultrasound on human motor cortical excitability is currently unknown. We apply ultrasound to the primary motor cortex in humans using a novel transcranial ultrasound and magnetic stimulation (TUMS) paradigm that allows for concurrent and concentric ultrasound stimulation with transcranial magnetic stimulation (TMS). This allows for non-invasive inspection of the effect of ultrasound on motor neuronal excitability using the motor evoked potential (MEP) generated by TMS. We test the effect of ultrasound on single pulse MEP recruitment curves and paired pulse protocols including short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). We also test the longevity of the effect and the effect of ultrasound on the cortical silent period in a small sub-sample of participants. In addition, we test the effect of ultrasound to motor cortex on a stimulus response reaction time task. Results show ultrasound inhibits the amplitude of single-pulse MEPs and attenuates intracortical facilitation but does not affect intracortical inhibition. Early evidence suggests that ultrasound does not affect cortical silent period duration and that the duration of inhibition may be related to the duration of stimulation. Finally, ultrasound reduces reaction time on a simple stimulus response task. This is the first report of the effect of ultrasound on human motor cortical excitability and motor behavior and confirms previous results in the somatosensory cortex that ultrasound results in effective neuronal inhibition that confers a performance advantage.
Structure of APP-C991-99and Implications for Role of Extra-Membrane Domains in Function and Oligomerization
Authors: Pantelopulos George A. , Straub John E. , Thirumalai D. , Sugita Yuji
Published: February 2018

The 99 amino acid C-terminal fragment of Amyloid Precursor Protein APP-C99 (C99) is cleaved by γ-secretase to form Aβ peptide, which plays a critical role in the etiology of Alzheimer’s Disease (AD). The structure of C99 consists of a single transmembrane domain flanked by intra and intercellular domains. While the structure of the transmembrane domain has been well characterized, little is known about the structure of the flanking domains and their role in C99 processing by γ-secretase. To gain insight into the structure of full-length C99, REMD simulations were performed for monomeric C99 in model membranes of varying thickness. We find equilibrium ensembles of C99 from simulation agree with experimentally-inferred residue insertion depths and protein backbone chemical shifts. In thin membranes, the transmembrane domain structure is correlated with extra-membrane structural states. Mean and variance of the transmembrane and G37G38hinge angles are found to increase with thinning membrane. The N-terminus of C99 forms β-strands that may seed aggregation of Aβ on the membrane surface, promoting amyloid formation. The N-terminus, which forms α-helices that interact with the nicastrin domain of γ-secretase. The C-terminus of C99 becomes more α-helical as the membrane thickens, forming structures that may be suitable for binding by cytoplasmic proteins, while C-terminal residues essential to cytotoxic function become α-helical as the membrane thins. The heterogeneous but discrete extra-membrane domain states analyzed here open the path to new investigations of the role of C99 structure and membrane in amyloidogenesis.
Herpes ICP8 protein stimulates homologous recombination in human cells
Authors: Valledor Melvys , Myers Richard S. , Schiller Paul C.
Published: February 2018

Recombineering has transformed functional genomic analysis. Genome modification by recombineering using the phage lambda Red SynExo homologous recombination proteins Beta inEscherichia colihas approached 100% efficiency. While highly efficient inE. coli, recombineering using the Red SynExo in other organisms declines in efficiency roughly correlating with phylogenetic distance fromE. coli. SynExo recombinases are common to double-stranded DNA viruses infecting a variety of organisms, including humans. Human Herpes virus Type 1 (HHV1) encodes a SynExo comprised of ICP8 synaptase and UL12 exonuclease. In a previous study, the Herpes SynExo was reconstitutedin vitroand shown to catalyze a model recombination reaction. Here we describe stimulation of gene targeting to edit a novel fluorescent protein gene in the human genome using ICP8 and compared its efficiency to that of a “humanized” version of Beta protein from phage λ. ICP8 significantly enhanced gene targeting rates in HEK 293 T cells while Beta was not only unable to catalyze recombineering but inhibited gene targeting using endogenous recombination functions, despite both synaptases being well-expressed and localized to the nucleus. This proof of concept encourages developing species-specific SynExo recombinases for genome engineering.

SIGNIFICANCE

Genome modification by recombineering using SynExo viral recombination proteins has transformed functional genomic analysis in bacteria. Single-stranded DNA (ssDNA) recombineering approaches 100% efficiency inE. coliusing Beta protein from bacteriophage lambda, but recombineering has not been extended to eukaryotic genomes. Efficient recombineering requires SynExos that co-evolved with a viral host, however SynExos are common to viruses infecting a variety of organisms, including humans. The ICP8 protein of Human Herpes virus Type 1 is a SynExo protein similar to Beta. In this pioneering study, Herpes ICP8 stimulated gene targeting in a human genome by homologous recombination while the bacterial virus Beta protein inhibited recombination in human cells. This is the first demonstration of host-specific recombineering in human cells using a human viral SynExo protein.
Nuclear localization of TORC1 and cellular co-localization of TORC1 and c-Fos in the visceral neuraxis after systemic LiCl injection
Authors: Kimbrough Adam , Houpt Thomas A.
Published: February 2018

Cyclic–AMP response element binding protein (CREB)-mediated gene expression is critical for the processing of visceral information, including learning about visceral stimuli (e.g. conditioned taste aversion). However, CREB requires additional co-factors to induce gene expression, including transducer of regulated CREB-activity (TORC). The nuclear localization of TORC1 has not been examined previously in the visceral neuraxis. c-Fos, a widely-used marker of activity, is induced by visceral stimulation. If CREB-mediated gene transcription is necessary for c-Fos induction in the visceral neuraxis after systemic LiCl injection, then TORC should be active following stimulation, and co-localized with c-Fos in activated neurons. We examined nuclear (activated) TORC1 in the visceral neuraxis at 30, 60, and 180 minutes after LiCl, as compared to c-Fos induction. Consistent with previous studies we found increases in c-Fos 60 min after LiCl in all regions. Nuclear TORC1 was also increased in the area postrema, NTS, and paraventricular nucleus after LiCl. Surprisingly, in the central amygdala, TORC1 was deactivated after LiCl, such that almost all TORC1 was cytoplasmic, whereas control rats had almost all nuclear TORC1. Fluorescent double-labeling of TORC1 and c-Fos after LiCl found that cellular co-localization of c-Fos and TORC1 was very low across the visceral neuraxis. Nuclear TORC1 expression reveals a population of cells in the visceral neuraxis, independent of c-Fos-positive cells, that are regulated by LiCl. TORC1, and in turn CREB-mediated gene transcription, may not be necessary for c-Fos induction in the visceral neuraxis after LiCl.
Sensations from a single M-cone depend on the activity of surrounding S-cones
Authors: Schmidt Brian P. , Sabesan Ramkumar , Tuten William S. , Neitz Jay , Roorda Austin
Published: February 2018

Color vision requires the activity of cone photoreceptors to be compared in post-receptoral circuitry. Decades of psychophysical measurements have quantified the nature of these comparative interactions on a coarse scale. How such findings generalize to a cellular scale remains unclear. To answer that question, we quantified the influence of surrounding light on the appearance of spots targeted to individual cones. The eye’s aberrations were corrected with adaptive optics and retinal position was precisely tracked in real-time to compensate for natural movement. Subjects reported the color appearance of each spot. A majority of L-and M-cones consistently gave rise to the sensation of white, while a smaller group repeatedly elicited hue sensations. When blue sensations were reported they were more likely mediated by M- than L-cones. Blue sensations were elicited from M-cones against a short-wavelength light that preferentially elevated the quantal catch in surrounding S-cones, while stimulation of the same cones against a white background elicited green sensations. In one of two subjects, proximity to S-cones increased the probability of blue reports when M-cones were probed. We propose that M-cone increments excited both green and blue opponent pathways, but the relative activity of neighboring cones favored one pathway over the other.
RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis
Authors: Chen Xin , Ma Anjun , McDermaid Adam , Zhang Hanyuan , Liu Chao , Cao Huansheng , Ma Qin
Published: February 2018

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, RECTA, for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA onLactococcus lactisMG1363 data to elucidate acid-response regulons.Lactococcus lactisis one of the most important Gram-positive lactic acid-producing bacteria, widely used in food industry and has been proved to have advantages in oral delivery of drug and vaccine. The pipeline carries out differential gene expression, gene co-expression analysis,cis-regulatory motif finding, and comparative genomics to predict and validate regulons related to acid stress response. A total of 51 regulonswere identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response with (i) known transcriptional factors in MEME suite database successfully mapped inLactococcus lactisMG1363; and (ii) differentially expressed genes between pH values of 6.5 (control) and 5.1 (treatment). Validated by 36 literature confirmed acid stress response related proteins and genes, 33 genes inLactococcus lactisMG1363 were found having orthologous genes using BLAST, associated to six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A,rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated to acid stress. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation. The predicted response pathways could serve as promising candidates for better acid tolerance engineering inLactococcus lactis. RECTA has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.
Growth potential ofListeria monocytogenesin twelve different types of RTE salads: impact of food matrix, storage temperature and shelf life
Authors: Ziegler Matthias , Kent David , Stephan Roger , Guldimann Claudia
Published: February 2018

Listeriosis is a food borne disease associated with high hospitalization and fatality rates; in 2014, EU member states reported 2194 cases with 98.9% hospitalization rates and 210 fatalities. Proper risk analysis and the development of effective food safety strategies critically depend on the knowledge of the growth characteristics ofL. monocytogeneson the product in question. Ready-to-eat (RTE) salads present a challenge in this context due to the absence of a heat treatment step before consumption and the interaction of pathogens with the plant microbial microbiota. This study provides challenge-test based data of the growth characteristics ofL. monocytogeneson twelve RTE salads. The food matrix, storage time and storage temperature were factors with a significant impact on the growth ofL. monocytogenes. While most tested salads permitted a significant increase ofL. monocytogenesin at least one of the tested conditions, no growth was observed on celeriac, carrot and corn salad products. There was a considerable increase in growth at 8 °C compared to 5 °C. Our data indicate that the reduction of the storage temperature at retail level to 5 °C and product shelf life could help mitigate the risk ofL. monocytogenesin RTE salads.
Regulation of ATM and ATR by Smarcal1 and BRG1
Authors: Sethy Ramesh , Rakesh Radhakrishnan , Patne Ketki , Arya Vijendra , Sharma Tapan , Haokip Dominic Thangminlen , Kumari Reshma , Muthuswami Rohini
Published: February 2018

The G2/M checkpoint is activated on DNA damage by the ATM and ATR kinases that are regulated by post-translational modifications. In this paper, the transcriptional co-regulation of ATM and ATR by SMARCAL1 and BRG1, both members of the ATP-dependent chromatin remodeling protein family, is described. SMARCAL1 and BRG1 co-localize on the promoters of ATM and ATR; downregulation of SMARCAL1/BRG1 results in transcriptional repression of ATM/ATR and therefore, overriding of the G2/M checkpoint leading to mitotic abnormalities. On doxorubicin-induced DNA damage, SMARCAL1 and BRG1 are upregulated and in turn, upregulate the expression of ATM/ATR.

Phosphorylation of ATM/ATR is needed for the transcriptional upregulation of SMARCAL1 and BRG1, and therefore, of ATM and ATR on DNA damage. The regulation of ATM/ATR is rendered non-functional if SMARCAL1 and/or BRG1 are absent or if the two proteins are mutated such that they are unable to hydrolyze ATP, as in for example in Schimke Immuno-Osseous Dysplasia and Coffin-Siris Syndrome. Thus, an intricate transcriptional regulation of DNA damage response genes mediated by SMARCAL1 and BRG1 is present in mammalian cells.
GWAS identifies 10 loci for objectively-measured physical activity and sleep with causal roles in cardiometabolic disease.
Authors: Doherty Aiden , Smith-Bryne Karl , Ferreira Teresa , Holmes Michael V , Holmes Chris , Pulit Sara L , Lindgren Cecilia M
Published: February 2018

Physical activity and sleep disorders are established risk factors for many diseases, but their etiology is poorly understood, partly due to a reliance on self-reported evidence. Here we report a genome-wide association study (GWAS) of wearable-defined and machine-learned physical activity and sleep phenotypes in 91,112 UK Biobank participants, and self-reported physical activity in 351,154 UK Biobank participants. While the self-reported activity analysis resulted in no significant (p<5x10-9) loci, the analysis of objectively-measured traits identified 10 loci, 6 of which are novel. These 10 loci account for 0.05% of activity and 0.33% of sleep phenotype variation, but genome-wide estimates suggest that common variation accounts for ~12% of phenotypic variation, indicating high polygenicity. Heritability was higher in women than in men for overall activity (Δh2 = 4%, p=6.3x10-5), moderate intensity activity (6%, p=6.7x10-8), and walking (5%, p=2.6x10-6). Heritability partitioning, enrichment and pathway analyses all indicate the central nervous system plays a role in activity behaviours. Mendelian randomization in publicly available GWAS data and in 278,367 UK Biobank participants, who were not included in our discovery analyses, suggest that overall activity might be causally related to lowering body fat percentage (beta per SD higher overall activity: -0.44, SE=0.047, p=2.70x10-21) and systolic blood pressure (beta per SD: -0.71, SE=0.125, p=1.38x10-8). Our current results advocate the value of physical activity for the reduction of adiposity and blood pressure.
Environmental DNA reveals the structure of phytoplankton assemblages along a 2900-km transect in the Mississippi River
Authors: Craine Joseph M. , Henson Michael W. , Thrash J. Cameron , Hanssen Jordan , Spooner Greg , Fleming Patrick , Pukonen Markus , Stahr Frederick , Spaulding Sarah , Fierer Noah
Published: February 2018

The environmental health of aquatic ecosystems is critical to society, yet traditional assessments of water quality have limited utility for some bodies of water such as large rivers. Sequencing of environmental DNA (eDNA) has the potential to complement if not replace traditional sampling of biotic assemblages for the purposes of reconstructing aquatic assemblages and, by proxy, assessing water quality. Despite this potential, there has been little testing of the ability of eDNA to reconstruct assemblages and their absolute and relative utility to infer water quality metrics. Here, we reconstruct phytoplankton communities by amplifying and sequencing DNA from a portion of the 23S rRNA region from filtered water samples along a 2900-km transect in the Mississippi River. Across the entire length, diatoms dominated the assemblage (72.6%) followed by cryptophytes (8.7%) and cyanobacteria (7.0%). There were no general trends in the abundances of these major taxa along the length of the river, but individual taxon abundance peaked in different regions. For example, the abundance of taxa genetically similar to Melosira tropica peaked at approximately 60% of all reads 2750 km upstream from the Gulf of Mexico, while taxa similar to Skeletonema marinoi began to increase below the confluence with the Missouri River until it reached approximately 30% of the reads at the Gulf of Mexico. There were four main clusters of samples based on phytoplankton abundance, two above the confluence with the Missouri and two below. Phytoplankton abundance was a poor predictor of NH4+ concentrations in the water, but predicted 61% and 80% of the variation in observed NO3-and PO43-concentrations, respectively. Phytoplankton richness increased with increasing distance along the river, but was best explained by phosphate concentrations and water clarity. Along the Mississippi transect, there was similar structure to phytoplankton and bacterial assemblages, indicating that the two sets of organisms are responding to similar environmental factors. In all, the research here demonstrates the potential utility of metabarcoding for reconstructing aquatic assemblages, which might aid in conducting water quality assessments.
Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogenTrichophyton rubrum
Authors: Persinoti Gabriela F. , Martinez Diego A. , Li Wenjun , Döğen Aylin , Billmyre R. Blake , Averette Anna , Goldberg Jonathan M. , Shea Terrance , Young Sarah , Zeng Qiandong , Oliver Brian G. , Barton Richard , Metin Banu , Hilmioğlu-Polat Süleyha , Ilkit Macit , Gräser Yvonne , Martinez-Rossi Nilce M. , White Theodore C. , Heitman Joseph , Cuomo Christina A.
Published: February 2018

Dermatophytes include fungal species that infect humans, as well as those which also infect other animals or only grow in the environment. The dermatophyte speciesTrichophyton rubrumis a frequent cause of skin infection in immunocompetent individuals. While members of theT. rubrumspecies complex have been further categorized based on various morphologies, the population structure and ability to undergo sexual reproduction are not well understood. In this study, we analyze a large set ofT. rubrumandTrichophyton interdigitaleisolates to examine mating types, evidence of mating, and genetic variation. We find that nearly all isolates ofT. rubrumare of a single mating type, and that incubation withT. rubrummorphotypemegniniiisolates of the other mating type failed to induce sexual development. While the region around the mating type locus is characterized by a higher frequency of SNPs compared to other genomic regions, we find that the population is remarkably clonal, with highly conserved gene content, low levels of variation, and little evidence of recombination These results support a model of recent transition to asexual growth when this species specialized to growth on human hosts.

Data access: Genome sequence data is available in NCBI under the Umbrella BioProject PRJNA186851.
Stronger connectivity of the resident gut microbiome lends resistance to invading bacteria
Authors: Herren Cristina M. , Baym Michael
Published: February 2018

Bacterial infection in the gut is often due to successful invasion of the host microbiome by an introduced pathogen. Ecological theory indicates that resident community members and their interactions should be strong determinants of whether an invading taxon can persist in a community. In the context of the gut microbiome, this suggests colonization resistance against newly introduced bacteria should depend on the instantaneous bacterial community composition within the gut and interactions between these constituent members. Here we develop a mathematical model of how metabolite-dependent biotic interactions between resident bacteria mediate invasion, and find that stronger biotic connectivity from metabolite cross-feeding and competition increases colonization resistance. We then introduce a statistical method for identifying invasive taxa in the human gut, and show empirically that greater connectivity of the resident gut microbiome is related to increased resistance to invading bacteria. Finally, we examined patient outcomes after fecal microbiota transplant (FMT) for recurring Clostridium difficile infection. Patients with lower connectivity of the gut microbiome after treatment were more likely to relapse, experiencing a later infection. Thus, simulation models and data from human subjects support the hypothesis that stronger interactions between bacteria in the gut repel invaders. These results demonstrate how ecological invasion theory can be applied to the gut microbiome, which might inform targeted microbiome manipulations and interventions. More broadly, this study provides evidence that low connectivity in gut microbial communities is a hallmark of community instability and susceptibility to invasion.
Removing Contaminants from Metagenomic Databases
Authors: Lu Jennifer , Salzberg Steven L.
Published: February 2018

Metagenomic sequencing of patient samples is a very promising method for the diagnosis of human infections. Sequencing has the ability to capture all the DNA or RNA from pathogenic organisms in a human sample. However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison. Thousands of genomes are now available, and as these numbers grow, the power of metagenomic sequencing for diagnosis should increase. However, recent studies have exposed the presence of contamination in published genomes, which when used for diagnosis increases the risk of falsely identifying the wrong pathogen.

To address this problem, we have developed a bioinformatics system for eliminating contamination as well as low-complexity genomic sequences in the draft genomes of eukaryotic pathogens. We applied this software to identify and remove human, bacterial, archaeal, and viral sequences present in a comprehensive database of all sequenced eukaryotic pathogen genomes. We also removed low-complexity genomic sequences, another source of false positives. Using this pipeline, we have produced a database of “clean” eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools. We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction in false positives.
Transcriptome and metabolome analysis provide insights into root and root released organic anion responses to phosphorus deficiency in oat
Authors: Wang Yanliang , Lysøe Erik , Armarego-Marriott Tegan , Erban Alexander , Paruch Lisa , van Eerde Andre , Bock Ralph , Liu-Clarke Jihong
Published: February 2018

Root and root-released organic anions play important roles in uptake of phosphorus (P), an essential macronutrient for food production. Oat, ranking sixth in the world’s cereal production, contains valuable nutritional compounds and can withstand poor soil conditions. The aim of this research was to investigate root transcriptional and metabolic responses of oat grown under P-deficient and P-sufficient conditions. We conducted a hydroponic experiment and measured root morphology, organic anions exudation, and analysed changes in the transcriptome and metabolome, to understand oat root adaptation to P deficiency. We found that oat roots showed enhanced citrate and malate exudation after four weeks of P-deficiency. After 10 days of P-deficiency, we identified 9371 differentially expressed transcripts with a two-fold or greater change (p < 0.05): forty-eight sequences predicted to be involved in organic anion biosynthesis and efflux were consistently up-regulated; twenty-four up-regulated transcripts in oat were also found up-regulated upon P starvation in rice and wheat under similar conditions. Phosphorylated metabolites (i.e. glucose-6-phosphate, myo-inositol-phosphate) reduced dramatically, while citrate and malate, some sugars and amino acids increased slightly in P-deficient oat roots. Our data provide new insights into the root responses to P deficiency and root-released organic anions in oat.

Highlight

We found oat- a monocot food crop, showed high exudation rate of citrate under phosphorus deficiency; root transcriptome and metabolome were then investigated to understand oat adaptation to P deficiency.
Genotypic and phenotypic diversity within the neonatal HSV-2 population
Authors: Akhtar Lisa N. , Bowen Christopher D. , Renner Daniel W. , Pandey Utsav , Della Fera Ashley N. , Kimberlin David W. , Prichard Mark N. , Whitley Richard J. , Weitzman Matthew D. , Szpara Moriah L.
Published: February 2018

More than 14,000 neonates are infected with herpes simplex virus (HSV) annually. Approximately half display manifestations limited to the skin, eyes, or mouth (SEM disease). The rest develop invasive infections that spread to the central nervous system (CNS disease or encephalitis) or systemically (disseminated disease). Invasive HSV disease is associated with significant morbidity and mortality, but viral and host factors that predispose neonates to these forms are unknown. To define viral diversity within the infected neonatal population, we evaluated ten HSV-2 isolates from newborns with a range of clinical presentations. To assess viral fitness independent of host immune factors, we measured viral growth characteristics in cultured cells and found diversein vitrophenotypes. Isolates from neonates with CNS disease were associated with larger plaque size and enhanced spread, with isolates from cerebrospinal fluid (CSF) exhibiting the most robust growth. We sequenced complete viral genomes of all ten neonatal viruses, providing new insights into HSV-2 genomic diversity in this clinical setting. We found extensive inter-host and intra-host genomic diversity throughout the viral genome, including amino acid differences in more than 90% of the viral proteome. The genes encoding glycoprotein G (gG, US4), gI (US7), gK (UL53), and viral proteins UL8, UL20, UL24, and US2 contained variants that were found in association with CNS isolates. Many of these viral proteins are known to contribute to cell spread and neurovirulence in mouse models of CNS disease. This study represents the first application of comparative pathogen genomics to neonatal HSV disease.

Importance

Herpes simplex virus (HSV) causes invasive disease in half of infected neonates, resulting in significant mortality and permanent cognitive morbidity. The factors that contribute to invasive disease are not understood. This study reveals diversity among HSV isolates from infected neonates, and makes the first associations between viral genetic variations and clinical disease manifestations. We found that viruses isolated from newborns with encephalitis show enhanced spread in culture. These viruses contain protein-coding variations not found in viruses causing non-invasive disease. Many of these variations are found in proteins known to impact neurovirulence and viral spread between cells. This work advances our understanding of HSV diversity in the neonatal population and how it may impact disease outcome.
Accelerated brain aging towards transcriptional inversion in a zebrafish model of familial Alzheimer’s disease
Authors: Hin Nhi , Newman Morgan , Kaslin Jan , Douek Alon M. , Lumsden Amanda , Zhou Xin-Fu , Ludington Alastair , Adelson David L. , Pederson Stephen , Lardelli Michael
Published: February 2018

Alzheimer’s disease (AD) develops silently over decades. We cannot easily access and analyse pre-symptomatic brains, so the earliest molecular changes that initiate AD remain unclear. Previously, we demonstrated that the genes mutated in early-onset, dominantly-inherited familial forms of AD (fAD) are evolving particularly rapidly in mice and rats. Fortunately, some non-mammalian vertebrates such as the zebrafish preserve fAD-relevant transcript isoforms of the PRESENILIN (PSEN1 and PSEN2) genes that these rodents have lost. Zebrafish are powerful vertebrate genetic models for many human diseases, but no genetic model of fAD in zebrafish currently exists. We edited the zebrafish genome to model the unique, protein-truncating fAD mutation of human PSEN2, K115fs. Analysing the brain transcriptome and proteome of young (6-month-old) and aged, infertile (24-month-old) wild type and heterozygous fAD-like mutant female sibling zebrafish supports accelerated brain aging and increased glucocorticoid signalling in young fAD-like fish, leading to a transcriptional ‘inversion’ into glucocorticoid resistance and vast changes in biological pathways in aged, infertile fAD-like fish. Notably, one of these changes involving microglia-associated immune responses regulated by the ETS transcription factor family is preserved between our zebrafish fAD model and human early-onset AD. Importantly, these changes occur before obvious histopathology and likely in the absence of Aβ. Our results support the contributions of early metabolic and oxidative stresses to immune and stress responses favouring AD pathogenesis and highlight the value of our fAD-like zebrafish genetic model for elucidating early changes in the brain that promote AD pathogenesis. The success of our approach has important implications for future modelling of AD.
A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078
Authors: Dingle Kate E. , Didelot Xavier , Quan T. Phuong , Eyre David W. , Stoesser Nicole , Marwick Charis A. , Coia John , Brown Derek , Buchanan Sarah , Ijaz Umer Z. , Goswami Cosmika , Douce Gill , Fawley Warren N. , Wilcox Mark H. , Peto Timothy E.A. , Walker A. Sarah , Crook Derrick W.
Published: February 2018

Farm animals have been identified as reservoirs of Clostridium difficile PCR-ribotype 078 (RT078). Since 2005, the incidence of human clinical cases (frequently severe), with this genotype has increased. We aimed to understand this change, by studying the recent evolutionary history of RT078. Phylogenetic analysis of international genomes (isolates from 2006–2014) revealed several recent clonal expansions. A common ancestor of each expansion had independently acquired different alleles of the tetracycline resistance gene tetM. Consequently, an unusually high proportion of RT078 genomes were tetM positive (76.5%). Additional tetracycline resistance determinants were also identified, some for the first time in C. difficile (efflux pump tet40). Each tetM-clonal expansion lacked geographic structure, indicating rapid international spread. Resistance determinants for C. difficile-infection-triggering antimicrobials including fluoroquinolones and clindamycin were comparatively rare in RT078. Tetracyclines are used intensively in agriculture; this selective pressure, plus rapid spread via the food-chain may explain the increased RT078 prevalence in humans.