bluuebunny/crossref_metadata_2025 huggingface dataset:
Maternal influences on beef calf rumen microbiome in the first 4 wk of life
Authors: Powell S , Cunningham H C , Austin K J , Cammack K M
Published: September 2018

The preruminant microbiome has the potential to set the stage for later life feed efficiency and is critical to proper development within the rumen. We hypothesized that the rumen microbiome is established at or near birth and is subject to maternal influences that can influence preruminant and postruminant microbial profiles. Our objective was to determine how mode of delivery and rearing affected the development of the rumen microbiome. Bred mature Charolais cows were randomly allocated to one of the three treatment groups: control (CON; n = 8), bottle reared (BOT; n = 8), and caesarian section (CSET; n = 8), where CON was vaginal birth and raised by their dam; BOT was vaginal birth, then removed 24-h post-parturition, and raised on commercial milk replacer; and CSET was born via caesarian section and raised by their respective dams. Calf rumen fluid was collected from calves at 1, 3, and 28 d of age via oral lavage and metagenomic shotgun sequencing was performed using the Illumina NextSeq 500 platform. Sequence data were analyzed utilizing Metataxa2 for taxonomic assignment followed by QIIME to determine α- and β-diversity differences. A total of 1,113 taxa had differential abundance when comparing day while 66 taxa had differential abundance across treatment groups. There were no differences across treatment group richness (P > 0.05), but day 28 was significantly more rich (P = 0.003) compared with days 1 and 3 with no difference between days 1 and 3 (P = 0.58). No differences in β-diversity were detected across treatment group with the exception of greater variance in the BOT and CSET compared with the CON (P = 0.048). Microbial profiles of day 1 are more similar to each other than day 3 or 28 (P = 0.03); day 3 is more similar to each other than day 1 or 28 (P = 0.03); and day 28 is more similar to each other than day 1 or 3 (P = 0.03). These data suggest that while treatment group did not have a large impact on microbial diversity, several specific taxa were affected by treatment group. Day affects the microbial diversity both within and among samples. Understanding how these profiles shift with age is critical to understanding key intervention periods for optimal alteration of the microbiome.
Crude glycerin alters beef cow ruminal fluid degradability of nutrients in vitro
Authors: Pillmore S L , Catey M M , Mercier C M , Lopez F A , Klump L T , Muro B J , Carey R E , Oosthuysen E R , Scholljegerdes E J , Löest C A
Published: September 2018

Crude glycerin (GLY) is used as an energy supplement for cattle and has been shown to increase propionate and decrease acetate concentrations in the rumen. Glycerin also decreases ruminal NH3, and therefore, we hypothesized that GLY in rumen fluid would decrease protein degradability of feedstuffs. The objective was to evaluate the effect of GLY in bovine rumen fluid on extent of protein degradability of alfalfa hay (ALF), dried distiller’s grains (DDG), and soybean meal (SBM). The study was conducted using an in vitro incubator with four incubation jars. Each incubation jar contained 18 filter bags with 0.5 g of ground feed sample (six bags contained ALF, six contained DDG, and six contained SBM), six blank bags, 1,600 mL of buffer solution, 400-mL rumen fluid (collected from two ruminally cannulated cows), and one of the two treatments. Treatments were 12.7 g of deionized water (−GLY) or 12.7 g of GLY (+GLY) added to the 2-liter contents of each jar. Incubation jars were purged with CO2 and allowed to incubate at 39°C for 48 h. The 48-h incubation period was repeated for a total of three runs (the study was a randomized complete block design). Fluid samples from incubation jars were collected at 0 and 48 h into 25-mL vials for measurement of pH and analysis of VFA and NH3. At the end of the 48-h incubation period, filter bags containing feed samples were collected for determination of DM, NDF, and CP disappearance. The pH and NH3 concentrations of the contents of jars were lower (P ≤ 0.01) and total VFA concentrations were greater (P < 0.01) for +GLY than −GLY after 48 h of incubation. Molar percentages of acetate, isobutyrate, and isovalerate were lower (P < 0.01) and molar percentages of propionate and valerate were greater (P ≤ 0.02), resulting in a lower (P < 0.01) acetate-to-propionate ratio for +GLY compared with −GLY after the 48-h incubation period. A GLY × feed interaction (P < 0.01) occurred for DM and CP disappearance, where +GLY decreased DM and CP disappearance of SBM more than that of ALF and DDG. Disappearance of NDF from ALF, DDG, and SBM was lower for +GLY compared with −GLY (GLY; P < 0.01). These results suggest that supplementing glycerin to ruminants may cause an increase in RUP fraction escaping to the small intestine for potential digestion and absorption.
Consequences of Long-Distance Dispersal for Epidemic Spread: Patterns, Scaling, and Mitigation
Authors: Severns Paul M. , Sackett Kathryn E. , Farber Daniel H. , Mundt Christopher C.
Published: September 2018

Epidemics caused by long-distance dispersed pathogens result in some of the most explosive and difficult to control diseases of both plants and animals (including humans). Yet the factors influencing disease spread, especially in the early stages of the outbreak, are not well-understood. We present scaling relationships, of potentially widespread relevance, that were developed from more than 15 years of field and in silico single focus studies of wheat stripe rust spread. These relationships emerged as a consequence of accounting for a greater proportion of the fat-tailed disease gradient that may be frequently underestimated in disease spread studies. Leptokurtic dispersal gradients (highly peaked and fat-tailed) are relatively common in nature and they can be represented by power law functions. Power law scale invariance properties generate patterns that repeat over multiple spatial scales, suggesting important and predictable scaling relationships between disease levels during the first generation of disease outbreaks and subsequent epidemic spread. Experimental wheat stripe rust outbreaks and disease spread simulations support theoretical scaling relationships from power law properties and suggest that relatively straightforward scaling approximations may be useful for projecting the spread of disease caused by long-distance dispersed pathogens. Our results suggest that, when actual dispersal/disease data are lacking, an inverse power law with exponent = 2 may provide a reasonable approximation for modeling disease spread. Furthermore, our experiments and simulations strongly suggest that early control treatments with small spatial extent are likely to be more effective at suppressing an outbreak caused by a long-distance dispersed pathogen than would delayed treatment of a larger area. The scaling relationships we detail and the associated consequences for disease control may be broadly applicable to plant and animal pathogens characterized by non-exponentially bound, fat-tailed dispersal gradients.
2018 Guide to Nursing Certification Boards
Authors: Bonsall Lisa Morris , Schnur Myrna Buiser , Fryling-Resare Kim , Lynch Lindsey
Published: September 2018

Nursing specialty certification is a way to demonstrate clinical and professional growth. Use this resource to learn about available certifications and contact the certifying body that meets your needs.
Effects of Physical Exercise on Depressive Symptoms in Patients With Cognitive Impairment
Authors: Leng Minmin , Liang Bing , Zhou Haiyan , Zhang Ping , Hu Mingyue , Li Guichen , Li Feng , Chen Li
Published: September 2018

We aimed to evaluate the efficacy of physical exercise in ameliorating depressive symptoms in patients with cognitive impairment. The databases of PubMed, EMBASE, Web of Science, the Cochrane Library, PsycINFO, China National Knowledge Infrastructure, WanFang, and WeiPu (VIP) were searched to identify randomized controlled trials (RCTs) that involved physical exercise for patients with cognitive impairment. A random effects model and a fixed effects model were used to calculate the pooled effect size. Twenty-one studies were identified. The meta-analysis showed that physical exercise significantly ameliorated depressive symptoms (standardized mean difference [SMD] = −0.23; 95% confidence interval [CI], −0.39 to −0.07; p = 0.004). In addition, beneficial improvements in neuropsychiatric symptoms (mean difference, −4.62; 95% CI, −9.07 to −0.16, p = 0.04), quality of life (SMD = 0.23; 95% CI, 0.01–0.46; p = 0.04), and activities of daily living (SMD = 0.27; 95% CI, 0.12–0.43; p = 0.0005) were observed in our study. No significant improvements were found in anxiety or apathy. Nevertheless, further high-quality, multicenter RCTs are needed to identify the clinical value of our results.
Exploring Resilience at Work Among First-Line Nurse Managers
Authors: Carpio Ron C. , Castro Laura P. , Huerto Heinrich M. , Highfield Martha E.F. , Mendelson Sherri
Published: September 2018

OBJECTIVES

This study explored the assessment of resilience at work among 1st-line nurse managers (NMs).

BACKGROUND

Resilience is the ability to cope with stress. NMs have stressful roles and may ultimately withdraw from management if they lack resilient behaviors. Having a measurement of resilience at work in NMs and other healthcare workers may facilitate resilience development approaches.

METHODS

In a descriptive, cross-sectional design, an electronic survey of 25-item, 7-subscale Resilience at Work (RAW) self-report assessment was distributed to 77 NMs.

RESULTS

The highest reported subscale was living authentically; lowest was maintaining perspective. Total years as NM was related to overall RAW mean, maintaining perspective, staying healthy.

CONCLUSION

The application of an instrument to determine resilience may focus support for NMs on maintaining perspective, for example. Further study exploring the application of the RAW assessment to healthcare workers is indicated.
Evaluation of Outcomes From an Online Nurse Residency Program
Authors: Wilson Thad , Weathers Nicole , Forneris Lori
Published: September 2018

OBJECTIVE

This retrospective study examined the nurse outcomes from new-graduate nurse residents completing an online nurse residency program (NRP).

BACKGROUND

Studies have shown that hospital-based NRPs help new graduates transition from beginners to competent nurses. However, NRPs can tax the resources of smaller institutions, making such a program unrealistic. Little is published exploring the efficacy of online programs for nursing residents.

METHODS

Surveys assessing the impact of the online program were completed by residents in an online NRP at initiation, 6 months, and at completion.

RESULTS

There were statistically significant improvements in organizational and prioritizing skills; confidence in communication with other healthcare providers, patients, and families; and improved leadership ability. The percentage of residents reporting negative safety practices and patient errors decreased over time.

CONCLUSIONS

An NRP using online educational modules results in nurse outcomes comparable to those reported from traditional models.
Hepatitis B Virus Infection
Authors: Jang Yeonsoo , Boo Sunjoo , Yoo Hyera
Published: September 2018

Fatigue is one of the most common patient-reported symptoms and can result in poor quality of life in patients with the hepatitis B virus (HBV). Little is known about the characteristics of fatigue in Korean patients with HBV. This study's purpose was to examine fatigue severity and explore health issues associated with fatigue in Korean patients with HBV. A mixed-methods research design was used. Quantitative data on fatigue severity were measured using the revised Piper Fatigue Scale (PFS) with 147 participants. Qualitative data on health issues induced by fatigue were collected via interviews with11 participants. Content analysis revealed three categories of health issues (physical, psychological, and social) and eight subcategories. Participants' overall fatigue level was moderate. The cognitive/mood dimension on the PFS had a significant negative correlation with age. Emotional and psychosocial issues associated with HBV-related fatigue may be more prevalent than physical issues in Korean patients.
Detection and Mitigation of Spurious Antisense Reads with RoSA
Authors: Mourão Kira , Schurch Nicholas J. , Lucoszek Radoslaw , Froussios Kimon , MacKinnon Katarzyna , Duc Céline , Simpson Gordon , Barton Geoffrey J.
Published: September 2018

Motivation

Antisense transcription is known to have a range of impacts on sense gene expression, including (but not limited to) impeding transcription initiation, disrupting post-transcriptional processes, and enhancing, slowing, or even preventing transcription of the sense gene. Strand-specific RNA-Seq protocols preserve the strand information of the original RNA in the data, and so can be used to identify where antisense transcription may be implicated in regulating gene expression. However, our analysis of 199 strand-specific RNA-Seq experiments reveals that spurious antisense reads are often present in these datasets at levels greater than 1% of sense gene expression levels. Furthermore, these levels can vary substantially even between replicates in the same experiment, potentially disrupting any downstream analysis, if the incorrectly assigned antisense counts dominate the set of genes with high antisense transcription levels. Currently, no tools exist to detect or correct for this spurious antisense signal.

Results

Our tool, RoSA (Removal of Spurious Antisense), detects the presence of high levels of spurious antisense read alignments in strand-specific RNA-Seq datasets. It uses incorrectly spliced reads on the antisense strand and/or ERCC spike-ins (if present in the data) to calculate both global and gene-specific antisense correction factors. We demonstrate the utility of our tool to filter out spurious antisense transcript counts in an Arabidopsis thaliana RNA-Seq experiment.

Availability

RoSA is open source software available under the GPL licence via the Barton Group GitHub page https://github.com/bartongroup.

Contact

g.j.barton@dundee.ac.uk, g.g.simpson@dundee.ac.uk
FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
Authors: Quan Jenai , Langelier Charles , Kuchta Alison , Batson Joshua , Teyssier Noam , Lyden Amy , Caldera Saharai , McGeever Aaron , Dimitrov Boris , King Ryan , Wilheim Jordan , Murphy Maxwell , Ares Lara Pesce , Travisano Katherine A. , Sit Rene , Amato Roberto , Mumbengegwi Davis R. , Smith Jennifer L. , Bennett Adam , Gosling Roly , Mourani Peter M. , Calfee Carolyn S. , Neff Norma F. , Chow Eric D. , Kim Peter S. , Greenhouse Bryan , DeRisi Joseph L. , Crawford Emily D.
Published: September 2018

The growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.
An introduction to MPEG-G, the new ISO standard for genomic information representation
Authors: Albert Claudio , Paridaens Tom , Voges Jan , Naro Daniel , Ahmad Junaid J. , Ravasi Massimo , Renzi Daniele , Zoia Giorgio , Ribeca Paolo , Ochoa Idoia , Mattavelli Marco , Delgado Jaime , Hernaez Mikel
Published: September 2018

The MPEG-G standardization initiative is a coordinated international effort to specify a compressed data format that enables large scale genomic data to be processed, transported and shared. The standard consists of a set of specifications (i.e., a book) describing: i) a nor-mative format syntax, and ii) a normative decoding process to retrieve the information coded in a compliant file or bitstream. Such decoding process enables the use of leading-edge com-pression technologies that have exhibited significant compression gains over currently used formats for storage of unaligned and aligned sequencing reads. Additionally, the standard provides a wealth of much needed functionality, such as selective access, data aggregation, ap-plication programming interfaces to the compressed data, standard interfaces to support data protection mechanisms, support for streaming and a procedure to assess the conformance of implementations. ISO/IEC is engaged in supporting the maintenance and availability of the standard specification, which guarantees the perenniality of applications using MPEG-G. Fi-nally, the standard ensures interoperability and integration with existing genomic information processing pipelines by providing support for conversion from the FASTQ/SAM/BAM file formats.

In this paper we provide an overview of the MPEG-G specification, with particular focus on the main advantages and novel functionality it offers. As the standard only specifies the decoding process, encoding performance, both in terms of speed and compression ratio, can vary depending on specific encoder implementations, and will likely improve during the lifetime of MPEG-G. Hence, the performance statistics provided here are only indicative baseline examples of the technologies included in the standard.
FlashPack: Fast and simple preparation of ultra-high performance capillary columns for LC-MS
Authors: Kovalchuk Sergey , Jensen Ole N. , Rogowska-Wrzesinska Adelina
Published: September 2018

Capillary ultra-high-pressure liquid chromatography (cUHPLC) is essential for in-depth characterization of complex biomolecule mixtures by LC-MS. We developed a simple and fast method called FlashPack for custom packing of capillary columns of 50-100 cm length with sub-2-μm sorbent particles. FlashPack uses high sorbent concentrations of 500-1000 mg/ml for packing at relatively low pressure of 100 bar. Column blocking by sorbent aggregation is avoided during the packing of sorbent particles by gentle mechanical tapping of the capillary proximal end by a slowly rotating magnet bar. Utilizing a standard 100 bar pressure bomb, Flashpack allows for production of 15-25 cm cUHPLC columns within a few minutes and of 50 cm cUHPLC columns in less than an hour. Columns exhibit excellent reproducibility of back-pressure, retention time and resolution (CV 8,7 %). FlashPack cUHPLC columns are inexpensive, robust and deliver performance comparable to commercially available cUHPLC columns. The FlashPack method is versatile and enables production of cUHPLC columns using a variety of sorbent materials.
BitterSweet: Building machine learning models for predicting the bitter and sweet taste of small molecules
Authors: Tuwani Rudraksh , Wadhwa Somin , Bagler Ganesh
Published: September 2018

The dichotomy of sweet and bitter tastes is a salient evolutionary feature of human gustatory system with an innate attraction to sweet taste and aversion to bitterness. A better understanding of molecular correlates of bitter-sweet taste gradient is crucial for identification of natural as well as synthetic compounds of desirable taste on this axis. While previous studies have advanced our understanding of the molecular basis of bitter-sweet taste and contributed models for their identification, there is ample scope to enhance these models by meticulous compilation of bitter-sweet molecules and utilization of a wide spectrum of molecular descriptors. Towards these goals, based on structured data compilation our study provides an integrative framework with state-of-the-art machine learning models for bitter-sweet taste prediction (BitterSweet). We compare different sets of molecular descriptors for their predictive performance and further identify important features as well as feature blocks. The utility of BitterSweet models is demonstrated by taste prediction on large specialized chemical sets such as FlavorDB, FooDB, SuperSweet, Super Natural II, DSSTox, and DrugBank. To facilitate future research in this direction, we make all datasets and BitterSweet models publicly available, and also present an end-to-end software for bitter-sweet taste prediction based on freely available chemical descriptors.
Dnmt1has an essential function despite the absence of CpG DNA methylation in the red flour beetleTribolium castaneum
Authors: Schulz Nora KE , Wagner C Isabel , Ebeling Julia , Raddatz Günter , Buhr Maike F Diddens-de , Lyko Frank , Kurtz Joachim
Published: September 2018

Epigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set ofDnmts.But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. The red flour beetle,Tribolium castaneum,lacksDnmt3but possessesDnmt1and it has been controversial whether it has a functional DNA methylation system.

Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we foundDnmt1expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown ofDnmt1caused a developmental arrest in offspring embryos.

We show thatDnmt1plays an essential role inT. castaneumembryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.
Computational estimation of ms-sec atomistic folding times
Authors: Adhikari Upendra , Mostofian Barmak , Copperman Jeremy , Petersen Andrew , Zuckerman Daniel M.
Published: September 2018

Despite the development of massively parallel computing hardware including inexpensive graphics processing units (GPUs), it has remained infeasible to simulate the folding of atomistic proteins at room temperature using conventional molecular dynamics (MD) beyond the µs scale. Here we report the folding of atomistic, implicitly solvated protein systems with folding times τf ranging from ∼100 µs to ∼1s using the weighted ensemble (WE) strategy in combination with GPU computing. Starting from an initial structure or set of structures, WE organizes an ensemble of GPU-accelerated MD trajectory segments via intermittent pruning and replication events to generate statistically unbiased estimates of rate constants for rare events such as folding; no biasing forces are used. Although the variance among atomistic WE folding runs is significant, multiple independent runs are used to reduce and quantify statistical uncertainty. Folding times are estimated directly from WE probability flux and from history-augmented Markov analysis of the WE data. Three systems were examined: NTL9 at low solvent viscosity (yielding τf = 0.8 − 9.0 μs), NTL9 at water-like viscosity (τf = 0.2 − 1.9 ms), and Protein G at low viscosity (τf = 3.3 - 200 ms). In all cases the folding time, uncertainty, and ensemble properties could be estimated from WE simulation; for Protein G, this characterization required significantly less overall computing than would be required to observe a single folding event with conventional MD simulations. Our results suggest that the use and calibration of force fields and solvent models for precise estimation of kinetic quantities is becoming feasible.
Characterization of the role of several COPI complex isoforms during the early acceptance of compatible pollen grains inArabidopsis thaliana
Authors: Gomez Daniel A. Cabada , Chavez M. Isabella , Indriolo Emily
Published: September 2018

COPI is a seven subunit coatomer complex, consisting of α, β, β′, γ, δ, ε, and ξ; inA. thaliana, COPI is necessary for retrograde transport from the Golgi to the Endoplasmic Reticulum, Golgi maintenance, and cell-plate formation in plant cells. Vesicle recruitment to the pollen contact point is required for pollen hydration and pollen tube penetration. To determine what other aspects of trafficking may be involved in the stigmatic papillae acceptance of compatible pollen, knock-out lines of several isoforms of the COPI complex were characterized in their roles during compatible pollination. Isoforms that were studied included α1-COPI, β-COPI, β′-COPI, γ-COPI and ε-COPI. Each mutant line was characterized in regards to pollen grain adherence, pollen tube penetration, and seed set. Of the mutant lines examined,α1-copihad the strongest phenotype with issues with compatible pollen grain adherence, tube germination and reduction in seed set while other lines had milder but visible retardation in compatible pollen acceptance. The data presented here are the first study of the role of the COPI complex in compatible pollinations and that certain subunit isoforms are required for compatible pollen acceptance.
The microbial basis of impaired wound healing: differential roles for pathogens, “bystanders”, and strain-level diversification in clinical outcomes
Authors: Kalan Lindsay , Meisel Jacquelyn S. , Loesche Michael A. , Horwinski Joseph , Soaita Ioana , Chen Xiaoxuan , Gardner Sue E. , Grice Elizabeth A.
Published: September 2018

Chronic, non-healing wounds are a major complication of diabetes associated with high morbidity and health care expenditures estimated at $9-13 billion annually in the US. Though microbial infection and critical colonization is hypothesized to impair healing and contribute to severe outcomes such as amputation, antimicrobial therapy is inefficacious and the role of microbes in tissue repair, regeneration, and healing remains unclear. Here, in a longitudinal prospective cohort study of 100 subjects with non-infected neuropathic diabetic foot ulcer (DFU), we performed metagenomic shotgun sequencing to elucidate microbial temporal dynamics at strain-level resolution, to investigate pathogenicity and virulence of the DFU microbiome with respect to outcomes, and to determine the influence of therapeutic intervention on the DFU microbiota. Slow healing DFUs were associated with signatures of biofilm formation, host invasion, and virulence. Though antibiotic resistance was widespread at the genetic level, debridement, rather than antibiotic treatment, significantly shifted the DFU microbiome in patients with more favorable outcomes. Primary clinical isolates ofS. aureus, C. striatum, andA. faecalisinduced differential biological responses in keratinocytes and in a murine model of diabetic wound healing, with theS. aureusstrain associated with non-healing wounds eliciting the most severe phenotype. Together these findings implicate strain-level diversification of the wound pathogenS. aureusin chronic wound outcomes, while revealing potential contributions from skin commensals and other previously underappreciated constituents of the wound microbiota.
The Spectrum of Asynchronous Dynamics in Spiking Networks: A Theory for the Diversity of Non-Rhythmic Waking states in Neocortex
Authors: Zerlaut Yann , Zucca Stefano , Panzeri Stefano , Fellin Tommaso
Published: September 2018

The cerebral cortex of awake animals exhibits frequent transitions between diverse non-rhythmic network states. However, it is still unclear how these different activity states emerge within the same network and how each state impacts network function. Here, we demonstrate that model networks of spiking neurons with moderate recurrent interactions dynamically change their asynchronous dynamics depending upon the level of afferent excitation. We found that the model network displayed a spectrum of asynchronous states, ranging from afferent input-dominated (AD) regimes, characterized by unbalanced synaptic currents and sparse firing, to recurrent input-dominated (RD) regimes, characterized by balanced synaptic currents and dense firing. The model predicted regime-specific relationships between several different neural biophysical properties which were all experimentally confirmed by intracellular recordings in the somatosensory cortex of awake mice. Moreover, theoretical analysis showed that AD regimes more precisely encode spatiotemporal patterns of presynaptic activity, while RD regimes better encoded the strength of afferent inputs. These results provide a theoretical foundation for how recurrent neocortical circuits generate non-rhythmic waking states and how these different states modulate the processing of incoming information.
Promoter activity of ORF-less gene cassettes isolated from the oral metagenome
Authors: Tansirichaiya Supathep , Mullany Peter , Roberts Adam P.
Published: September 2018

Integrons are genetic elements consisting of a functional platform for recombination and expression of gene cassettes (GCs). GCs usually carry promoter-less open reading frames (ORFs), encoding proteins with various functions including antibiotic resistance. The transcription of GCs relies mainly on a cassette promoter (PC), located upstream of an array of GCs. Some integron GCs, called ORF-less GCs, contain no identifiable ORF with a small number shown to be involved in antisense mRNA mediated gene regulation.

In this study, promoter sequences were identified, usingin silicoanalysis, within GCs PCR amplified from the oral metagenome. The promoter activity of ORF-less GCs was verified by cloning them upstream of agusAreporter, proving they can function as a promoter, presumably allowing bacteria to adapt to multiple stresses within the complex physico-chemical environment of the human oral cavity. A bi-directional promoter detection system was also developed allowing direct identification of clones with promoter-containing GCs on agar plates. Novel promoter-containing GCs were identified from the human oral metagenomic DNA using this construct, called pBiDiPD.

This is the first demonstration and detection of promoter activity of ORF-less GCs and the development of an agar plate-based detection system will enable similar studies in other environments.
Screening for insulin-independent pathways that modulate glucose homeostasis identifies androgen receptor antagonists
Authors: Mullapudi Sri Teja , Helker Christian S. M. , Boezio Giulia L.M. , Maischein Hans-Martin , Sokol Anna M. , Graumann Johannes , Guenther Stefan , Matsuda Hiroki , Kubicek Stefan , Carol Yang Yu Hsuan , Stainier Didier Y.R.
Published: September 2018

Pathways modulating glucose homeostasis independently of insulin would open new avenues to combat insulin resistance and diabetes. Here, we report the establishment, characterization and employment of a vertebrate ‘insulin-free’ model to identify insulin-independent modulators of glucose metabolism. insulin knockout zebrafish recapitulate core characteristics of diabetes and survive only up to larval stages. Utilizing a highly efficient endoderm transplant technique, we generated viable chimeric adults that provide the large numbers of insulin mutant larvae required for our screening platform. Using glucose as a disease-relevant readout, we screened 2233 molecules and identified 3 that consistently reduced glucose levels in insulin mutants. Most significantly, we uncovered an insulin-independent beneficial role for androgen receptor antagonism in hyperglycemia, mostly by reducing fasting glucose levels. Our study proposes therapeutic roles for androgen signaling in diabetes and, more broadly, offers a novel in vivo model for rapid screening and decoupling of insulin-dependent and -independent mechanisms.
The structural basis for forkhead box family specificity revealed by the crystal structure of human FOXN1 in complex with DNA
Authors: Newman Joseph A. , Aitkenhead Hazel , Gravard Angeline , Rota Ioanna A. , Handel Adam E. , Hollander Georg A. , Gileadi Opher
Published: September 2018

Significance

FOXN1 is a transcription factor that is essential for the development of the thymus and the production of T-lymphocytes. It is a member of a large family of transcription factors which recognize DNA sequences through the conserved Forkhead (FH) domain. FOXN1 recognizes a DNA sequence that is different from the common consensus binding sequence of FH domains, although key binding residues are identical. We present crystal structures of the FH domain of FOXN1, free and DNA-bound, which shed light on the different binding specificities; the structure also revelas the basis of the immunocompromisednudemutation, as well as a preferential binding to non-methylated CpG motifs.

FOXN1 is a member of the forkhead box (FOX) family of transcription factors, and plays an important role in thymic epithelial cell differentiation and function. FOXN1 mutations in humans and mice give rise to the "nude" phenotype which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognize an alternate consensus sequence (GACGC), which is different from the more widely-recognized canonical sequence consensus RYAAAYA. Here, we present the structure of FOXN1 in complex with DNA at 1.6 Å resolution, in which the DNA sequence is recognised by a mixture of direct and water-mediated contacts provided by residues in an a-helix inserted in the DNA major groove (the recognition helix). Comparisons with other FOX family structures reveal that the canonical and alternate DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identify a single alternate rotamer within the recognition helix itself as an important determinant of DNA specificity, and indicate sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally we demonstrate that FOXN1 has a significantly reduced affinity for DNA containing 5-methylcytosine, which may have implications for the role of FOXN1 in thymic senescence.
Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes
Authors: Pucker Boas , Brockington Samuel F.
Published: September 2018

Most eukaryotic genes comprise exons and introns thus requiring the precise removal of introns from pre-mRNAs to enable protein biosynthesis. U2 and U12 spliceosomes catalyze this step by recognizing motifs on the transcript in order to remove the introns. A process which is dependent on precise definition of exon-intron borders by splice sites, which are consequently highly conserved across species. Only very few combinations of terminal dinucleotides are frequently observed at intron ends, dominated by the canonical GT-AG splice sites on the DNA level.

Here we investigate the occurrence of diverse combinations of dinucleotides at predicted splice sites. Analyzing 121 plant genome sequences based on their annotation revealed strong splice site conservation across species, annotation errors, and true biological divergence from canonical splice sites. The frequency of non-canonical splice sites clearly correlates with their divergence from canonical ones indicating either an accumulation of probably neutral mutations, or evolution towards canonical splice sites. Strong conservation across multiple species and non-random accumulation of substitutions in splice sites indicate a functional relevance of non-canonical splice sites. The average composition of splice sites across all investigated species is 98.7% for GT-AG, 1.2% for GC-AG, 0.06% for AT-AC, and 0.09% for minor non-canonical splice sites. RNA-Seq data sets of 35 species were incorporated to validate non-canonical splice site predictions through gaps in sequencing reads alignments and to demonstrate the expression of affected genes. We conclude thatbona fidenon-canonical splice sites are present and appear to be functionally relevant in most plant genomes, if at low abundance.
Uncovering hidden members and functions of the soil microbiome using de novo metaproteomics
Authors: Lee Joon-Yong , Mitchell Hugh D. , Burnet Meagan C. , Wu Ruonan , Jenson Sarah C. , Merkley Eric D. , Nakayasu Ernesto S. , Nicora Carrie D. , Jansson Janet K. , Burnum-Johnson Kristin E. , Payne Samuel H.
Published: September 2018

Metaproteomics has been increasingly utilized for high-throughput molecular characterization in complex environments and has been demonstrated to provide insights into microbial composition and functional roles in soil systems. Despite its potential for the study of microbiomes, significant challenges remain in data analysis, including the creation of a sample-specific protein sequence database as the taxonomic composition of soil is often unknown. Almost all metaproteome analysis tools require this database and their accuracy and sensitivity suffer when the database is incomplete or contains extraneous sequences from organisms which are not present. Here, we leverage a de novo peptide sequencing approach to identify sample composition directly from metaproteomic data. First, we created a deep learning model, Kaiko, to predict the peptide sequences from mass spectrometry data, and trained it on 5 million peptide-spectrum matches from 55 phylogenetically diverse bacteria. After training, Kaiko successfully identified unsequenced soil isolates directly from proteomics data. Finally, we created a pipeline for metaproteome database generation using Kaiko. We tested the pipeline on native soils collected in Kansas, showing that the de novo sequencing model can be employed to construct the sample-specific protein database instead of relying on (un)matched metagenomes. Our pipeline identified all highly abundant taxa from 16S ribosomal RNA sequencing of the soil samples and also uncovered several additional species which were strongly represented only in proteomic data. Our pipeline offers an alternative and complementary method for metaproteomic data analysis by creating a protein database directly from proteomic data, thus removing the need for metagenomic sequencing.

Significance Statement

Proteomic characterization of environmental samples, or metaproteomics, reveals microbial activity critical to our understanding of climate, nutrient cycling and human health. Metaproteomic samples originate from diverse environs, such as soil and oceans. One option for data analysis is a de novo interpretation of the mass spectra. Unfortunately, the current generation of de novo algorithms were primarily trained on data originating from human proteins. Therefore, these algorithms struggle with data from environmental samples, limiting our ability to analyze metaproteomics data. To address this challenge, we trained a new algorithm with data from dozens of diverse environmental bacteria and achieved significant improvements in accuracy across a broad range of organisms. This generality opens proteomics to the world of natural isolates and microbiomes.
DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity
Authors: Nechemia-Arbely Yael , Miga Karen H. , Shoshani Ofer , Aslanian Aaron , McMahon Moira A. , Lee Ah Young , Fachinetti Daniele , Yates John R. , Ren Bing , Cleveland Don W.
Published: September 2018

Chromatin assembled with the histone H3 variant CENP-A is the heritable epigenetic determinant of human centromere identity. Using genome-wide mapping and reference models for 23 human centromeres, CENP-A is shown in early G1 to be assembled into nucleosomes within megabase, repetitive α-satellite DNAs at each centromere and onto 11,390 transcriptionally active sites on the chromosome arms. Here we identify that DNA replication acts as an error correction mechanism to sustain centromere identity through the removal of the sites of CENP-A loading on the chromosome arms, while maintaining centromere-bound CENP-A with the same DNA sequence preferences as in its initial loading.
Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine
Authors: Zaim Samir Rachid , Kenost Colleen , Berghout Joanne , Zhang Helen Hao , Lussier Yves A.
Published: September 2018

Background

Gene expression profiling has benefited medicine by providing clinically relevant insights at the molecular candidate and systems levels. However, to adopt a more ‘precision’ approach that integrates individual variability including ‘omics data into risk assessments, diagnoses, and therapeutic decision making, whole transcriptome expression analysis requires methodological advancements. One need is for users to confidently be able to make individual-level inferences from whole transcriptome data. We propose that biological replicates in isogenic conditions can provide a framework for testing differentially expressed genes (DEGs) in a single subject (ss) in absence of an appropriate external reference standard or replicates.

Methods

Eight ss methods for identifying genes with differential expression (NOISeq, DEGseq, edgeR, mixture model, DESeq, DESeq2, iDEG, and ensemble) were compared inYeast(parental line versus snf2 deletion mutant; n=42/condition) andMCF7breast-cancer cell (baseline and stimulated with estradiol; n=7/condition) RNA-Seq datasets where replicate analysis was used to build reference standards from NOISeq, DEGseq, edgeR, DESeq, DESeq2. Each dataset was randomly partitioned so that approximately two-thirds of the paired samples were used to construct reference standards and the remainder were treated separately as single-subject sample pairs and DEGs were assayed using ss methods. Receiver-operator characteristic (ROC) and precision-recall plots were determined for all ss methods against each RSs in both datasets (525 combinations).

Results

Consistent with prior analyses of these data,~50% and ~15% DEGs were respectively obtained in Yeast and MCF7 reference standard datasets regardless of the analytical method. NOISeq, edgeR and DESeq were the most concordant and robust methods for creating a reference standard. Single-subject versions of NOISeq, DEGseq, and an ensemble learner achieved the best median ROC-area-under-the-curve to compare two transcriptomes without replicates regardless of the type of reference standard (>90% in Yeast, >0.75 in MCF7).

Conclusion

Better and more consistent accuracies are obtained by an ensemble method applied to singlesubject studies across different conditions. In addition, distinct specific sing-subject methods perform better according to different proportions of DEGs. Single-subject methods for identifying DEGs from paired samples need improvement, as no method performs with both precision>90% and recall>90%.http://www.lussiergroup.org/publications/EnsembleBiomarker
The bacterial DNA binding protein MatP involved in linking the nucleoid terminal domain to the divisome at midcell interacts with lipid membranes
Authors: Monterroso Begoña , Zorrilla Silvia , Sobrinos-Sanguino Marta , Robles-Ramos Miguel Ángel , Alfonso Carlos , Söderström Bill , Meiresonne Nils Y , Verheul Jolanda , den Blaauwen Tanneke , Rivas Germán
Published: September 2018

Division ring formation at midcell is controlled by various mechanisms inEscherichia coli, one of them being the linkage between the chromosomal Ter macrodomain and the Z-ring mediated by MatP, a DNA binding protein that organizes this macrodomain and contributes to the prevention of premature chromosome segregation. Here we show that, during cell division, just before splitting the daughter cells, MatP seems to localize close to the cytoplasmic membrane, suggesting that this protein might interact with lipids. To test this hypothesis, we investigated MatP interaction with lipidsin vitro. We found that MatP, when encapsulated inside microdroplets generated by microfluidics and giant vesicles, accumulates at phospholipid bilayers and monolayers matching the lipid composition in theE. coliinner membrane. MatP binding to lipids was independently confirmed using lipid coated microbeads and bio-layer interferometry assays. Interaction of MatP with the lipid membranes also occurs in the presence of the DNA sequences specifically targeted by the protein but there is no evidence of ternary membrane/protein/DNA complexes. We propose that the interaction of MatP with lipids may modulate its spatiotemporal localization and its recognition of other ligands.

IMPORTANCE

The division of anE. colicell into two daughter cells with equal genomic information and similar size requires duplication and segregation of the chromosome and subsequent scission of the envelope by a protein ring, the Z-ring. MatP is a DNA binding protein that contributes both to the positioning of the Z-ring at midcell and the temporal control of nucleoid segregation. Our integratedin vivoandin vitroanalysis provides evidence that MatP can interact with lipid membranes comprising the phospholipid mixture in theE. coliinner membrane, without concomitant recruitment of the short DNA sequences specifically targeted by MatP. This observation strongly suggests that the membrane may play a role in the regulation of the function and localization of MatP, which could be relevant for the coordination of the two fundamental processes in which this protein participates, nucleoid segregation and cell division.
A high-resolution map of non-crossover events reveals impacts of genetic diversity on mammalian meiotic recombination
Authors: Li Ran , Bitoun Emmanuelle , Altemose Nicolas , Davies Robert W , Davies Benjamin , Myers Simon R
Published: September 2018

During meiotic recombination in most mammals, hundreds of programmed DNA Double-Strand Breaks (DSBs) occur across all chromosomes in each cell at sites bound by the protein PRDM9. Faithful DSB repair using the homologous chromosome is essential for fertility, yielding either non-crossovers, which are frequent but difficult to detect, or crossovers. In certain hybrid mice, high sequence divergence causes PRDM9 to bind each homologue at different sites, 'asymmetrically', and these mice exhibit meiotic failure and infertility, by unknown mechanisms. To investigate the impact of local sequence divergence on recombination, we intercrossed two mouse subspecies over five generations and deep-sequenced 119 offspring, whose high heterozygosity allowed detection of thousands of crossover and non-crossover events with unprecedented power and spatial resolution. Both crossovers and non-crossovers are strongly depleted at individual asymmetric sites, revealing that PRDM9 not only positions DSBs but also promotes their homologous repair by binding to the unbroken homologue at each site. Unexpectedly, we found that non-crossovers containing multiple mismatches repair by a different mechanism than single-mismatch sites, which undergo GC-biased gene conversion. These results demonstrate that local genetic diversity profoundly alters meiotic repair pathway decisions via at least two distinct mechanisms, impacting genome evolution and Prdm9-related hybrid infertility.