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El Niño events in the Central Pacific may be changing due to climate change, but long records to support this are lacking. Here, the authors present sea surface temperature reconstructions from tree cellulose for the last 800 years which suggest the variability of Central Pacific El Niño events has increased.

Abstract Background Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. Results Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. Conclusions Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.

Summary: Adaptation of influenza A viruses to new hosts are rare events but are the basis for emergence of new influenza pandemics in the human population. Thus, understanding the processes involved in such events is critical for anticipating potential pandemic threats. In 2013, the first case of human infection by an avian H10N8 virus was reported, yet the H10 hemagglutinin (HA) maintains avian receptor specificity. However, the 150-loop of H10 HA, as well as related H7 and H15 subtypes, contains a two-residue insert that can potentially block human receptor binding. Mutation of the 150-loop on the background of Q226L and G228S mutations, which arose in the receptor-binding site of human pandemic H2 and H3 viruses, resulted in acquisition of human-type receptor specificity. Crystal structures of H10 HA mutants with human and avian receptor analogs, receptor-binding studies, and tissue staining experiments illustrate the important role of the 150-loop in H10 receptor specificity. : Introduction and subsequent circulation of avian and other zoonotic influenza viruses in the human population requires changes to the hemagglutinin-binding specificity. Tzarum et al. report on mutations that can alter the receptor specificity of hemagglutinin H10 using a glycan array, tissue staining, and structural analysis. Keywords: influenza A virus, hemagglutinin, HA, host specificity, H10N8, 150-loop, glycan array, crystal structure

Kyungho Jang,1,2,* Min-Kyoung Kim,3,4,* Jaeseong Oh,1 SeungHwan Lee,1 Joo-Youn Cho,1 Kyung-Sang Yu,1 Tai Kiu Choi,3 Sang-Hyuk Lee,3,4 Kyoung Soo Lim4 1Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, Seoul, 2Center for Clinical Pharmacology and Biomedical Research Institute, Chonbuk National University Medical School, Jeonju, 3Department of Psychiatry, 4Department of Clinical Pharmacology and Therapeutics, CHA University School of Medicine and CHA Bundang Medical Center, Seongnam, Republic of Korea *These authors contributed equally to this work Purpose: Oseltamivir is widely used in the treatment and prophylaxis of influenza A and B viral infections. It is ingested as an oral prodrug that is rapidly metabolized by carboxylesterase 1 (CES1) to its active form, oseltamivir carboxylate. Dexamethasone is also used in the treatment of acute respiratory distress syndrome, a severe complication of influenza; however, its influence on the pharmacokinetics (PK) of oseltamivir is controversial. The aim of this study was to investigate the effects of coadministering oseltamivir and dexamethasone on the PK of oseltamivir in healthy volunteers. Methods: An open-label, two-period, one-sequence, multiple-dose study was conducted in 19 healthy male volunteers. Oseltamivir (75 mg) was orally administered on Day 1 and Day 8, and dexamethasone (1.5 mg) was administered once daily from Day 3 to Day 8. Serial blood and urine samples were collected for PK analysis of oseltamivir and oseltamivir carboxylate on Day 1 and Day 8. Oseltamivir and oseltamivir carboxylate concentrations in plasma and urine were determined using liquid chromatography–tandem mass spectrometry. Results: Area under the plasma concentration–time curve (AUC) of oseltamivir and oseltamivir carboxylate decreased after dexamethasone treatment for 6 days. The geometric mean ratio (90% confidence interval) of the metabolic ratio (oseltamivir carboxylate AUC0–48h/oseltamivir AUC0–48h) was 0.92 (0.87–0.97). The amount of unchanged oseltamivir excreted in urine increased by 14% after dexamethasone treatments. Conclusion: Coadministration of dexamethasone with oseltamivir slightly decreased systemic exposure to oseltamivir and oseltamivir carboxylate in healthy volunteers. This result suggests that CES1 is inhibited by dexamethasone in humans. However, coadministration of oseltamivir and dexamethasone did not appear to have a clinically relevant effect on the PK of oseltamivir; based on these results, dexamethasone can be coadministered with oseltamivir. Keywords: carboxylesterase, steroid, influenza, ARDS

Genetics: Variant may increase cancer risk in pre-menopausal black women A gene variant found in people of African descent may increase the risk of breast cancer—but only among pre-menopausal women. In a study of more than 14,000 women of African ancestry, a team led by Maureen Murphy from the Wistar Institute in Philadelphia, Pennsylvania, USA, and Christine Ambrosone from Roswell Park Cancer Institute in Buffalo, NY, USA, tested for an association between breast cancer and a rare genetic polymorphism in the TP53 gene that’s found almost exclusively in African-descent populations. This variant alters the p53 tumor suppressor protein and has been shown to increase cancer risk in a mouse model. Murphy and colleagues showed that the variant increased risk by about 72% in women who had not yet experienced menopause—which could help explain the earlier onset of the disease among women of African ancestry.

Emergence and intercontinental spread of highly pathogenic avian influenza A(H5Nx) virus clade 2.3.4.4 is unprecedented. H5N8 and H5N2 viruses have caused major economic losses in the poultry industry in Europe and North America, and lethal human infections with H5N6 virus have occurred in Asia. Knowledge of the evolution of receptor-binding specificity of these viruses, which might affect host range, is urgently needed. We report that emergence of these viruses is accompanied by a change in receptor-binding specificity. In contrast to ancestral clade 2.3.4 H5 proteins, novel clade 2.3.4.4 H5 proteins bind to fucosylated sialosides because of substitutions K222Q and S227R, which are unique for highly pathogenic influenza virus H5 proteins. North American clade 2.3.4.4 virus isolates have retained only the K222Q substitution but still bind fucosylated sialosides. Altered receptor-binding specificity of virus clade 2.3.4.4 H5 proteins might have contributed to emergence and spread of H5Nx viruses.

The main objective of this study was to estimate past and future dynamics of forest carbon pools in South Korea, as classified by the Intergovernmental Panel on Climate Change (IPCC) Good Practice Guidance (GPG) and to test the Carbon Budget Model of the Canadian Forest Sector 3 (CBM-CFS3). Inventory data required in CBM-CFS3 were extracted from Korea’s 3rd Forest Type Map. The site index in the inventory data was estimated through regression models developed using 5th National Forest Inventory (NFI) data with 4000 plots. Necessary yield tables to a stand age of over 100 years, stratified by species, were prepared through the estimation of volume per ha with tree species, site index and stand age. We considered thinning and cutting regulations for sustainable forest management announced by the Korean Forest Service and that the forest area was constant over from 1992 to 2092. We estimated the carbon stocks and their changes of aboveground (AGB) and belowground (BGB) biomass, litter (L), dead wood (DW), and soil organic matter (SOM). Validation was conducted based on the 5th NFI and statistical data. Our results showed that the carbon content of the total forest area increased from 509.7 Tg C to 1007.3 Tg C at a rate of 11.8 Tg C yr-1 during 1992-2034. Results also showed that AGB, BGB, DW, L and SOM changed from 54.6, 30.2, 15.9, 43.6, and 373.9 Tg C in 1992 to 455.6, 100.77, 32.89, 65.46, and 369.2 Tg C in 2034, respectively. However, the amount of forest carbon was projected to decrease due to large increases in harvest rates as most of the forest reaches the legislated cutting age during 2035-2045. Our simulation estimated that by 2045 AGB, BGB, and SOM decreased to 347.8, 78.2, and 368.9 Tg C, respectively, while DW and L increased to 46.8 and 89.1 Tg C, respectively. The carbon content of the total forested area starts to stabilize after 2045 as the annual stand growth gradually decreases. Finally in 2092, the carbon content of AGB, BGB, DW, L, and SOM was estimated as 422.3, 93.9, 31.2, 63.0, and 365.1 Tg C, respectively. Through harvesting, over the 100 year period more than 200 Tg C were transferred from South Korea’s forests to meet demands for timber, fiber and energy. Good agreement between model results, NFI data and independent studies, demonstrates the applicability of CBM-CFS3 for estimating past and future forest carbon budgets in South Korean forests and for exploring forest management activity impacts in managed forests.

Md Al-Amin, Jiafu Cao, Muhammad Naeem, Hasanul Banna, Min-Soo Kim, Yunjin Jung, Hae Young Chung, Hyung Ryong Moon, Jin-Wook Yoo College of Pharmacy, Pusan National University, Busan, South Korea Abstract: Hyperpigmentation caused by melanin overproduction is a major skin disorder in humans. Inhibition of tyrosinase, a key regulator of melanin production, has been used as an effective strategy to treat hyperpigmentation. In this study, we investigated the use of solid lipid nanoparticles (SLNs) as a highly effective and nontoxic means to deliver a newly synthesized potent tyrosinase inhibitor, MHY498, and to target melanocytes through the skin. MHY498-loaded SLNs (MHY-SLNs) were prepared by an oil-in-water emulsion solvent-evaporation method, and their morphological and physicochemical properties were characterized. MHY-SLNs showed a prolonged drug-release profile and higher skin permeation than that of MHY solution. In an in vivo evaluation of antimelanogenic activity, MHY-SLNs showed a prominent inhibitory effect against ultraviolet B-induced melanogenesis, resulting in no change in the skin color of C57BL/6 mouse, compared with that observed in an MHY solution-treated group and an untreated control group. The antimelanogenic effect of MHY-SLNs was further confirmed through Fontana–Masson staining. Importantly, MHY-SLNs did not induce any toxic effects in the L929 cell line. Overall, these data indicate that MHY-SLNs show promise in the topical treatment of hyperpigmentation. Keywords: melanogenesis, hyperpigmentation, MHY498, solid lipid nanoparticles, skin delivery

Editorial

The aim of this paper is to explore the fit between the cognitive concept of writing self-efficacy and a socially constructed epistemology of writing. Socially constructed perspectives on writing emphasise context and community and include academic literacies, rhetorical genre theory, and the writing across the curriculum movement. These perspectives have been prominent in theoretical discussions of writing since the 1980s. This paper argues that the measurement of writing self-efficacy has continued to prioritise assessing writing self-efficacy as ability to successfully accomplish superficial writing product and process features, while the social context of writing and its resultant impacts on the identity forming, relational, emotional and creative impacts on writing self-efficacy have been largely ignored. The historical context of paradigmatic shifts in writing theory will be discussed with a lens towards proposing a synthesis of three constructionist situated perspectives - activity theory, rhetorical genre theory, and communities of practice - and how these situated perspectives may inform a more complete view of how writing self-efficacy should be assessed and measured. How practitioners may consider the merger of these theories in writing pedagogy will be introduced to inspire future research.

There is increasing recognition that the underlying genetic variation contributing to complex traits influences transcriptional regulation and can be detected at a population level as expression quantitative trait loci. At the level of an individual, allelic variation in transcriptional regulation of individual genes can be detected by measuring allele-specific expression in RNAseq data. We reasoned that extreme variants in gene expression could be identified by analysis of inbred progeny with shared grandparents. Commercial chickens have been intensively selected for production traits. Selection is associated with large blocks of linkage disequilibrium with considerable potential for co-selection of closely linked “hitch-hiker alleles” affecting traits unrelated to the feature being selected, such as immune function, with potential impact on the productivity and welfare of the animals. To test this hypothesis that there is extreme allelic variation in immune-associated genes we sequenced a founder population of commercial broiler and layer birds. These birds clearly segregated genetically based upon breed type. Each genome contained numerous candidate null mutations, protein-coding variants predicted to be deleterious and extensive non-coding polymorphism. We mated selected broiler-layer pairs then generated cohorts of F2 birds by sibling mating of the F1 generation. Despite the predicted prevalence of deleterious coding variation in the genomic sequence of the founders, clear detrimental impacts of inbreeding on survival and post-hatch development were detected in only one F2 sibship of 15. There was no effect on circulating leukocyte populations in hatchlings. In selected F2 sibships we performed RNAseq analysis of the spleen and isolated bone marrow-derived macrophages (with and without lipopolysaccharide stimulation). The results confirm the predicted emergence of very large differences in expression of individual genes and sets of genes. Network analysis of the results identified clusters of co-expressed genes that vary between individuals and suggested the existence of trans-acting variation in the expression in macrophages of the interferon response factor family that distinguishes the parental broiler and layer birds and influences the global response to lipopolysaccharide. This study shows that the impact of inbreeding on immune cell gene expression can be substantial at the transcriptional level, and potentially opens a route to accelerate selection using specific alleles known to be associated with desirable expression levels.

Optogenetics is a state-of-the-art tool for interrogating neural circuits. In the cerebellum, Purkinje cells serve as the sole output of the cerebellar cortex where they synapse on neurons in the deep cerebellar nuclei (DCN). To investigate the properties of this synaptic connection, we sought to elicit time-locked single action potentials from Purkinje cell axons. Using optical stimulation of channelrhodopsin-2 (ChR2)-expressing Purkinje cells combined with patch-clamp recordings of Purkinje cells and DCN neurons in acute cerebellar slices, we determine the photostimulation parameters required to elicit single time-locked action potentials from Purkinje cell axons. We show that axons require longer light pulses than somata do to elicit single action potentials and that Purkinje cell axons are also more susceptible to light perturbations. We then demonstrate that these empirically determined photostimulation parameters elicit time-locked synaptic currents from postsynaptic cells in the DCN. Our results highlight the importance of optimizing optogenetic stimulation conditions to interrogate synaptic connections.

ABSTRACT The human pathogens Neisseria gonorrhoeae and Neisseria meningitidis share high genome identity. Retrospective analysis of surveillance data from New Zealand indicates the potential cross-protective effect of outer membrane vesicle (OMV) meningococcal serogroup B vaccine (MeNZB) against N. gonorrhoeae. A licensed OMV-based MenB vaccine, MenB-4C, consists of a recombinant FHbp, NhbA, NadA, and the MeNZB OMV. Previous work has identified several abundantly expressed outer membrane proteins (OMPs) as major components of the MenB-4C OMV with high sequence similarity between N. gonorrhoeae and N. meningitidis, suggesting a mechanism for cross-protection. To build off these findings, we performed comparative genomic analysis on 970 recent N. gonorrhoeae isolates collected through a U.S surveillance system against N. meningitidis serogroup B (NmB) reference sequences. We identified 1,525 proteins that were common to both Neisseria species, of which 57 proteins were predicted to be OMPs using in silico methods. Among the MenB-4C antigens, NhbA showed moderate sequence identity (73%) to the respective gonococcal homolog, was highly conserved within N. gonorrhoeae, and was predicted to be surface expressed. In contrast, the gonococcal FHbp was predicted not to be surface expressed, while NadA was absent in all N. gonorrhoeae isolates. Our work confirmed recent observations (E. A. Semchenko, A. Tan, R. Borrow, and K. L. Seib, Clin Infect Dis, 2018, https://doi.org/10.1093/cid/ciy1061) and describes homologous OMPs from a large panel of epidemiologically relevant N. gonorrhoeae strains in the United States against NmB reference strains. Based on our results, we report a set of OMPs that may contribute to the previously observed cross-protection and provide potential antigen targets to guide the next steps in gonorrhea vaccine development. IMPORTANCE Gonorrhea, a sexually transmitted disease, causes substantial global morbidity and economic burden. New prevention and control measures for this disease are urgently needed, as strains resistant to almost all classes of antibiotics available for treatment have emerged. Previous reports demonstrate that cross-protection from gonococcal infections may be conferred by meningococcal serogroup B (MenB) outer membrane vesicle (OMV)-based vaccines. Among 1,525 common proteins shared across the genomes of both N. gonorrhoeae and N. meningitidis, 57 proteins were predicted to be surface expressed (outer membrane proteins [OMPs]) and thus preferred targets for vaccine development. The majority of these OMPs showed high sequence identity between the 2 bacterial species. Our results provide valuable insight into the meningococcal antigens present in the current OMV-containing MenB-4C vaccine that may contribute to cross-protection against gonorrhea and may inform next steps in gonorrhea vaccine development.

Although both exercise and thyroid hormone (TH) status can cause cellular and metabolic changes in skeletal muscle, the impact of TH status on exercise-associated changes is not well understood. Here, we examined the effects of TH status on muscle fiber type, cell signaling, and metabolism in a rabbit model of exercise training – chronic motor nerve stimulation (CMNS). Five rabbits were rendered hypothyroid for 7–8 weeks and three rabbits were made hyperthyroid for 2 weeks prior to CMNS of the left peroneal nerve for 10 days. We then measured markers of muscle fiber type, autophagy, and nutrient- or energy-sensing proteins, and metabolic intermediates. CMNS increased MHC-I expression in hypothyroid rabbits, whereas it was unchanged in hyperthyroid rabbits. CMNS also increased p-AMPK, p-ATGL, CPT-1α, p-Akt, GLUT4, and p-70S6K in hypothyroid rabbits. In contrast, p-AMPK and p-AKT were increased at baseline in hyperthyroid rabbits, but CMNS did not further increase them or any of the other markers. CMNS also increased TCA cycle and acylcarnitine metabolites in hypothyroid rabbits; whereas, acylcarnitines were already elevated in hyperthyroid rabbits, and were only slightly increased further by CMNS. In summary, CMNS effects on cell signaling and metabolism of skeletal muscle were more pronounced in the hypothyroid than the hyperthyroid state. Interestingly, in the hypothyroid state, CMNS caused concomitant activation of two signaling pathways that are usually reciprocally regulated – AMPK and mTOR signaling – which manifested as increased β-oxidation, MHC-I expression, and protein synthesis. Thus, our findings provide insight into the role of TH status on exercise response in muscle. Our observations suggest that TH status of patients may be an important determinant and predictor of their response to exercise training in skeletal muscle.

ABSTRACT “Candidatus Synechococcus feldmannii” is a facultative intracellular symbiont of the Atlanto-Mediterranean sponge Petrosia ficiformis. Genomic information of sponge-associated cyanobacteria derives thus far from the obligate and extracellular symbiont “Candidatus Synechococcus spongiarum.” Here we utilized a differential methylation-based approach for bacterial DNA enrichment combined with metagenomics to obtain the first draft genomes of “Ca. Synechococcus feldmannii.” By comparative genomics, we revealed that some genomic features (e.g., iron transport mediated by siderophores, eukaryotic-like proteins, and defense mechanisms, like CRISPR-Cas [clustered regularly interspaced short palindromic repeats-associated proteins]) are unique to both symbiont types and absent or rare in the genomes of taxonomically related free-living cyanobacteria. These genomic features likely enable life under the conditions found inside the sponge host. Interestingly, there are many genomic features that are shared by “Ca. Synechococcus feldmannii” and free-living cyanobacteria, while they are absent in the obligate symbiont “Ca. Synechococcus spongiarum.” These include genes related to cell surface structures, genetic regulation, and responses to environmental stress, as well as the composition of photosynthetic genes and DNA metabolism. We speculate that the presence of these genes confers on “Ca. Synechococcus feldmannii” its facultative nature (i.e., the ability to respond to a less stable environment when free-living). Our comparative analysis revealed that distinct genomic features depend on the nature of the symbiotic interaction: facultative and intracellular versus obligate and extracellular. IMPORTANCE Given the evolutionary position of sponges as one of the earliest phyla to depart from the metazoan stem lineage, studies on their distinct and exceptionally diverse microbial communities should yield a better understanding of the origin of animal-bacterium interactions. While genomes of several extracellular sponge symbionts have been published, the intracellular symbionts have, so far, been elusive. Here we compare the genomes of two unicellular cyanobacterial sponge symbionts that share an ancestor but followed different evolutionary paths—one became intracellular and the other extracellular. Counterintuitively, the intracellular cyanobacteria are facultative, while the extracellular ones are obligate. By sequencing the genomes of the intracellular cyanobacteria and comparing them to the genomes of the extracellular symbionts and related free-living cyanobacteria, we show how three different cyanobacterial lifestyles are reflected by adaptive genomic features.

Students will take independent action to improve their writing when they believe those actions will have a positive effect. The data presented focuses on the self-regulatory writing behaviours of nursing students in their third year. The purpose was to explore patterns of writing self-efficacy, anxiety levels, and student grade point average (GPA) in relation to student choices with help seeking, advanced planning of writing, revision habits, and response to feedback. Low writing self-efficacy, high anxiety students sought help from more sources, reported their feedback made them feel negative about their capabilities as writers, and were less likely to report reading and applying feedback to future writing efforts. No patterns of writing self-efficacy or anxiety levels emerged with respect to student revision habits or their choice to begin their assignments in advance of the due date. GPA was also not associated with the writing self-regulatory choices assessed. As the primary writing support for students in the later years of a nursing program, educators should consider interventions that encourage help seeking, facilitate students’ understanding and integration of the feedback they receive into their assignment revisions, and normalize the negative emotions that interfere with the self-efficacy levels required to write well.Les étudiants vont prendre des mesures indépendantes afin d’améliorer leur écriture quand ils pensent que ces mesures vont avoir des résultats positifs. Les données présentées se concentrent sur les comportements d’auto-régulation d’étudiants de troisième année en sciences infirmières. L’objectif était d’explorer les tendances de l’auto-efficacité de l’écriture, les niveaux d’anxiété et la moyenne générale des étudiants par rapport aux choix des étudiants pour chercher à se faire aider, planifier l’écriture à l’avance, leurs habitudes de révision et la réponse au feedback. Les étudiants ayant une mauvaise auto-efficacité de l’écriture et qui étaient anxieux ont cherché à se faire aider auprès de davantage de sources, ils ont rapporté que leur feedback leur avait donné un sentiment négatif concernant leurs capacités en tant que rédacteurs et ils avaient moins tendance à rapporter leurs lectures et à appliquer le feedback reçu à leurs efforts futurs en rédaction. Aucune tendance d’auto-efficacité de l’écriture ou de niveaux d’anxiété ne sont apparus en ce qui concerne les habitudes de révision des étudiants ou leurs choix pour commencer leurs travaux à l’avance par rapport à la date où ceux-ci devaient être remis. La moyenne générale n’était également pas liée aux choix évalués d’auto-efficacité de l’écriture. En tant que soutien de rédaction principal des étudiants au cours des dernières années du programme de soins infirmiers, les éducateurs devraient envisager des interventions qui encouragent les étudiants à chercher de l’aide, à faciliter leur compréhension et l’intégration du feedback qu’ils reçoivent dans les révisions de leurs travaux, et à normaliser les émotions négatives qui perturbent les niveaux d’auto-efficacité indispensables pour bien écrire.

The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides, and draught power. The global water buffalo population is predominantly found in Asia, and per head of population more people depend upon the buffalo than on any other livestock species. Despite its agricultural importance, there are comparatively fewer genomic and transcriptomic resources available for buffalo than for other livestock species. We have generated a large-scale gene expression atlas covering multiple tissue and cell types from all major organ systems collected from three breeds of riverine water buffalo (Mediterranean, Pandharpuri and Bhadawari) and used the network analysis tool Graphia Professional to identify clusters of genes with similar expression profiles. Alongside similar data, we and others have generated for ruminants as part of the Functional Annotation of Animal Genomes Consortium; this comprehensive transcriptome supports functional annotation and comparative analysis of the water buffalo genome.

ABSTRACT Microorganisms can have a profound and varying effect on the chemical character of environments and, thereby, ecological health. Their capacity to consume or transform contaminants leads to contrasting outcomes, such as the dissipation of nutrient pollution via denitrification, the breakdown of spilled oil, or eutrophication via primary producer overgrowth. Recovering the genomes of organisms directly from the environment is useful to gain insights into resource usage, interspecies collaborations (producers and consumers), and trait acquisition. Microbial data can also be considered alongside the broader biological character of an environment through the co-recovery of eukaryotic DNA. The contributions of individual microorganisms (bacteria, archaea, and protists) to snapshots of ecosystem processes can be determined by integrating genomics with functional methods. This combined approach enables a detailed understanding of how microbial communities drive biogeochemical cycles, and although currently limited by scale, key attributes can be effectively extrapolated with lower-resolution methods to determine wider ecological relevance.

Background: MicroRNAs have been implicated in the pathogenesis of rheumatoid arthritis (RA), obesity, and altered metabolism. Although RA is associated with both obesity and altered metabolism, expression of RA-related microRNA in the setting of these cardiometabolic comorbidities is unclear. Our objective was to determine relationships between six RA-related microRNAs and RA disease activity, inflammation, body composition, and metabolic function.Methods: Expression of plasma miR-21, miR-23b, miR-27a, miR-143, miR-146a, and miR-223 was measured in 48 persons with seropositive and/or erosive RA (mean DAS-28-ESR 3.0, SD 1.4) and 23 age-, sex-, and BMI-matched healthy controls. Disease activity in RA was assessed by DAS-28-ESR. Plasma cytokine concentrations were determined by ELISA. Body composition was assessed using CT scan to determine central and muscle adipose and thigh muscle tissue size and tissue density. Plasma and skeletal muscle acylcarnitine, amino acid, and organic acid metabolites were measured via mass-spectroscopy. Plasma lipoproteins were measured via nuclear magnetic resonance (NMR) spectroscopy. Spearman correlations were used to assess relationships for microRNA with inflammation and cardiometabolic measures. RA and control associations were compared using Fisher transformations.Results: Among RA subjects, plasma miR-143 was associated with plasma IL-6 and IL-8. No other RA microRNA was positively associated with disease activity or inflammatory markers. In RA, microRNA expression was associated with adiposity, both visceral adiposity (miR-146a, miR-21, miR-23b, and miR-27a) and thigh intra-muscular adiposity (miR-146a and miR-223). RA miR-146a was associated with greater concentrations of cardiometabolic risk markers (plasma short-chain dicarboxyl/hydroxyl acylcarnitines, triglycerides, large VLDL particles, and small HDL particles) and lower concentrations of muscle energy substrates (long-chain acylcarnitines and pyruvate). Despite RA and controls having similar microRNA levels, RA, and controls differed in magnitude and direction for several associations with cytokines and plasma and skeletal muscle metabolic intermediates.Conclusion: Most microRNAs thought to be associated with RA disease activity and inflammation were more reflective of RA adiposity and impaired metabolism. These associations show that microRNAs in RA may serve as an epigenetic link between RA inflammation and cardiometabolic comorbidities.

Objectives: Considering the critical role of microRNAs (miRNAs) in regulation of cell activation, we investigated their role in circulating type-2 conventional dendritic cells (cDC2s) of patients with primary Sjögren's syndrome (pSS) compared to healthy controls (HC).Methods: CD1c-expressing cDC2s were isolated from peripheral blood. A discovery cohort (15 pSS, 6 HC) was used to screen the expression of 758 miRNAs and a replication cohort (15 pSS, 11 HC) was used to confirm differential expression of 18 identified targets. Novel targets for two replicated miRNAs were identified by SILAC in HEK-293T cells and validated in primary cDC2s. Differences in cytokine production between pSS and HC cDC2s were evaluated by intracellular flow-cytometry. cDC2s were cultured in the presence of MSK1-inhibitors to investigate their effect on cytokine production.Results: Expression of miR-130a and miR-708 was significantly decreased in cDC2s from pSS patients compared to HC in both cohorts, and both miRNAs were downregulated upon stimulation via endosomal TLRs. Upstream mediator of cytokine production MSK1 was identified as a novel target of miR-130a and overexpression of miR-130a reduced MSK1 expression in cDC2s. pSS cDC2s showed higher MSK1 expression and an increased fraction of IL-12 and TNF-α-producing cells. MSK1-inhibition reduced cDC2 activation and production of IL-12, TNF-α, and IL-6.Conclusions: The decreased expression of miR-130a and miR-708 in pSS cDC2s seems to reflect cell activation. miR-130a targets MSK1, which regulates pro-inflammatory cytokine production, and we provide proof-of-concept for MSK1-inhibition as a therapeutic avenue to impede cDC2 activity in pSS.

Background: Increasing albumin to creatinine ratio (ACR) within the normal range is a risk factor for cardiovascular disease in the general population. Clinical and epidemiological studies often store urine samples for long durations prior to ACR assessment. The stability of ACR at the lowest urinary albumin concentrations during prolonged storage has not been previously studied because routine clinical assays can’t quantify very low concentrations of albumin. Aim: To determine the stability of urinary albumin and creatinine over 12 months in samples stored at −20 °C and −80 °C using an assay which enables assessment of previously undetectable levels of albumin and to investigate if additives can be used to prevent urinary albumin degradation. Method: ACR was measured in 30 urine samples from healthy subjects on the day of collection. Each sample was divided into 5 portions, each receiving a different treatment; alkalisation, protease inhibiter, boric acid, low protein binding tubes and no treatment (control). Samples were stored at −20 °C and −80 °C and ACR was analysed again after 12 months. Results: Mean (95% CI) percent change in ACR was −34.3% (−47.2 to −21.4; p

Background: STRRIDE (Studies Targeting Risk Reduction Interventions through Defined Exercise) was an eight-month exercise study conducted from 1998–2003. Subjects were randomized to control or one of three exercise groups differing in intensity and amount. To determine if there were legacy effects, we invited 161 individuals who completed the intervention phase to return for a 10-year Reunion study.Methods: Subjects completed medical history and physical activity questionnaires. Height, body weight, blood pressure, waist circumference, and peak VO2 were measured. Fasting blood samples were analyzed for glucose, insulin and lipids. Of 161 original subjects, 153 were within 10 years of STRRIDE completion. Of these, 28 were lost to follow-up and 21 declined to participate in the Reunion study. Overall, 104 subjects (83% eligible) participated. Change over time was computed as the 10-year Reunion value minus the pre-intervention value. Significant within group changes were calculated using two-tailed t-tests. ANCOVA determined differences among groups with pre-intervention values as covariates. Bonferroni corrections were applied to account for multiple comparisons.Results: Ten years after completing STRRIDE, there were a number of group-specific health and fitness legacy effects. Original participation in either the moderate intensity exercise or control group resulted in a 10.5% decrease in peak VO2 over the ensuing 10 years. Conversely, both vigorous intensity groups experienced only a 4.7% decrement in cardiorespiratory fitness over that time period. As compared to controls, all three exercise groups experienced smaller increases in waist circumference. Those who participated in moderate intensity exercise experienced the greatest 10-year reduction in fasting insulin. Compared to all other groups, the moderate intensity subjects had greater reductions in mean arterial pressure at the Reunion timepoint.Summary: Ten years after completing a randomized eight-month exercise training intervention, previously sedentary individuals exhibited group-specific differences consistent with an intervention-based legacy effect on cardiorespiratory fitness and cardiometabolic parameters. These findings highlight the critical need to better understand the sustained legacy health effects of exercise training interventions.

Spirochaetes of the Borrelia burgdorferi sensu lato complex, which includes those that cause Lyme disease, have not been identified in Australia. Nevertheless, Australian patients exist, some of whom have not left the country, who have symptoms consistent with so-called "chronic Lyme disease". Blood specimens from these individuals may be tested in Australian laboratories and in specialist laboratories outside Australia and sometimes conflicting results are obtained. Such discrepancies cause the patients to question the results from the Australian laboratories and seek assistance from the Australian Government in clarifying why the discrepancies occur. The aim of this study was to determine the level of agreement in results between commonly used B. burgdorferi serology assays in specimens of known status, and between results reported by different laboratories when they use the same serology assay. Five immunoassays and five immunoblots used in Australia and elsewhere were examined for the detection of IgG antibodies to Borrelia burgdorferi sensu lato. Predominantly, archived specimens previously tested for Lyme disease were used for the study and included 639 contributed by seven clinical laboratories located either in Australia or in areas endemic for Lyme disease. Also included were 308 prospectively collected Australian blood donor specimens. All clinical specimens were tested in all 10 assays whereas blood donor specimens were tested in all immunoassays and a subset was tested on immunoblots. With the exception of one immunoblot, the results between the assays agreed with each other in a known positive specimen population ≥ 77% of the time and in a known negative population, 88% of the time or greater. The test results obtained during the study were different from the participating laboratory's less than 2% of the time when the same assay was used. These findings suggest that discordance in results between laboratories is more likely due to variation in algorithms or in the use of assays with different sensitivities or specificities rather than conflicting results being reported from the same assay in different laboratories. In the known negative population, specificities of the immunoassays ranged between 87.7% and 99.7%. In Australia's low prevalence population, this would translate to a positive predictive value of < 4%.

INTRODUCTION:The additional value of ST analysis during labour is uncertain. In ST analysis, a T/QRS baseline value is calculated from the fetal electrocardiogram and successive T/QRS ratios are compared to this baseline. However, variation in the orientation of the electrical heart axis between fetuses may yield different T/QRS baseline values. In case of a higher T/QRS baseline value more ST events are encountered, although not always related to perinatal outcome. We hypothesised that we can partly correct for this effect by analysing T/QRS rises as a percentage from baseline (relative ST analysis). This study aimed to explore whether relative ST analysis has better diagnostic value for cord acidaemia compared to conventional ST analysis, where predefined fixed T/QRS ratios are used. METHODS AND MATERIALS:A case-control study was performed in 20 term human fetuses during labour; 10 cases (umbilical cord artery pH 7.20) were included. The fetal electrocardiogram was recorded using a STAN monitor. We electronically extracted all T/QRS values, baseline and episodic ST events from the STAN monitor and calculated the relative T/QRS changes. The cut-off for relative ST events was determined in a receiver operator characteristic (ROC) curve at optimal specificity for cord acidaemia. Parameters of interest were area under the curve (AUC) of the ROC curve for relative ST events and test performance of both conventional and relative ST analysis. RESULTS:Relative ST analysis showed an AUC of 0.99. The optimal cut-off value for relative T/QRS rise was determined at 0.70. Relative vs conventional (absolute) ST analysis showed a specificity of 100% vs 40% (p = 0.031); sensitivity 90% vs 90%; positive likelihood ratio infinity vs 1.5; negative likelihood ratio 0.10 vs 0.25, respectively. CONCLUSION:Relative ST analysis seems to be a promising method to detect impending fetal acidaemia during labour. Further studies are required to determine the diagnostic accuracy.

The objectives of this study were to explore the goodness of fit between the bereaved peoples' needs and the support offered by their social networks; to ascertain whether this support was experienced as helpful or unhelpful by bereaved people; and to explore both the types of social networks that offer effective support and the characteristics of the communities that encourage and nurture such networks. This study was based on qualitative interviews from twenty bereaved people, in Western Australia, interviewed in 2013. A framework analysis of these interviews was undertaken using a deductive approach based on the goodness of fit framework. Much of this support is provided informally in community settings by a range of people already involved in the everyday lives of those recently bereaved; and that support can be helpful or unhelpful depending on its amount, timing, function and structure. Improving the fit between the bereaved person's needs and the support offered may thus involve identifying and enhancing the caring capacity of existing networks. An important strategy for achieving this is to train community members in mapping and developing these naturally occurring networks. Some such networks will include relationships of long standing, others may be circles of care formed during a period of caring. Peer support bereavement networks develop from these existing networks and may also recruit new members who were not part of the caring circle. The findings endorse social models of bereavement care that fit within a public health approach rather than relying solely on professional care. As exemplified by Compassionate Communities policies and practices, establishing collaboration between community networks and professional services is vital for effective and sustainable bereavement care.

ABSTRACT Recent reports suggest that mosaic-like sequences within the mtr (multiple transferable resistance) efflux pump locus of Neisseria gonorrhoeae, likely originating from commensal Neisseria sp. by transformation, can increase the ability of gonococci to resist structurally diverse antimicrobials. Thus, acquisition of numerous nucleotide changes within the mtrR gene encoding the transcriptional repressor (MtrR) of the mtrCDE efflux pump-encoding operon or overlapping promoter region for both along with those that cause amino acid changes in the MtrD transporter protein were recently reported to decrease gonococcal susceptibility to numerous antimicrobials, including azithromycin (Azi) (C. B. Wadsworth, B. J. Arnold, M. R. A. Satar, and Y. H. Grad, mBio 9:e01419-18, 2018, https://doi.org/10.1128/mBio.01419-18). We performed detailed genetic and molecular studies to define the mechanistic basis for why such strains can exhibit decreased susceptibility to MtrCDE antimicrobial substrates, including Azi. We report that a strong cis-acting transcriptional impact of a single nucleotide change within the −35 hexamer of the mtrCDE promoter as well gain-of-function amino acid changes at the C-terminal region of MtrD can mechanistically account for the decreased antimicrobial susceptibility of gonococci with a mosaic-like mtr locus. IMPORTANCE Historically, after introduction of an antibiotic for treatment of gonorrhea, strains of N. gonorrhoeae emerge that display clinical resistance due to spontaneous mutation or acquisition of resistance genes. Genetic exchange between members of the Neisseria genus occurring by transformation can cause significant changes in gonococci that impact the structure of an antibiotic target or expression of genes involved in resistance. The results presented here provide a framework for understanding how mosaic-like DNA sequences from commensal Neisseria that recombine within the gonococcal mtr efflux pump locus function to decrease bacterial susceptibility to antimicrobials, including antibiotics used in therapy of gonorrhea.

Background: Central haemodynamic parameters derived from reservoir pressure analysis (RPA-parameters) exhibit prognostic utility. Alterations in reservoir function could have an unfavourable influence on target organs, such as the kidneys. We determined in older adults whether these RPA-parameters would be associated with the reduction in estimated glomerular filtration rate (eGFR) during a 3-year follow-up period. Methods: We studied 544 individuals (69.4 ± 7.9 yrs, 195F, 235CVD) at baseline and after 3 years. RPA-parameters including reservoir pressure integral (INTPR), peak reservoir pressure, excess pressure integral, systolic and diastolic rate constants were obtained by radial artery tonometry. Results: After 3 years, 95 individuals (72.4 ± 7.6 yrs, 26F) had an eGFR reduction of more than 5 ml/min/1.73 m2/year. A multivariate logistic regression analysis revealed that baseline INTPR was independently associated with the eGFR reduction after adjusting for conventional risk factors and baseline renal function [odds ratio 0.975 (95% CI, 0.958–0.993), p < 0.01]. When the eGFR reduction was expressed as a continuous variable, baseline INTPR was also independently associated with changes in eGFR (β = 0.115, p < 0.01; multivariate linear regression with adjustment for conventional risk factors and baseline renal function). These associations remained unchanged after further adjustments for central artery stiffness or traditional central haemodynamic parameters. No other RPA-parameters exhibited significant associations. Conclusions: These findings demonstrate that baseline INTPR is independently associated with the eGFR reduction in older adults, suggesting that INTPR may play a role in the functional decline of the kidneys.

Obesity prevalence among Hispanic children is twice that of non-Hispanic white children; Hispanic children may also engage in less physical activity (PA) compared to non-Hispanic white children. A large number of U.S. preschool-aged children are cared for in Family Child Care Homes (FCCH), yet few studies have examined PA levels and ethnicity differences in PA levels among these children. We examine baseline data from a cluster-randomized trial (Healthy Start/Comienzos Sanos) to improve food and PA environments in FCCHs. Children aged 2-to-5-years (n = 342) wore triaxial accelerometers for two days in FCCHs. Variables examined include percentage of time (%) spent in sedentary, and light, moderate, and vigorous PA. The full dataset (n = 342) indicated sedentary behavior 62% ± 11% of the time and only 10% ± 5% of the time spent in moderate-to-vigorous PA. Among children in the upper-median half of wear-time (n = 176), Hispanic children had significantly greater % sedentary time vs. Non-Hispanic children (66.2% ± 8.3% vs. 62.6% ± 6.9%, p = 0.007), and lower % light PA (25.4% ± 6.3% vs. 27.7% ± 4.9%, p = 0.008) and moderate PA (5.5% ± 2.1% vs. 6.4% ± 2.2%, p = 0.018). Our results highlight that PA levels were lower among our sample compared to previous studies, and that Hispanic children were more sedentary and less active compared to non-Hispanic white children.

Fish swimming performance is strongly influenced by flow hydrodynamics, but little is known about the relation between fine-scale fish movements and hydrodynamics based on in-situ investigations. In the presented study, we validated the etho-hydraulic fish swimming direction model presented in the River Mandal from Southern Norway, using similar behavioral and hydraulic data on salmon smolts from the River Orkla in Central Norway. The re-parametrized model explained the variation of the swimming direction of fish in the Orkla system in same degree as the original model performed in the Mandal system (R2: 84% in both cases). The transferability of the model when using it from one river to predict swimming direction in the other river was lower (R2: 21% and 26%), but nevertheless relatively high given that the two localities differed in hydraulic conditions. The analyses thus provide support for the fact that the identified hydraulic parameters and their interaction affected smolt behavior in a similar way at the two sites, but that local parametrization of the base model is required. The developed etho-hydraulic models can provide important insights into fish behavior and fish migration trajectories and can be developed into prediction models important for the future development of behavioral downstream migration solutions.

Myxomatous mitral valve disease (MMVD) is the most common cardiac disease in dogs. It varies from dogs without clinical signs to those developing left-sided congestive heart failure, leading to death. Cavalier King Charles Spaniels (CKCSs) are particularly susceptible to MMVD. We hypothesised that within the elderly CKCS population, there is a sub-cohort of MMVD-affected dogs that do not have cardiac remodelling. The objectives of the present study were (i) to determine the prevalence and the degree of cardiac remodelling associated with MMVD; and (ii) assess the effect of age, gender, and body weight on echocardiographic status in a population of aged CKCSs. A total of 126 CKCSs ≥ 8 years old were prospectively included. They all had a physical and echocardiographic examination. A systolic murmur was detected in 89% of dogs; the presence of clinical signs was reported in 19% of them; and echocardiographic evidence of MMVD was described in 100%. Despite the high prevalence, 44.4% of the dogs were clear of echocardiographic signs of cardiac remodelling. Age was significantly associated with the presence and severity of cardiac remodelling and mitral valve prolapse. Our results showed that a proportion of elderly CKCS with confirmed MMVD did not undergo advanced stages of this pathology.