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Campylobacter jejuni is a significant cause of human gastroenteritis worldwide and all strains express an N-glycan that is added to at least 80 different proteins. We characterized 98 C. jejuni isolates from infants from seven low- and middle-income countries and identified 4 isolates unreactive with our N-glycan-specific antiserum that was raised against the C. jejuni heptasaccharide composed of GalNAc-GalNAc-GalNAc(Glc)-GalNAc-GalNAc-diNAcBac. Mass spectrometric analyses indicated these isolates express a hexasaccharide lacking the glucose branch. Although all 4 strains encode the PglI glucosyltransferase (GTase), one aspartate in the DXDD motif was missing, an alteration also present in ~4% of all available PglI sequences. Deleting this residue from an active PglI resulted in a non-functional GTase when the protein glycosylation system was reconstituted in E. coli, while replacement with Glu/Ala was not deleterious. Molecular modelling proposed a mechanism for how the DXDD residues and the structure/length beyond the motif influences activity. Mouse vaccination with an E. coli strain expressing the full-length heptasaccharide produced N-glycan-specific antibodies and a corresponding reduction in Campylobacter colonization and weight loss following challenge. However, the antibodies did not recognize the hexasaccharide and were unable to opsonize C. jejuni isolates lacking glucose suggesting this should be considered when designing N-glycan based vaccines to prevent campylobacteriosis.

A state-of-the-art canopy modelling framework was used to predict changes in crop carbon uptake after Rubisco substitutions. We provide a new perspective and improve predictions from previous Rubisco modelling studies at the leaf level., Improving the performance of the CO2-fixing enzyme Rubisco is among the targets for increasing crop yields. Here, Earth system model (ESM) representations of canopy C3 and C4 photosynthesis were combined with species-specific Rubisco parameters to quantify the consequences of bioengineering foreign Rubiscos into C3 and C4 crops under field conditions. The ‘two big leaf’ (sunlit/shaded) model for canopy photosynthesis was used together with species-specific Rubisco kinetic parameters including maximum rate (Kcat), Michaelis–Menten constant for CO2 at ambient atmospheric O2 (Kc21%O2), specificity for CO2 to O2 (Sc/o), and associated heat activation (Ha) values. Canopy-scale consequences of replacing native Rubiscos in wheat, maize, and sugar beet with foreign enzymes from 27 species were modelled using data from Ameriflux and Fluxnet databases. Variation among the included Rubisco kinetics differentially affected modelled carbon uptake rates, and Rubiscos from several species of C4 grasses showed the greatest potential of >50% carbon uptake improvement in wheat, and >25% improvement in sugar beet and maize. This study also reaffirms the need for data on fully characterized Rubiscos from more species, and for better parameterization of ‘Vcmax’ and temperature response of ‘Jmax’ in ESMs.

A diverse array of organisms induce plants to form galls. This phenomenon is one of the most striking instances of convergent evolution, yet the underlying mechanism is only well understood in gall-inducing microbes. To determine if gall induction by insects is associated with bacterial symbiosis, we used 16S rRNA gene sequencing to examine the microbiome of a variety of gall-inducing and non-gall-inducing insects. Overall, we did not find any bacterial signature of gall induction among the insect species we surveyed. There were no specific bacterial taxa that were consistently associated with gall induction. Microbiome diversity differed significantly among species of host insects, but not between gall- and non-gall-inducing insect species. Bacterial community composition also differed strongly among insect species, but not in a systematic way between gall-inducing and non-gall-inducing species. Furthermore, two gall-inducing species harbored highly variable microbiomes with relatively few bacterial sequences, characteristics that suggest a lack of abundant bacterial symbionts. Together, these findings argue that gall induction is not consistently mediated by a bacterial symbiont or bacterial community and may be symbiont-independent, at least in some insect species. While symbionts may still contribute to gall induction in specific instances, we suggest that the convergent evolution of gall induction is more typically driven by endogenous mechanisms, with potential contributions from horizontal gene transfer.

There is limited guidance on how to assess the ethical acceptability of research risks that extend beyond research participants to third parties (or "research bystanders"). Community or stakeholder engagement has been proposed as one way to address potential harms to community members, including bystanders. Despite widespread agreement on the importance of community engagement in biomedical research, this umbrella term includes many different goals and approaches, agreement on which is ethically required or recommended for a particular context. We analyse the case of a potential Zika virus human challenge trial to assess whether and how community engagement can help promote the ethical acceptability of research posing risks to bystanders. We conclude that, in addition to having intrinsic value, community engagement can improve the identification of bystander risks, effective approaches to minimizing them, and transparency about bystander risks for host communities.

Postoperative vomiting (POV) in children is frequent. Dextrose-containing intravenous fluids in the perioperative period have shown improvement of POV in adults. Similar studies have not been done in children. The primary purpose was to study the efficacy of intraoperative intravenous dextrose for antiemetic prophylaxis in children undergoing ambulatory surgery. A non-inferiority randomized clinical trial of healthy children (three to nine years old) undergoing ambulatory dental surgery was conducted. The control group received dexamethasone (0.15 mg·kg−1 iv) and ondansetron (0.05 mg·kg−1 iv); the intervention group received dexamethasone (0.15 mg·kg−1 iv) and intravenous 5% dextrose in 0.9% normal saline according to a weight-based maintenance rate. The primary outcome was POV in the postanesthetic care unit (PACU) within two hr after surgery. Secondary outcomes included POV within 24 hr from discharge and unplanned hospital admission. A non-inferiority analysis was conducted on the primary outcome using an absolute risk difference of 7.5% as the non-inferiority margin. Data from 290 patients were analyzed. Demographics and intraoperative anesthetic management were similar between groups. Vomiting in the PACU occurred in 7.6% and 3.5% of the dextrose and ondansetron groups, respectively, with a risk difference of 4.2% (95% confidence interval [CI], -1.0 to 9.5). Given that the upper limit of the 95% CI exceeded our non-inferiority margin, non-inferiority of dextrose compared with ondansetron was not shown. These results do not support the use of intravenous dextrose as a satisfactory alternative to ondansetron to prevent POV in ambulatory pediatric dental surgery patients. www.clinicaltrials.gov (NCT 01912807); registered 18 July 2013.

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study ofgcof adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA in 2016 and 2017). Five genomic regions significantly associated withgcwere resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction ofgcin locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control ofgcand have the potential to help breeders more effectively develop drought-tolerant maize for target environments.Article summaryThe cuticle serves as the major barrier to water loss when stomata are closed at night and under water-limited conditions and potentially relevant to drought tolerance in crops. We performed a genome-wide association study to elucidate the genetic architecture of natural variation for maize leaf cuticular conductance. We identified epidermally expressed candidate genes that are potentially involved in cuticle biosynthesis, trafficking and deposition, cutin polymerization, and cell wall modification. Finally, we observed moderately high predictive abilities for whole-genome prediction of leaf cuticular conductance. Collectively, these findings may help breeders more effectively develop drought-tolerant maize.

Highlights • First description of Elastic Light Scatter analysis for characterisation of Arcobacter species. • Discrimination of pathogenic from environmental Arcobacter species in shellfish achieved. • Significant growth rate differences between species documented., An increasing number of Arcobacter species (including several regarded as emerging human foodborne pathogens) have been isolated from shellfish, an important food commodity. A method to distinguish these species and render viable isolates for further analysis would benefit epidemiological and ecological studies. We describe a method based on Elastic Light Scatter analysis (ELSA) for the detection and discrimination of eleven shellfish-associated Arcobacter species. Although substantive differences in the growth rates of some taxa were seen, ELSA was able to differentiate all the species studied, apart from some strains of A. butzleri and A. cryaerophilus, which were nonetheless distinguished from all other species examined. ELSA appears to be a promising new approach for the detection and identification of Arcobacter species in shellfish and may also be applicable for studies in other foods and matrices.

This paper re-examines the taxonomic positions of recently described Poseidonibacter (P. parvum and P. antarcticus ), Aliarcobacter (‘Al. vitoriensis’), Halarcobacter (‘H. arenosus’) and Arcobacter ( A. caeni , A. lacus ) species, and other species proposed to represent novel genera highly related to the genus Arcobacter . Phylogenomic and several overall genome relatedness indices (OGRIs) were applied to a total of 118 representative genomes for this purpose. Phylogenomic analyses demonstrated the Arcobacter clade to be distinct from other Epsilonproteobacteria , clearly defined and containing closely related species. Aliarcobacter butzleri and Malaciobacter pacificus did not cluster with other members of these proposed genera, indicating incoherence of these genera. Every OGRI measure applied indicated a high level of relatedness among all Arcobacter clade species, including the recently described taxa studied here, and substantially lower between type species representatives for other Epsilonproteobacteria. Where published guidelines were available, OGRI values for Arcobacter clade species were either unsupportive of division into other genera or were at the lowest boundary range (for average amino acid identity). We propose that Aliarcobacter , Halarcobacter , Malaciobacter , Pseudarcobacter , Poseidonibacter and Arcobacter sensu stricto be considered members of a single genus, Arcobacter , and subsequently transfer P. parvum, P. antarcticus , ‘ Al. vitoriensis ’ and ‘H. arenosus’ to Arcobacter as Arcobacter parvum comb. nov., Arcobacter antarcticus comb. nov., Arcobacter vitoriensis comb. nov. and Arcobacter arenosus comb. nov.

Background Rare variants in gene coding regions likely have a greater impact on disease-related phenotypes than common variants through disruption of their encoded protein. We searched for rare variants associated with onset of end stage kidney disease (ESKD) in individuals with type 1 diabetes at advanced kidney disease stage. Methods Gene-based exome array analysis of 15,449 genes in 5 large incidence cohorts of individuals with type 1 diabetes and proteinuria were analyzed for survival time-to-ESKD, testing the top gene in a 6th cohort (N=2,372/1,115 events all cohorts) and replicating in two retrospective case-control studies (N=1,072 cases, 752 controls). Deep resequencing of the top associated gene in 5 cohorts confirmed the findings. We performed immunohistochemistry and gene expression experiments in human control and diseased cells, and in mouse ischemia reperfusion and aristolochic acid nephropathy models. Results Protein coding variants in the hydroxysteroid 17-beta dehydrogenase 14 gene (HSD17B14), predicted to affect protein structure, had a net protective effect against development of ESKD at exome-wide significance (N=4,196; p-value=3.3x10-7). The HSD17B14 gene and encoded enzyme were robustly expressed in healthy human kidney, maximally in proximal tubular cells. Paradoxically, gene and protein expression were attenuated in human diabetic proximal tubules and in mouse kidney injury models. Expressed HSD17B14 gene and protein levels remained low without recovery after 21 days in a murine ischemic reperfusion injury model. Decreased gene expression was found in other chronic kidney disease-associated renal pathologies. Conclusions HSD17B14 gene is mechanistically involved in diabetic kidney disease. The encoded sex steroid enzyme is a druggable target, potentially opening a new avenue for therapeutic development.

Arcobacter anaerophilus was originally described as the first obligate anaerobe in this genus by Sasi Jyothsna et al. 2013. The complete genome sequence of the type strain of this species was determined and analysed. Genes characteristic for organisms capable of aerobic growth were identified, and the ability of the organism to grow under microaerobic and aerobic conditions was confirmed in two independent laboratories. The description of A. anaerophilus is thus emended and the wider ramifications of these findings are discussed.

Early life stress (ELS) may accelerate frontoamygdala development related to socioemotional processing, serving as a potential source of resilience. Whether this circuit is associated with other proposed measures of accelerated development is unknown. In a sample of young adolescents, we examined the relations among ELS, frontoamygdala circuitry during viewing of emotional faces, cellular aging as measured by telomere shortening, and pubertal tempo. We found that greater cumulative severity of ELS was associated with stronger negative coupling between bilateral centromedial amygdala and the ventromedial prefrontal cortex, a pattern that may reflect more mature connectivity. More negative frontoamygdala coupling (for distinct amygdala subdivisions) was associated with slower telomere shortening and pubertal tempo over 2 years. These potentially protective associations of negative frontoamygdala connectivity were most pronounced in adolescents who had been exposed to higher ELS. Our findings provide support for the formulation that ELS accelerates maturation of frontoamygdala connectivity and provide novel evidence that this neural circuitry confers protection against accelerated biological aging, particularly for adolescents who have experienced higher ELS. Although negative frontoamygdala connectivity may be an adaptation to ELS, frontoamygdala connectivity, cellular aging, and pubertal tempo do not appear to be measures of the same developmental process.

The walnut twig beetle, Pityophthorus juglandis Blackman (Coleoptera: Scolytidae), vectors a phytopathogenic fungus, Geosmithia morbida Kolařik et al. (Hypocreales), which causes thousand cankers disease (TCD) in walnut (Juglans sp.) and wingnut (Pterocarya sp., both Juglandaceae) trees. We investigated an early point in disease inception in two walnut species – Juglans californica S. Wats. and Juglans major (Torr. ex Sitsgr.) Heller – native to riparian forests of the western USA by comparing P. juglandis flight and landing responses to small‐diameter branch sections. Twenty unbaited branch sections (10 each of J. californica and J. major) were presented in a completely randomized design to populations of P. juglandis at the USDA Agricultural Research Service, National Clonal Germplasm Repository (NCGR) Juglans collection located at Wolfskill Experimental Orchards (Winters, CA, USA) and at the California State University, Chico, Agricultural Teaching and Research Center (ATRC, Chico, CA). These assays were carried out within a 4‐ to 6‐year period when weekly flight surveys with aggregation pheromone‐baited multiple funnel traps revealed that P. juglandis flight activity–abundance was higher at the NCGR than at the ATRC. For the landing rate assays, adhesive‐coated acetate sheets were wrapped around the branch sections and exchanged weekly. Three assays were completed at the NCGR (assays 1–3), whereas one assay was completed at the ATRC (assay 4). Landing rates on these traps were compared between J. californica and J. major. Two additional assays (5 and 6) were completed at the NCGR to compare responses to branch sections of J. californica and to similarly sized cardboard tubes (negative control). All six assays were completed over a 4‐year span during the 4‐ to 6‐year weekly flight survey period. Pooled landing rates of male and female P. juglandis (assays 1–4) demonstrated a preference by both sexes for J. californica over J. major. In assay 5 there was no preference by males or females for J. californica over the negative control, perhaps due to the low flight activity–abundance of P. juglandis during the assay. When repeated at a time of higher flight activity–abundance (assay 6), male and female landing rates on J. californica exceeded those on the negative control. Females of the invasive fruit‐tree pinhole borer (an ambrosia beetle), Xyleborinus saxeseni (Ratzeburg), and an invasive bark beetle, Hypothenemus eruditus Westwood (both Coleoptera: Scolytidae), showed relatively higher flight responses than either sex of P. juglandis during most assays, suggesting higher population densities of these two other invasive species at the two orchards or a greater sensitivity to host volatiles. Xyleborinus saxeseni and H. eruditus preferred to land on J. major over J. californica and on J. californica over the negative control. Similarly, an invasive longhorned beetle, Nathrius brevipennis (Mulsant) (Coleoptera: Cerambycidae), showed a significant preference for J. major over J. californica, but not for J. californica over the negative control. More male N. brevipennis were trapped than females at both study sites [sex ratio ranged from 5:1 (assay 6) to 39:1 (assay 4)], and flight occurred only in the spring and early summer months. Another ambrosia beetle trapped at the NCGR and ATRC, Xyleborus affinis Eichhoff, represented the first records of this species from western North America. In summary, flight responses recorded in some of our assays for P. juglandis and several other subcortical insects on Juglans indicate that host preference by these insects may be determined by long‐range olfactory cues that do not involve pheromones.

The first record of the Jefferson ground sloth, Megalonyx jeffersonii, in New York is reported. The specimen consists of a partial synsacrum recovered from a peat deposit near Newburgh, Orange County. Compared to other synsacra of Megalonyx, the number of vertebrae is anomalous with one less caudal vertebra than expected. Stable isotope analysis of the bone shows a δ13C value of 20.5‰ and implies a diet of only C3 plants. The specimen has a radiocarbon date of 11,450 ± 55 BP indicating the presence of this taxon in the region immediately prior to the extinction of the North American Pleistocene megafauna.

Campylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining their pathogenic potential. Eight C. showae genomes were assessed, four strains isolated from inflamed gut tissues from paediatric Crohn’s disease patients, three strains from colonic adenomas, and one from a gastroenteritis patient stool. Genome assemblies were analyzed alongside the only 3 deposited C. showae genomes. The pangenome from these 11 strains consisted of 4686 unique protein families, and the core genome size was estimated at 1050 ± 15 genes with each new genome contributing an additional 206 ± 16 genes. Functional assays indicated that colonic strains segregated into 2 groups: adherent/invasive vs. non-adherent/non-invasive strains. The former possessed Type IV secretion machinery and S-layer proteins, while the latter contained Cas genes and other CRISPR associated proteins. Comparison of gene profiles with strains in Human Microbiome Project metagenomes showed that gut-derived isolates share genes specific to tongue dorsum and supragingival plaque counterparts. Our findings indicate that C. showae strains are phenotypically and genetically diverse and suggest that secretion systems may play an important role in virulence potential.

Unseasonal fire occurrence is increasing globally, driven by climate change and other human activity. Changed timing of fire can inhibit postfire seedling recruitment through interactions with plant phenology (the timing of key processes, e.g., flower initiation, seed production, dispersal, germination), and therefore threaten the persistence of many plant species. Although empirical evidence from winter-rainfall ecosystems shows that optimal seedling recruitment is expected following summer and autumn (dry season) fires, we sought experimental evidence isolating the mechanisms of poor recruitment following unseasonal (wet season) fire. We implemented a seed-sowing experiment using nine species native to fire-prone, Mediterranean-climate woodlands in southwestern Australia to emulate the timing of postfire recruitment and test key mechanisms of fire seasonality effects. For seeds sown during months when fire is unseasonal (i.e., August-September: end of the wet winter season), seedling recruitment was reduced by up to 99% relative to seeds sown during seasonal fire months (i.e., May-June: end of the dry summer season) because of varying seed persistence, seedling emergence, and seedling survival. We found that up to 70 times more seedlings emerged when seeds were sown during seasonal fire months compared to when seeds were sown during unseasonal fire months. The few seedlings that emerged from unseasonal sowings all died with the onset of the dry season. Of the seeds that failed to germinate from unseasonal sowings, only 2% survived exposure on the soil surface over the ensuing hot and dry summer. Our experimental results demonstrate the potential for unseasonal fire to inhibit seedling recruitment via impacts on pregermination seed persistence and seedling establishment. As ongoing climate change lengthens fire seasons (i.e., unseasonal wildfires become more common) and managed fires are implemented further outside historically typical fire seasons, postfire seedling recruitment may become more vulnerable to failure, causing shifts in plant community composition towards those with fewer species solely dependent on seeds for regeneration.

BACKGROUND AND OBJECTIVE: Proliferative vitreoretinopathy (PVR) is the leading cause of retinal detachment repair failure. However, the molecular pathogenesis remains incompletely understood. Determining the proteome of PVR will help to identify novel therapeutic targets. MATERIALS AND METHODS: Preretinal tissue samples, delaminated during surgery from six PVR cases and one idiopathic epiretinal membrane (ERM) were analyzed by mass spectrometry. Tandem mass spectra were extracted using the UniProt database, generating a list of 896 proteins, which were subjected to pathway set and fold-change (ERM vs PVR) analyses. RESULTS: Two pathways were enriched in PVR: extracellular matrix (ECM) organization and extracellular structure organization. A fold-change analysis comparing mean total spectral counts from PVR to an ERM control identified fibronectin, the ECM glycoprotein, as the protein most significantly elevated in PVR compared to ERM. CONCLUSION: These data identify pathwayskey to PVR progression, including thoseinvolved in cell-mediated ECM assembly and thus tractional force generation at the cellular level. [ Ophthalmic Surg Lasers Imaging Retina . 2021;52:S5–S12.]

Background Skeletal muscle atrophy, whether caused by chronic disease, acute critical illness, disuse or aging, is characterized by tissue-specific decrease in oxidative capacity and broad alterations in metabolism that contribute to functional decline. However, the underlying mechanisms responsible for these metabolic changes are largely unknown. One of the most highly upregulated genes in atrophic muscle is AMP deaminase 3 (AMPD3: AMP → IMP + NH3), which controls the content of intracellular adenine nucleotides (AdN; ATP + ADP + AMP). Given the central role of AdN in signaling mitochondrial gene expression and directly regulating metabolism, we hypothesized that overexpressing AMPD3 in muscle cells would be sufficient to alter their metabolic phenotype similar to that of atrophic muscle. Methods AMPD3 and GFP (control) were overexpressed in mouse tibialis anterior (TA) muscles via plasmid electroporation and in C2C12 myotubes using adenovirus vectors. TA muscles were excised one week later, and AdN were quantified by UPLC. In myotubes, targeted measures of AdN, AMPK/PGC-1α/mitochondrial protein synthesis rates, unbiased metabolomics, and transcriptomics by RNA sequencing were measured after 24 h of AMPD3 overexpression. Media metabolites were measured as an indicator of net metabolic flux. At 48 h, the AMPK/PGC-1α/mitochondrial protein synthesis rates, and myotube respiratory function/capacity were measured. Results TA muscles overexpressing AMPD3 had significantly less ATP than contralateral controls (−25%). In myotubes, increasing AMPD3 expression for 24 h was sufficient to significantly decrease ATP concentrations (−16%), increase IMP, and increase efflux of IMP catabolites into the culture media, without decreasing the ATP/ADP or ATP/AMP ratios. When myotubes were treated with dinitrophenol (mitochondrial uncoupler), AMPD3 overexpression blunted decreases in ATP/ADP and ATP/AMP ratios but exacerbated AdN degradation. As such, pAMPK/AMPK, pACC/ACC, and phosphorylation of AMPK substrates, were unchanged by AMPD3 at this timepoint. AMPD3 significantly altered 191 out of 639 detected intracellular metabolites, but only 30 transcripts, none of which encoded metabolic enzymes. The most altered metabolites were those within purine nucleotide, BCAA, glycolysis, and ceramide metabolic pathways. After 48 h, AMPD3 overexpression significantly reduced pAMPK/AMPK (−24%), phosphorylation of AMPK substrates (−14%), and PGC-1α protein (−22%). Moreover, AMPD3 significantly reduced myotube mitochondrial protein synthesis rates (−55%), basal ATP synthase-dependent (−13%), and maximal uncoupled oxygen consumption (−15%). Conclusions Increased expression of AMPD3 significantly decreased mitochondrial protein synthesis rates and broadly altered cellular metabolites in a manner similar to that of atrophic muscle. Importantly, the changes in metabolites occurred prior to reductions in AMPK signaling, gene expression, and mitochondrial protein synthesis, suggesting metabolism is not dependent on reductions in oxidative capacity, but may be consequence of increased AMP deamination. Therefore, AMP deamination in skeletal muscle may be a mechanism that alters the metabolic phenotype of skeletal muscle during atrophy and could be a target to improve muscle function during muscle wasting.

Campylobacter jejuni is the leading bacterial cause of gastroenteritis worldwide with excessive incidence in low-and middle-income countries (LMIC). During a survey for C. jejuni from putative animal hosts in a town in the Peruvian Amazon, we were able to isolate and whole genome sequence two C. jejuni strains from domesticated guinea pigs (Cavia porcellus). The C. jejuni isolated from guinea pigs had a novel multilocus sequence type that shared some alleles with other C. jejuni collected from guinea pigs. Average nucleotide identity and phylogenetic analysis with a collection of C. jejuni subsp. jejuni and C. jejuni subsp. doylei suggest that the guinea pig isolates are distinct. Genomic comparisons demonstrated gene gain and loss that could be associated with guinea pig host specialization related to guinea pig diet, anatomy, and physiology including the deletion of genes involved with selenium metabolism, including genes encoding the selenocysteine insertion machinery and selenocysteine-containing proteins.

COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. To expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients, including matched analysis of the whole-blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate herein the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide., Graphical Abstract, Sullivan et al. describe the development of a multidimensional dataset for the study of COVID-19 known as the COVIDome, which includes diverse clinical, transcriptome, proteome, metabolome, and immune cell datasets. A researcher portal known as the COVIDome Explorer was created to enable global data access and analysis.

Oyster habitat restoration seeks to recover lost ecosystem services including increased provisioning of refuge and foraging habitat for fish and invertebrate communities. The goal of this study was to quantify the ecosystem service benefit of habitat provisioning in Ninigret Pond, RI, following oyster restoration. Four metrics were measured, abundance, biomass, species richness, and diversity, as well as isotopic composition in fish and invertebrates collected seasonally from restored oyster, aquaculture, and bare sediment sites, to examine whether the oyster habitat outperformed the bare sediment habitat. Sampling locations were chosen in Foster's Cove north and south, Grassy Point, South Sanctuary, and an Aquaculture lease; each had two restored oyster sites and one bare sediment site. Each site was sampled using a box trap, seine net, shrimp trap, and minnow trap. Oyster habitats had significantly greater metrics than did bare sediment habitats in some comparisons from the box trap and seine net samples. Restored oyster sites at South Sanctuary had lower metric values than the other oyster sites. Metrics from the Aquaculture sites were comparable to the Foster's Cove and Grassy Point restored oyster sites and often outperformed South Sanctuaryrestored oyster sites. Seasonally, spring and autumn samples tended to have higher abundance and biomass values than summer samples. Isotopic composition of five species occurring at both restored oyster and bare sediment sites demonstrated some differences in the trophic levels between species but not between habitat types. In Ninigret Pond, fish and invertebrate abundance, biomass, species richness, and diversity benefit from the use of oyster and bare sediment habitats. Coastal zone managers interested in restoring the ecological function of oyster reefs to support fish and invertebrate communities should consider strategically locating restoration projects within the mosaic of structured habitats and monitoring them for selected ecosystem services.

During a sampling of wild red foxes (Vulpes vulpes) for the detection of Epsilonproteobacteria, 14 strains were isolated from the caecal contents of 14 epidemiologically-unrelated animals. A genus-specific PCR indicated that the isolates belonged to the genus Campylobacter. Based on the results of a species-specific PCR, the isolates were initially identified as C. upsaliensis. However, multi-locus sequence typing (MLST) revealed that the isolates were significantly different from the C. upsaliensis present in the MLST database. A polyphasic study, including conventional biochemical and tolerance characteristics, morphology by transmission electron microscopy (TEM), MALDI-TOF analysis, and genetic comparisons based on partial 16S rDNA and atpA gene sequences, was undertaken. Finally, the complete genome sequence of the type strain 251/13T and the draft genome sequences of the other isolates were determined. Average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization analyses confirmed that the isolates represent a novel taxon for which the name Campylobacter vulpis sp. nov. is proposed, with isolate 251/13T (=CCUG 70587T = LMG 30110T) as the type strain. In order to allow a rapid discrimination of C. vulpis from the closely-related C. upsaliensis, a specific PCR test was designed, based on atpA gene sequences.

New antibiotics are urgently needed to address the mounting resistance challenge. In early drug discovery, one of the bottlenecks is the elucidation of targets and mechanisms. To accelerate antibiotic research, we provide a proteomic approach for the rapid classification of compounds into those with precedented and unprecedented modes of action. We established a proteomic response library of Bacillus subtilis covering 91 antibiotics and comparator compounds, and a mathematical approach was developed to aid data analysis., New antibiotics are urgently needed to address the mounting resistance challenge. In early drug discovery, one of the bottlenecks is the elucidation of targets and mechanisms. To accelerate antibiotic research, we provide a proteomic approach for the rapid classification of compounds into those with precedented and unprecedented modes of action. We established a proteomic response library of Bacillus subtilis covering 91 antibiotics and comparator compounds, and a mathematical approach was developed to aid data analysis. Comparison of proteomic responses (CoPR) allows the rapid identification of antibiotics with dual mechanisms of action as shown for atypical tetracyclines. It also aids in generating hypotheses on mechanisms of action as presented for salvarsan (arsphenamine) and the antirheumatic agent auranofin, which is under consideration for repurposing. Proteomic profiling also provides insights into the impact of antibiotics on bacterial physiology through analysis of marker proteins indicative of the impairment of cellular processes and structures. As demonstrated for trans-translation, a promising target not yet exploited clinically, proteomic profiling supports chemical biology approaches to investigating bacterial physiology.

Staphylococcus aureus is the most common bacteria causing purulent skin and soft tissue infections. Many disease-causing S aureus strains are methicillin resistant; thus, empiric therapy should be given to cover methicillin-resistant S aureus. Bacterial wound cultures are important for characterizing local susceptibility patterns. Definitive antibiotic therapy is warranted, although there are no compelling data demonstrating superiority of any one antibiotic over another. Antibiotic choice is predicated by the infection severity, local susceptibility patterns, and drug-related safety, tolerability, and cost. Response to therapy is expected within the first days; 5 to 7 days of therapy is typically adequate to achieve cure.

We have examined the draft genomes of five isolates from two different Klebsiella species obtained from intensive care unit patients at two geographically distributed hospitals to examine the genomic diversity of hospital acquired organisms in this understudied population.

Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens., In September 2018, Hurricane Florence caused extreme flooding in eastern North Carolina, USA, a region highly dense in concentrated animal production, especially swine and poultry. In this study, floodwater samples (n = 96) were collected as promptly post-hurricane as possible and for up to approximately 30 days and selectively enriched for Campylobacter using Bolton broth enrichment and isolation on modified charcoal cefoperazone deoxycholate agar (mCCDA) microaerobically at 42°C. Only one sample yielded Campylobacter, which was found to be Campylobacter jejuni with the novel sequence type 2866 (ST-2866). However, the methods employed to isolate Campylobacter readily yielded Arcobacter from 73.5% of the floodwater samples. The Arcobacter isolates failed to grow on Mueller-Hinton agar at 25, 30, 37, or 42°C microaerobically or aerobically but could be readily subcultured on mCCDA at 42°C microaerobically. Multilocus sequence typing of 112 isolates indicated that all were Arcobacter butzleri. The majority (85.7%) of the isolates exhibited novel sequence types (STs), with 66 novel STs identified. Several STs, including certain novel ones, were detected in diverse waterbody types (channel, isolated ephemeral pools, floodplain) and from multiple watersheds, suggesting the potential for regionally dominant strains. The genotypes were clearly partitioned into two major clades, one with high representation of human and ruminant isolates and another with an abundance of swine and poultry isolates. Surveillance of environmental waters and food animal production systems in this animal agriculture-dense region is needed to assess potential regional prevalence and temporal stability of the observed A. butzleri strains as well as their potential association with specific types of food animal production. IMPORTANCE Climate change and associated extreme weather events can have massive impacts on the prevalence of microbial pathogens in floodwaters. However, limited data are available on foodborne zoonotic pathogens such as Campylobacter or Arcobacter in hurricane-associated floodwaters in rural regions with intensive animal production. With a high density of intensive animal production as well as pronounced vulnerability to hurricanes, eastern North Carolina presents unique opportunities in this regard. Our findings revealed widespread incidence of the emerging zoonotic pathogen Arcobacter butzleri in floodwaters from Hurricane Florence. We encountered high and largely unexplored diversity while also noting the potential for regionally abundant and persistent clones. We noted pronounced partitioning of the floodwater genotypes into two source-associated clades. The data will contribute to elucidating the poorly understood ecology of this emerging pathogen and highlight the importance of surveillance of floodwaters associated with hurricanes and other extreme weather events for Arcobacter and other zoonotic pathogens.

SUMMARYE-cadherin junctions facilitate the assembly and disassembly of cell-cell contacts that drive development and homeostasis of epithelial tissues. The stability of E-cadherin-based junctions highly depends on their attachment to the actin cytoskeleton, but little is known about how the assembly of junctional actin filaments is regulated. Formins are a conserved group of proteins responsible for the formation and elongation of filamentous actin (F-actin). In this study, using Xenopus embryonic kidney and Madin-Darby canine kidney (MDCK) cells, we investigate the role of the Wnt/ planar cell polarity (PCP) formin protein Daam1 (Dishevelled-associated activator of morphogenesis 1) in regulating E-cadherin based intercellular adhesion. Using live imaging we show that Daam1 localizes to newly formed cell-cell contacts in the developing nephron. Furthermore, analyses of junctional F-actin upon Daam1 depletion indicate a decrease in microfilament localization and their slowed turnover. We also show that Daam1 is necessary for efficient and timely localization of junctional E-cadherin, which is mediated by Daam1’s formin homology domain 2 (FH2). Finally, we establish that Daam1 signaling is essential for promoting organized movement of renal cells. This study demonstrates that Daam1 formin junctional activity is critical for epithelial tissue organization.

Felid semen has historically been frozen using an egg yolk-based cryopreservation medium. However, the use of egg introduces several potential concerns, such as variability in composition, microbial contamination, and regulatory issues. In the present study, our aim was to compare a chemically-defined, soy-based medium (SOY) to a commercial egg yolk-based medium (TEY) for the cryopreservation of sperm in four imperiled small cat species. Semen was collected from adult male cats (n = 6 black-footed cats; n = 6 sand cats; n = 4 fishing cats; and n = 7 Pallas’ cats) via electroejaculation, split into two aliquots, and cryopreserved in SOY or TEY. Frozen-thawed samples were evaluated for sperm motility and rate of progressive motility (up to 24 h post-thaw) and acrosome status (0 and 6 h). No difference in post-thaw traits were observed between treatments in all four species. Heterologous IVF using oocytes collected laparoscopically from domestic cats demonstrated no difference among freezing treatments in percentage of mature oocytes that cleaved or the mean number of blastomeres at 48 h post-insemination. More spermatozoa frozen with SOY were bound to the zona pellucida in the sand cat (P = 0.018), but no treatment effect was observed in the other three species. These findings collectively demonstrate that SOY may be a preferable alternative to TEY for sperm cryopreservation in these four wild felid species.

Blood culture (BC) often fails to detect bloodstream microorganisms in sepsis. However, molecular diagnostics hold great potential. The molecular method PCR/electrospray ionization-mass spectrometry (PCR/ESI-MS) can detect DNA from hundreds of different microorganisms in whole blood. The aim of the present study was to evaluate the performance of this method in a multicenter study including 16 teaching hospitals in the United States (n = 13) and Europe (n = 3)., Blood culture (BC) often fails to detect bloodstream microorganisms in sepsis. However, molecular diagnostics hold great potential. The molecular method PCR/electrospray ionization-mass spectrometry (PCR/ESI-MS) can detect DNA from hundreds of different microorganisms in whole blood. The aim of the present study was to evaluate the performance of this method in a multicenter study including 16 teaching hospitals in the United States (n = 13) and Europe (n = 3). First, on testing of 2,754 contrived whole blood samples, with or without spiked microorganisms, PCR/ESI-MS produced 99.1% true-positive and 97.2% true-negative results. Second, among 1,460 patients with suspected sepsis (sepsis-2 definition), BC and PCR/ESI-MS on whole blood were positive in 14.6% and 25.6% of cases, respectively, with the following result combinations: BC positive and PCR/ESI-MS negative, 4.3%; BC positive and PCR/ESI-MS positive, 10.3%; BC negative and PCR/ESI-MS positive, 15.3%; and BC negative and PCR/ESI-MS negative, 70.1%. Compared with BC, PCR/ESI-MS showed the following sensitivities (coagulase-negative staphylococci not included): Gram-positive bacteria, 58%; Gram-negative bacteria, 78%; and Candida species, 83%. The specificities were >94% for all individual species. Patients who had received prior antimicrobial medications (n = 603) had significantly higher PCR/ESI-MS positivity rates than patients without prior antimicrobial treatment—31% versus 22% (P

Evidence suggests that insulin deficiency and hyperglycemia may disrupt the normal function of the female reproductive system, leading to delayed menarche and premature ovarian aging. We compared the length of the reproductive period of women with T1D and women without diabetes. We assessed age at menarche and natural menopause in women with childhood-onset T1D (diagnosed in 1950-80) who participated in the Pittsburgh EDC study’s 2010-16 follow-up (where reproductive history was assessed) and nondiabetic participants from the Pittsburgh site of the SWAN study. Women who had not yet reached natural menopause, had a hysterectomy/oophorectomy before menopause or received sex hormone therapy during the menopausal transition were excluded from analyses. In EDC, covariate data were selected from the follow-up visit where chronological age was closest to the baseline age in SWAN. Reproductive history was self-reported. The Women’s Ischemia Syndrome Evaluation historical and hormonal algorithms were also used to assess menopause status. Women with T1D (n=105) were younger (42.8 vs. 46.0 yrs, p=.0003), more likely to be white (96.2% vs. 68.3%, p Disclosure Y. Yi: None. S.R. El Khoudary: None. R.G. Miller: None. D. Rubinstein: None. K.A. Matthews: None. T.J. Orchard: None. T. Costacou: None. Funding National Institutes of Health (DK34818); Rossi Memorial Fund; National Institute on Aging; National Institute of Nursing Research; Office of Research on Women’s Health

We describe the epidemiologic and microbiologic characteristics of patients co-colonized with different species of carbapenem-resistant Enterobacteriaceae (CRE) from 5 hospitals in 4 states. Twenty-eight of 313 patients (8.9%) were co-colonized with at least 2 different CRE species. Different species within the same patient showed identical mechanism resistance in 18/28 (64%) cases.

Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1, always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders.

The rise of antibiotic resistance, coupled with increased expectations for mobility in later life, is creating a need for biofilm inhibitors and delivery systems that will reduce surgical implant infection. A limitation of some of these existing delivery approaches is toxicity exhibited toward host cells. Here, we report the application of a novel inhibitor of the enzyme, methylthioadenosine nucleosidase (MTAN), a key enzyme in bacterial metabolic pathways, which include S-adenosylmethionine catabolism and purine nucleotide recycling, in combination with a poly(vinyl alcohol)-tyramine-based (PVA-Tyr) hydrogel delivery system. We demonstrate that a lead MTAN inhibitor, selected from a screened library of 34 candidates, (2S)-2-(4-amino-5H-pyrrolo3,2-dpyrimidin-7-ylmethyl)aminoundecan-1-ol (31), showed a minimum biofilm inhibitory concentration of 2.2 ± 0.4 μM against a clinical staphylococcal species isolated from an infected implant. We observed that extracellular DNA, a key constituent of biofilms, is significantly reduced when treated with 10 μM compound 31, along with a decrease in biofilm thickness. Compound 31 was incorporated into a hydrolytically degradable photo-cross-linked PVA-Tyr hydrogel and the release profile was evaluated by HPLC studies. Compound 31 released from the PVA-hydrogel system significantly reduced biofilm formation (77.2 ± 8.4% biofilm inhibition). Finally, compound 31 released from PVA-Tyr showed no negative impact on human bone marrow stromal cell (MSC) viability, proliferation, or morphology. The results demonstrate the potential utility of MTAN inhibitors in treating infections caused by Gram-positive bacteria, and the development of a nontoxic release system that has potential for tunability for time scale of delivery.

The Middle Shale Member of the Amdeh Formation is interpreted to be of Early Ordovician age based on its trace fossils, stratigraphic context and a newly discovered fauna of conodonts. The member abruptly overlies the Lower Quartzite Member, which may be Early Cambrian, and passes gradationally-upward into the Upper Quartzite Member, which is probably Early–Middle Ordovician. The 542.5 m thick Middle Shale Member can be divided into two parts: a shaly lower part, and a sandy upper part that contains an influx of heavy minerals. Bioturbation by marine trace fossils is one of the most obvious characteristics of the member. The shales and sandstones are interpreted to be ofCruzianaandSkolithosichnofacies and represent shallow-marine shelf, shoreface, beach and coastal deposits. Sparse shelly fossils occur in the sandy upper part, principally bivalves, inarticulate brachiopods, ostracods and conodonts. The small assemblage of conodonts includes elements interpreted to be Tremadocian (Tetraprioniodus,Drepanoistodus,Drepanodus,Scolopodus, ?Tropodus,SemiacontiodusandTeridontus), and others which may be Floian or ancestral forms of Floian taxa (Balognathidae gen. et sp. indet. A & B and aff.Erraticodon). No acritarchs have been recovered, probably due to high temperatures experienced during burial to >6 km. It is likely that the Middle Shale Member is the seaward equivalent of the Mabrouk and Barakat formations, and an outcrop gamma-ray log supports such a correlation. The trace fossils, sedimentology, conodont fauna and the general lack of macrofossils are in keeping with the regional Tremadocian–Floian of the Arabian margin of Gondwana.

Aims: This study inquires the relationship between Campylobacter jejuni isolated from broiler meat carcasses (n = 97) and human clinical samples (n = 72) in Belgium, from 2011 to 2013. Methods and Results: The evaluation of the relation was based on the characteristics determined using multilocus sequence typing (MLST) alone and combined with flagellin gene A restriction fragment length polymorphism (flaA-RFLP) typing, antibiotic microbiological resistance profiling (AMRp), lipooligosaccharide class typing or virulence gene profiling (Vp). Clusters containing both human and broiler meat strains were more common when MLST was used alone, followed by MLST/flaA-RFLP and then by MLST/AMRp. More logical chronologically relations broiler-human were obtained for MLST/flaA-RFLP, then for MLST, and finally for MLST/AMRp: i.e. the isolates would first be detected in the broiler meat and at the same time or later in humans. Conclusions: In several cases, the C. jejuni strains isolated from the consumed broiler meat and from the campylobacteriosis case had the same profile, according to the used typing methods. The circulating Campylobacter strains appear to have remained the same from 2011 till 2013 in Belgium. Significance and Impact of the Study: This study corroborates previously published data from Belgium that suggest a strong correlation between C. jejuni strains isolated from broiler meat and from campylobacteriosis patients.

Irish moss (Chondrus crispus Stackhouse) is a red alga that is common in Atlantic Canada. A unique strain of this species, the giant Irish moss, grows in a single location and is under strict protection. Unlike the common coastal form, the giant Irish moss reproduces solely by fragmentation and is found in gametophyte form. A 99.9% decline in giant Irish moss abundance (1999–2012) prompted this study to address two questions: whether the giant Irish moss remains 100% vegetative and gametophytic, and whether such decline is related to factors leading to a reduction in photosynthetic health. Six populations of the common Irish moss strain were compared with two populations of giant Irish moss, and their life history phases determined using a resorcinol method. The common Irish moss populations exhibited a 65%–86% ratio of gametophytic:tetrasporophytic fronds, while both giant strain populations were 100% gametophytic. Photosynthetic efficiency was measured with Pulse-Amplitude-Modulation (PAM) fluorometry and neither giant moss population had significantly different quantum yield values from the littoral populations. Hence, these analyses provided no evidence of giant Irish moss being exposed to particular sources of stress linked to water or habitat quality and alternative factors explaining the decline of this unique strain are proposed.

Synaptic vesicles (SVs) transmit signals by releasing neurotransmitters from specialized synaptic regions of neurons. In the synaptic region, SVs are tightly clustered around small structures called active zones. The motor KIF1A transports SVs outward through axons until they are captured in the synaptic region. This transport must be guided in the forward direction because it is opposed by the dynein motor, which causes SVs to reverse direction multiple times en route. The core synapse stability (CSS) system contributes to both guided transport and capture of SVs. We identified Sentryn as a CSS protein that contributes to the synaptic localization of SVs in Caenorhabditis elegans. Like the CSS proteins SAD Kinase and SYD-2 (Liprin-α), Sentryn also prevents dynein-dependent accumulation of lysosomes in dendrites in strains lacking JIP3. Genetic analysis showed that Sentryn and SAD Kinase each have at least one nonoverlapping function for the stable accumulation of SVs at synapses that, when combined with their shared functions, enables most of the functions of SYD-2 (Liprin-α) for capturing SVs. Also like other CSS proteins, Sentryn appears enriched at active zones and contributes to active zone structure, suggesting that it is a novel, conserved active zone protein. Sentryn is recruited to active zones by a process dependent on the active zone-enriched CSS protein SYD-2 (Liprin-α). Our results define a specialized group of active zone enriched proteins that can affect motorized transport throughout the neuron and that have roles in both guided transport and capture of SVs.

Dense core vesicles (DCVs) can transmit signals by releasing neuropeptides from specialized synaptic regions called active zones. DCVs reach the active zone by motorized transport through a long axon. A reverse motor frequently interrupts progress by taking DCVs in the opposite direction. “Guided transport” refers to the mechanism by which outward movements ultimately dominate to bring DCVs to the synaptic region. After guided transport, DCVs alter their interactions with motors and enter a “captured” state. The mechanisms of guided transport and capture of DCVs are unknown. Here, we discovered two proteins that contribute to both processes in Caenorhabditis elegans. SAD kinase and a novel conserved protein we named Sentryn are the first proteins found to promote DCV capture. By imaging DCVs moving in various regions of single identified neurons in living animals, we found that DCV guided transport and capture are linked through SAD kinase, Sentryn, and Liprin-α. These proteins act together to regulate DCV motorized transport in a region-specific manner. Between the cell body and the synaptic region, they promote forward transport. In the synaptic region, where all three proteins are highly enriched at active zones, they promote DCV pausing by inhibiting transport in both directions. These three proteins appear to be part of a special subset of active zone-enriched proteins because other active zone proteins do not share their unique functions.

We document Neogene benthic foraminiferal biofacies changes on a depth transect of six Gulf of Mexico industry wells (sidewall and cutting samples) that is oblique to the coast and extends from Main Pass to Green Canyon (offshore Alabama to Louisiana, USA). Calcareous nannofossil and planktonic foraminiferal biostratigraphic control provides the framework to make interwell comparisons of the benthic foraminiferal biofacies; these comparisons provide the basis for paleobathymetric and paleoenvironmental interpretations and to identify useful benthic foraminiferal biostratigraphic markers in this region.Benthic foraminiferal faunas indicate that Neogene paleodepths were slightly shallower at the eastern wells and deepened towards the western wells. Calcareous benthic foraminiferal biofacies dominated by Uvigerina spp. indicate that paleoenvironments characterized by low-oxygen conditions and/or high productivity occurred periodically during deposition along the transect. This is supported by repeated occurrences of a distinctive assemblage of agglutinated foraminifera (known as the “Agua Salada Fauna”) that is typical of dysaerobic environments.Evidence of intensified low-oxygen/high-productivity environments are recorded in lowermost Middle Miocene sediments at some locations and are present at all wells in Upper Miocene deposits. In Upper Miocene-Pliocene sediments, oxygen levels appear to have been related to paleodepth, indicating that the development of lower oxygen conditions was the result of an expansion or migration of the oxygen minimum zone. Our results are consistent with a global cause for the expansion of the oxygen minumum zone during the Late Miocene and widespread increase in export production. Our study shows that despite problems in well cuttings (cavings, inconsistent sampling) and complications in regional salt and fault tectonics, well transects can provide coherent benthic foraminiferal biofacies patterns that reveal paleobathymetric and paleoenvironmental changes in the Gulf of Mexico.

Galls are modified, invariably symmetrical, naturally developing plant structures that arise because of messages from certain specialist insects, mostly from the Thysanoptera, Hemiptera, Diptera, and Hymenoptera, and in a lesser frequency from the Lepidoptera and Coleoptera. Several species of the Eriophyoidea (Acari) induce galls and wherever appropriate, we have considered examples from the Eriophyoidea as well, generically referred under the term “insects”. The insects live within them, deriving nourishment and shelter. When these insects attack plant tissues, osmotic-change–related stress increases, thus stimulating alterations in gas exchange and subcellular metabolic functions. The osmotic stress alters the electrical properties of the plant-cell plasma membranes and impacts on indole-acetic acid synthesis and activity, which, in turn, affects the H+-transport. Insect action stimulates parts of host-cell wall to break down and the degenerated wall materials in the cytoplasm act as elicitors. In such contexts the susceptible plants use flexible strategies to mitigate stress, which generally manifest as galls. Inherited traits also play a role in providing specific shapes to the gall, which is coordinated by the innate correlating morphogenetic factors that operate normally in the plant. The gall-inducing Diptera (Cecidomyiidae), Hemiptera (Sternorrhyncha), and Hymenoptera (Cynipidae) induce galls of highly defined and exquisite shapes. Almost all of these insects are known for their specificity to plants. The gall-inducing insects, unlike many of their free-living relatives, discriminate between plants and choose from them. Selection of a particular plant by a gall-inducing insect is not a matter of chance, given that the insect encounters varied plant taxa in the natural environment. The gall-inducing insects preferentially feed on specific plant organs, or parts of these, and on specific plant species. One recent explanation is that the gall-inducing insects prefer certain plants or parts of those plants, because they need the lipidic materials, e.g., sterols, available in those plant parts, which the insects utilize for building hormones critically necessary for their metamorphosis. Because of the sedentary nature of the juvenile stages of the inducing insect, the gravid females endowed with specialized sensory structures play a key role in selecting the site precisely for oviposition and thus for the progeny. Although a majority of gall-inducing insects are restricted to specific plant taxa, some of them, as we presently know, are indicated to be capable of inducing galls on plant species closely related to their mostpreferred hosts, thus demonstrating some level of oligophagy. A few species of Asphondyliina and Schizomyiina (Cecidomyiidae) are presently indicated as polyphagous. Clearly demonstrated host shifts and adaptive radiation in some of the European and North-American gall-inducing Tephritidae populations explain the evolution of sympatric host races, more because of changes either in the preference of feeding and/or oviposition sites or by acquiring “new” physiological adaptations to new plants or through assortative mating. Differences in the temporally regulated flowering and leafing phenologies in the susceptible plants possibly play a role in isolating gall-inducing insect populations, which enable divergence and diversification via genetic drift. The general understanding, as of now, is that host shifts and radiation in gall-inducing insects are more complex than what is known in their non-gallinducing allies. Such a complexity is attributed to intricate relationships of gall-inducing insects with plants and the dispersal of gall-inducing insects through different biogeographical realms, mainly influenced by the abundance and variety of plant species. The gall-inducing insects, as a highly evolved group,... This abstract has been truncated. To view the complete abstract please download the PDF.

Biliverdin reductase B (BLVRB) is a newly identified cellular redox regulator that catalyzes the NADPH-dependent reduction of multiple substrates. Through mass spectrometry analysis, we identified high levels of BLVRB in mature red blood cells, highlighting the importance of BLVRB in redox regulation. The BLVRB conformational changes that occur during conezyme/substrate binding and the role of dynamics in BLVRB function, however, remain unknown. Through a combination of NMR, kinetics, and isothermal titration calorimetry studies, we determined that BLVRB binds its coenzyme 500-fold more tightly than its substrate. While the active site of apo BLVRB is highly dynamic on multiple timescales, active site dynamics are largely quenched within holo BLVRB, in which dynamics are redistributed to other regions of the enzyme. We show that a single point mutation of Arg78➔Ala leads to both an increase in active site micro-millisecond motions and an increase in the microscopic rate constants of coenzyme binding. This demonstrates that altering BLVRB active site dynamics can directly cause a change in functional characteristics. Our studies thus address the solution behavior of apo and holo BLVRB and identify a role of enzyme dynamics in coenzyme binding.

Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.

Fresh water cyanobacterial algal blooms represent a major health risk because these organisms produce cylindrospermopsin, a toxic, structurally complex, zwitterionic uracil-guanidine alkaloid recognized by the EPA as a dangerous drinking water contaminant. At present, the ability to detect and quantify the presence of cylindrospermospin in water samples is severely hampered by the lack of an isotopically labeled standard for analytical mass spectrometry. Herein, we present a concise, scaled total synthesis of 15N cylindrospermosin from 15N ammonium chloride, which leverages a unique stereoselective intramolecular double conjugate addition step to assemble the tricyclic guanidine core. In addition to providing the first pure isotopically labeled probe for precise quantification of this potent biotoxin in fresh water sources, our results demonstrate how unique constraints associated with isotope incorporation compel novel solutions to synthesis design.

Increasing extreme wildfire occurrence globally is boosting demand to understand the fuel dynamics and fire risk of fire-prone areas. This is particularly pressing in fire-prone, Mediterranean climate-type vegetation, such as the Banksia woodlands surrounding metropolitan Perth, southwestern Australia. Despite an extensive wildland-urban interface and frequent fire occurrence, fuel accumulation and the spatial variation in fuel risk is not well quantified across the broad extent of this ecosystem. Using a space for time sampling approach to generate a chronosequence of time since fire, we selected sites that spanned across two distinct sandy soil types (Spearwood and Bassendean sands) and a rainfall gradient (550 to 750 mm north–south). We examined 82 sites in Banksia woodlands, southwestern Australia. Of the 82 sites, 44 burnt during the measurement period (2016 to 2021), which provided the opportunity for fuel measurements following fire (resulting in total N = 126). We wanted to answer two key questions: 1) How do measures of fuel load (mass) and arrangement (structure and continuity) vary across space and time, particularly with respect to time since the last fire? 2) How do biophysical drivers, such as soil type and rainfall, influence fuel accumulation and arrangement, and do these covariates improve litter fuel modelling beyond traditional asymptotic models? We found that fine surface fuel loads (litter and small twigs) differed between sand types, accumulating faster and reaching a higher peak on Spearwood sands (7–9 Mg ha−1) compared to Bassendean sands (6–7 Mg ha−1). Shrub layer fuel loads also accumulated faster on Spearwood sands than on Bassendean sands. While shrub layer fuels on Spearwood sands peaked at 14 years and declined thereafter, those on Bassendean sand did not decline over time but have lower overall connectivity. Total fine fuels (fine surface plus fine shrub layer fuels) had no significant decline over the same time period, on either sand type. Total fine fuel loads reached a peak of 9–10 Mg ha−1 between 13- and 20-years following fire, depending on the underlying sand type. Our quantitative fuel accumulation models confirmed the strength of time since fire as a predictor of hazard, but nonetheless included up to 40% unexplained variance. Importantly, while components fluctuated over time, the combined total of fine fuels did not decline with the long absence of fire, suggesting fire risk does not necessarily decrease in long unburned vegetation.

The mechanisms that mediate durable protection against Staphylococcus aureus skin reinfections are unclear, as recurrences are common despite high antibody titers and memory T cells. Here, we developed a mouse model of S. aureus skin reinfection to investigate protective memory responses. In contrast with WT mice, IL-1β-deficient mice exhibited poor neutrophil recruitment and bacterial clearance during primary infection that was rescued during secondary S. aureus challenge. The γδ T cells from skin-draining LNs utilized compensatory T cell-intrinsic TLR2/MyD88 signaling to mediate rescue by trafficking and producing TNF and IFN-γ, which restored neutrophil recruitment and promoted bacterial clearance. RNA-sequencing (RNA-seq) of the LNs revealed a clonotypic S. aureus-induced γδ T cell expansion with a complementarity-determining region 3 (CDR3) aa sequence identical to that of invariant Vγ5+ dendritic epidermal T cells. However, this T cell receptor γ (TRG) aa sequence of the dominant CDR3 sequence was generated from multiple gene rearrangements of TRGV5 and TRGV6, indicating clonotypic expansion. TNF- and IFN-γ-producing γδ T cells were also expanded in peripheral blood of IRAK4-deficient humans no longer predisposed to S. aureus skin infections. Thus, clonally expanded γδ T cells represent a mechanism for long-lasting immunity against recurrent S. aureus skin infections.

Adult neurogenesis, a complex process by which stem cells in the hippocampal brain region differentiate and proliferate into new neurons and other resident brain cells, is known to be affected by many intrinsic and extrinsic factors, including diet. Neurogenesis plays a critical role in neural plasticity, brain homeostasis, and maintenance in the central nervous system and is a crucial factor in preserving the cognitive function and repair of damaged brain cells affected by aging and brain disorders. Intrinsic factors such as aging, neuroinflammation, oxidative stress, and brain injury, as well as lifestyle factors such as high-fat and high-sugar diets and alcohol and opioid addiction, negatively affect adult neurogenesis. Conversely, many dietary components such as curcumin, resveratrol, blueberry polyphenols, sulforaphane, salvionic acid, polyunsaturated fatty acids (PUFAs), and diets enriched with polyphenols and PUFAs, as well as caloric restriction, physical exercise, and learning, have been shown to induce neurogenesis in adult brains. Although many of the underlying mechanisms by which nutrients and dietary factors affect adult neurogenesis have yet to be determined, nutritional approaches provide promising prospects to stimulate adult neurogenesis and combat neurodegenerative diseases and cognitive decline. In this review, we summarize the evidence supporting the role of nutritional factors in modifying adult neurogenesis and their potential to preserve cognitive function during aging.

Objective: Rett syndrome (RTT) and epileptic encephalopathy (EE) are devastating neurodevelopmental disorders with distinct diagnostic criteria. However, highly heterogeneous and overlapping clinical features often allocate patients into the boundary of the two conditions, complicating accurate diagnosis and appropriate medical interventions. Therefore, we investigated the specific molecular mechanism that allows an understanding of the pathogenesis and relationship of these two conditions. Methods: We screened novel genetic factors from 34 RTT-like patients without MECP2 mutations, which account for ∼90% of RTT cases, by whole exome sequencing. The biological function of the discovered variants was assessed in cell culture and Xenopus tropicalis models. Results: We identified a recurring de novo variant in GABAB receptor R2 (GABBR2) that reduces the receptor function, whereas different GABBR2 variants in EE patients possess a more profound effect in reducing receptor activity and are more responsive to agonist rescue in an animal model. Interpretation: GABBR2 is a genetic factor that determines RTT- or EE-like phenotype expression depending on the variant positions. GABBR2-mediated GABA signaling is a crucial factor in determining the severity and nature of neurodevelopmental phenotypes. This article is protected by copyright. All rights reserved.

Protein O-glycosylation is a diverse, common, and important post-translational modification of both proteins inside the cell and those that are secreted or membrane-bound. Much work has shown that O-glycosylation can alter the structure, function, and physical properties of the proteins to which it is attached. One gap remaining in our understanding of O-glycoproteins is how O-glycans might affect the folding of proteins. Here, we took advantage of synthetic, homogeneous O-glycopeptides to show that certain glycosylation patterns have an intrinsic effect, independent of any cellular folding machinery, on the folding pathway of a model O-glycoprotein, a carbohydrate binding module (CBM) derived from the Trichoderma reesei cellulase TrCel7A. The strongest effect, a 6-fold increase in overall folding rate, was observed when a single O-mannose was the glycan, and the glycosylation site was near the N-terminus of the peptide sequence. We were also able to show that glycosylation patterns affected the kinetics of each step in unique ways, which may help to explain the observations made here. This work is a first step toward quantitative understanding of how O-glycosylation might control, through intrinsic means, the folding of O-glycoproteins. Such an understanding is expected to facilitate future investigations into the effects of glycosylation on more biological processes related to protein folding.