Growth of the Ballena fan delta on the Gulf of California (Mexico) at the close of the Pliocene Warm Period

Tectonic uplift on the shores of Bahía San Rafael in Mexico’s upper Gulf of California exposed a Pliocene delta system that covers a map area of 4 km². Subaerial dissection by arroyos entrenched during Pleistocene and post-Pleistocene time carved cross-sectional slices through the delta, showing its dominant construction resulting from massive transfers of siliciclastic sand derived from the breakdown of igneous rocks (tonolite) in a well-defined terrestrial basin. Restoration of the sedimentary structure by elimination of Pleistocene arroyos and linkage of former topographic lines reveals a triangular shape recognizable as a classic fan delta. The complex includes an alluvial fan that emerges from a small opening in the landscape connected to a semi-circular, high-walled basin with a map area of 2.6 km². Through a strictly longitudinal sequence, estimates of the excavated basin’s volume and the delta’s sedimentary volume were conducted as a mass-balance exercise that yielded a strong match. The lower central part of the delta features dense concentrations of sand dollars (Dendraster granti) that form a distinct limestone coquina not previously recognized elsewhere in Baja California. Through the regional biostratigraphy of concurrent range zones supplemented by absolute age dates from inter-bedded volcanics in other places, a later Pliocene age around 3–2 Ma is suggested for the sand dollars and the delta complex in which they are buried. Such timing corresponds to the close of the Pliocene Warm Period, during which a persistent El Niño climate brought tropical storms and excessive rainfall to the upper Gulf of California. Comparisons with other Pliocene deltas throughout the Gulf of California underscore the unique status of the complex named the Ballena fan delta.     

Changes in the associations of race and rurality with SARS-CoV-2 infection,mortality, and case fatality in the United States from February 2020 to March 2021: A population-based cohort study

BackgroundWe examined whether key sociodemographic and clinical risk factors for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and mortality changed over time in a population-based cohort study.Methods and findingsIn a cohort of 9,127,673 persons enrolled in the United States Veterans Affairs (VA) healthcare system, we evaluated the independent associations of sociodemographic and clinical characteristics with SARS-CoV-2 infection (n = 216,046), SARS-CoV-2–related mortality (n = 10,230), and case fatality at monthly intervals between February 1, 2020 and March 31, 2021. VA enrollees had a mean age of 61 years (SD 17.7) and were predominantly male (90.9%) and White (64.5%), with 14.6% of Black race and 6.3% of Hispanic ethnicity. Black (versus White) race was strongly associated with SARS-CoV-2 infection (adjusted odds ratio [AOR] 5.10, [95% CI 4.65 to 5.59], p-value <0.001), mortality (AOR 3.85 [95% CI 3.30 to 4.50], p-value < 0.001), and case fatality (AOR 2.56, 95% CI 2.23 to 2.93, p-value < 0.001) in February to March 2020, but these associations were attenuated and not statistically significant by November 2020 for infection (AOR 1.03 [95% CI 1.00 to 1.07] p-value = 0.05) and mortality (AOR 1.08 [95% CI 0.96 to 1.20], p-value = 0.21) and were reversed for case fatality (AOR 0.86, 95% CI 0.78 to 0.95, p-value = 0.005). American Indian/Alaska Native (AI/AN versus White) race was associated with higher risk of SARS-CoV-2 infection in April and May 2020; this association declined over time and reversed by March 2021 (AOR 0.66 [95% CI 0.51 to 0.85] p-value = 0.004). Hispanic (versus non-Hispanic) ethnicity was associated with higher risk of SARS-CoV-2 infection and mortality during almost every time period, with no evidence of attenuation over time. Urban (versus rural) residence was associated with higher risk of infection (AOR 2.02, [95% CI 1.83 to 2.22], p-value < 0.001), mortality (AOR 2.48 [95% CI 2.08 to 2.96], p-value < 0.001), and case fatality (AOR 2.24, 95% CI 1.93 to 2.60, p-value < 0.001) in February to April 2020, but these associations attenuated over time and reversed by September 2020 (AOR 0.85, 95% CI 0.81 to 0.89, p-value < 0.001 for infection, AOR 0.72, 95% CI 0.62 to 0.83, p-value < 0.001 for mortality and AOR 0.81, 95% CI 0.71 to 0.93, p-value = 0.006 for case fatality). Throughout the observation period, high comorbidity burden, younger age, and obesity were consistently associated with infection, while high comorbidity burden, older age, and male sex were consistently associated with mortality. Limitations of the study include that changes over time in the associations of some risk factors may be affected by changes in the likelihood of testing for SARS-CoV-2 according to those risk factors; also, study results apply directly to VA enrollees who are predominantly male and have comprehensive healthcare and need to be confirmed in other populations.ConclusionsIn this study, we found that strongly positive associations of Black and AI/AN (versus White) race and urban (versus rural) residence with SARS-CoV-2 infection, mortality, and case fatality observed early in the pandemic were ameliorated or reversed by March 2021.

George Ioannou and co-workers study the distribution of SARS-CoV-2 infections and outcomes among the United States population.     

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive Cysteines

Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation.     

Characterization of EPG waveforms for the tea green leafhopper, Empoasca vitis Göthe (Hemiptera: Cicadellidae), on tea plants and their correlation with stylet activities

The stylet probing activities of the tea green leafhopper Empoasca vitis Gothe (Hemiptera: Cicadellidae) were studied using the DC electrical penetration graph (EPG) technique. Seven different EPG waveforms (i.e., Np, E1, E2, E3, E4, E5 and E6) were distinguished and characterized on susceptible tea leaves. In addition, four of them (i.e., Np, E1, E2, E3), together accounting for 97.08% of the total recording time, were behaviorally correlated with probing and non-probing activities using artificial diet observation with high-magnification video recording. At the start of stylet probing, waveform E1 always occurred at a variable voltage. E1, with all three of its waveform sub-types (E1-A to E1-C), was correlated with production of the salivary sheath trunk, stylet laceration, and channel cutting in viscous artificial diet. Afterwards, two types of high-amplitude waveforms, E2 and E3, followed. E2 had a highly regular, quasi-square wave, repetitive appearance, and lasted the longest duration of all E. vitis probing waveforms. E3 usually appeared after E2, and also exhibited a quasi-square wave feature similar to E2, but had much higher amplitude. Both waveforms E2 and E3 were correlated with active ingestion in liquid artificial diet. In addition, secretion of watery, enzymatic saliva was likely during E2. The active stylet movements and channel-cutting observed during the probing process indicate that E. vitis is a cell rupture feeder, not a salivary sheath feeder, as aphids and other leafhoppers. Thus, hopperburn damage to the tea plant is probably due to the cell rupture feeding strategy, similar to other hopperburning Empoasca species.     

Behavioral evidence that the precibarial sensilla of leafhoppers are chemosensory and function in host discrimination

Leafhoppers (Homoptera: Cicadellidae) possess epi-and hypopharyngeal chemosensilla within the head. In this paper, we describe the behaviors of leafhoppers (Graphocephala atropunctata Signoret) which have had two of the four main nerves to these sensilla cut. Insects with severed nerves (treated) and control insects (both sham-operated and normal) were offered a choice of two small mustard leaves infused with either distilled water or a 5% sucrose solution. The control insects showed a preference for the 5% sucrose leaf, whereas the treated leafhoppers did not; they distributed themselves on both leaves with similar frequency. Thus, severing the nerves of only half of the precibarial chemosensilla (epipharyngeal organ) resulted in major changes in leafhopper feeding behavior. This evidence supports the hypothesis that the precibarial chemosensilla mediate gustatory discrimination of chemical compounds within the plant.

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Résumé Les cicadelles (Homoptera) possèdent dans la tête des sensilles gustatives sur l'épi et l'hypopharynx. Cette note décrit le comportement de Graphocephala atropunctata Signoret dont deux des quatre principaux nerfs de ces sensilles ont été coupés. Le choix entre des petites feuilles de moutarde infusées, soit dans de l'eau distillée, soit dans une solution de sucrose à 5%, a été proposé à ces insectes et à deux catégories de témoins, les uns intacts, les autres ayant subi une opération à blanc. Les témoins ont montré une préférence pour les feuilles traitées au sucrose, mais pas les cicadelles aux nerfs sectionnés. Les insectes sectionnés ont perforé les deux types de feuilles avec les mêmes fréquences. Ainsi la section de la moitié seulement des nerfs des sensilles gustatives précibariales (organe épipharyngien) a induit un changement fondamental du comportement alimentaire des cicadelles. Cette expérience appuie l'hypothèse selon laquelle les sensilles précibariales fournissent la discrimination gustative des composés chimiques de la plante.

     

Mass spectral characterization of fatty acid amides from alfalfa trichomes and their deterrence against the potato leafhopper

A homologous series of N-(3-methylbutyl)amides of normal saturated C14, C15, C16, C17 and C18 fatty acids were identified as major components of glandular trichome extracts from Medicago sativa G98A, an alfalfa genotype resistant to the potato leafhopper, Empoasca fabae. A second homologous series of N-(2-methylpropyl)amides of C14 through C18 normal fatty acids were minor components. Saturated free fatty acids C12, C13, C14, C15, C16, C17 and C18 were present in trace amounts, as was the N-(3-methylbutyl)amide of linoleic acid (C18:2). N-(3-methylbutyl)amides and N-(2-methylpropyl)amides of C14 through C18 fatty acids, along with the N-(3-methylbutyl)amide of linoleic acid, were synthesized and bioassayed for leafhopper deterrence by applying the compounds to the surface of a sachet containing an artificial diet. Leafhoppers were then offered a two-way choice between diet surfaces treated with the synthetic amides or an untreated control. N-(3-methylbutyl)amides and N-(2-methylpropyl)amides of C14 through C18 fatty acids did not deter leafhopper settling in a dose-dependent fashion. In contrast, when tested singly, N-(3-methylbutyl)amide of linoleic acid exhibited dose-dependent deterrence against leafhopper settling. Fatty acid amides localized in alfalfa glandular trichomes likely contribute to leafhopper resistance.     

Extracellular signal-regulated kinase 1/2 plays a pro-life role in experimental brain stem death via MAPK signal-interacting kinase at rostral ventrolateral medulla

Background  

As the origin of a life-and-death signal detected from systemic arterial pressure, which sequentially increases (pro-life) and decreases (pro-death) to reflect progressive dysfunction of central cardiovascular regulation during the advancement towards brain stem death in critically ill patients, the rostral ventrolateral medulla (RVLM) is a suitable neural substrate for mechanistic delineation of this fatal phenomenon. The present study assessed the hypothesis that extracellular signal-regulated kinase 1/2 (ERK1/2), a member of the mitogen-activated protein kinases (MAPKs) that is important for cell survival and is activated specifically by MAPK kinase 1/2 (MEK1/2), plays a pro-life role in RVLM during brain stem death. We further delineated the participation of MAPK signal-interacting kinase (MNK), a novel substrate of ERK in this process.     

Bloat in sheep (Ovis aries)

1. Most of the field studies on bloat are conducted with cattle and most of the laboratory experiments seeking to explain the various parameters associated with bloat are done with sheep. 2. Based on grazing behaviour, it would be expected that sheep might bloat more severely than cattle because they selectively choose to eat leaves over stems and chew what they ingest more frequently than cattle. Furthermore, sheep appear to select legumes over grasses because the legumes can be eaten more rapidly. However, because they are selective, sheep eat more slowly than cattle. Despite a higher bloat expectation, bloating in sheep is reported to be less of a problem than in cattle. 3. Although frothing of rumen ingesta was described earlier in cattle as the cause of acute legume bloat, experiments with frothy bloat in sheep preceded those in cattle. 4. Anti-frothing agents were used in sheep before cattle to treat acute legume bloat. 5. Experiments devoted to the study of eructation in ruminants were carried out on sheep, then cattle. 6. Convincing evidence that rumen motility does not cease during acute legume bloat was gathered using sheep. 7. Although the transected tracheal technique for the determination of the volume of eructated gas was developed with cattle, the pathway of eructated gas was confirmed with sheep. 8. All the current evidence accumulated from experiments with sheep supports the hypothesis that death due to legume bloat is caused by acute neural, respiratory, and cardiovascular insult resulting from the effect of the distended rumen on thoracic viscera, diaphragm, intercostal muscles, and the abdominal vena cava. 9. Experiments with sheep and cattle being fed scabrous and nonscabrous diets similar in chemical composition show that sheep are more resistant than cattle to the increase in intrarumen pressure, decline in rumen contraction amplitude, and decrease in rumen contraction frequency caused by nonscabrous diets. 10. The sequence of events in the reticulorumen during primary and secondary contractions previously described following visual and palpation experiments with cattle was confirmed by the use of myoelectrodes implanted in the various sacs of the reticulorumen of sheep. 11. Elevated intrarumen pressure is associated with an increase in the frequency of primary (mixing) and secondary (eructation) contractions (more secondaries than primaries).(ABSTRACT TRUNCATED AT 400 WORDS)     

Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

Background

Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs.

Results

We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5′ or 3′ positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for genes involved in xenobiotic metabolism and mitochondrial function, suggesting these eQTLs may have adaptive origins. Several strong eQTLs (CDK5RAP2, NBPFs) coincide with regions of reported human lineage selection. The intersection of new kidney and plaque eQTLs with related GWAS suggest possible gene prioritization. For example, butyrophilins are now linked to arterial pathogenesis via multiple genetic and expression studies. Expression QTL and GWAS results are made available as a community resource through the NHLBI GRASP database [http://apps.nhlbi.nih.gov/grasp/].

Conclusions

Expression QTLs inform the interpretation of human trait variability, and may account for a greater fraction of phenotypic variability than protein-coding variants. The synthesis of available tissue eQTL data highlights many strong cis-eQTLs that may have important biologic roles and could serve as positive controls in future studies. Our results indicate some strong tissue-ubiquitous eQTLs may have adaptive origins in humans. Efforts to expand the genetic, splicing and tissue coverage of known eQTLs will provide further insights into human gene regulation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-532) contains supplementary material, which is available to authorized users.     

Absence of cue-recruitment for extrinsic signals: sounds, spots, and swirling dots fail to influence perceived 3D rotation direction after training

The visual system can learn to use information in new ways to construct appearance. Thus, signals such as the location or translation direction of an ambiguously rotating wire frame cube, which are normally uninformative, can be learned as cues to determine the rotation direction. This perceptual learning occurs when the formerly uninformative signal is statistically associated with long-trusted visual cues (such as binocular disparity) that disambiguate appearance during training. In previous demonstrations, the newly learned cue was intrinsic to the perceived object, in that the signal was conveyed by the same image elements as the object itself. Here we used extrinsic new signals and observed no learning. We correlated three new signals with long-trusted cues in the rotating cube paradigm: one crossmodal (an auditory signal) and two within modality (visual). Cue recruitment did not occur in any of these conditions, either in single sessions or in ten sessions across as many days. These results suggest that the intrinsic/extrinsic distinction is important for the perceptual system in determining whether it can learn and use new information from the environment to construct appearance. Extrinsic cues do have perceptual effects (e.g. the "bounce-pass" illusion and McGurk effect), so we speculate that extrinsic signals must be recruited for perception, but only if certain conditions are met. These conditions might specify the age of the observer, the strength of the long-trusted cues, or the amount of exposure to the correlation.