Improved Metabolic Health Alters Host Metabolism in Parallel with Changes in Systemic Xeno-Metabolites of Gut Origin

Novel plasma metabolite patterns reflective of improved metabolic health (insulin sensitivity, fitness, reduced body weight) were identified before and after a 14–17 wk weight loss and exercise intervention in sedentary, obese insulin-resistant women. To control for potential confounding effects of diet- or microbiome-derived molecules on the systemic metabolome, sampling was during a tightly-controlled feeding test week paradigm. Pairwise and multivariate analysis revealed intervention- and insulin-sensitivity associated: (1) Changes in plasma xeno-metabolites (“non-self” metabolites of dietary or gut microbial origin) following an oral glucose tolerance test (e.g. higher post-OGTT propane-1,2,3-tricarboxylate [tricarballylic acid]) or in the overnight-fasted state (e.g., lower γ-tocopherol); (2) Increased indices of saturated very long chain fatty acid elongation capacity; (3) Increased post-OGTT α-ketoglutaric acid (α-KG), fasting α-KG inversely correlated with Matsuda index, and altered patterns of malate, pyruvate and glutamine hypothesized to stem from improved mitochondrial efficiency and more robust oxidation of glucose. The results support a working model in which improved metabolic health modifies host metabolism in parallel with altering systemic exposure to xeno-metabolites. This highlights that interpretations regarding the origins of peripheral blood or urinary “signatures” of insulin resistance and metabolic health must consider the potentially important contribution of gut-derived metabolites toward the host''s metabolome.     

Comparative Analysis of Predicted Plastid-Targeted Proteomes of Sequenced Higher Plant Genomes

Plastids are actively involved in numerous plant processes critical to growth, development and adaptation. They play a primary role in photosynthesis, pigment and monoterpene synthesis, gravity sensing, starch and fatty acid synthesis, as well as oil, and protein storage. We applied two complementary methods to analyze the recently published apple genome (Malus × domestica) to identify putative plastid-targeted proteins, the first using TargetP and the second using a custom workflow utilizing a set of predictive programs. Apple shares roughly 40% of its 10,492 putative plastid-targeted proteins with that of the Arabidopsis (Arabidopsis thaliana) plastid-targeted proteome as identified by the Chloroplast 2010 project and ∼57% of its entire proteome with Arabidopsis. This suggests that the plastid-targeted proteomes between apple and Arabidopsis are different, and interestingly alludes to the presence of differential targeting of homologs between the two species. Co-expression analysis of 2,224 genes encoding putative plastid-targeted apple proteins suggests that they play a role in plant developmental and intermediary metabolism. Further, an inter-specific comparison of Arabidopsis, Prunus persica (Peach), Malus × domestica (Apple), Populus trichocarpa (Black cottonwood), Fragaria vesca (Woodland Strawberry), Solanum lycopersicum (Tomato) and Vitis vinifera (Grapevine) also identified a large number of novel species-specific plastid-targeted proteins. This analysis also revealed the presence of alternatively targeted homologs across species. Two separate analyses revealed that a small subset of proteins, one representing 289 protein clusters and the other 737 unique protein sequences, are conserved between seven plastid-targeted angiosperm proteomes. Majority of the novel proteins were annotated to play roles in stress response, transport, catabolic processes, and cellular component organization. Our results suggest that the current state of knowledge regarding plastid biology, preferentially based on model systems is deficient. New plant genomes are expected to enable the identification of potentially new plastid-targeted proteins that will aid in studying novel roles of plastids.     

The Neural Code for Auditory Space Depends on Sound Frequency and Head Size in an Optimal Manner

A major cue to the location of a sound source is the interaural time difference (ITD)–the difference in sound arrival time at the two ears. The neural representation of this auditory cue is unresolved. The classic model of ITD coding, dominant for a half-century, posits that the distribution of best ITDs (the ITD evoking a neuron’s maximal response) is unimodal and largely within the range of ITDs permitted by head-size. This is often interpreted as a place code for source location. An alternative model, based on neurophysiology in small mammals, posits a bimodal distribution of best ITDs with exquisite sensitivity to ITDs generated by means of relative firing rates between the distributions. Recently, an optimal-coding model was proposed, unifying the disparate features of these two models under the framework of efficient coding by neural populations. The optimal-coding model predicts that distributions of best ITDs depend on head size and sound frequency: for high frequencies and large heads it resembles the classic model, for low frequencies and small head sizes it resembles the bimodal model. The optimal-coding model makes key, yet unobserved, predictions: for many species, including humans, both forms of neural representation are employed, depending on sound frequency. Furthermore, novel representations are predicted for intermediate frequencies. Here, we examine these predictions in neurophysiological data from five mammalian species: macaque, guinea pig, cat, gerbil and kangaroo rat. We present the first evidence supporting these untested predictions, and demonstrate that different representations appear to be employed at different sound frequencies in the same species.     

Signalling for survival and death in neurones: the role of stress-activated kinases, JNK and p38

The pathways involved in neuronal survival or death have been extensively studied mainly in cell lines. Recent evidence has suggested that activation of the stress activated pathways, jun N-terminal kinase (JNK) and p38 may play important roles in neuronal cell death or regeneration. In this review we will discuss these pahtways in detail. We will examine the evidence that these pathways are important in neuronal cell death. Finally we will review the evidence that inhibitors of these pathways have a neuroprotective effect both in vitro and in vivo.     

Development of Vegetation and Aquatic Habitat in Restored Riparian Sites of California's North Coast Rangelands

The preponderance of short‐term objectives and lack of systematic monitoring of restoration projects limits opportunities to learn from past experience and improve future restoration efforts. We conducted a retrospective, cross‐sectional survey of 89 riparian revegetation sites and 13 nonrestored sites. We evaluated 36 restoration metrics at each site and used project age (0–39 years) to quantify plant community and aquatic habitat trajectories with a maximum likelihood model selection approach to compare linear and polynomial relationships. We found significant correlations with project age for 16 of 21 riparian vegetation, and 11 of 15 aquatic habitat attributes. Our results indicated improvements in multiple ecosystem services and watershed functions such as diversity, sedimentation, carbon sequestration, and available habitat. Ten riparian vegetation metrics, including native tree and exotic shrub density, increased nonlinearly with project age, while litter and native shrub density increased linearly. Species richness and cover of annual plants declined over time. Improvements in aquatic habitat metrics, such as increasing pool depth and decreasing bankfull width‐to‐depth ratio, indicated potentially improved anadromous fish habitats at restored sites. We hypothesize that certain instream metrics did not improve because of spatial and/or temporal limitations of riparian vegetation to affect aquatic habitat. Restoration managers should be prepared to maintain or enhance understory diversity by controlling exotic shrubs or planting shade‐tolerant native species as much as 10 years after revegetation.     

Micro-structure and chemical composition of vateritic deformities occurring in the bivalve Corbicula fluminea (Müller, 1774)

Vateritic deformities occurring in the invasive heterodont bivalve Corbicula fluminea from several locations in the UK were characterised in detail for the first time using scanning electron microscopy, X-ray diffraction and different geochemical techniques (electron microprobe, ICP-AES, and mass spectrometry). Large volumes of vaterite are produced abnormally in the animals' shells in the form of yellow-green bulges. These are distinguished from the aragonitic parts of the shell by their characteristic micro-structures, content of organic material, trace elemental composition and carbon stable isotope signatures. The most commonly observed micro-structures include columnar vaterite, lamellar vaterite and different irregular structures occurring in all parts of the shell. There are indications that organic material is present largely as intracrystalline impurities or nano-scale phases and not as envelopes around microstructural units. These micro-structures are novel, nothing equivalent having yet been described for other vateritic systems. Euhedral vaterite crystals also occur occasionally. The vaterite has generally higher Mg/Ca and lower Na/Ca, K/Ca than the aragonite. In addition, δ13C is also always lower. Microstructural characteristics would suggest loss of biological control probably due to physiological stress(es) inducing the switch to vaterite production. The vaterite might be stabilised by its higher content of organic material and magnesium.     

<Emphasis Type="Italic">Protungulatum</Emphasis>, Confirmed Cretaceous Occurrence of an Otherwise Paleocene Eutherian (Placental?) Mammal

Neither pre-Cenozoic crown eutherian mammals (placentals) nor archaic ungulates (“condylarths”) are known with certainty based on the fossil record. Herein we report a new species of the Paleocene archaic ungulate (“condylarth”) Protungulatum from undisputed Late Cretaceous aged rocks in Montana USA based on an isolated last upper premolar, indicating rare representatives of these common early Tertiary mammals appeared in North America a minimum of 300 k  years before the extinction of non-avian dinosaurs. The other 1200 mammal specimens from the locality are characteristic Late Cretaceous taxa. This discovery overturns the current hypothesis that archaic ungulates did not appear in North America until after the Cretaceous/Tertiary (K/T) boundary and also suggests that other reports of North American Late Cretaceous archaic ungulates may be correct. Recent studies, including ours, cannot determine whether Protungulatum does or does not belong to the crown clade Placentalia.     

A Multi-Country Non-Inferiority Cluster Randomized Trial of Frontloaded Smear Microscopy for the Diagnosis of Pulmonary Tuberculosis

Background

More than 50 million people around the world are investigated for tuberculosis using sputum smear microscopy annually. This process requires repeated visits and patients often drop out.

Methods and Findings

This clinical trial of adults with cough ≥2 wk duration (in Ethiopia, Nepal, Nigeria, and Yemen) compared the sensitivity/specificity of two sputum samples collected “on the spot” during the first visit plus one sputum sample collected the following morning (spot-spot-morning [SSM]) versus the standard spot-morning-spot (SMS) scheme. Analyses were per protocol analysis (PPA) and intention to treat (ITT). A sub-analysis compared just the first two smears of each scheme, spot-spot and spot-morning.In total, 6,627 patients (3,052 SSM/3,575 SMS) were enrolled; 6,466 had culture and 1,526 were culture-positive. The sensitivity of SSM (ITT, 70.2%, 95% CI 66.5%–73.9%) was non-inferior to the sensitivity of SMS (PPA, 65.9%, 95% CI 62.3%–69.5%). Similarly, the specificity of SSM (ITT, 96.9%, 95% CI 93.2%–99.9%) was non-inferior to the specificity of SMS (ITT, 97.6%, 95% CI 94.0%–99.9%). The sensitivity of spot-spot (ITT, 63.6%, 95% CI 59.7%–67.5%) was also non-inferior to spot-morning (ITT, 64.8%, 95% CI 61.3%–68.3%), as the difference was within the selected −5% non-inferiority limit (difference ITT = 1.4%, 95% CI −3.7% to 6.6%). Patients screened using the SSM scheme were more likely to provide the first two specimens than patients screened with the SMS scheme (98% versus 94.2%, p<0.01). The PPA and ITT analysis resulted in similar results.

Conclusions

The sensitivity and specificity of SSM are non-inferior to those of SMS, with a higher proportion of patients submitting specimens. The scheme identifies most smear-positive patients on the first day of consultation.

Trial Registration

Current Controlled Trials ISRCTN53339491 Please see later in the article for the Editors'' Summary