The Effect of Iron Limitation on the Transcriptome and Proteome of Pseudomonas fluorescens Pf-5

One of the most important micronutrients for bacterial growth is iron, whose bioavailability in soil is limited. Consequently, rhizospheric bacteria such as Pseudomonas fluorescens employ a range of mechanisms to acquire or compete for iron. We investigated the transcriptomic and proteomic effects of iron limitation on P. fluorescens Pf-5 by employing microarray and iTRAQ techniques, respectively. Analysis of this data revealed that genes encoding functions related to iron homeostasis, including pyoverdine and enantio-pyochelin biosynthesis, a number of TonB-dependent receptor systems, as well as some inner-membrane transporters, were significantly up-regulated in response to iron limitation. Transcription of a ribosomal protein L36-encoding gene was also highly up-regulated during iron limitation. Certain genes or proteins involved in biosynthesis of secondary metabolites such as 2,4-diacetylphloroglucinol (DAPG), orfamide A and pyrrolnitrin, as well as a chitinase, were over-expressed under iron-limited conditions. In contrast, we observed that expression of genes involved in hydrogen cyanide production and flagellar biosynthesis were down-regulated in an iron-depleted culture medium. Phenotypic tests revealed that Pf-5 had reduced swarming motility on semi-solid agar in response to iron limitation. Comparison of the transcriptomic data with the proteomic data suggested that iron acquisition is regulated at both the transcriptional and post-transcriptional levels

I’m so tired: biological and genetic mechanisms of cancer-related fatigue

Objective The goal of this paper is to discuss cancer-related fatigue (CRF) and address issues related to the investigation into potential biological and genetic causal mechanisms. The objectives are to: (1) describe CRF as a component of quality of life (QOL); (2) address measurement issues that have slowed progress toward an understanding of mechanisms underlying this symptom; (3) review biological pathways and genetic approaches that have promise for the exploration of causal mechanisms of CRF; and (4) offer directions for future research. Methods Review, synthesis, and interpretation of the literature. Results Until recently, CRF and QOL have been understood primarily as subjective patient-reported experiences. With increased understanding of human genetics, theories and research are being expanded to incorporate biological and genetic understandings of these subjective experiences. Proposed biological and genetic mechanisms of CRF that have been examined include cytokine dysregulation, hypothalamic-pituitary-adrenal (HPA) axis dysfunction, five hydroxy tryptophan (5-HT) neurotransmitter dysregulation, circadian rhythm disruption, alterations in adenosine triphosphate (ATP) and muscle metabolism, and vagal afferent activation. Approaches to the study of genetic mechanisms have also been addressed including candidate genes, genome-wide scanning, and gene expression. Based on the review and synthesis of the literature, directions for future research are proposed. Conclusions Understanding the biological and genetic basis of CRF has the potential to contribute to a more complete understanding of the genetic determinants of QO

Pieces of the puzzle: Lack of significant C4in the late Miocene of southern California

The stable carbon isotope ratios of tooth enamel from 89 herbivores from the Dove Spring Formation (DSF) of the El Paso Basin, western Mojave Desert, California, were analyzed to determine if C4plants may have been present in the late Miocene of southern California. Taxa analyzed include antilocaprids, castorids, camelids, equids, gomphotheriids, merycoidodontids, and rhinocerotids. The atmospheric CO2-δ13C value has varied significantly in the geologic past, leading to changes in the δ13C values of plants and tooth enamel. The estimated δ13C value of atmospheric CO2in the middle to late Miocene is − 5.8 ± 0.2‰, making the pure C3diet cutoff value higher than the modern by ~ 2‰. Given this, much of the evidence of an early spread of C4, which inappropriately uses the modern C3diet cutoff value, may be a false signal from water-stressed C3plants and the amount of C4biomass in the geologic past may have been over-estimated. The enamel-δ13C values of all taxa sampled are − 10.1 ± 1.1‰ (n = 89). Accounting for the changes in the δ13C values of atmospheric CO2, enamel-δ13C values from the DSF indicate that herbivores from that area had C3diets and lived in an environment dominated by C3plants. Serial enamel isotope data from the DSF revealed negligible intra-tooth variations in the δ13C values, confirming that these herbivores consumed C3plants year-round. If the C4photosynthetic pathway did spread to southern California prior to the rapid, global rise in C4in the late Miocene, the taxa sampled did not incorporate C4biomass into their diets. The results of the stable carbon isotope analysis, along with the evidence from the rock record and the life habits of the fossil taxa present, indicate that the El Paso Basin consisted of diverse habitats including C3grasslands, wooded C3grasslands, and riparian forests

Photosynthetic pathway of grass fossils from the upper Miocene Dove Spring Formation, Mojave Desert, California

The spread of grasslands in the Miocene and of C4 grasses in the late Miocene-Pliocene represents a major development in terrestrial plant evolution that affected the climate system and faunal evolution. The macrofossil record of grasses is sparse, likely due to the limited preservation potential of grasses. Diagnosis of the C3 or C4 photosynthetic pathway depends on preservation of both cellular structures and organic carbon for isotope analysis. Here we analyze the anatomical and isotopic composition of newly-collected grass fossils from the Dove Spring Formation, Red Rock Canyon State Park, California, USA, located in the El Paso Basin on the western side of the Basin and Range Province, a site previously identified as one of the earliest known C4 grass fossil bearing localities. We analyzed the anatomical and geochemical characteristics of these new grass fossils dated to 12.01–12.15 Ma. The fossils analyzed in this study include grass shoots and in cross-section display anatomy indicative of the C3 photosynthetic pathway. We isolated organic carbon from the stem fossils and determined the carbon isotopic composition to be − 24.8 ± 0.5‰. Together, the anatomical and geochemical analyses confirm that these plants used the C3 photosynthetic pathway. Our findings are consistent with dietary evidence based on tooth enamel from grazing mammals of available C3 resources in the same sections. These newly reported Miocene-age C3 grass fossils contribute to a sparse macrofossil record of grass evolution. Overall, paleoecological reconstructions at this site indicate more humid conditions during the Miocene compared to the modern Mojave Desert with C3 grasses and diverse grazing mammals

Detection of pneumococcal DNA in blood by polymerase chain reaction for diagnosing pneumococcal pneumonia in young children From low- and middle-income countries

Background We investigated the performance of polymerase chain reaction (PCR) on blood in the diagnosis of pneumococcal pneumonia among children from 7 low- and middle-income countries. Methods We tested blood by PCR for the pneumococcal autolysin gene in children aged 1–59 months in the Pneumonia Etiology Research for Child Health (PERCH) study. Children had World Health Organization–defined severe or very severe pneumonia or were age-frequency–matched community controls. Additionally, we tested blood from general pediatric admissions in Kilifi, Kenya, a PERCH site. The proportion PCR-positive was compared among cases with microbiologically confirmed pneumococcal pneumonia (MCPP), cases without a confirmed bacterial infection (nonconfirmed), cases confirmed for nonpneumococcal bacteria, and controls. Results In PERCH, 7.3% (n = 291/3995) of cases and 5.5% (n = 273/4987) of controls were blood pneumococcal PCR-positive (P Discussion The utility of pneumococcal PCR on blood for diagnosing childhood pneumococcal pneumonia in the 7 low- and middle-income countries studied is limited by poor specificity and by poor sensitivity among MCPP cases.</p

Evaluation of pneumococcal load in blood by polymerase chain reaction for the diagnosis of pneumococcal pneumonia in young children in the PERCH Study

Background. Detection of pneumococcus by lytA polymerase chain reaction (PCR) in blood had poor diagnostic accuracy for diagnosing pneumococcal pneumonia in children in 9 African and Asian sites. We assessed the value of blood lytA quantification in diagnosing pneumococcal pneumonia. Methods. The Pneumonia Etiology Research for Child Health (PERCH) case-control study tested whole blood by PCR for pneumococcus in children aged 1-59 months hospitalized with signs of pneumonia and in age-frequency matched community controls. The distribution of load among PCR-positive participants was compared between microbiologically confirmed pneumococcal pneumonia (MCPP) cases, cases confirmed for nonpneumococcal pathogens, nonconfirmed cases, and controls. Receiver operating characteristic analyses determined the "optimal threshold" that distinguished MCPP cases from controls. Results. Load was available for 290 of 291 cases with pneumococcal PCR detected in blood and 273 of 273 controls. Load was higher in MCPP cases than controls (median, 4.0 × 10 3 vs 0.19 × 10 3 copies/mL), but overlapped substantially (range, 0.16-989.9 × 10 3 copies/mL and 0.01-551.9 × 10 3 copies/mL, respectively). The proportion with high load (≥2.2 log 10 copies/mL) was 62.5% among MCPP cases, 4.3% among nonconfirmed cases, 9.3% among cases confirmed for a nonpneumococcal pathogen, and 3.1% among controls. Pneumococcal load in blood was not associated with respiratory tract illness in controls (P = .32). High blood pneumococcal load was associated with alveolar consolidation on chest radiograph in nonconfirmed cases, and with high ( > 6.9 log 10 copies/mL) nasopharyngeal/oropharyngeal load and C-reactive protein ≥40 mg/L (both P < .01) in nonconfirmed cases but not controls. Conclusions. Quantitative pneumococcal PCR in blood has limited diagnostic utility for identifying pneumococcal pneumonia in individual children, but may be informative in epidemiological studies