Revisiting the timetable of tuberculosis.
Ontology highlight
ABSTRACT:
SUBMITTER: Behr MA
PROVIDER: S-EPMC6105930 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundWe have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence.ResultsOn the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates.ConclusionsWe observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.
| S-EPMC395783 | biostudies-literature
Project description:A convenient way to estimate internal body time (BT) is essential for chronotherapy and time-restricted feeding, both of which use body-time information to maximize potency and minimize toxicity during drug administration and feeding, respectively. Previously, we proposed a molecular timetable based on circadian-oscillating substances in multiple mouse organs or blood to estimate internal body time from samples taken at only a few time points. Here we applied this molecular-timetable concept to estimate and evaluate internal body time in humans. We constructed a 1.5-d reference timetable of oscillating metabolites in human blood samples with 2-h sampling frequency while simultaneously controlling for the confounding effects of activity level, light, temperature, sleep, and food intake. By using this metabolite timetable as a reference, we accurately determined internal body time within 3 h from just two anti-phase blood samples. Our minimally invasive, molecular-timetable method with human blood enables highly optimized and personalized medicine.
| S-EPMC3443163 | biostudies-literature
Project description:IntroductionBreaking the sub-2-h marathon in an official event has attracted growing interest in recent times with commercial and international momentum building. Here it is shown that predicting how likely and when the sub-2-h barrier will be broken are statistically coupled considerations.MethodsUsing a nonlinear limiting exponential model and calculating prediction intervals, a statistical timetable for the sub-2-h event is produced over a range of likelihoods.ResultsAt the benchmark odds level (1 in 10, or 10% likely), the expected sub-2-h arrival time is found to be May 2032. By estimating the model for male and female world record progressions, I find that limiting marathon times for males and females (at 1 in 10) are 1 h 58 min 5 s and 2 h 5 min 31 s, respectively. These times equate to a performance gap of 2.9% and 8.6%, respectively. The male estimate has remarkable similarity (~7 s) to Joyner's 1991 limiting human physiological estimate. Finally, I provide an estimate of the equivalent "sub-2-h" threshold for females and argue that a threshold of 130 min ("sub-130") could be an appropriate choice.ConclusionThe study is the first to address all three related aspects of world record marathon performance (sub-2 h, limits, gender equivalence) in a single, unified modeling framework and provides many avenues for further exploration and insight.
| S-EPMC6613719 | biostudies-literature
Project description:Climate change is expected to increase temperature and decrease summer precipitation in Central Europe. Little is known about how warming and drought will affect phenological patterns of oaks, which are considered to possess excellent adaptability to these climatic changes. Here, we investigated bud burst and intra-annual shoot growth of Quercus robur, Q. petraea and Q. pubescens grown on two different forest soils and exposed to air warming and drought. Phenological development was assessed over the course of three growing seasons. Warming advanced bud burst by 1-3 days °C⁻¹ and led to an earlier start of intra-annual shoot growth. Despite this phenological shift, total time span of annual growth and shoot biomass were not affected. Drought changed the frequency and intensity of intra-annual shoot growth and advanced bud burst in the subsequent spring of a severe summer drought by 1-2 days. After re-wetting, shoot growth recovered within a few days, demonstrating the superior drought tolerance of this tree genus. Our findings show that phenological patterns of oaks are modified by warming and drought but also suggest that ontogenetic factors and/or limitations of water and nutrients counteract warming effects on the biomass and the entire span of annual shoot growth.
| S-EPMC3933646 | biostudies-literature
Project description:Mycobacterium tuberculosis, the agent of human tuberculosis has developed different virulence mechanisms and virulence-associated tools during its evolution to survive and multiply inside the host. Based on previous reports and by analogy with other bacteria, phospholipases C (PLC) of M. tuberculosis were thought to be among these tools. To get deeper insights into the function of PLCs, we investigated their putative involvement in the intracellular lifestyle of M. tuberculosis, with emphasis on phagosomal rupture and virulence, thereby re-visiting a research theme of longstanding interest. Through the construction and use of an M. tuberculosis H37Rv PLC-null mutant (?PLC) and control strains, we found that PLCs of M. tuberculosis were not required for induction of phagosomal rupture and only showed marginal, if any, impact on virulence of M. tuberculosis in the cellular and mouse infection models used in this study. In contrast, we found that PLC-encoding genes were strongly upregulated under phosphate starvation and that PLC-proficient M. tuberculosis strains survived better than ?PLC mutants under conditions where phosphatidylcholine served as sole phosphate source, opening new perspectives for studies on the role of PLCs in the lifecycle of M. tuberculosis.
| S-EPMC4658479 | biostudies-literature
Project description:IQG-607 is a metal complex previously reported as a promising anti-tuberculosis (TB) drug against isoniazid (INH)-resistant strains of Mycobacterium tuberculosis Unexpectedly, we found that INH-resistant clinical isolates were resistant to IQG-607. Spontaneous mutants resistant to IQG-607 were subjected to whole-genome sequencing, and all sequenced colonies carried alterations in the katG gene. The katG(S315T) mutation was sufficient to confer resistance to IQG-607 in both MIC assays and inside macrophages. Moreover, overexpression of the InhA(S94A) protein caused IQG-607's resistance.
| S-EPMC5786794 | biostudies-literature
Project description:Slaughterhouse or meat factory surveillance to detect factory lesions (FL) at slaughter is an important part of the bovine tuberculosis (bTB) eradication program in Ireland. The objective of this study was to quantify the effectiveness of Irish slaughterhouses or factories in submitting FL and the proportion of those submitted FL confirmed as being due to bTB in slaughtered cattle, and to identify and quantify the association of risk factors at animal, herd, and factory level with FL submission and confirmation. The data consisted of 6,611,854 animals slaughtered in Irish factories from 2014 to 2018 obtained from the Department of Agriculture, Food and Marine (DAFM), Ireland. Selected risk factors for this study included factory, year and month of slaughter, age, sex, breed, animal movement, ever inconclusive in the standard or severe skin test, herd type, herd size, and bTB history. The association of each risk factor on the FL submission and confirmation risk were analysed with univariable followed by a multivariable logistic regression with herd as random effect. Factories were ranked and compared based on the odds ratio (OR) obtained from the univariable (crude OR) and multivariable (adjusted OR) analysis. The average submission risk of all factories was 20 per 10,000 animals slaughtered, ranging from 1 to 42 per 10,000 animals slaughtered, and the average confirmation risk over all factories was 40.72%, ranging from 0.00 to 61.84%. The odds of submitting and confirming FL as bTB positive were higher in animals over eight years old compared to animals 1-2 years old (OR = 1.91, 95 CI 95% 1.77-2.06 and OR = 4.05, 95% CI 3.17-5.18, respectively), and were higher in animals that ever had inconclusive skin result based on severe interpretation (OR = 2.83, 95% CI 2.44-3.27 and OR = 4.48, 95% CI 2.66-7.54, respectively), animals originating from sucklers herds (OR = 1.08, 95% CI 1.02-1.14 and OR = 1.31, 95% CI 1.11-1.55, respectively), or herds with bTB history in the past three years (OR = 4.46, 95% CI 4.28-4.66 and OR = 319.90, 95% CI 237.98-430.04, respectively). The odds of FL submission and confirmation decreased as the herd size increased (OR = 0.95, 95% CI 0.93-0.96 and OR = 0.82, 95% CI 0.78-0.86, respectively). An inverse relationship of FL submission and confirmation was present for variable sex and inconclusive skin result with standard interpretation, where submission odds were higher in males (OR = 1.05, 95% CI 1.00-1.10) and ever inconclusive animals (OR = 74.24, 95% CI 69.39-79.43), although the confirmation odds were lower (males OR = 0.66, 95% CI 0.56-0.76; ever inconclusive OR = 0.44, 95% CI 0.36-0.54). The crude and adjusted ranking of factories did not differ greatly for FL submission, indicating that factory-related factors may contribute significantly to the submission variation between factories. However, a substantial difference between crude and adjusted confirmation ranking was present which may indicate that animal and herd-related factors were associated to variation in confirmation risk between factories.
| S-EPMC9543943 | biostudies-literature
Project description:Gene expression analysis is a widely used and powerful method for investigating the transcriptional behavior of biological systems, for classifying cell states in disease and for many other purposes. Recent studies indicate that common assumptions currently embedded in experimental and analytical practices can lead to misinterpretation of global gene expression data. We discuss these assumptions and describe solutions that should minimize erroneous interpretation of gene expression data from multiple analysis platforms. RNA was extracted from cells expressing low or high levels of c-Myc. A panel of synthetic RNA's was added to these populations, based on cell number. Total RNA was then extracted and processed on Affymetrix microarrays in biological duplicate.
2012-10-25 | E-GEOD-40782 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2012-10-25 | GSE40784 | GEO
Project description:Of the diverse lineages of the Phylum Oomycota, saprotrophic oomycetes from the salt marsh and mangrove habitats are still understudied, despite their ecological importance. Salisapiliaceae, a monophyletic and monogeneric taxon of the marine and estuarine oomycetes, was introduced to accommodate species with a protruding hyaline apical plug, small hyphal diameter and lack of vesicle formation during zoospore release. At the time of description of Salisapilia, only few species of Halophytophthora, an ecologically similar, phylogenetically heterogeneous genus from which Salisapilia was segregated, were included. In this study, a revision of the genus Salisapilia is presented, and five new combinations (S. bahamensis, S. elongata, S. epistomia, S. masteri, and S. mycoparasitica) and one new species (S. coffeyi) are proposed. Further, the species description of S. nakagirii is emended for some exceptional morphological and developmental characteristics. A key to the genus Salisapilia is provided and its generic circumscription and character evolution in cultivable Peronosporales are discussed.
| S-EPMC7252517 | biostudies-literature