Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and non-canonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments1. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago2, conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum AtDt (in which ‘t’ indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups

Hypocalcification and hypoplasia in primary teeth of pre-school children from different ethnic groups in South Africa

A study was completed in 1985/86 which examined the dental health of pre-school children from different ethnic groups and communities in South Africa: rural black, urban black, urban colored, urban Indian, and urban white. Enamel defects were recorded in primary teeth by use of the HHI, an index developed to measure hypocalcification and hypoplasia of enamel. The findings showed that colored children had the greatest number of enamel defects. The teeth most commonly affected were the maxillary anterior teeth and mandibular molar teeth. It is suggested that further epidemiological studies utilizing the HHI should be undertaken in pre-school children, especially from developing countries, to gain more information on the causes of enamel defects in the primary dentition and the possible use of such findings to predict nutritional health of individuals.TS2016.http://journals.sagepub.com/doi/pdf/10.1177/0895937489003002070

Effluent Organic Nitrogen (EON): Bioavailability and Photochemical and Salinity-Mediated Release

The goal of this study was to investigate three potential ways that the soluble organic nitrogen (N) fraction of wastewater treatment plant (WWTP) effluents, termed effluent organic N (EON), could contribute to coastal eutrophication - direct biological removal, photochemical release of labile compounds, and salinity-mediated release of ammonium (NH4+). Effluents from two WWTPs were used in the experiments. For the bioassays, EON was added to water from four salinities (similar to 0 to 30) collected from the James River (VA) in August 2008, and then concentrations of N and phosphorus compounds were measured periodically over 48 h. Bioassay results, based on changes in DON concentrations, indicate that some fraction of the EON was removed and that the degree of EON removal varied between effluents and with salinity. Further, we caution that bioassay results should be interpreted within a broad context of detailed information on chemical characterization. EON from both WWTPs was also photoreactive, with labile NH4+ and dissolved primary amines released during exposure to sunlight. We also present the first data that demonstrate that when EON is exposed to higher salinities, increasing amounts of NH4+ are released, further facilitating EON use as effluent transits from freshwater through estuaries to the coast

Field Validation of Multi-Species Laboratory Test Systems for Estuarine Benthic Communities

The aim of this project was to evaluate the validity of using multi-species laboratory systems to assess the response of eatuarine benthic communities to an introduced stress. Over a 5- year period experiments in Apalachicola Bay, Florida, and the York River, Virginia, sought to (1) develop criteria for microcosm tests for evaluating the capacity of microcosms to model natural communities in the presence and absence of a pollution-induced stress, and (2) assess the validity of extrapolating test results from one location to another. Procedures for constructing, maintaining and sampling microcosms were tested and refined over the study period. A large number of laboratory and field tests were conducted synoptically over this period, including experiments in which microcosms and field sites were dosed with toxicants (mixed hydrocarbons in some and pentachlorophenol in others). We have investigated various methodologies for analysing and interpreting data derived from microcosm tests

Regional scale dryland vegetation classification with an integrated lidar-hyperspectral approach

The sparse canopy cover and large contribution of bright background soil, along with the heterogeneous vegetation types in close proximity, are common challenges for mapping dryland vegetation with remote sensing. Consequently, the results of a single classification algorithm or one type of sensor to characterize dryland vegetation typically show low accuracy and lack robustness. In our study, we improved classification accuracy in a semi-arid ecosystem based on the use of vegetation optical (hyperspectral) and structural (lidar) information combined with the environmental characteristics of the landscape. To accomplish this goal, we used both spectral angle mapper (SAM) and multiple endmember spectral mixture analysis (MESMA) for optical vegetation classification. Lidar-derived maximum vegetation height and delineated riparian zones were then used to modify the optical classification. Incorporating the lidar information into the classification scheme increased the overall accuracy from 60% to 89%. Canopy structure can have a strong influence on spectral variability and the lidar provided complementary information for SAM’s sensitivity to shape but not magnitude of the spectra. Similar approaches to map large regions of drylands with low uncertainty may be readily implemented with unmixing algorithms applied to upcoming space-based imaging spectroscopy and lidar. This study advances our understanding of the nuances associated with mapping xeric and mesic regions, and highlights the importance of incorporating complementary algorithms and sensors to accurately characterize the heterogeneity of dryland ecosystems

The structure of the PapD-PapGII pilin complex reveals an open and flexible P5 pocket

P pili are hairlike polymeric structures that mediate binding of uropathogenic Escherichia coli to the surface of the kidney via the PapG adhesin at their tips. PapG is composed of two domains: a lectin domain at the tip of the pilus followed by a pilin domain that comprises the initial polymerizing subunit of the 1,000-plus-subunit heteropolymeric pilus fiber. Prior to assembly, periplasmic pilin domains bind to a chaperone, PapD. PapD mediates donor strand complementation, in which a beta strand of PapD temporarily completes the pilin domain's fold, preventing premature, nonproductive interactions with other pilin subunits and facilitating subunit folding. Chaperone-subunit complexes are delivered to the outer membrane usher where donor strand exchange (DSE) replaces PapD's donated beta strand with an amino-terminal extension on the next incoming pilin subunit. This occurs via a zip-in-zip-out mechanism that initiates at a relatively accessible hydrophobic space termed the P5 pocket on the terminally incorporated pilus subunit. Here, we solve the structure of PapD in complex with the pilin domain of isoform II of PapG (PapGIIp). Our data revealed that PapGIIp adopts an immunoglobulin fold with a missing seventh strand, complemented in parallel by the G1 PapD strand, typical of pilin subunits. Comparisons with other chaperone-pilin complexes indicated that the interactive surfaces are highly conserved. Interestingly, the PapGIIp P5 pocket was in an open conformation, which, as molecular dynamics simulations revealed, switches between an open and a closed conformation due to the flexibility of the surrounding loops. Our study reveals the structural details of the DSE mechanism

Improved ventricular function during inhalation of PGI(2) aerosol partly relies on enhanced myocardial contractility

Inhaled prostacyclin (PGI(2)) aerosol induces selective pulmonary vasodilation. Further, it improves right ventricular ( RV) function, which may largely rely on pulmonary vasodilation, but also on enhanced myocardial contractility. We investigated the effects of the inhaled PGI(2) analogs epoprostenol (EPO) and iloprost (ILO) on RV function and myocardial contractility in 9 anesthetized pigs receiving aerosolized EPO (25 and 50 ng center dot kg(-1) center dot min(-1)) and, consecutively, ILO (60 ng center dot kg(-1) center dot min(-1)) for 20 min each. We measured pulmonary artery pressure ( PAP), RV ejection fraction (RVEF) and RV end-diastolic-volume (RV-EDV), and left ventricular end-systolic pressure-volume-relation (end-systolic elastance, E-es). EPO and ILO reduced PAP, increased RVEF and reduced RVEDV. E-es was enhanced during all doses tested, which reached statistical significance during EPO25ng and ILO, but not during EPO50ng. PGI(2) aerosol enhances myocardial contractility in healthy pigs, contributing to improve RV function. Copyright (C) 2005 S. Karger AG, Basel

Application of Jain and Munczek's bound-state approach to gamma gamma-processes of pi0, eta_c and eta_b

We point out the problems affecting most quark--antiquark bound state approaches when they are faced with the electromagnetic processes dominated by Abelian axial anomaly. However, these problems are resolved in the consistently coupled Schwinger-Dyson and Bethe-Salpeter approach. Using one of the most successful variants of this approach, we find the dynamically dressed propagators of the light u and d quarks, as well as the heavy c and b quarks, and find the Bethe-Salpeter amplitudes for their bound states pi0, eta_c and \eta_b. Thanks to incorporating the dynamical chiral symmetry breaking, the pion simultaneously appears as the (pseudo)Goldstone boson. We give the theoretical predictions for the gamma-gamma decay widths of pi0, eta_c and eta_b, and for the pi0 gamma* -> gamma transition form factor, and compare them with experiment. In the chiral limit, the axial-anomaly result for pi0->gamma-gamma is reproduced analytically in the consistently coupled Schwinger-Dyson and Bethe-Salpeter approach, provided that the quark-photon vertex is dressed consistently with the quark propagator, so that the vector Ward-Takahashi identity of QED is obeyed. On the other hand, the present approach is also capable of quantitatively describing systems of heavy quarks, concretely eta_c and possibly eta_b, and their gamma-gamma decays. We discuss the reasons for the broad phenomenological success of the bound-state approach of Jain and Munczek.Comment: RevTeX, 37 pages, 7 eps figures, submitted to Int. J. Mod. Phys.

Prenatal exposures and exposomics of asthma

This review examines the causal investigation of preclinical development of childhood asthma using exposomic tools. We examine the current state of knowledge regarding early-life exposure to non-biogenic indoor air pollution and the developmental modulation of the immune system. We examine how metabolomics technologies could aid not only in the biomarker identification of a particular asthma phenotype, but also the mechanisms underlying the immunopathologic process. Within such a framework, we propose alternate components of exposomic investigation of asthma in which, the exposome represents a reiterative investigative process of targeted biomarker identification, validation through computational systems biology and physical sampling of environmental medi