Ligand Specificity of Bean Leaf Soluble Auxin-binding Protein

The soluble bean leaf auxin-binding protein (ABP) has a high affinity for a range of auxins including indole-3-acetic acid (IAA), α-napthaleneacetic acid, phenylacetic acid, 2,4,5-trichlorophenoxyacetic acid, and structurally related auxins. A large number of nonauxin compounds that are nevertheless structurally related to auxins do not displace IAA from bean ABP. Bean ABP has a high affinity for auxin transport inhibitors and antiauxins. The specificity of pea ABP for representative auxins is similar to that found for bean ABP. The bean ABP auxin binding site is similar to the corn endoplasmic reticulum auxin-binding sites in specificity for auxins and sensitivity to thiol reagents and azide. Qualitative similarities between the ligand specificity of bean ABP and the specificity of auxin-induced bean leaf hyponasty provide further evidence, albeit circumstantial, that ABP (ribulose 1,5-bisphosphate carboxylase) can bind auxins in vivo. The high incidence of ABP in bean leaves and the high affinity of this protein for auxins and auxin transport inhibitors suggest possible functions for ABP in auxin transport and/or auxin sequestration.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.     

A Global Perspective on Drinking-Water and Sanitation Classification: An Evaluation of Census Content

Following the recent expiry of the United Nations’ 2015 Millennium Development Goals (MDGs), new international development agenda covering 2030 water, sanitation and hygiene (WASH) targets have been proposed, which imply new demands on data sources for monitoring relevant progress. This study evaluates drinking-water and sanitation classification systems from national census questionnaire content, based upon the most recent international policy changes, to examine national population census’s ability to capture drinking-water and sanitation availability, safety, accessibility, and sustainability. In total, 247 censuses from 83 low income and lower-middle income countries were assessed using a scoring system, intended to assess harmonised water supply and sanitation classification systems for each census relative to the typology needed to monitor the proposed post-2015 indicators of WASH targets. The results signal a lack of international harmonisation and standardisation in census categorisation systems, especially concerning safety, accessibility, and sustainability of services in current census content. This suggests further refinements and harmonisation of future census content may be necessary to reflect ambitions for post-2015 monitoring.     

Altered Energetics of Exercise Explain Risk of Rhabdomyolysis in Very Long-Chain Acyl-CoA Dehydrogenase Deficiency

Rhabdomyolysis is common in very long-chain acyl-CoA dehydrogenase deficiency (VLCADD) and other metabolic myopathies, but its pathogenic basis is poorly understood. Here, we show that prolonged bicycling exercise against a standardized moderate workload in VLCADD patients is associated with threefold bigger changes in phosphocreatine (PCr) and inorganic phosphate (Pi) concentrations in quadriceps muscle and twofold lower changes in plasma acetyl-carnitine levels than in healthy subjects. This result is consistent with the hypothesis that muscle ATP homeostasis during exercise is compromised in VLCADD. However, the measured rates of PCr and Pi recovery post-exercise showed that the mitochondrial capacity for ATP synthesis in VLCADD muscle was normal. Mathematical modeling of oxidative ATP metabolism in muscle composed of three different fiber types indicated that the observed altered energy balance during submaximal exercise in VLCADD patients may be explained by a slow-to-fast shift in quadriceps fiber-type composition corresponding to 30% of the slow-twitch fiber-type pool in healthy quadriceps muscle. This study demonstrates for the first time that quadriceps energy balance during exercise in VLCADD patients is altered but not because of failing mitochondrial function. Our findings provide new clues to understanding the risk of rhabdomyolysis following exercise in human VLCADD.     

Plant community composition as a driver of decomposition dynamics in riparian wetlands

Riparian wetlands are well known for providing the important ecosystem service of carbon storage. However, changes in land-use regimes surrounding riparian wetlands have been shown to result in alterations to the wetland plant community. These plant community changes have the potential to alter litter quality, decomposition rates, and ultimately the capacity of riparian wetlands to store carbon. To determine the effects of plant community shifts associated with disturbance on decomposition and carbon inputs, we performed a yearlong decomposition experiment using in situ herbaceous material, leaf litter, and control litter and examined biomass inputs in six headwater riparian wetlands in central Pennsylvania. Two sites were classified as Hemlock-Mixed Hardwood Palustrine Forest, two were classified as Broadleaf Palustrine Forest, and two were classified as Reed Canary Grass-Floodplain Grassland (Zimmerman et al. 2012). Plant matter with greater initial percent C, percent lignin, and lignin:N ratios decomposed more slowly while plant matter with greater initial cellulose decomposed more quickly. However, no significant differences were found between plant community types in decomposition rate or amount of carbon remaining at the end of the experiment, indicating that the differences in plant community type did not have a large impact on decomposition in riparian wetlands. This work has important implications for studies that examine the decomposition dynamics of a few select species, as they may not capture the decomposition dynamics of the plant community and thus extrapolating results from these studies to the larger ecosystem may be inappropriate.     

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.      

Modelling parasite aggregation: disentangling statistical and ecological approaches

The overdispersion in macroparasite infection intensity among host populations is commonly simulated using a constant negative binomial aggregation parameter. We describe an alternative to utilising the negative binomial approach and demonstrate important disparities in intervention efficacy projections that can come about from opting for pattern-fitting models that are not process-explicit. We present model output in the context of the epidemiology and control of soil-transmitted helminths due to the significant public health burden imposed by these parasites, but our methods are applicable to other infections with demonstrable aggregation in parasite numbers among hosts.