Quantifying a stress gradient: An objective approach to variable selection,standardization and weighting in ecosystem assessment

Quantifying relative habitat quality is an important means of ecosystem assessment, and an essential step in the development and validation of indices of biotic integrity (IBI). Variables included in multi-metric IBIs are selected on the basis of their correlation with a human disturbance gradient, and the IBI is tested by examining correlation between IBI scores and rankings on the human disturbance gradient for an independent suite of sites. We present an objective approach to develop a disturbance gradient that ranks sites based on local-level measurements of physical and chemical stress; however, it could equally be applied to GIS-derived data. We measured 52 variables at three types of wetland in Alberta: reference wetlands, oil sands reclamation wetlands exposed to mine tailings, and reclamation wetlands free from tailings contamination. We used the data's correlation structure to select a sub-set of variables that minimized redundancy while retaining sensitivity and interpretability. The optimal sub-set included eight variables: chloride, cation and nitrogen content of water; water and oil content of sediment; water depth and amplitude and Secchi depth/total depth. We combined these eight environmental variables using different combinations of standardization (conversion to a common unit) and weighting schemes to produce six multi-metric stress indices. We evaluated the stress indices on their ability to discriminate among our three wetland types. The indices differed in their sensitivity to stress. Standardization had greater influence on index score than weighting. While all stress indices detected a difference among the three wetland types, only two were able to discriminate between the two classes of reclamation wetlands, both of which used percentile binning to standardize variables. The optimal stress index was standardized by percentile binning and weighted such that water quality, sediment chemistry, physical structure, and the level of tailings contamination were weighted equally. The approach we developed is repeatable and produced a sensitive index of wetland condition that is easily interpreted and relies minimally on best professional judgment. It may be suitable for measuring restoration success or the impact of any anthropogenic disturbance in a variety of ecosystem types.     

Evolution of <Emphasis Type="Italic">trappin</Emphasis> genes in mammals

Background  

Trappin is a multifunctional host-defense peptide that has antiproteolytic, antiinflammatory, and antimicrobial activities. The numbers and compositions of trappin paralogs vary among mammalian species: human and sheep have a single trappin-2 gene; mouse and rat have no trappin gene; pig and cow have multiple trappin genes; and guinea pig has a trappin gene and two other derivativegenes. Independent duplications of trappin genes in pig and cow were observed recently after the species were separated. To determine whether these trappin gene duplications are restricted only to certain mammalian lineages, we analyzed recently-developed genome databases for the presence of duplicate trappin genes.     

In Vitro and Ex Vivo Testing of Tenofovir Shows It Is Effective As an HIV-1 Microbicide

Background

Tenofovir gel has entered into clinical trials for use as a topical microbicide to prevent HIV-1 infection but has no published data regarding pre-clinical testing using in vitro and ex vivo models. To validate our findings with on-going clinical trial results, we evaluated topical tenofovir gel for safety and efficacy. We also modeled systemic application of tenofovir for efficacy.

Methods and Findings

Formulation assessment of tenofovir gel included osmolality, viscosity, in vitro release, and permeability testing. Safety was evaluated by measuring the effect on the viability of vaginal flora, PBMCs, epithelial cells, and ectocervical and colorectal explant tissues. For efficacy testing, PBMCs were cultured with tenofovir or vehicle control gels and HIV-1 representing subtypes A, B, and C. Additionally, polarized ectocervical and colorectal explant cultures were treated apically with either gel. Tenofovir was added basolaterally to simulate systemic application. All tissues were challenged with HIV-1 applied apically. Infection was assessed by measuring p24 by ELISA on collected supernatants and immunohistochemistry for ectocervical explants. Formulation testing showed the tenofovir and vehicle control gels were >10 times isosmolar. Permeability through ectocervical tissue was variable but in all cases the receptor compartment drug concentration reached levels that inhibit HIV-1 infection in vitro. The gels were non-toxic toward vaginal flora, PBMCs, or epithelial cells. A transient reduction in epithelial monolayer integrity and epithelial fracture for ectocervical and colorectal explants was noted and likely due to the hyperosmolar nature of the formulation. Tenofovir gel prevented HIV-1 infection of PBMCs regardless of HIV-1 subtype. Topical and systemic tenofovir were effective at preventing HIV-1 infection of explant cultures.

Conclusions

These studies provide a mechanism for pre-clinical prediction of safety and efficacy of formulated microbicides. Tenofovir was effective against HIV-1 infection in our algorithm. These data support the use of tenofovir for pre-exposure prophylaxis.     

The efficacy and sterilisation of human decellularised dermal allografts with combinations of cupric ions and hydrogen peroxide

Decellularised tissue allografts have been used in reconstructive surgical applications and transplantation for many years. Some of the current methods of sterilisation have a detrimental effect on the tissue graft structure and function. The anti-microbial activity of cupric ions and hydrogen peroxide (H₂O₂) are well known however their combined application is not currently utilised as a decontamination agent in the tissue banking world sector. The aim of this study was to determine the combined concentrations of copper chloride (CuCl₂) and H₂O₂ that have the optimal bactericidal and sporicidal activity on decellularised (dCELL) human dermis. The first part of this study established the decimal reduction time (D-value) of CuCl₂ (0.1 mg/L and 1 mg/L) together with H₂O₂ (0.01, 0.1, 0.5 and 1%) for Staphylococcus epidermidis, Escherichia coli and Bacillus subtilis spores. The second part of this study identified the most effective CuCl₂ and H₂O₂ concentration that decontaminated dCELL human dermis inoculated with these pathogens. Of all the concentrations tested, 0.1 mg/L CuCl₂ in combination with 1% H₂O₂ had the shortest D-value; S. epidermidis D = 3.15 min, E. coli D = 2.62 min and B. subtilis spores D = 18.05 min. However when adsorbed onto dCELL dermis, S. epidermidis and E. coli were more susceptible to 1 mg/L CuCl₂ together with 0.5% H₂O₂. These studies show promise of CuCl₂–H₂O₂ formulations as potential sterilants for decellularised dermal allografts.     

CTGF/CCN2 activates canonical Wnt signalling in mesangial cells through LRP6: implications for the pathogenesis of diabetic nephropathy

We describe the activation of Wnt signalling in mesangial cells by CCN2. CCN2 stimulates phosphorylation of LRP6 and GSK-3β resulting in accumulation and nuclear localisation of β-catenin, TCF/LEF activity and expression of Wnt targets. This is coincident with decreased phosphorylation of β-catenin on Ser 33/37 and increased phosphorylation on Tyr142. DKK-1 and LRP6 siRNA reversed CCN2’s effects. Microarray analyses of diabetic patients identified differentially expressed Wnt components. β-Catenin is increased in type 1 diabetic and UUO mice and in in vitro models of hyperglycaemia and hypertension. These findings suggest that Wnt/CCN2 signalling plays a role in the pathogenesis of diabetic nephropathy.     

The Non-Classical MAP Kinase ERK3 Controls T Cell Activation

The classical mitogen-activated protein kinases (MAPKs) ERK1 and ERK2 are activated upon stimulation of cells with a broad range of extracellular signals (including antigens) allowing cellular responses to occur. ERK3 is an atypical member of the MAPK family with highest homology to ERK1/2. Therefore, we evaluated the role of ERK3 in mature T cell response. Mouse resting T cells do not transcribe ERK3 but its expression is induced in both CD4⁺ and CD8⁺ T cells following T cell receptor (TCR)-induced T cell activation. This induction of ERK3 expression in T lymphocytes requires activation of the classical MAPK ERK1 and ERK2. Moreover, ERK3 protein is phosphorylated and associates with MK5 in activated primary T cells. We show that ERK3-deficient T cells have a decreased proliferation rate and are impaired in cytokine secretion following in vitro stimulation with low dose of anti-CD3 antibodies. Our findings identify the atypical MAPK ERK3 as a new and important regulator of TCR-induced T cell activation.     

Sorghum Phytochrome B Inhibits Flowering in Long Days by Activating Expression of SbPRR37 and SbGHD7, Repressors of SbEHD1, SbCN8 and SbCN12

Light signaling by phytochrome B in long days inhibits flowering in sorghum by increasing expression of the long day floral repressors PSEUDORESPONSE REGULATOR PROTEIN (SbPRR37, Ma1) and GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGHD7, Ma6). SbPRR37 and SbGHD7 RNA abundance peaks in the morning and in the evening of long days through coordinate regulation by light and output from the circadian clock. 58 M, a phytochrome B deficient (phyB-1, ma3^R) genotype, flowered ∼60 days earlier than 100 M (PHYB, Ma3) in long days and ∼11 days earlier in short days. Populations derived from 58 M (Ma1, ma3^R, Ma5, ma6) and R.07007 (Ma1, Ma3, ma5, Ma6) varied in flowering time due to QTL aligned to PHYB/phyB-1 (Ma3), Ma5, and GHD7/ghd7-1 (Ma6). PHYC was proposed as a candidate gene for Ma5 based on alignment and allelic variation. PHYB and Ma5 (PHYC) were epistatic to Ma1 and Ma6 and progeny recessive for either gene flowered early in long days. Light signaling mediated by PhyB was required for high expression of the floral repressors SbPRR37 and SbGHD7 during the evening of long days. In 100 M (PHYB) the floral activators SbEHD1, SbCN8 and SbCN12 were repressed in long days and de-repressed in short days. In 58 M (phyB-1) these genes were highly expressed in long and short days. Furthermore, SbCN15, the ortholog of rice Hd3a (FT), is expressed at low levels in 100 M but at high levels in 58 M (phyB-1) regardless of day length, indicating that PhyB regulation of SbCN15 expression may modify flowering time in a photoperiod-insensitive manner.     

Magnetic Resonance Imaging and Spectroscopy Assessment of Lower Extremity Skeletal Muscles in Boys with Duchenne Muscular Dystrophy: A Multicenter Cross Sectional Study

Introduction

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder that results in functional deficits. However, these functional declines are often not able to be quantified in clinical trials for DMD until after age 7. In this study, we hypothesized that ¹H₂O T₂ derived using ¹H-MRS and MRI-T₂ will be sensitive to muscle involvement at a young age (5–7 years) consistent with increased inflammation and muscle damage in a large cohort of DMD subjects compared to controls.

Methods

MR data were acquired from 123 boys with DMD (ages 5–14 years; mean 8.6 SD 2.2 years) and 31 healthy controls (age 9.7 SD 2.3 years) using 3-Tesla MRI instruments at three institutions (University of Florida, Oregon Health & Science University, and Children’s Hospital of Philadelphia). T₂-weighted multi-slice spin echo (SE) axial images and single voxel ¹H-MRS were acquired from the lower leg and thigh to measure lipid fraction and ¹H₂O T₂.

Results

MRI-T₂, ¹H₂O T₂, and lipid fraction were greater (p<0.05) in DMD compared to controls. In the youngest age group, DMD values were different (p<0.05) than controls for the soleus MRI-T₂, ¹H₂O T₂ and lipid fraction and vastus lateralis MRI-T₂ and ¹H₂O T₂. In the boys with DMD, MRI-T₂ and lipid fraction were greater (p<0.05) in the oldest age group (11–14 years) than the youngest age group (5–6.9 years), while ¹H₂O T₂ was lower in the oldest age group compared to the young age group.

Discussion

Overall, MR measures of T₂ and lipid fraction revealed differences between DMD and Controls. Furthermore, MRI-T₂ was greater in the older age group compared to the young age group, which was associated with higher lipid fractions. Overall, MR measures of T₂ and lipid fraction show excellent sensitivity to DMD disease pathologies and potential therapeutic interventions in DMD, even in the younger boys.     

Yield Results and Stability Analysis from the Sorghum Regional Biomass Feedstock Trial

Sorghum [Sorghum bicolor (L.) Moench] is one of four herbaceous dedicated bioenergy crops the U.S. Department of Energy identified as critical to annually produce one billion tons of dry biomass. Of these four crops, sorghum is unique as it is a drought-tolerant, annual crop established from seed that is readily tractable to genetic improvement. The purpose of this study was to assess the yield potential and stability of sorghums grown across diverse production environments in the USA. For this study, six sorghum genotypes (one cultivar, five hybrids) were grown in yield trials in seven locations in six states for 5 years (2008–2012). Variation in dry and fresh yield was attributable to not only genotypes, but also to the effects of year, location, and year × location. Even with the highest yielding genotype, environmental conditions were a major factor in determining the yield in a given year. This variability affects the consistency of the biomass supply for ethanol production. In general, the southeastern USA had the highest mean yields for fresh weight and dry weight, indicating that this area may be the most reliable for biomass production. A significant variation was detected among genotypes for fresh weight, dry weight, moisture content, and brix, revealing that sufficient variation within sorghum exists for continued improvement and that certain hybrids are more tractable for biomass/bioenergy production. With dedicated bioenergy sorghum germplasm and proper production environments, sorghum will be a valuable tool in the goal of the sustainable production of one billion tons of dry biomass each year in the USA.     

Retracted: Tusk shells in trouble? Physiology and behavior in response to changing temperature in a scaphopod (Mollusca: Scaphopoda: Dentaliida)

Scaphopods (tusk shells) are infaunal marine predators that occur at locally high densities in coastal and deep‐sea mud habitats, and as consumers of foraminifera they are important in carbon cycling. We investigated oxygen metabolism and burying behavior of the scaphopod Rhabdus rectius and its responses to altered temperatures. These are the first measurements of oxygen uptake rates for any member of this taxonomic class. In response to elevated temperatures, oxygen uptake rates increased, but the ability of animals to bury themselves in sediment was compromised. Female scaphopods were significantly larger than males and, when corrected for body mass, oxygen uptake rates were consistently higher for female individuals than for males. This is consistent with previous anecdotal observations of females in other scaphopod species being larger and potentially more active. In conditions of declining oxygen availability, individuals of Rhabdus rectius showed strong oxyregulatory ability by maintaining the same oxygen uptake rate displayed in normoxic conditions. The ability to maintain normal metabolic functioning even in conditions of oxygen limitation would benefit a species living in a benthic environment that may be prone to temporary or transient anoxic events. Yet the decrease in normal escape response in moderately elevated temperatures indicates these animals may be at risk from rising sea temperatures.