The Planktonic Index of Biotic Integrity (P-IBI): An approach for assessing lake ecosystem health

Using historical (1970) and more recent (1996) Lake Erie plankton and trophic status data, we developed a Planktonic Index of Biotic Integrity (P-IBI) to measure changes in lake ecosystem health. We used discriminant analysis to determine phytoplankton and zooplankton community characteristics (metrics) that distinguished among levels of impairment. Traditional measures of lake trophic status classes (i.e., oligotrophic, mesotrophic, eutrophic), such as chlorophyll a and total phosphorus concentrations, were used to classify sites on a gradient of impairment. We then judged the ability of plankton metrics to distinguish among trophic status classes. Because of the temporal variability found in plankton communities, we conducted analyses on a monthly basis (May–September). For June, July and August we found five unique metrics that could distinguish among trophic status classes. The P-IBI showed an increase in water quality in Lake Erie between 1970 (<3 = eutrophic) and the mid-1990s (1996 and 1997) (3–4 = mesotrophic) (which reflected mean (±standard error) total phosphorus concentrations (μg/L) 1970 > 1996; western basin (41.53 ± 2.68 > 29.75 ± 1.39), eastern basin (14.84 ± 0.82 > 7.74 ± 0.28) and mean (±standard error) chlorophyll a concentrations (μg/L) uncorrected for pheophytin 1970 > 1996; western basin (12.58 ± 1.82 > 5.40 ± 0.22), central basin (5.90 ± 0.36 > 3.17 ± 0.54), and eastern basin (5.17 ± 0.38 > 1.67 ± 0.18)), with declining water quality in the late 1990s (1998 and 1999) (3) and 2002 (<3). We recommend that the techniques used in creating the P-IBI be investigated for determining ecosystem health of other lakes.     

The timing and specificity of prenatal immune risk factors for autism modeled in the mouse and relevance to schizophrenia

Autism is a highly heritable condition, but there is strong epidemiological evidence that environmental factors, especially prenatal exposure to immune challenge, contribute to it. This evidence is largely indirect, and experimental testing is necessary to directly examine causal mechanisms. Mouse models reveal that prenatal immune perturbation disrupts postnatal brain maturation with alterations in gene and protein expression, neurotransmitter function, brain structure and behavioral indices reminiscent of, but not specific to, autism. This likely reflects a neurodevelopmental spectrum in which autism and schizophrenia share numerous genetic and environmental risk factors for difficulties in social interaction, communication, emotion processing and executive function. Recent epidemiological studies find that early rather than late pregnancy infection confers the greater risk of schizophrenia. The autism literature is more limited, but exposures in the 2nd half of pregnancy may be important. Mouse models of prenatal immune challenge help dissect these observations and show some common consequences of early and late gestational exposures, as well as distinct ramifications potentially relevant to schizophrenia and autism. Although nonspecificity of immune-stimulated mouse models could be considered a disadvantage, we propose a broadened perspective, exploiting the possibility that advances made investigating a target condition can contribute towards the understanding of related conditions.     

Temperature-induced reversible conformational change in the first 100 residues of alpha-synuclein

Natively disordered proteins are a growing class of anomalies to the structure-function paradigm. The natively disordered protein alpha-synuclein is the primary component of Lewy bodies, the cellular hallmark of Parkinson's disease. We noticed a dramatic difference in dilute solution 1H-15N Heteronuclear Single Quantum Coherence (HSQC) spectra of wild-type alpha-synuclein and two disease-related mutants (A30P and A53T), with spectra collected at 35 degrees C showing fewer cross-peaks than spectra acquired at 10 degrees C. Here, we show the change to be the result of a reversible conformational exchange linked to an increase in hydrodynamic radius and secondary structure as the temperature is raised. Combined with analytical ultracentrifugation data showing alpha-synuclein to be monomeric at both temperatures, we conclude that the poor quality of the 1H-15N HSQC spectra obtained at 35 degrees C is due to conformational fluctuations that occur on the proton chemical shift time scale. Using a truncated variant of alpha-synuclein, we show the conformational exchange occurs in the first 100 amino acids of the protein. Our data illustrate a key difference between globular and natively disordered proteins. The properties of globular proteins change little with solution conditions until they denature cooperatively, but the properties of natively disordered proteins can vary dramatically with solution conditions.     

Effects of Metformin and Weight Loss on Serum Alanine Aminotransferase Activity in the Diabetes Prevention Program

Nonalcoholic fatty liver disease (NAFLD) is associated with obesity, insulin resistance, and impaired glucose tolerance. We investigated whether metformin or changes in metabolic measurements (weight, fasting plasma glucose (FPG), or fasting insulin (FI)) improved serum alanine aminotransferase (ALT) activity, as a marker for NAFLD, in the Diabetes Prevention Program (DPP). From 1996 to 1999, 2,153 participants without marked elevations of serum ALT at baseline were randomized (1,081 to placebo, 1,072 to metformin) and treated for an average of 3.2 years. ALT increased during the first 2 years of the study, and was slightly but significantly lower in the participants randomized to metformin. In regression models adjusted for sex, baseline age, FPG, and FI, these differences remained significant, but disappeared after adjustment for weight, FPG, and FI changes at each examination. The 3‐year cumulative incidence for development of abnormal ALT concentrations was not significantly different ((mean ± s.e.) 21.4 ± 1.4% and 24.6 ± 1.4%, P = 0.11) in the metformin vs. placebo groups but was lower in individuals in both groups that lost more weight by the end of year 1 (metformin: 19.4 ± 2.4% vs. 27.5 ± 3.7%, for highest vs. lowest quartile of weight loss; placebo: 18.7 ± 3.4% vs. 28.8 ± 2.6%). Over 3 years of follow‐up in persons at high risk for development of diabetes, serum ALT was consistently lower in those treated with metformin compared with placebo. This effect was mediated by weight loss, indicating that the effects of metformin therapy on ALT is via its effects on weight.     

Autistic Disorders and Schizophrenia: Related or Remote? An Anatomical Likelihood Estimation

Shared genetic and environmental risk factors have been identified for autistic spectrum disorders (ASD) and schizophrenia. Social interaction, communication, emotion processing, sensorimotor gating and executive function are disrupted in both, stimulating debate about whether these are related conditions. Brain imaging studies constitute an informative and expanding resource to determine whether brain structural phenotype of these disorders is distinct or overlapping. We aimed to synthesize existing datasets characterizing ASD and schizophrenia within a common framework, to quantify their structural similarities. In a novel modification of Anatomical Likelihood Estimation (ALE), 313 foci were extracted from 25 voxel-based studies comprising 660 participants (308 ASD, 352 first-episode schizophrenia) and 801 controls. The results revealed that, compared to controls, lower grey matter volumes within limbic-striato-thalamic circuitry were common to ASD and schizophrenia. Unique features of each disorder included lower grey matter volume in amygdala, caudate, frontal and medial gyrus for schizophrenia and putamen for autism. Thus, in terms of brain volumetrics, ASD and schizophrenia have a clear degree of overlap that may reflect shared etiological mechanisms. However, the distinctive neuroanatomy also mapped in each condition raises the question about how this is arrived in the context of common etiological pressures.     

Epithelial sodium channel regulation by cell surface-associated serum- and glucocorticoid-regulated kinase 1

Serum- and glucocorticoid-regulated kinase 1 (sgk1) participates in diverse biological processes, including cell growth, apoptosis, and sodium homeostasis. In the cortical collecting duct of the kidney, sgk1 regulates sodium transport by stimulating the epithelial sodium channel (ENaC). Control of subcellular localization of sgk1 may be an important mechanism for modulating specificity of sgk1 function; however, which subcellular locations are required for sgk1-regulated ENaC activity in collecting duct cells has yet to be established. Using cell surface biotinylation studies, we detected endogenous sgk1 at the apical cell membrane of aldosterone-stimulated mpkCCD(c14) collecting duct cells. The association of sgk1 with the cell membrane was enhanced when ENaC was co-transfected with sgk1 in kidney cells, suggesting that ENaC brings sgk1 to the cell surface. Furthermore, association of endogenous sgk1 with the apical cell membrane of mpkCCD(c14) cells could be modulated by treatments that increase or decrease ENaC expression at the apical membrane; forskolin increased the association of sgk1 with the apical surface, whereas methyl-β-cyclodextrin decreased the association of sgk1 with the apical surface. Single channel recordings of excised inside-out patches from the apical membrane of aldosterone-stimulated A6 collecting duct cells revealed that the open probability of ENaC was sensitive to the sgk1 inhibitor GSK650394, indicating that endogenous sgk1 is functionally active at the apical cell membrane. We propose that the association of sgk1 with the apical cell membrane, where it interacts with ENaC, is a novel means by which sgk1 specifically enhances ENaC activity in aldosterone-stimulated collecting duct cells.     

High-Sensitivity Monoclonal Antibodies Specific for Homoserine Lactones Protect Mice from Lethal Pseudomonas aeruginosa Infections

A number of bacteria, including pathogens like Pseudomonas aeruginosa, utilize homoserine lactones (HSLs) as quorum sensing (QS) signaling compounds and engage in cell-to-cell communication to coordinate their behavior. Blocking this bacterial communication may be an attractive strategy for infection control as QS takes a central role in P. aeruginosa biology. In this study, immunomodulation of HSL molecules by monoclonal antibodies (MAbs) was used as a novel approach to prevent P. aeruginosa infections and as tools to detect HSLs in bodily fluids as a possible first clue to an undiagnosed Gram-negative infection. Using sheep immunization and recombinant antibody technology, a panel of sheep-mouse chimeric MAbs were generated which recognized HSL compounds with high sensitivity (nanomolar range) and cross-reactivity. These MAbs retained their nanomolar sensitivity in complex matrices and were able to recognize HSLs in P. aeruginosa cultures grown in the presence of urine. In a nematode slow-killing assay, HSL MAbs significantly increased the survival of worms fed on the antibiotic-resistant strain PA058. The therapeutic benefit of these MAbs was further studied using a mouse model of Pseudomonas infection in which groups of mice treated with HSL-2 and HSL-4 MAbs survived, 7 days after pathogen challenge, in significantly greater numbers (83 and 67%, respectively) compared with the control groups. This body of work has provided early proof-of-concept data to demonstrate the potential of HSL-specific, monoclonal antibodies as theranostic clinical leads suitable for the diagnosis, prevention, and treatment of life-threatening bacterial infections.     

Methylome analysis identifies a Wilms tumor epigenetic biomarker detectable in blood

Background

Wilms tumor is the most common pediatric renal malignancy and there is a clinical need for a molecular biomarker to assess treatment response and predict relapse. The known mutated genes in this tumor type show low mutation frequencies, whereas aberrant methylation at 11p15 is by far the most common aberration. We therefore analyzed the epigenome, rather than the genome, to identify ubiquitous tumor-specific biomarkers.

Results

Methylome analysis of matched normal kidney and Wilms tumor identifies 309 preliminary methylation variable positions which we translate into three differentially methylated regions (DMRs) for use as tumor-specific biomarkers. Using two novel algorithms we show that these three DMRs are not confounded by cell type composition. We further show that these DMRs are not methylated in embryonic blastema but are intermediately methylated in Wilms tumor precursor lesions. We validate the biomarker DMRs using two independent sample sets of normal kidney and Wilms tumor and seven Wilms tumor histological subtypes, achieving 100% and 98% correct classification, respectively. As proof-of-principle for clinical utility, we successfully use biomarker DMR-2 in a pilot analysis of cell-free circulating DNA to monitor tumor response during treatment in ten patients.

Conclusions

These findings define the most common methylated regions in Wilms tumor known to date which are not associated with their embryonic origin or precursor stage. We show that this tumor-specific methylated DNA is released into the blood circulation where it can be detected non-invasively showing potential for clinical utility.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0434-y) contains supplementary material, which is available to authorized users.