GSEA-SNP identifies genes associated with Johne’s disease in cattle

SNP-based gene-set enrichment analysis from single nucleotide polymorphisms, or GSEA-SNP, is a tool to identify candidate genes based on enrichment analysis of sets of genes rather than single SNP associations. The objective of this study was to identify modest-effect genes associated with Mycobacterium avium subsp. paratuberculosis (Map) tissue infection or fecal shedding using GSEA-SNP applied to KEGG pathways or Gene Ontology (GO) gene sets. The Illumina Bovine SNP50 BeadChip was used to genotype 209 Holstein cows for the GSEA-SNP analyses. For each of 13,744 annotated genes genome-wide located within 50 kb of a Bovine SNP50 SNP, the single SNP with the highest Cochran-Armitage Max statistic was used as a proxy statistic for that gene’s strength of affiliation with Map. Gene-set enrichment was tested using a weighted Kolmogorov-Smirnov-like running sum statistic with data permutation to adjust for multiple testing. For tissue infection and fecal shedding, no gene sets in KEGG pathways or in GO sets for molecular function or cellular component were enriched for signal. The GO biological process gene set for positive regulation of cell motion (GO:0051272, q = 0.039, 5/11 genes contributing to the core enrichment) was enriched for Map tissue infection, while no GO biological process gene sets were enriched for fecal shedding. GSEA-SNP complements traditional SNP association approaches to identify genes of modest effects as well as genes with larger effects as demonstrated by the identification of one locus that we previously found to be associated with Map tissue infection using a SNP-by-SNP genome-wide association study.     

Evaluation of nicotine and cotinine analogs as potential neuroprotective agents for Alzheimer’s disease

The currently available therapies for Alzheimer’s disease (AD) and related forms of dementia are limited by modest efficacy, adverse side effects, and the fact that they do not prevent the relentless progression of the illness. The purpose of the studies described here was to investigate the neuroprotective effects of the nicotine metabolite cotinine as well as a small series of cotinine and nicotine analogs (including stereoisomers) and to compare their effects to the four clinically prescribed AD therapies.     

Probabilistic and multiple regression modeling of the biologist’s decision processes and its implications for medical diagnosis

Current psychological research into the inference (diagnostic) process is briefly reviewed, using as a vehicle an investigation of the prediction of the probability of success of hypothetical applicants to a graduate program in biology. Brunswik’s lens model and multiple regression analysis are used, as is a Bayesian approach. Four judges’ (biologists’) predictions are analyzed. Some general conclusions about inference, drawn from the current data in psychology, are presented. This investigation was supported by PHS Research Grant No. MH-17487-01 from the National Institute of Mental Health.     

Therapeutic and pharmacokinetic characterizations of an anti-amyloidogenic bis-styrylbenzene derivative for Alzheimer’s disease treatment

Alzheimer’s disease drug discovery regarding exploration into the molecules and processes has focused on the intrinsic causes of the brain disorder correlated with the accumulation of amyloid-β. An anti-amyloidogenic bis-styrylbenzene derivative, KMS80013, showed excellent oral bioavailability (F = 46.2%), facilitated brain penetration (26%, iv) in mouse and target specific in vivo efficacy in acute AD mouse model attenuating the cognitive deficiency in Y-maze test. Acute toxicity (LD₅₀ >2000 mg/kg) and hERG channel inhibition (14% at 10 μM) results indicated safety of KMS80013.     

Co-occurrence of five Fusarium toxins in corn-Dried Distiller’s Grains with Solubles in Thailand and comparison of ELISA and LC-MS/MS for fumonisin analysis

Dried Distiller’s Grains with Solubles (DDGS), a by-product of bio-ethanol production from maize and other cereals, is increasingly used as a feed additive. In this study, five Fusarium toxins, including fumonisin B₁ (FB₁), fumonisin B₂ (FB₂), deoxynivalenol (DON), zearalenone (ZEN) and beauvericin (BEA) were quantified by LC-MS/MS in 59 corn-DDGS samples. In addition, the fumonisin level in 30 randomly selected-samples was compared using an ELISA detection technique. No sample was free from mycotoxin contamination, and 50.8 % of the samples were co-contaminated with all five mycotoxins. Moreover, toxin levels were generally high, with mean levels of 9 mg kg^?1 FB₁, 6 mg kg^?1 FB₂, 1.2 mg kg^?1 DON, 0.9 mg kg^?1 ZEN, and 0.35 mg kg^?1 BEA. Maximum levels for FB₁ (143 mg kg^?1) and FB₂ (125 mg kg^?1) are of acute toxicological relevance. The ELISA method had a tendency to underestimate the fumonisin content when compared with LC-MS/MS. Finally, this is the first reported beauvericin contamination in corn-DDGS.     

Deoxynivalenol in commercial beer — screening for the toxin with an indirect competitive ELISA

Antibodies specific for deoxynivalenol (DON) were prepared by immunizing rabbits with a deoxynivalenol-hemiglutaryl-HSA conjugate. The antibody showed cross-reactivity with DON, 15a-acetyl-DON (15-Ac DON), and 3a-acotyl-DON (3-Ac DON) of 100%, 216%, and 260%, respectively. No cross-reactivity was observed against 20 further trichothecenes of the A-, B-, and C-type. An indirect competitive ELISA procedure was set up for the detection of DON in liquid matrices occurring in the brewing process, Including beer. ELISA was sensitive down to 3.8 ng/mL. Detection limit for DON in tenfold diluted beer was 50 ppb. Recovery of the toxin in spiked beer was 45%, 77%, and 83% at toxin levels of 50; 500; and 1,000 ppb, respectively. ELISA results corresponded quite well with HPLC data. 196 commercial beers from several German breweries, including 36 gushing-positive samples, were assayed for DON. Screening revealed toxin levels from not detectable to 569 ppb. 69% of the gushing beers had marked levels of DON. 37% of the gushing-negative beer samples contained DON in detectable amounts with a maximum content of 172 ppb. Wheat beers had significantly higher DON-contents than beers derived from barley. Concentration of the toxin was significantly higher in gushing beers than in nongushing beers from both cereal sources.     

Development and Evaluation of an In Vitro Vaginal Model for Assessment of Drug’s Biopharmaceutical Properties: Curcumin

Vaginal administration is a promising alternative to the per-oral route in achieving systemic or local therapeutic effects, when intestinal drug absorption is hindered by problematic biopharmaceutical drug properties. The aim of this study was to establish an in vitro vaginal model and use it to characterize biopharmaceutical properties of liposomally associated curcumin destined for vaginal delivery. The in vitro permeability, metabolism, and tissue retention of high/low permeable compounds were assessed on cow vaginal mucosa and compared to the permeabilities determined through Caco-2 cells and rat jejunum in vitro. The results showed that the intestinal mucosa was superior to the vaginal one in categorizing drugs based on their permeabilities in high/low permeable classes. Passive diffusion was found to be the main mechanism of drug penetration through vaginal mucosa and it was not affected by transporter–enzyme alliance, as their expression/activity was significantly reduced compared to the intestinal tract. Curcumin permeability from the solution form was the lowest of all tested substances due to its significant tissue retention and curcumin–mucus interactions. The permeability of liposomally associated curcumin was even lower but the binding of liposomally associated curcumin to the vaginal tissue was significantly higher. The permeability and tissue retention of liposomal curcumin were vesicle size dependent. Vaginal application of liposomally associated curcumin provides relatively high levels of curcumin in vaginal tissue, with limited systemic absorption.KEY WORDS: curcumin, intestinal models, liposomes, permeability, vaginal mucosa     

Variation of a test’s sensitivity and specificity with disease prevalence

Background:

Anecdotal evidence suggests that the sensitivity and specificity of a diagnostic test may vary with disease prevalence. Our objective was to investigate the associations between disease prevalence and test sensitivity and specificity using studies of diagnostic accuracy.

Methods:

We used data from 23 meta-analyses, each of which included 10–39 studies (416 total). The median prevalence per review ranged from 1% to 77%. We evaluated the effects of prevalence on sensitivity and specificity using a bivariate random-effects model for each meta-analysis, with prevalence as a covariate. We estimated the overall effect of prevalence by pooling the effects using the inverse variance method.

Results:

Within a given review, a change in prevalence from the lowest to highest value resulted in a corresponding change in sensitivity or specificity from 0 to 40 percentage points. This effect was statistically significant (p < 0.05) for either sensitivity or specificity in 8 meta-analyses (35%). Overall, specificity tended to be lower with higher disease prevalence; there was no such systematic effect for sensitivity.

Interpretation:

The sensitivity and specificity of a test often vary with disease prevalence; this effect is likely to be the result of mechanisms, such as patient spectrum, that affect prevalence, sensitivity and specificity. Because it may be difficult to identify such mechanisms, clinicians should use prevalence as a guide when selecting studies that most closely match their situation.Diagnostic accuracy plays a central role in the evaluation of medical diagnostic tests. Test accuracy may be expressed as sensitivity and specificity, as positive and negative predictive values or as positive and negative likelihood ratios.¹ Some feel that the positive and negative predictive values of a test are more clinically relevant measures than sensitivity and specificity. However, predictive values directly depend on disease prevalence and can therefore not directly be translated from one situation to another.² In contrast, a test’s sensitivity and specificity are commonly believed not to vary with disease prevalence.^3–5Stability of sensitivity and specificity is an assumption that underlies the use of Bayes theorem in clinical diagnosis. Bayes theorem can be applied in clinical practice by using the likelihood ratio of a test and the probability of the disease before the test was done (pretest probability) to estimate the probability of disease after the test was done.² Because likelihood ratios are a function of sensitivity and specificity, it is assumed that the likelihood ratios also remain the same when prevalence varies.A number of studies have shown that sensitivity and specificity may not be as stable as thought.^6–10 We previously summarized the possible mechanisms through which differences in disease prevalence may lead to changes in a test’s sensitivity and specificity.¹⁰ Prevalence affects diagnostic accuracy because of clinical variability or through artifactual differences, as described in the theoretical framework in 6^,7 Artifactual differences can result from using additional exclusion criteria, verification bias or an imperfect reference standard. For example, using an imperfect reference standard may lead to an underestimate of diagnostic accuracy, but as prevalence increases, the extent to which this happens will vary.^8,9

Table 1:

Theoretical framework of how disease prevalence and test accuracy may be related¹⁰

Predictive association of copper metabolism proteins with Alzheimer’s disease and Parkinson’s disease: a preliminary perspective

Neurodegenerative diseases, Alzheimer’s disease (AD) and Parkinson’s disease (PD), constitute a major worldwide health problem. Several hypothesis have been put forth to elucidate the basis of onset and pathogenesis of AD and PD; however, till date, none of these seems to clearly elucidate the complex pathoetiology of these disorders. Notably, copper dyshomeostasis has been shown to underlie the pathophysiology of several neurodegenerative diseases including AD and PD. Numerous studies have concluded beyond doubt that imbalance in copper homeostatic mechanisms in conjunction with aging causes an acceleration in the copper toxicity elicited oxidative stress, which is detrimental to the central nervous system. Amyloid precursor protein and α-synuclein protein involved in AD and PD are copper binding proteins, respectively. In this review, we have discussed the possible association of copper metabolism proteins with AD and PD along with briefly outlining the expanding proportion of “copper interactome” in human biology. Using network biology, we found that copper metabolism proteins, superoxide dismutase 1 and ceruloplasmin may represent direct and indirect link with AD and PD, respectively.     

Arsenic concentration in the urine of patients with Blackfoot disease and Bowen’s disease

Extensive epidemiological study implicates that high arsenic content in artesian well water is the causal factor responsible for Blackfoot disease. We determine the arsenic concentration in urine samples of patients with Blackfoot and Bowen’s diseases and examine whether there exists any discrepancy of urinary arsenic concentrations among patients and the normal population. The analyses were made by hydride atomic absorption spectrophotometry (AAS) and the analytical reliability of the method was checked with a standard urine sample (ORTHO Bi-Level Urine Metal Control). The results show that the mean urinary arsenic concentration in 100 healthy adults is 63.4±29.7 μg/L, and those means for 23 and 11 patients with Blackfoot disease and Bowen’s disease are 75.7±39.1 μg/L (P vs controls >0.05) and 201±58 μg/L (P vs controls <0.001), respectively. From the analytical results obtained, we cannot conclude that urinary arsenic is associated with Blackfoot disease, as was disclosed from the epidemiological studies. However, urinary arsenic concentrations are possibly very closely associated with Bowen’s disease.     

Ubiquitin-protein ligase parkin and its role in the development of Parkinson’s disease

Parkin is a protein encoded by the corresponding parkin gene. It exhibits ubiquitin-protein ligase activity. In this review, we analyze domain structure, substrate specificity, subcellular localization of parkin, and regulation of its activity. Then we discuss data on the effects of various mutations in the parkin gene on structure and functions of this protein and results obtained with parkin knock-out animals. Better understanding of parkin biochemistry, its compartmentalization, functions, and altered functions would help the development of new approaches for the treatment of both inherited and sporadic cases of Parkinson’s disease. Published in Russian in Biokhimiya, 2006, Vol. 71, No. 8, pp. 1050–1061.     

Cohen’s h for detection of disease association with rare genetic variants

Background

The power of the genome wide association studies starts to go down when the minor allele frequency (MAF) is below 0.05. Here, we proposed the use of Cohen’s h in detecting disease associated rare variants. The variance stabilizing effect based on the arcsine square root transformation of MAFs to generate Cohen’s h contributed to the statistical power for rare variants analysis. We re-analyzed published datasets, one microarray and one sequencing based, and used simulation to compare the performance of Cohen’s h with the risk difference (RD) and odds ratio (OR).

Results

The analysis showed that the type 1 error rate of Cohen’s h was as expected and Cohen’s h and RD were both less biased and had higher power than OR. The advantage of Cohen’s h was more obvious when MAF was less than 0.01.

Conclusions

Cohen’s h can increase the power to find genetic association of rare variants and diseases, especially when MAF is less than 0.01.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-875) contains supplementary material, which is available to authorized users.     

Mitochondrial DNA polymorphisms as risk factors for Parkinson’s disease and Parkinson’s disease dementia

The activity of complex I of the mitochondrial respiratory chain has been found to be decreased in patients with Parkinsons disease (PD), but no mutations have been identified in genes encoding complex I subunits. Recent studies have suggested that polymorphisms in mitochondrial DNA (mtDNA)-encoded complex I genes (MTND) modify susceptibility to PD. We hypothesize that the risk of PD is conveyed by the total number of nonsynonymous substitutions in the MTND genes in various mtDNA lineages rather than by single mutations. To test this possibility, we determined the number of nonsynonymous substitutions of the seven MTND genes from 183 Finns. The differences in the total number of nonsynonymous substitutions and the nonsynonymous to synonymous substitution rate ratio (K_a/K_s) of MTND genes between the European mtDNA haplogroup clusters (HV, JT, KU, IWX) were analysed by using a statistical approach. Patients with PD (n=238) underwent clinical examination together with mtDNA haplogroup analysis and the clinical features between patient groups defined by the number of nonsynonymous substitutions were compared. Our analysis revealed that the haplogroup clusters HV and KU had a lower average number of amino acid replacements and a lower K_a/K_s ratio in the MTND genes than clusters JT and IWX. Supercluster JTIWX with the highest number of amino acid replacements was more frequent among PD patients and even more frequent among patients with PD who developed dementia. Our results suggest that a relative excess of nonsynonymous mutations in MTND genes in supercluster JTWIX is associated with an increased risk of PD and the disease progression to dementia.     

Identifying candidate genes for discrimination of ulcerative colitis and Crohn’s disease

In this study we aimed to screen effective biomarkers for differential diagnosis of ulcerative colitis (UC) and Crohn’s disease (CD). By using the gene expression profile dataset GSE24287 including 47 ileal CD, 27 UC and 25 non-inflammatory bowel diseases control downloaded from Gene Expression Omnibus database, we identified the differentially expressed genes (DEGs) between UC patients and controls as well as between CD patients and controls (|log₂FC(fold change)| > 1 and p < 0.05). Then Gene Ontology (GO) functional enrichment analyses were performed for these DEGs in two groups, followed by the construction of weight PPI (protein–protein interaction) networks. Subnets enriched for the PPIs and differentially expressed genes were constructed based on the weight PPI networks. The overlapping genes between the genes in the top 10 subnets with smallest p value and the DEGs were selected as the candidate genes of disease. A total of 75 DEGs were identified in UC group and 87 ones in CD group. There were 69 and 57 specific DEGs in CD group and UC group, respectively. The DEGs in CD group were mainly enriched in “inflammatory response” and “defense response”, while the most significantly enriched GO terms in UC group were “anion transport” and “chemotaxis”. FOS and SOCS3 were identified as candidate genes for CD and other three genes HELB, ZBTB16 and FAM107A were candidate genes for UC. In conclusion, there were distinct genetic alterations between UC and CD. The candidate genes identified in current study may be used as biomarkers for differential diagnosis of CD and UC.     

New cyclopentaquinoline hybrids with multifunctional capacities for the treatment of Alzheimer’s disease

Alzheimer’s disease (AD) is the most common progressive form of brain neurodegeneration and the most prevailing cause of dementia. Unfortunately, the aetiology of AD is not completely studied but different factors are associated with the development of AD such as among others low level of acetylcholine, aggregation of β-amyloid (Aβ), hyperphosphorylated tau protein, oxidative stress, and inflammation. The study encompass organic syntheses of 2,3-dihydro-1H-cyclopenta[b]quinoline with 5,6-dichloronicotinic acid and suitable linkers derivatives as multifunctional agents for AD treatment. Afterwards self-induced amyloid beta aggregation, inhibition studies of acetylcholinesterase and butyrylcholinesterase and molecular docking studies were performed. The results showed that 3b compound exhibited the best acetylcholinesterase inhibitory activity, with IC₅₀ value of 0.052?µM which is lower compared to references. Besides, all synthesised compounds showed good butyrylcholinesterase inhibitory activity with IC₅₀ values from 0.071 to 0.797?µM. Compound 3b exhibited strong Aβ_1–42 aggregation inhibitory effect with 25.7% at 5?µM to 92.8% at 100?µM as well as good anti-inflammatory effect. Thus, new compounds could create new perspectives for further development as a multi-target-directed agent for AD treatment.     

Tackling neurodegenerative diseases: animal models of Alzheimer’s disease and Parkinson’s disease

Our ageing society is confronted with a dramatic increase in incidence of age-related neurodegenerative diseases; biomedical research leading to novel therapeutic strategies is crucial to address this problem. Animal models of neurodegenerative conditions are invaluable in improving our understanding of the molecular basis of pathology, potentially revealing novel targets for intervention. Here, we review transgenic animal models of Alzheimer’s and Parkinson’s disease reported in mice, zebrafish, Caenorhabditis elegans and Drosophila melanogaster. This information will enable researchers to compare different animal models targeting disease-associated molecules by genomic engineering and to facilitate the development of novel animal models for any particular study, depending on the ultimate research goals.     

Calmodulin’s flexibility allows for promiscuity in its interactions with target proteins and peptides

The small bilobal calcium regulatory protein calmodulin (CaM) activates numerous target enzymes in response to transient changes in intracellular calcium concentrations. Binding of calcium to the two helix-loop-helix calcium-binding motifs in each of the globular domains induces conformational changes that expose a methionine-rich hydrophobic patch on the surface of each domain of the protein, which it uses to bind to peptide sequences in its target enzymes. Although these CaM-binding domains typically have little sequence identity, the positions of several bulky hydrophobic residues are often conserved, allowing for classification of CaM-binding domains into recognition motifs, such as the 1–14 and 1–10 motifs. For calcium-independent binding of CaM, a third motif known as the IQ motif is also common. Many CaM-peptide complexes have globular conformations, where CaM’s central linker connecting the two domains unwinds, allowing the protein to wrap around a single predominantly α-helical target peptide sequence. However, novel structures have recently been reported where the conformation of CaM is highly dissimilar to these globular complexes, in some instances with less than a full compliment of bound calcium ions, as well as novel stoichiometries. Furthermore, many divergent CaM isoforms from yeast and plant species have been discovered with unique calcium-binding and enzymatic activation characteristics compared to the single CaM isoform found in mammals.