Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans

African Americans (AAs) are an admixed population with widely varying proportion of West African ancestry (WAA). Here we report the correlation of WAA to gene expression and DNA methylation in AA-derived hepatocytes, a cell type important in disease and drug response. We perform mediation analysis to test whether methylation is a mediator of the effect of ancestry on expression. GTEx samples and a second cohort are used as validation. One hundred and thirty-one genes are associated with WAA (FDR < 0.10), 28 of which replicate and represent 220 GWAS phenotypes. Among PharmGKB pharmacogenes, VDR, PTGIS, ALDH1A1, CYP2C19, and P2RY1 nominally associate with WAA (p < 0.05). We find 1037 WAA-associated, differentially methylated regions (FDR < 0.05), with hypomethylated genes enriched in drug-response pathways. In conclusion, WAA contributes to variability in hepatocyte expression and DNA methylation with identified genes previously implicated for diseases disproportionately affecting AAs, including cardiovascular (PTGIS, PLAT) and renal (APOL1) disease, and drug response (CYP2C19).

COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer

COSMIC (http://cancer.sanger.ac.uk) is an expert-curated database of somatic mutations in human cancer. Broad and comprehensive in scope, recent releases in 2016 describe over 4 million coding mutations across all human cancer disease types. Mutations are annotated across the entire genome, but expert curation is focused on over 400 key cancer genes. Now encompassing the majority of molecular mutation mechanisms in oncogenetics, COSMIC additionally describes 10 million non-coding mutations, 1 million copy-number aberrations, 9 million gene-expression variants, and almost 8 million differentially methylated CpGs. This information combines a consistent interpretation of the data from the major cancer genome consortia and cancer genome literature with exhaustive hand curation of over 22,000 gene-specific literature publications. This unit describes the graphical Web site in detail; alternative protocols overview other ways the entire database can be accessed, analyzed, and downloaded. © 2016 by John Wiley & Sons, Inc.

Electron paramagnetic resonance in human fingernails: the sponge model implication

The most significant problem of electron paramagnetic resonance (EPR) fingernail dosimetry is the presence of two signals of non-radiation origin that overlap the radiation-induced signal (RIS), making it almost impossible to perform dose measurements below 5 Gy. Historically, these two non-radiation components were named mechanically induced signal (MIS) and background signal (BKS). In order to investigate them in detail, three different methods of MIS and BKS mutual isolation have been developed and implemented. After applying these methods, it is shown here that fingernail tissue, after cut, can be modeled as a deformed sponge, where the MIS and BKS are associated with the stress from elastic and plastic deformations, respectively. A sponge has a unique mechanism of mechanical stress absorption, which is necessary for fingernails in order to perform its everyday function of protecting the fingertips from hits and trauma. Like a sponge, fingernails are also known to be an effective water absorber. When a sponge is saturated with water, it tends to restore to its original shape, and when it loses water, it becomes deformed again. The same happens to fingernail tissue. It is proposed that the MIS and BKS signals of mechanical origin be named MIS1 and MIS2 for MISs 1 and 2, respectively. Our suggested interpretation of the mechanical deformation in fingernails gives also a way to distinguish between the MIS and RIS. The results obtained show that the MIS in irradiated fingernails can be almost completely eliminated without a significant change to the RIS by soaking the sample for 10 min in water. The proposed method to measure porosity (the fraction of void space in spongy material) of the fingernails gave values of 0.46-0.48 for three of the studied samples. Existing results of fingernail dosimetry have been obtained on mechanically stressed samples and are not related to the "real" in vivo dosimetric properties of fingernails. A preliminary study of these properties of pre-soaked (unstressed) fingernails has demonstrated their significant difference from fingernails stressed by cut. They show a higher stability signal, a less intensive non-radiation component, and a nonlinear dose dependence. The findings in this study set the stage for understanding fingernail EPR dosimetry and doing in vivo measurements in the future.

Virulence attenuation of a UDP-galactose/N-acetylglucosamine beta1,4 galactosyltransferase expressing Leishmania donovani promastigote

Protozoan parasites of the genus Leishmania are the causative agent of leishmaniasis, a disease whose manifestations in humans range from mild cutaneous lesions to fatal visceral infections. Human visceral leishmaniasis is caused by Leishmania donovani. Long-term culture in vitro leads to the attenuation of the parasite. This loss of parasite virulence is associated with the expression of a developmentally regulated UDP-Galactose/N-acetylglucosamine beta 1-4 galactosyltransferase and galactose terminal glycoconjugates as determined by their agglutination with the pea nut agglutinin (PNA). Thus, all promastigotes passaged for more than 11 times were 100% agglutinated with PNA, and represent a homogeneous population of avirulent parasites. Identical concentrations of PNA failed to agglutinate promastigotes passaged for < or =5 times. These PNA(-) promastigotes were virulent. Promastigotes passaged from 5 to 10 times showed a mixed population. The identity of populations defined by virulence and PNA agglutination was confirmed by isolating PNA(+) avirulent and PNA(-) virulent clones from the 7th passage promastigotes. Only the PNA(+) clones triggered macrophage microbicidal activity. The PNA(+) clones lacked lipophosphoglycan. Intravenous administration of [(14)C] galactose-labeled parasite in BALB/c mice resulted in rapid clearance of the parasite from blood with a concomitant accumulation in the liver. By enzymatic assay and RT-PCR we have shown the association of a UDP-Galactose/N-acetylglucosamine beta1,4 galactosyltransferase with only the attenuated clones. By immunofluorescence we demonstrated that the enzyme is located in the Golgi apparatus. By western blot analysis and SDS-PAGE of the affinity-purified protein, we have been able to identify a 29 KDa galactose terminal protein from the avirulent clones.

Infectivity and attenuation of Leishmania donovani promastigotes. II: Association of the loss of parasite infectivity with the terminal galactosylation of precursor acceptors present in virulent parasites by the developmentally regulated galactosyltransferase

The beta1-4 galactosyltransferase enzyme of the Leishmania donovani promastigotes, was found to be developmentally regulated and expressed only in the attenuated parasites. The enzymatic product of soluble determinants of virulent promastigotes and the galactosyltransferase enzyme was found to stimulate the macrophage burst activity but inhibit in vitro intracellular parasitism. In contrast, removal of terminal galactose moieties from soluble determinants of attenuated parasites resulted in the inhibition of macrophage respiratory burst activity but did not now inhibit intracellular parasitism. We propose that the terminal galactosylation of acceptor substrates present in virulent parasites by the developmentally regulated galactosyltransferase is associated with loss of parasite virulence.

Depression in acutely medically ill elderly inpatients: a pilot study of early identification and intervention by formal psychogeriatric consultation

BACKGROUND

Depressive disorders are common among acutely medically ill elderly inpatients, but they are poorly recognised and treated. A single blind, randomised and controlled pilot study evaluating the efficacy of early identification of depression and intervention by a psychogeriatric consultation was undertaken.

METHOD

A two-stage screening procedure, using the Geriatric Depression Scale (GDS) and the Brief Assessment Schedule (BAS), was used to identify patients with depression. They were randomised into two groups: one received a psychogeriatric consultation and the other acted as a control group. Patients were followed-up at 10 weeks and 1 year interval.

RESULTS

There were no differences between the intervention group and the control group on any outcome measure at 10 week and 1 year follow-up. There was poor concordance between recommended interventions and their implementation by the geriatricians in the intervention group. Also, there were no differences between the intervention and control groups in terms of the interventions received by the patient. The whole sample improved on almost all outcome measures from baseline to 10 weeks and 1 year follow-up.

CONCLUSIONS

Reasons for the absence of efficacy of psychogeriatric consultation and suggestions for improved methodology are discussed.

Macrophage heterogeneity, antigen presentation, and membrane fluidity: implications in visceral Leishmaniasis

Morphological and functional heterogeneity of the splenic macrophage (M phi) population was studied in Leishmania donovani (LD) infected BALB/c mice. On a discontinuous percoll gradient two distinct M phi populations were separated. They differed significantly in size as evident from Scanning Electron Microscopy (SEM). Morphologically, the bigger M phi (LM) showed surface projections, whereas the smaller M phi (SM) was round. As regards the antigen-presenting abilities, the LM of infected animals showed defective antigen-presenting abilities at a later stage of the disease, i.e. 6 months post infection ((6)I-LM) but not earlier, whereas the SM population remained functionally intact throughout the course of the infection. Further, the (6)I-LM showed a much enhanced Ad status as compared to their controls. Interestingly, both the (6)I-LM and the control set showed a comparable level of binding of a known A(d) restricted peptide. Despite the presence of sufficient A(d) molecules and the ability to bind the appropriate peptide, (6)I-LM were unable to stimulate peptide specific T-cell hybridoma. Further, the (6)I-LM showed an increase in membrane fluidity and distorted morphology with membrane fissure and blebs as evident from SEM. It is possible that an increase in the membrane fluidity may lead to the defective antigen-presenting ability of (6)I-LM. Thus, the LD infection functionally keep the (6)I-LM out of antigen presentation and this may contribute to the defective cell mediated immune response in leishmaniasis.

Use of an attenuated leishmanial parasite as an immunoprophylactic and immunotherapeutic agent against murine visceral leishmaniasis

The ability of the leishmanial parasite UR6 to act as an immunoprophylactic and immunotherapeutic agent against Leishmania donovani infection in BALB/c mice was investigated. Unlike the virulent L. donovani AG83 (MOHOM/IN/1983/AG83), UR6 given through intracardiac route failed to induce visceral infection, but when it was injected subcutaneously, UR6 induced a short-lived and localized self-healing skin lesion. Priming of peritoneal macrophages with UR6 in vitro induced superoxide (O(2)(-)) generation, whereas similar experiments with virulent AG83 inhibited O(2)(-) generation. It was observed that priming of mice with either live or sonicated UR6 in the absence of any adjuvant provided strong protection against subsequent virulent challenge. Further, UR6-primed infected mice not only displayed a strong antileishmanial delayed-type hypersensitivity (DTH) response but also showed an elevated level of the serum antileishmanial immunoglobulin G2a (IgG2a) isotype, whereas infected mice failed to mount any antileishmanial DTH response and showed an elevated level of IgG1. This indicates that UR6 priming and subsequent L. donovani infection allowed the expansion of Th1 cells. Our studies indicate that UR6 has potential to be used as an immunoprophylactic and immunotherapeutic agent against experimental visceral leishmaniasis.

Infectivity and attenuation of Leishmania donovani promastigotes: association of galactosyl transferase with loss of parasite virulence

During the course of long-term in vitro cultivation of Leishmania donovani parasites, the promastigotes were found to lose their infectivity. Lectin agglutination studies revealed that there is an up-regulation of terminally exposed galactose residues on the noninfective promastigotes. The enzyme galactosyl transferase was absent in the infective form but present in the non-infective form of the parasites. An association between galactosylation and loss of infectivity was also observed. We propose that the enzyme galactosyl transferase is developmentally regulated and induces galactosylation of surface carbohydrates.

Documented evidence of depression in medical and nursing case-notes and its implications in acutely ill geriatric inpatients

Depression is common among acutely ill elderly medical inpatients. Identification of such depression by geriatric medicine staff would allow early treatment. The impact of a depression screening procedure on documentation of depressive signs and symptoms in the medical and nursing case-notes was examined. Thirty-five sets of medical and nursing case-notes of medically ill elderly inpatients, for whom data from the Brief Assessment Schedule and the short Geriatric Depression Scale (GDS) were also available, were examined for documentation of signs and symptoms of depression, prescription of antidepressants, and referral to the psychogeriatric service. Depressive signs and symptoms were documented in only a few medical (29%) and nursing (11%) case-notes. Only a small number of depressed patients were prescribed antidepressants (20%) or were referred to the psychogeriatric service (13%). The frequency of documentation of depressive signs and symptoms after the screening procedure with the short GDS was associated with subsequent prescription of antidepressants and referral to the psychogeriatric service. The screening procedure itself may increase the general awareness of depressive signs and symptoms and effect its management. These results require replication.

The effect of an educational intervention package about aggressive behaviour directed at the nursing staff on a continuing care psychogeriatric ward

INTRODUCTION

Levels of aggressive behaviour on continuing care wards are high. Various staffing factors, potentially amenable to improvement by training, are important in reducing and preventing aggressive behaviour.

METHOD

The efficacy of an educational package, directed at the nursing staff, in reducing aggressive behaviour on a psychogeriatric continuing care ward was prospectively evaluated over an 18-week period. The package was administered during the middle 6-week period. Aggressive behaviour was measured using the RAGE and SOAS scales.

RESULTS

Aggressive behaviour on both these scales was reduced after the educational package, and the educational intervention package may explain this reduction.

CONCLUSIONS

The educational package may have genuinely reduced aggressive behaviour or improved the nursing staffs tolerance and reporting threshold for aggressive behaviour. Studies with improved methodology in several different settings are suggested.

Suicide and the elderly

Impending demographic changes mean that the proportion of the elderly in the population will increase. Suicide rates increase with age. The literature on elderly suicide, with emphasis on methodology, cross-national rates and trends, correlates, cultural factors, location and method, attempted suicides and prevention, is critically reviewed in this paper.

The relationship between two scales measuring aggressive behavior among continuing-care psychogeriatric inpatients

Aggressive behavior among the elderly is a neglected area of research. An 18-week prospective study of aggressive behavior on a continuing-care psychogeriatric ward provided data to examine the relationship between two aggression scales (SOAS and RAGE). There was a strong and significant correlation between the SOAS and RAGE scales for the total and the subscale scores. Both these scales appear useful in measuring aggressive behavior among continuing-care psychogeriatric inpatients. Also, the nursing staff can be trained to complete these scales effectively.

Purification and kinetic studies of an alpha-L-fucosidase of Venus mercenaria

An alpha-L-fucosidase activity has been isolated from the liver (hepatopancreas) of the common edible clam, Venus mercenaria, and has been purified approximately 300-fold (11% yield) by affinity chromatography on agarose-epsilon-amino-caproylfucosamine. Isoelectric focusing profiles were heterogeneous, revealing several isoenzymes. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated the presence of a single subunit of Mr 50,000. The purified enzyme preparation contained only trace amounts of other alpha- and beta-D-glycosidases tested. In addition to p-nitrophenyl alpha-L-fucopyranoside, the enzyme hydrolyzed natural substrates such as fucose-containing milk pentasaccharides, thyroglobulin glycopeptides, human salivary glycoproteins, and blood-group-active glycosphingolipids. The enzyme preparation had a broad pH optimum range between 4.5 and 5.5. The apparent Km value with respect to p-nitrophenyl alpha-L-fucopyranoside was 0.26mM.