Complementation testing identifies genes mediating effects at quantitative trait loci underlying fear-related behavior

Knowing the genes involved in quantitative traits provides an entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six quantitative trait loci (QTLs) by quantitative complementation, and identified six genes. Four genes, Lamp, Ptprd, Nptx2, and Sh3gl, have known roles in synapse function; the fifth, Psip1, was not previously implicated in behavior; and the sixth is a long non-coding RNA, 4933413L06Rik, of unknown function. Variation in transcriptome and epigenetic modalities occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results relieve a bottleneck in using genetic mapping of QTLs to uncover biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

Complementation testing identifies causal genes at quantitative trait loci underlying fear related behavior

Knowing the genes involved in quantitative traits provides a critical entry point to understanding the biological bases of behavior, but there are very few examples where the pathway from genetic locus to behavioral change is known. Here we address a key step towards that goal by deploying a test that directly queries whether a gene mediates the effect of a quantitative trait locus (QTL). To explore the role of specific genes in fear behavior, we mapped three fear-related traits, tested fourteen genes at six QTLs, and identified six genes. Four genes, Lsamp, Ptprd, Nptx2 and Sh3gl, have known roles in synapse function; the fifth gene, Psip1, is a transcriptional co-activator not previously implicated in behavior; the sixth is a long non-coding RNA 4933413L06Rik with no known function. Single nucleus transcriptomic and epigenetic analyses implicated excitatory neurons as likely mediating the genetic effects. Surprisingly, variation in transcriptome and epigenetic modalities between inbred strains occurred preferentially in excitatory neurons, suggesting that genetic variation is more permissible in excitatory than inhibitory neuronal circuits. Our results open a bottleneck in using genetic mapping of QTLs to find novel biology underlying behavior and prompt a reconsideration of expected relationships between genetic and functional variation.

Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription

Relating genetic variants to behavior remains a fundamental challenge. To assess the utility of DNA methylation marks in discovering causative variants, we examined their relationship to genetic variation by generating single-nucleus methylomes from the hippocampus of eight inbred mouse strains. At CpG sequence densities under 40 CpG/Kb, cells compensate for loss of methylated sites by methylating additional sites to maintain methylation levels. At higher CpG sequence densities, the exact location of a methylated site becomes more important, suggesting that variants affecting methylation will have a greater effect when occurring in higher CpG densities than in lower. We found this to be true for a variant's effect on transcript abundance, indicating that candidate variants can be prioritized based on CpG sequence density. Our findings imply that DNA methylation influences the likelihood that mutations occur at specific sites in the genome, supporting the view that the distribution of mutations is not random.

Improving Activity Estimation in Passive Gamma Scanning for Radioactive Waste Drums

A method to improve radioactive waste drum activity estimation in Segmented Gamma Scanning (SGS) systems was developed for homogenous content. We describe a method to quantify the activity of spatially distributed gamma-emitting isotopes (‘hot spots’) in homogenous content waste drums without the use of a collimator. Instead of averaging all the detector's readings we treat it as many different spatial samples as if we have multiple detectors surrounding the waste drum ("virtual detectors"). From these readings, we form a general linear model. Next, we derive the Maximum Likelihood Estimator (MLE) for the multiple sources position and activity. We solve this hyper-dimensional search problem using an Alternating Projections (AP) technique which transforms the problem into a simpler one-dimensional maximization problem. We tested this method using a mathematical simulation with a various number of sources, at random activities and positions for several energy bands. The preliminary results are consistent and show large improvement of the accuracy with comparison to industrial SGS systems and the same accuracy as new methods which exploits the spatial samples. Furthermore, since this method eliminates the need for heavy led collimator, none of the sources is blocked for the whole measurement period, which provides increased count rates and decreases the total measurement time.

Abstract P6-03-03: The Q-CROC-3 project reveals novel genomic alterations in triple negative breast cancers in residual tumors after neoadjuvant chemotherapy

The prognosis of triple negative breast cancer that shows resistance and/or incomplete response to cytotoxic chemotherapy is poor. In order to understand the mechanisms of resistance to chemotherapy and the genomic evolution of TNBCs treated with chemotherapy, an international multi-center biopsy-driven clinical trial was created for the collection and study of drug-resistant primary and metastatic freshly frozen tumors (Q-CROC-03: NCT01276899). We consented 60 patients with operable TNBC undergoing neoadjuvant Anthracycline/Taxane-based chemotherapy for pre and post-treatment biopsies as well as collection of residual tumor at the time of surgery and serial blood sampling. In 12-15 patients, adequate residual tumor material was available for genomic studies, which included whole exome sequencing, array CGH, gene expression microarray profiling and RNAseq of paired tumors. Whole exome sequencing revealed clonal shifts as well as the relatively infrequent appearance of novel mutations in individual tumors, without any recurrently detected variants. Array CGH revealed a remarkable stability in the number of DNA copy number alterations with a few functional alterations enriched for in the residual tumor, including an amplicon involving the NFIB gene. Finally, gene expression profiling showed shifts towards the immune-modulatory and basal TNBC subtypes after chemotherapy as well as an increase in the expression of several targetable genes, including DUSP1, a dual specificity phosphatase. In the 4 cases of primary and matching metastatic tumors, the post-NAC residual tumor had acquired changes many of which persisted in the metastatic sites, indicating that the analysis of the residual tumors can provide a partial picture of genomic changes present in metastases but not in the primary tumor. In summary, the genomic characterization of residual post-NAC tumor tissue provides important information for the development of novel therapeutic strategies for drug-resistant TNBCs as well as a portrait of genomic evolution of TNBCs subjected to chemotherapy.

Citation Format: Basik M, Aguilar-Mahecha A, Lafleur J, Bareke E, Przybytkowski E, Alirezaie N, Discepola F, Légaré S, Kovacina B, Lan C, Mihalcioiu CL, Robidoux A, Marcus E, Roy J-A, Pelmus M, Aleynikova O, Nabavi S, Tonellato P, Majewski J. The Q-CROC-3 project reveals novel genomic alterations in triple negative breast cancers in residual tumors after neoadjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-03.

Evidence for effective interventions to reduce mental health-related stigma and discrimination in the medium and long term: systematic review

BACKGROUND

Most research on interventions to counter stigma and discrimination has focused on short-term outcomes and has been conducted in high-income settings.

AIMS

To synthesise what is known globally about effective interventions to reduce mental illness-based stigma and discrimination, in relation first to effectiveness in the medium and long term (minimum 4 weeks), and second to interventions in low- and middle-income countries (LMICs).

METHOD

We searched six databases from 1980 to 2013 and conducted a multi-language Google search for quantitative studies addressing the research questions. Effect sizes were calculated from eligible studies where possible, and narrative syntheses conducted. Subgroup analysis compared interventions with and without social contact.

RESULTS

Eighty studies (n = 422 653) were included in the review. For studies with medium or long-term follow-up (72, of which 21 had calculable effect sizes) median standardised mean differences were 0.54 for knowledge and -0.26 for stigmatising attitudes. Those containing social contact (direct or indirect) were not more effective than those without. The 11 LMIC studies were all from middle-income countries. Effect sizes were rarely calculable for behavioural outcomes or in LMIC studies.

CONCLUSIONS

There is modest evidence for the effectiveness of anti-stigma interventions beyond 4 weeks follow-up in terms of increasing knowledge and reducing stigmatising attitudes. Evidence does not support the view that social contact is the more effective type of intervention for improving attitudes in the medium to long term. Methodologically strong research is needed on which to base decisions on investment in stigma-reducing interventions.

Significance and outcome of left heart hypoplasia in fetal congenital diaphragmatic hernia

OBJECTIVE

In patients with a left-sided congenital diaphragmatic hernia (CDH), the left ventricle (LV) is often compressed and smaller than normal. The objective of this study was to investigate whether small left heart dimensions prenatally normalize after birth in patients with CDH, or whether prenatal indices of left heart size and flow predict postnatal outcome.

METHODS

Clinical and echocardiographic data were reviewed for patients diagnosed with left-sided CDH prenatally. Cardiac dimensions and flows were compared with normative data. Among liveborn patients, pre- and postnatal Z-scores of left heart structures were compared, and associations between prenatal indices and outcome were assessed.

RESULTS

Of 125 patients diagnosed prenatally with CDH, 111 had a left-sided defect. Of these, 85 were liveborn, including 20 with congenital heart disease. Gestational age-adjusted dimensions of fetal left heart structures, including aortic valve diameter, mitral valve (MV) diameter, LV long-axis, LV short-axis and LV volume, were all smaller than normal (P < 0.001). On average, the LV contributed 33 +/- 8% of combined ventricular output, lower than the normal 40-50%. Z-scores of left heart structures increased from the prenatal echocardiogram to the postnatal study, with average changes ranging from 0.56 +/- 1.68 (aortic valve) to 1.39 +/- 1.85 (LV volume). Among liveborn patients, there was no association between prenatal left heart Z-scores and postnatal survival.

CONCLUSIONS

Hypoplasia of and reduced flow through the left heart are common among fetuses with CDH. After birth and CDH repair, left heart dimensions generally normalize, with adequate size to support a biventricular circulation, even when there is very low flow through the left heart in mid- and late-gestation.

Conformational requirements of suramin to target angiogenic growth factors

The conformational requirements of suramin for its binding to basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF) were examined by molecular modeling and docking simulations using the conformational features of suramin determined by the present proton nuclear magnetic resonance (1H-NMR) studies and the crystal structures of growth factors reported previously. The assignment of resonances of suramin to individual protons was accomplished by the combined analysis of the coupling constants, two-dimensional correlated spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY). The NOESY data obtained for suramin were utilized in a conformational search algorithm with constraints to generate a family of conformers which were further refined by restrained energy minimization. A family of nine conformers generated by restrained modeling falls primarily into one of two categories, either the conformer's two naphthyl rings are far apart, approximately 28-30 A, from one another or the conformer's two naphthyl rings are relatively close, approximately 16-18 A. The NMR data provide evidence for the presence of more than one conformer in solution. The modeling and docking simulation studies suggest that suramin binds efficiently to bFGF and PDGF by an induced-fit mechanism, wherein suramin complements bFGF or PDGF by adjusting its conformational freedom around the two pairs of single bonds that link the middle phenyl rings to the secondary amide backbone. The interaction of suramin with bFGF or PDGF primarily involves ion-pair, hydrophobic and hydrogen bonding interactions, in addition to van der Waals' contacts. The results indicate that suramin not only sterically blocks the receptor binding loop of the growth factors, but also competes for the binding sites of agonists such as heparin. The results suggest that suramin's propensity to bind to several polypeptides of varying size and structure is due to its conformational flexibility. Collectively, the data emphasize that conformationally constrained suramin analogs that selectively and competitively target angiogenic growth factors could be designed to reduce non-specific binding and, accordingly, toxicity.

Giant Hamartoma of the Breast

Hamartoma of the breast is a rare clinico-pathologic entity. Its clinical diagnosis can be extremely difficult; however, diagnosis is not difficult when it is made on the basis of a combination of radiologic and pathologic features. Its differential diagnosis includes a circumscribed fibrocystic mass, fibroadenoma, lipoma, cystosarcoma phylloides, and various carcinomas. A high index of suspicion is mandatory. In this study, we report a case of giant hamartoma of the breast in a young postlactational female patient, including treatment of the tumor by excisional biopsy and correction of the resulting breast deformity by mastopexy. Clinical, radiologic, and pathologic features are discussed.

Structure of human salivary histatin 5 in aqueous and nonaqueous solutions

The solution structure of human salivary histatin 5 (D-S-H-A-K-R-H-H-G-Y-K-R-K-F-H-E-K-H-H-S-H-R-G-Y) was examined in water (pH 3.8) and dimethyl sulfoxide solutions using 500 MHz homo- and heteronuclear two-dimensional (2D) nmr. The resonance assignment of peptide backbone and side-chain protons was accomplished by 2D total correlated spectroscopy and nuclear Overhauser effect (NOE) spectroscopy. The high JNH-C alpha H values (> or = 7.4 Hz), absence of any characteristic NH-NH (i, i + 1) or C alpha H-C beta H (i, i + 3) NOE connectivities, high d delta/dT values (> or = 0.004 ppm K-1) and the fast 1H/2H amide exchange suggest that histatin 5 molecules remain unstructured in aqueous solution at pH 3.8. In contrast, histatin 5 prefers largely alpha-helical conformation in dimethyl sulfoxide solution as evident from the JNH-C alpha H values (< or = 6.4 Hz), slow 1H/2H exchange, low d delta/dT values (< or = 0.003 ppm K-1) observed for amide resonances of residues 6-24, and the characteristic NH-NH (i, i + 1) and C alpha H-C beta H (i, i + 3) NOE connectivities. All backbone amide 15N-1H connectivities fall within 6 ppm on the 15N scale in the 2D heteronuclear single quantum correlated spectrum, and the restrained structure calculations using DIANA suggest the prevalence of alpha-helical conformations stabilized by 19 (5-->1) intramolecular backbone amide hydrogen bonds in polar aprotic medium such as dimethyl sulfoxide. The interside-chain hydrogen bonding and salt-bridge type interactions that normally stabilize the helical structure of linear peptides in aqueous solutions are not observed. Histatin 5, unlike other naturally occurring antimicrobial polypeptides such as magainins, defensins, and tachyplesins, does not adopt amphiphilic structure, precluding its insertion into microbial membranes and formation of ion channels across membranes. Electrostatic (ionic type) and hydrogen bonding interactions of the positively charged and polar residues with the head groups of microbial membranes or with a membrane-bound receptor could be the initial step involved in the mechanism of antimicrobial activity of histatins.

Reconstruction of 3-dimensional right ventricular shape and volume from 3 orthogonal planes

This study validates a reconstructive technique that describes 3-dimensional right ventricular (RV) shape and volume with the use of 3 standard echocardiographic planes. The volume of 24 cast models of lamb right ventricles (12 normal, 12 hypertensive) was determined by water displacement. Reconstruction of the cast shapes was calculated from 2 sets of digitized data: cast cross-sectional digitized tracings and echocardiographic cross-sectional tracings. Regional volume ratios from both data sets were assessed to quantitatively specify RV regional volume differences between normotensive and hypertensive right ventricles. This method described the 3-dimensional RV shape with no differences between reconstructed volumes and true volumes for either normotensive or hypertensive casts. Between hypertensive and normal groups, regional volume ratios yielded a difference in free wall ratios that was observed to be greater in the hypertensive cast group (P =.007).

Breast cancer screening, diagnosis, and treatment

The incidence of breast cancer in US women remains disturbingly high, and unfortunately primary care physicians still frequently encounter patients in whom the disease is suspected or, even worse, confirmed. Fortunately, however, the body of knowledge surrounding the disease has grown dramatically during the past decade, and major advances have been made in the understanding of breast cancer risk, prevention, diagnosis, and treatment. Controversies persist, particularly those concerning the screening of younger women, but consensus now exists regarding many clinical issues relevant to primary care practice. Although multidisciplinary subspecialty expertise must be made available to all women with known or suspected breast cancer, the primary care physician has an important role to play when dealing with patients with this condition. The following article focuses on what primary care practitioners need to know to expertly contribute to the diagnosis, counseling, and initial treatment of women with this disease.

How confounding are breast pain confounders?

Nine thousand four hundred evaluable patients with breast complaints were consecutively studied from 1984 to 1994. Their ages ranged between 15-65 years with a median of 33 years. Five thousand, six hundred and seventy-five of these presented on account of pain and a mass was the cause of pain in 74%. Gross fibrocystic disease of the breast was the commonest tumour encountered in this group. Seven hundred and thirty eight patients were found to have 'referred' pain, and splenomegaly was the commonest cause of this 'referred' pain. At present, a simple breast biopsy remains the cheapest and most effective method of investigating this organ in most developing countries.

Delineation of an active fragment and poly(L-proline) II conformation for candidacidal activity of bactenecin 5

Bactenecin 5 and its fragments [BN22 (1-22), BN16 (7-22), and BC24 (20-43)] were synthesized by solid-phase methods. Their antifungal activities on Candida albicans have been studied and compared with those of the native bactenecin 5. The conformational preferences of these peptides in aqueous and nonaqueous solutions and in lipid vesicles were examined by circular dichroism. The highly active N-terminal fragment (BN16) was examined in aqueous solution using 500 MHz two-dimensional NMR. Bactenecin 5 and its fragments are potent candidacidal agents against C. albicans. The N-terminal fragments (BN22 and BN16) of bactenecin 5 are relatively more active than the C-terminal fragment BC24, especially at lower concentrations. The N-terminal region (7-22) which retains the activity of the whole molecule appears to be the functional domain for candidacidal activity. The CD spectra of bactenecin 5 and its fragments are reminiscent of the CD spectrum of poly(L-proline) type II structure in aqueous and nonaqueous solutions and also in lipid vesicles. The temperature dependence of NH chemical shifts and 1H/2H exchange effect on amide resonances suggest the absence of intramolecularly hydrogen-bonded NH groups. The coupling constant (JNH-CalphaH) values, conformational restriction offered by the Pro residues (phi = -60 degrees +/- 15 degrees), the set of medium- and short-range nuclear Overhauser effects observed for the active N-terminal fragment (BN16), and the restrained structure calculation using DIANA suggest that poly(L-proline) type II conformers of the peptide molecules could be significantly populated in aqueous solution. The ability of bactenecin peptides to induce disruption of lipid vesicles correlates well with their activity. Our results suggest that poly(L-proline) type II structure may, indeed, be the biologically active conformation for candidacidal activity of bactenecin peptides.

Finding the global minimum: a fuzzy end elimination implementation

The 'fuzzy end elimination theorem' (FEE) is a mathematically proven theorem that identifies rotameric states in proteins which are incompatible with the global minimum energy conformation. While implementing the FEE we noticed two different aspects that directly affected the final results at convergence. First, the identification of a single dead-ending rotameric state can trigger a 'domino effect' that initiates the identification of additional rotameric states which become dead-ending. A recursive check for dead-ending rotameric states is therefore necessary every time a dead-ending rotameric state is identified. It is shown that, if the recursive check is omitted, it is possible to miss the identification of some dead-ending rotameric states causing a premature termination of the elimination process. Second, we examined the effects of removing dead-ending rotameric states from further considerations at different moments of time. Two different methods of rotameric state removal were examined for an order dependence. In one case, each rotamer found to be incompatible with the global minimum energy conformation was removed immediately following its identification. In the other, dead-ending rotamers were marked for deletion but retained during the search, so that they influenced the evaluation of other rotameric states. When the search was completed, all marked rotamers were removed simultaneously. In addition, to expand further the usefulness of the FEE, a novel method is presented that allows for further reduction in the remaining set of conformations at the FEE convergence. In this method, called a tree-based search, each dead-ending pair of rotamers which does not lead to the direct removal of either rotameric state is used to reduce significantly the number of remaining conformations. In the future this method can also be expanded to triplet and quadruplet sets of rotameric states. We tested our implementation of the FEE by exhaustively searching ten protein segments and found that the FEE identified the global minimum every time. For each segment, the global minimum was exhaustively searched in two different environments: (i) the segments were extracted from the protein and exhaustively searched in the absence of the surrounding residues; (ii) the segments were exhaustively searched in the presence of the remaining residues fixed at crystal structure conformations. We also evaluated the performance of the method for accurately predicting side chain conformations. We examined the influence of factors such as type and accuracy of backbone template used, and the restrictions imposed by the choice of potential function, parameterization and rotamer database. Conclusions are drawn on these results and future prospects are given.