Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned

Major depressive disorder (MDD) is a common complex disorder with a partly genetic etiology. We conducted a genome-wide association study of the MDD2000+ sample (2431 cases, 3673 screened controls and >1 M imputed single-nucleotide polymorphisms (SNPs)). No SNPs achieved genome-wide significance either in the MDD2000+ study, or in meta-analysis with two other studies totaling 5763 cases and 6901 controls. These results imply that common variants of intermediate or large effect do not have main effects in the genetic architecture of MDD. Suggestive but notable results were (a) gene-based tests suggesting roles for adenylate cyclase 3 (ADCY3, 2p23.3) and galanin (GAL, 11q13.3); published functional evidence relates both of these to MDD and serotonergic signaling; (b) support for the bipolar disorder risk variant SNP rs1006737 in CACNA1C (P=0.020, odds ratio=1.10); and (c) lack of support for rs2251219, a SNP identified in a meta-analysis of affective disorder studies (P=0.51). We estimate that sample sizes 1.8- to 2.4-fold greater are needed for association studies of MDD compared with those for schizophrenia to detect variants that explain the same proportion of total variance in liability. Larger study cohorts characterized for genetic and environmental risk factors accumulated prospectively are likely to be needed to dissect more fully the etiology of MDD.

Relationship between muscle output and functional MRI-measured brain activation

The relationship between functional MRI (fMRI)-measured brain signal and muscle force and or electromyogram (EMG) is critical in interpreting fMRI data and understanding the control mechanisms of voluntary motor actions. We designed a system that could record joint force and surface EMG online with fMRI data. High-quality force and EMG data were obtained while maintaining the quality of the fMRI brain images. Using this system, we determined the relationship between fMRI-measured brain activation and handgrip force and between fMRI-measured brain signal and EMG of extrinsic finger muscles. Ten volunteers participated in the experiments (only seven subjects' data were analyzed due to excessive noise in the fMRI data of three subjects). The participants exerted 20%, 35%, 50%, 65%, and 80% of the maximal force. During each contraction period, handgrip force, surface EMG of the finger flexor and extensor muscles, and fMRI brain images were acquired. The degree of muscle activation (force and EMG) was directly proportional to the amplitude of the brain signal determined by fMRI in the entire brain and in a number of motor function-related cortical fields, including primary motor, sensory regions, supplementary motor area, premotor, prefrontal, parietal and cingulate cortices, and cerebellum. All the examined brain areas demonstrated a similar relationship between the fMRI signal and force. A stronger fMRI signal during higher force indicates that more cortical output neurons and/or interneurons may participate in generating descending commands and/or processing additional sensory information. The similarity in the relationship between muscle output and fMRI signal in the cortical regions suggests that correlated or networked activation among a number of cortical fields may be necessary for controlling precise static force of finger muscles.

Relationship between motor activity-related cortical potential and voluntary muscle activation

The purpose of this study was to investigate the relationship between EEG-derived motor activity-related cortical potential (MRCP) and voluntary muscle activation. Eight healthy volunteers participated in two experimental sessions. In one session, subjects performed isometric elbow-flexion contractions at four intensity levels [10%, 35%, 60%, and 85% maximal voluntary contraction (MVC)]. In another session, a given elbow-flexion force (35% MVC) was generated at three different rates (slow, intermediate, and fast). Thirty to 40 contractions were performed at each force level or rate. EEG signals were recorded from the scalp overlying the supplementary motor area (SMA) and contralateral sensorimotor cortex, and EMG signals were recorded from the skin surface overlying the belly of the biceps brachii and brachioradialis muscles during all contractions. In each trial, the force was used as the triggering signal for MRCP averaging. MRCP amplitude was measured from the beginning to the peak of the negative slope. The magnitude of MRCP from both EEG recording locations (sensorimotor cortex and SMA) was highly correlated with elbow-flexion force, rate of rising of force, and muscle EMG signals. These results suggest that MRCP represents cortical motor commands that scale the level of muscle activation.

Garlic and associated allyl sulfur components inhibit N-methyl-N-nitrosourea induced rat mammary carcinogenesis

Our previous studies demonstrated that dietary garlic powder supplementation inhibits N-nitrosamine induced DNA alkylation in liver and mammary tissue. The present studies compared the impact of dietary supplementation with garlic powder or two garlic constituents, water-soluble S-allyl cysteine (SAC) and oil-soluble diallyl disulfide (DADS), on the incidence of mammary tumorigenesis induced by N-methyl-N-nitrosourea (MNU). Female Sprague-Dawley rats were fed semi-purified casein based diets with or without supplements of garlic powder(20g/kg), SAC (57 micromol/kg) or DADS (57 micromol/kg) for 2 weeks prior to treatment with MNU (15 mg/kg body wt). Garlic powder, SAC and DADS supplementation significantly delayed the onset of mammary tumors compared to rats receiving the unsupplemented diet. Tumor incidence 23 weeks after MNU treatment was reduced by 76, 41 and 53% in rats fed garlic, SAC and DADS, respectively, compared to controls (P<0.05). Total tumor number was reduced 81, 35 and 65% by these supplements, respectively (P<0.05). In a separate study the quantity of mammary DNA alkylation occurring 3 h after MNU treatment was reduced in rats fed garlic, SAC or DADS (P<0.05). Specifically, O(6)-methylguanine adducts were reduced by 27, 18 and 23% in rats fed supplemental garlic, SAC and DADS, respectively, compared to controls. N(7)-Methylguanine adducts decreased by 48, 22 and 21% respectively, compared to rats fed the control diet. These studies demonstrate that garlic and associated allyl sulfur components, SAC and DADS, are effective inhibitors of MNU-induced mammary carcinogenesis.

DNA-binding and photocleavage studies of cobalt(III) mixed-polypyridyl complexes containing 2-(2-chloro-5-nitrophenyl)imidazo [4,5-f][1,10]phenanthroline

The ligand 2-(2-chloro-5-nitrophenyl)imidazo[4,5-f][1,10]phenanthroline(CNOIP) and its complexes [Co(bpy)(2)(CNOIP)](3+) (1) and [Co(phen)(2)(CNOIP)](3+) (2) (bpy=2,2'-bipyridine; phen=1,10-phenanthroline) have been synthesized and characterized. Binding of the two complexes with calf thymus DNA has been investigated by spectroscopic methods, cyclic voltammetry, viscosity, and electrophoresis measurements. The experimental results indicate that both complexes bind to DNA through an intercalative mode. In comparison with their parent complexes containing PIP ligand (PIP=2-phenylimidazo[4,5-f][1,10]phenanthroline), the introduction of NO(2) and Cl groups to the PIP ligand decreased the binding affinity of complexes 1 and 2 to CT DNA. Both complexes have also been found to promote the photocleavage of plasmid pBR 322 DNA, the hydroxyl radical (OH*) is suggested to be the reactive species responsible for the cleavage.

Older adults exhibit a reduced ability to fully activate their biceps brachii muscle

BACKGROUND

Voluntary muscle strength declines significantly in older adults. One contributing factor to the strength loss is muscle atrophy developed in old age. Whether the ability to maximally activate the muscle decreases with age, however, is unknown. This study was intended to determine if the central nervous system command to maximally activate the biceps brachii muscle deteriorates with age.

METHODS

Electrical stimulation pulses were applied to the skin overlying the biceps brachii muscle during maximal voluntary elbow-flexion contractions. The magnitude of force evoked on the maximal voluntary force was measured to determine the activation level (AL) of the muscle.

RESULTS

The AL was 94% for the elderly group and 97% for the young group (100% AL indicates complete activation). The AL for both the elderly and young groups was significantly (p<.05) lower than 100%. The AL of the elderly group was significantly (p<.05) lower than that of the young group.

CONCLUSIONS

The loss of voluntary strength in older adults is a mixed result of muscle atrophy and a reduced ability to fully activate muscle.

Simultaneous measurement of human joint force, surface electromyograms, and functional MRI-measured brain activation

Functional magnetic resonance imaging (fMRI) has been increasingly used in studying human brain function given its non-invasive feature and good spatial resolution. However, difficulties in acquiring data from peripheral (e.g. information from muscle) during fMRI studies of motor function hinder interpretation of fMRI data and designing more sophisticated investigations. Here we describe a system that was designed to concurrently measure handgrip force, surface electromyograms (EMG) of finger flexor and extensor muscles, and fMRI of human brain. The system included a pressure transducer built in a hydraulic environment, a heavily shielded EMG recording element, and a visual feedback structure for online monitoring of force and/or EMG signal, by the subject positioned in the scanner during an fMRI experiment. System evaluation and subsequent fMRI motor function studies have indicated that by using this system, high quality force and EMG signals can be recorded without sacrificing the quality of the fMRI data.

optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants

Motivation: Existing microarray genotype-calling algorithms adopt either SNP-by-SNP (SNP-wise) or sample-by-sample (sample-wise) approaches to calling. We have developed a novel genotype-calling algorithm for the Illumina platform, optiCall, that uses both SNP-wise and sample-wise calling to more accurately ascertain genotypes at rare, low-frequency and common variants.

Results: Using data from 4537 individuals from the 1958 British Birth Cohort genotyped on the Immunochip, we estimate the proportion of SNPs lost to downstream analysis due to false quality control failures, and rare variants misclassified as monomorphic, is only 1.38% with optiCall, in comparison to 3.87, 7.85 and 4.09% for Illuminus, GenoSNP and GenCall, respectively. We show that optiCall accurately captures rare variants and can correctly account for SNPs where probe intensity clouds are shifted from their expected positions.

Availability and implementation: optiCall is implemented in C++ for use on UNIX operating systems and is available for download at http://www.sanger.ac.uk/resources/software/opticall/.

Contact:optiCall@sanger.ac.uk

Skilled finger movement exercise improves hand function

BACKGROUND

Aging is accompanied by a marked decline in muscle strength and ability to maintain steady submaximal force. Studies have shown that exercise programs can improve age-related regression of hand function in elderly individuals. The purpose of this study was to train elderly subjects to perform skilled finger movements and to evaluate the changes in hand function involving skillful use of finger pinch.

METHODS

Grip strength, maximum pinch force (MPF), steadiness of pinch force at 5%, 10%, and 20% MPF, M wave, and Hoffman (H) reflex were measured. Fourteen elderly subjects were trained with skilled finger movements, and their performance involving finger pinch was measured.

RESULTS

Compared with untrained elderly subjects, the trained older adults significantly (p <.05) improved their ability to control submaximal pinch force, to maintain a steady hand posture, and to relocate a small object quickly with finger grip. The amplitude of H reflex increased significantly for the trained group.

CONCLUSIONS

Skilled finger movement training improves the ability to control submaximal pinch force, hand steadiness, and manual speed in elderly subjects; these improvements may be due to training-induced adaptations in the central and peripheral nervous systems.

Dietary garlic suppresses DNA adducts caused by N-nitroso compounds

The present studies examined the impact of a processed garlic powder on the in vivo occurrence of DNA adducts caused by N-nitroso compounds (NOC) in rats. Addition of 2% garlic powder to diets containing aminopyrine and sodium nitrite (each at 600 mg/kg) reduced the occurrence of both 7-N-methyldeoxyguanosine (7-N-mG) and 6-O-methyldeoxyguanosine (6-O-mG) adducts to rat liver DNA by approximately 55%; and over 80% when 4% garlic was provided. Dietary supplementation with garlic powder (2 and 4%) also reduced the occurrence of 7-N-mG and 6-O-mG adducts by approximately 40 and 60% respectively, in rats intubated with N-nitrosodimethylamine (150 mg/kg body wt). The quantity of 7-N-mG and 6-O-mG adducts in mammary tissue of rats given intravenous N-methyl-N-nitrosourea (50 mg/kg body wt) was reduced over 50% in rats fed 2% garlic compared to controls. The depression in the occurrence of these adducts was approximately 70% when dietary garlic was increased to 4%. These experiments suggest the reduction in DNA adducts caused by processed garlic powder likely reflects a depression in the formation of NOC from precursors and changes in the bioactivation and/or denitrosation of NOC.

Brain activation during human finger extension and flexion movements

Corticospinal projections to the motor neuron pool of upper-limb extensor muscles have been reported to differ from those of the flexor muscles in humans and other primates. The influence of this difference on the central nervous system control for extension and flexion movements is unknown. Cortical activation during thumb extension and flexion movements of eight human volunteers was measured using functional magnetic resonance imaging (fMRI), which detects signal changes caused by an alteration in the local blood oxygenation level. Although the relative activity of the extensor and flexor muscles of the thumb was similar, the brain volume activated during extension was substantially larger than that during flexion. These fMRI results were confirmed by measurements of EEG-derived movement-related cortical potential. Higher brain activity during thumb extension movement may be a result of differential corticospinal, and possibly other pathway projections to the motoneuron pools of extensor and flexor muscles of upper the extremities.

Reported in vivo splice-site mutations in the factor IX gene: severity of splicing defects and a hypothesis for predicting deleterious splice donor mutations

Small consensus sequences have been defined for RNA splicing, but questions about splicing in humans remain unanswered. Analysis of germline mutations in the factor IX gene offers a highly advantageous system for studying the mutational process in humans. In a sample of 860 families with hemophilia B, 9% of independent mutations are likely to disrupt splicing as their primary mode of action. This includes 26 splicing mutations reported herein. When combined with the factor IX splice mutations reported by others, at least 104 independent mutations have been observed, 80 of which are single base substitutions within the splice donor and splice acceptor consensus sequences. After analysis of these mutations, the following inferences emerge: (1) the susceptibility of a splice donor sequence to deleterious mutation depends on the degree of similarity with the donor consensus sequence, suggesting a simple "5-6 hypothesis" for predicting deleterious vs. neutral mutations; (2) the great majority of mutations that disrupt the splice donor or splice acceptor sequences result in at least a 100-fold decrement in factor IX coagulant activity, indicating that the mutations at these sites generally function as an on/off switch; (3) mutations that create cryptic splice junctions or that shorten but do not interrupt the polypyrimidine tract in the splice acceptor sequence can reduce splicing by a variable amount; and (4) there are thousands of potential donor-acceptor consensus sequence combinations in the 38-kb factor IX gene region apparently not reduced by evolutionary selective pressure, presenting an apparent paradox; i.e., mutations in the donor and acceptor consensus sequences at intron/exon splice junctions can dramatically alter normal splicing, yet, appropriately spaced, good matches to the consensus sequences do not predispose to significant amounts of alternative splicing.