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1.  Plant-Pathogenic Oomycetes, Escherichia coli Strains, and Salmonella spp. Frequently Found in Surface Water Used for Irrigation of Fruit and Vegetable Crops in New York State 
Applied and Environmental Microbiology  2014;80(16):4814-4820.
In the United States, surface water is commonly used to irrigate a variety of produce crops and can harbor pathogens responsible for food-borne illnesses and plant diseases. Understanding when pathogens infest water sources is valuable information for produce growers to improve the food safety and production of these crops. In this study, prevalence data along with regression tree analyses were used to correlate water quality parameters (pH, temperature, turbidity), irrigation site properties (source, the presence of livestock or fowl nearby), and precipitation data to the presence and concentrations of Escherichia coli, Salmonella spp., and hymexazol-insensitive (HIS) oomycetes (Phytophthora and Pythium spp.) in New York State surface waters. A total of 123 samples from 18 sites across New York State were tested for E. coli and Salmonella spp., of which 33% and 43% were positive, respectively. Additionally, 210 samples from 38 sites were tested for HIS oomycetes, and 88% were found to be positive, with 10 species of Phytophthora and 11 species of Pythium being identified from the samples. Regression analysis found no strong correlations between water quality parameters, site factors, or precipitation to the presence or concentration of E. coli in irrigation sources. For Salmonella, precipitation (≤0.64 cm) 3 days before sampling was correlated to both presence and the highest counts. Analyses for oomycetes found creeks to have higher average counts than ponds, and higher turbidity levels were associated with higher oomycete counts. Overall, information gathered from this study can be used to better understand the food safety and plant pathogen risks of using surface water for irrigation.
doi:10.1128/AEM.01012-14
PMCID: PMC4135776  PMID: 24878603
2.  Comorbid medical illness in bipolar disorder 
The British Journal of Psychiatry  2014;205(6):465-472.
Background
Individuals with a mental health disorder appear to be at increased risk of medical illness.
Aims
To examine rates of medical illnesses in patients with bipolar disorder (n = 1720) and to examine the clinical course of the bipolar illness according to lifetime medical illness burden.
Method
Participants recruited within the UK were asked about the lifetime occurrence of 20 medical illnesses, interviewed using the Schedules for Clinical Assessment in Neuropsychiatry (SCAN) and diagnosed according to DSM-IV criteria.
Results
We found significantly increased rates of several medical illnesses in our bipolar sample. A high medical illness burden was associated with a history of anxiety disorder, rapid cycling mood episodes, suicide attempts and mood episodes with a typically acute onset.
Conclusions
Bipolar disorder is associated with high rates of medical illness. This comorbidity needs to be taken into account by services in order to improve outcomes for patients with bipolar disorder and also in research investigating the aetiology of affective disorder where shared biological pathways may play a role.
doi:10.1192/bjp.bp.114.152249
PMCID: PMC4248234  PMID: 25359927
3.  Antibacterial gene transfer across the tree of life 
eLife  2014;3:e04266.
Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group.
DOI: http://dx.doi.org/10.7554/eLife.04266.001
eLife digest
Living things inherit most of their genetic material from their parents, so genes tend to be passed on from one generation to the next—from ancestors to descendants. Sometimes, however, DNA is transferred from one organism to another by other means. These events, collectively called horizontal gene transfer, are fairly common in nature; genes have been passed between different species as well as between different groups of organisms. For example, genes that confer resistance to antibacterial drugs have transferred from one species of bacteria to another, and other genes have also ‘jumped’ from bacteria to plants or animals.
Now Metcalf et al. have studied a gene that first arose in bacteria and that encodes an enzyme called a lysozyme. This enzyme breaks down the outer casing of a bacterial cell: a step that is required for a bacterium to reproduce and divide in two. When Metcalf et al. searched for relatives of the lysozyme gene, they found copies in many other species of bacteria and revealed that this gene has been repeatedly transferred between different bacteria. Members of the lysozyme gene family have also ‘jumped out’ of bacteria and into other organisms at least four times. Metcalf et al. found related lysozyme genes in a plant, an insect, many species of fungi, and a single-celled microbe (called an archaeon) that lives at hot, deep-sea vents.
A gene family being spread this widely across the tree of life has not been seen before. Nevertheless, as DNA is a common biological language to all living things, it is likely that all the different species that have received a lysozyme gene might use it for similar purposes.
Metcalf et al. reveal that the lysozyme could be being used as an antibacterial molecule. The archaeon lysozyme can kill a broad range of bacteria; and when the gene was transferred into Escherichia coli bacteria, only the bacteria that mutated the lysozyme gene to render it useless were able to survive. Metcalf et al. also revealed that the archaeon microbe produces more of the enzyme if bacteria are present, which allows it to outcompete these bacteria.
These findings suggest that there may be a number of horizontally transferred genes that have antibacterial activity against a wide range of bacteria. Searching for these genes—particularly in the largely underexplored group of archaea—might reveal new sources for antibiotic drugs to treat bacterial infections.
DOI: http://dx.doi.org/10.7554/eLife.04266.002
doi:10.7554/eLife.04266
PMCID: PMC4241558  PMID: 25422936
horizontal gene transfer; antibiotic; lysin; archaea; other
4.  Immunodepletion Plasma Proteomics by TripleTOF 5600 and Orbitrap Elite/LTQ-Orbitrap Velos/Q Exactive Mass Spectrometers 
Journal of proteome research  2013;12(10):10.1021/pr400307u.
Plasma proteomic experiments performed rapidly and economically using several of the latest high-resolution mass spectrometers were compared. Four quantitative hyperfractionated plasma proteomics experiments were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments. Each experiment compared two iTRAQ isobaric-labeled immunodepleted plasma proteomes, provided as 30 labeled peptide fractions. 480 LC-MS/MS runs delivered >250 GB of data in two months. Several analysis algorithms were compared. At 1 % false discovery rate, the relative comparative findings concluded that the Thermo Scientific Q Exactive Mass Spectrometer resulted in the highest number of identified proteins and unique sequences with iTRAQ quantitation. The confidence of iTRAQ fold-change for each protein is dependent on the overall ion statistics (Mascot Protein Score) attainable by each instrument. The benchmarking also suggested how to further improve the mass spectrometry parameters and HPLC conditions. Our findings highlight the special challenges presented by the low abundance peptide ions of iTRAQ plasma proteome because the dynamic range of plasma protein abundance is uniquely high compared with cell lysates, necessitating high instrument sensitivity.
doi:10.1021/pr400307u
PMCID: PMC3817719  PMID: 24004147
immunodepletion; Seppro; IgY14; iTRAQ; EMMOL normalization; TripleTOF; Orbitrap; Q Exactive
5.  Gene expression in whole lung and pulmonary macrophages reflects the dynamic pathology associated with airway surface dehydration 
BMC Genomics  2014;15(1):726.
Background
Defects in airway mucosal defense, including decreased mucus clearance, contribute to the pathogenesis of human chronic obstructive pulmonary diseases. Scnn1b-Tg mice, which exhibit chronic airway surface dehydration from birth, can be used as a model to study the pathogenesis of muco-obstructive lung disease across developmental stages. To identify molecular signatures associated with obstructive lung disease in this model, gene expression analyses were performed on whole lung and purified lung macrophages collected from Scnn1b-Tg and wild-type (WT) littermates at four pathologically relevant time points. Macrophage gene expression at 6 weeks was evaluated in mice from a germ-free environment to understand the contribution of microbes to disease development.
Results
Development- and disease-specific shifts in gene expression related to Scnn1b over-expression were revealed in longitudinal analyses. While the total number of transgene-related differentially expressed genes producing robust signals was relatively small in whole lung (n = 84), Gene Set Enrichment Analysis (GSEA) revealed significantly perturbed biological pathways and interactions between normal lung development and disease initiation/progression. Purified lung macrophages from Scnn1b-Tg mice exhibited numerous robust and dynamic gene expression changes. The expression levels of Classically-activated (M1) macrophage signatures were significantly altered at post-natal day (PND) 3 when Scnn1b-Tg mice lung exhibit spontaneous bacterial infections, while alternatively-activated (M2) macrophage signatures were more prominent by PND 42, producing a mixed M1-M2 activation profile. While differentially-regulated, inflammation-related genes were consistently identified in both tissues in Scnn1b-Tg mice, there was little overlap between tissues or across time, highlighting time- and tissue-specific responses. Macrophages purified from adult germ-free Scnn1b-Tg mice exhibited signatures remarkably similar to non-germ-free counterparts, indicating that the late-phase macrophage activation profile was not microbe-dependent.
Conclusions
Whole lung and pulmonary macrophages respond independently and dynamically to local stresses associated with airway mucus stasis. Disease-specific responses interact with normal developmental processes, influencing the final state of disease in this model. The robust signatures observed in Scnn1b-Tg lung macrophages highlight their critical role in disease pathogenesis. These studies emphasize the importance of region-, cell-type-, and time-dependent analyses to fully dissect the natural history of disease and the consequences of disease on normal lung development.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-726) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-726
PMCID: PMC4247008  PMID: 25204199
Scnn1b-Tg mice; Pulmonary macrophage activation; Inflammation; Mucus clearance defect; Gene expression profiling; Lung development; Airway surface liquid dehydration
6.  Adverse childhood experiences and associations with health-harming behaviours in young adults: surveys in eight eastern European countries 
Abstract
Objective
To evaluate the association between adverse childhood experiences – e.g. abuse, neglect, domestic violence and parental separation, substance use, mental illness or incarceration – and the health of young adults in eight eastern European countries.
Methods
Between 2010 and 2013, adverse childhood experience surveys were undertaken in Albania, Latvia, Lithuania, Montenegro, Romania, the Russian Federation, The former Yugoslav Republic of Macedonia and Turkey. There were 10 696 respondents – 59.7% female – aged 18–25 years. Multivariate modelling was used to investigate the relationships between adverse childhood experiences and health-harming behaviours in early adulthood including substance use, physical inactivity and attempted suicide.
Findings
Over half of the respondents reported at least one adverse childhood experience. Having one adverse childhood experience increased the probability of having other adverse childhood experiences. The number of adverse childhood experiences was positively correlated with subsequent reports of health-harming behaviours. Compared with those who reported no adverse experiences, respondents who reported at least four adverse childhood experiences were at significantly increased risk of many health-harming behaviours, with odds ratios varying from 1.68 (95% confidence interval, CI: 1.32–2.15) – for physical inactivity – to 48.53 (95% CI: 31.98–76.65) – for attempted suicide. Modelling indicated that prevention of adverse childhood experiences would substantially reduce the occurrence of many health-harming behaviours within the study population.
Conclusion
Our results indicate that individuals who do not develop health-harming behaviours are more likely to have experienced safe, nurturing childhoods. Evidence-based programmes to improve parenting and support child development need large-scale deployment in eastern European.
doi:10.2471/BLT.13.129247
PMCID: PMC4208567  PMID: 25378755
7.  UV Light Inactivation of Human and Plant Pathogens in Unfiltered Surface Irrigation Water 
Fruit and vegetable growers continually battle plant diseases and food safety concerns. Surface water is commonly used in the production of fruits and vegetables and can harbor both human- and plant-pathogenic microorganisms that can contaminate crops when used for irrigation or other agricultural purposes. Treatment methods for surface water are currently limited, and there is a need for suitable treatment options. A liquid-processing unit that uses UV light for the decontamination of turbid juices was analyzed for its efficacy in the treatment of surface waters contaminated with bacterial or oomycete pathogens, i.e., Escherichia coli, Salmonella enterica, Listeria monocytogenes, Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato, and Phytophthora capsici. Five-strain cocktails of each pathogen, containing approximately 108 or 109 CFU/liter for bacteria or 104 or 105 zoospores/liter for Ph. capsici, were inoculated into aliquots of two turbid surface water irrigation sources and processed with the UV unit. Pathogens were enumerated before and after treatment. In general, as the turbidity of the water source increased, the effectiveness of the UV treatment decreased, but in all cases, 99.9% or higher inactivation was achieved. Log reductions ranged from 10.0 to 6.1 and from 5.0 to 4.2 for bacterial pathogens and Ph. capsici, respectively.
doi:10.1128/AEM.02964-13
PMCID: PMC3911201  PMID: 24242253
8.  Isolation and Characterization of the Herpes Simplex Virus 1 Terminase Complex 
Journal of Virology  2014;88(1):225-236.
During herpes simplex virus 1 (HSV-1) infection, empty procapsids are assembled and subsequently filled with the viral genome by means of a protein complex called the terminase, which is comprised of the HSV-1 UL15, UL28, and UL33 proteins. Biochemical studies of the terminase proteins have been hampered by the inability to purify the intact terminase complex. In this study, terminase complexes were isolated by tandem-affinity purification (TAP) using recombinant viruses expressing either a full-length NTAP-UL28 fusion protein (vFH476) or a C-terminally truncated NTAP-UL28 fusion protein (vFH499). TAP of the UL28 protein from vFH476-infected cells, followed by silver staining, Western blotting, and mass spectrometry, identified the UL15, UL28, and UL33 subunits, while TAP of vFH499-infected cells confirmed previous findings that the C terminus of UL28 is required for UL28 interaction with UL33 and UL15. Analysis of the oligomeric state of the purified complexes by sucrose density gradient ultracentrifugation revealed that the three proteins formed a complex with a molecular mass that is consistent with the formation of a UL15-UL28-UL33 heterotrimer. In order to assess the importance of conserved regions of the UL15 and UL28 proteins, recombinant NTAP-UL28 viruses with mutations of the putative UL28 metal-binding domain or within the UL15 nuclease domain were generated. TAP of UL28 complexes from cells infected with each domain mutant demonstrated that the conserved cysteine residues of the putative UL28 metal-binding domain and conserved amino acids within the UL15 nuclease domain are required for the cleavage and packaging functions of the viral terminase, but not for terminase complex assembly.
doi:10.1128/JVI.02632-13
PMCID: PMC3911699  PMID: 24155374
9.  Relationship between obesity and the risk of clinically significant depression: Mendelian randomisation study 
Background
Obesity has been shown to be associated with depression and it has been suggested that higher body mass index (BMI) increases the risk of depression and other common mental disorders. However, the causal relationship remains unclear and Mendelian randomisation, a form of instrumental variable analysis, has recently been employed to attempt to resolve this issue.
Aims
To investigate whether higher BMI increases the risk of major depression.
Method
Two instrumental variable analyses were conducted to test the causal relationship between obesity and major depression in RADIANT, a large case-control study of major depression. We used a single nucleotide polymorphism (SNP) in FTO and a genetic risk score (GRS) based on 32 SNPs with well-established associations with BMI.
Results
Linear regression analysis, as expected, showed that individuals carrying more risk alleles of FTO or having higher score of GRS had a higher BMI. Probit regression suggested that higher BMI is associated with increased risk of major depression. However, our two instrumental variable analyses did not support a causal relationship between higher BMI and major depression (FTO genotype: coefficient –0.03, 95% CI –0.18 to 0.13, P = 0.73; GRS: coefficient –0.02, 95% CI –0.11 to 0.07, P = 0.62).
Conclusions
Our instrumental variable analyses did not support a causal relationship between higher BMI and major depression. The positive associations of higher BMI with major depression in probit regression analyses might be explained by reverse causality and/or residual confounding.
doi:10.1192/bjp.bp.113.130419
PMCID: PMC4076654  PMID: 24809401
10.  Complementary MS Methods Assist Conformational Characterization of Antibodies with Altered S–S Bonding Networks 
As therapeutic monoclonal antibodies (mAbs) become a major focus in biotechnology and a source of the next-generation drugs, new analytical methods or combination methods are needed for monitoring changes in higher order structure and effects of post-translational modifications. The complexity of these molecules and their vulnerability to structural change provide a serious challenge. We describe here the use of complementary mass spectrometry methods that not only characterize mutant mAbs but also may provide a general framework for characterizing higher order structure of other protein therapeutics and biosimilars. To frame the challenge, we selected members of the IgG2 subclass that have distinct disulfide isomeric structures as a model to evaluate an overall approach that uses ion mobility, top-down MS sequencing, and protein footprinting in the form of fast photochemical oxidation of proteins (FPOP). These three methods are rapid, sensitive, respond to subtle changes in conformation of Cys→Ser mutants of an IgG2, each representing a single disulfide isoform, and may be used in series to probe higher order structure. The outcome suggests that this approach of using various methods in combination can assist the development and quality control of protein therapeutics.
doi:10.1007/s13361-013-0582-4
PMCID: PMC3651811  PMID: 23483515
Antibody characterization; Protein structure; Fast photochemical oxidation of proteins (FPOP); Top-down; Ion mobility; Antibody mutants; IgG2
11.  Replication of bipolar disorder susceptibility alleles and identification of 2 novel genome-wide significant associations in a new bipolar disorder case-control sample 
Molecular psychiatry  2012;18(12):1302-1307.
We have conducted a genotyping study using a custom Illumina Infinium HD genotyping array, the ImmunoChip, in a new UK sample of 1,218 bipolar disorder cases and 2,913 controls that have not been used in any studies previously reported independently or in meta-analyses. The ImmunoChip was designed prior to the publication of the Psychiatric GWAS Consortium Bipolar Disorder Working Group (PGC-BD) meta-analysis data. As such 3106 SNPs with a P value less than 1×10−3 from the bipolar disorder meta-analysis by Ferreira et al., 2008 were genotyped. We report support for two of the three most strongly associated chromosomal regions in the Ferreira study, CACNA1C (rs1006737, p=4.09×10−4) and 15q14 (rs2172835, p=0.043) but not ANK3 (rs10994336, p=0.912). We have combined our ImmunoChip data (569 quasi-independent SNPs from the 3016 SNPs genotyped) with the recently published PGC-BD meta-analysis data, using either the PGC-BD combined discovery and replication data where available or just the discovery data where the SNP was not typed in a replication sample in PGC-BD. Our data provide support for two regions, at ODZ4 and CACNA1C, with prior evidence for genome-wide significant association in PGC-BD meta-analysis. In addition, the combined analysis shows two novel genome-wide significant associations. First, rs7296288 (P = 8.97 × 10−9, OR = 0.9), an intergenic polymorphism on chromosome 12 located between RHEBL1 and DHH. Secondly, rs3818253 (P = 3.88 × 10−8, OR = 1.16), an intronic SNP on chromosome 20q11.2 in the gene TRPC4AP which lies in a high linkage disequilibrium region along with the genes GSS and MYH7B.
doi:10.1038/mp.2012.142
PMCID: PMC3971368  PMID: 23070075
Bipolar disorder; genome-wide significant association; ImmunoChip; PGC-BD; rs7296288; rs3818253
12.  Strong genetic evidence for a selective influence of GABAA receptors on a component of the bipolar disorder phenotype 
Molecular psychiatry  2008;15(2):146-153.
Despite compelling evidence for a major genetic contribution to risk of bipolar mood disorder, conclusive evidence implicating specific genes or pathophysiological systems has proved elusive. In part this is likely to be related to the unknown validity of current phenotype definitions and consequent aetiological heterogeneity of samples. In the recent Wellcome Trust Case Control Consortium (WTCCC) genome-wide association analysis of bipolar disorder (1868 cases, 2938 controls) one of the most strongly associated polymorphisms lay within the gene encoding the GABAA receptor β1 subunit, GABRB1. Aiming to increase biological homogeneity, we sought the diagnostic subset that showed the strongest signal at this polymorphism and used this to test for independent evidence of association with other members of the GABAA receptor gene family. The index signal was significantly enriched in the 279 cases meeting Research Diagnostic Criteria for schizoaffective disorder, bipolar type (p=3.8×10−6). Independently, these cases showed strong evidence that variation in GABAA receptor genes influences risk for this phenotype (independent system-wide p=6.6×10−5) with association signals also at GABRA4, GABRB3, GABRA5 and GABRR1. Our findings have the potential to inform understanding of presentation, pathogenesis and nosology of bipolar disorders. Our method of phenotype refinement may be useful in studies of other complex psychiatric and non-psychiatric disorders.
doi:10.1038/mp.2008.66
PMCID: PMC3967096  PMID: 19078961
13.  Genome Wide Association Analysis of Copy Number Variation in Recurrent Depressive Disorder 
Molecular psychiatry  2011;18(2):183-189.
Large, rare copy number variants (CNV) have been implicated in a variety of psychiatric disorders, but the role of CNVs in recurrent depression is unclear. We performed a genome-wide analysis of large, rare CNVs in 3,106 cases of recurrent depression, 459 controls screened for lifetime-absence of psychiatric disorder and 5,619 unscreened controls from phase 2 of the Wellcome Trust Case Control Consortium (WTCCC2). We compared the frequency of cases with CNVs against the frequency observed in each control group, analysing CNVs over the whole genome, genic, intergenic, intronic and exonic regions. We found that deletion CNVs were associated with recurrent depression while duplications were not. The effect was significant when comparing cases to WTCCC2 controls (p=7.7×10−6, OR =1.25 (95% CI 1.13 - 1.37)) and to screened controls (p=5.6×10−4, OR=1.52 (95% CI 1.20 - 1.93). Further analysis showed that CNVs deleting protein coding regions were largely responsible for the association. Within an analysis of regions previously implicated in schizophrenia, we found an overall enrichment of CNVs in our cases when compared to screened controls (p=0.019). We observe an ordered increase of samples with deletion CNVs, with the lowest proportion seen in screened controls, the next highest in unscreened controls and the highest in cases. This may suggest that the absence of deletion CNVs, especially in genes, is associated with resilience to recurrent depression.
doi:10.1038/mp.2011.144
PMCID: PMC3939438  PMID: 22042228
15.  Mood disorders and parity – A clue to the aetiology of the postpartum trigger 
Journal of Affective Disorders  2014;152-154(100):334-339.
Background
Episodes of postpartum psychosis have been associated with first pregnancies in women with bipolar I disorder. It is unclear, however, if the effect extends to episodes at other times in relation to childbirth and to women with other mood disorders such as major depression and bipolar II disorder. This primiparity effect, which is also seen in other pregnancy related conditions such as pre-eclampsia, is a potentially important clue to the aetiology of childbirth related mood episodes.
Methods
Participants were interviewed and case notes reviewed. Best-estimate diagnoses were made according to DSM-IV criteria. Data on the occurrence of episodes in pregnancy and the postpartum were available on 3345 full term deliveries from 1667 participants, 934 with bipolar I disorder (BD-I), 278 with bipolar II disorder (BD-II) and 455 with recurrent major depression (RMD).
Results
Onsets of psychosis/mania within 6 weeks of childbirth were overrepresented in primiparae (p=0.007) with BD-I. Although primiparity was not associated with perinatal bipolar depression, there was an association with the onset of depression within 6 weeks in women with RMD (p=0.035). Whilst women experiencing a postpartum episode were less likely to go on to have further children, this did not account for the association with primiparity.
Limitations
Data were collected retrospectively. Information on pharmacological treatment was not available.
Conclusions
Primiparity is associated not only with postpartum psychosis/mania in BD-I, but also with postpartum depression in RMD. Psychosocial factors and biological differences between first and subsequent pregnancies may play a role and are candidates for examination in further studies.
doi:10.1016/j.jad.2013.09.034
PMCID: PMC4025607  PMID: 24446553
Women mental health; Postpartum mood disorders; Bipolar disorder; Recurrent major depression
16.  Toward a definition of “fresh” whole blood: an in vitro characterization of coagulation properties in refrigerated whole blood for transfusion 
Transfusion  2011;51(1):10.1111/j.1537-2995.2010.02772.x.
Background
The hemostatic property of “fresh” whole blood (WB) has been observed in military application and cardiac surgery and is associated with reduced blood loss, transfusion requirements, and donor exposures. The time from donation to transfusion defining “fresh” has not been systematically studied. We undertook an in vitro study of coagulation properties of refrigerated WB stored for 31 days.
Study design and methods
Twenty-one WB units were obtained from healthy volunteer donors and stored under standard AABB refrigerated conditions. Samples were obtained on the day after donation and again on Days 2, 4, 7, 11, 14, 17, 21, 24, and 31. Tests included complete blood count, pH, pO2, pCO2, glucose, lactate, thromboelastography (TEG), and platelet function by light transmission aggregometry (LTA).
Results
There was progressive decline in pH, pO2, glucose, and sodium, but progressive increase in potassium, pCO2, and lactate. TEG variables in all units were normal through Day 11; abnormal values in some variables in some units began on Day 14. Final aggregation levels exhibited no change from Day 1 to Day 21 with adenosine diphosphate and epinephrine, but a decline with collagen (Day 7) and ristocetin (Day 17).
Conclusion
This in vitro study of coagulation properties demonstrates preservation of normal integrated coagulation function to a minimum of 11 days under standard conditions of refrigerated storage of WB for transfusion. These observations strongly suggest that the hemostatic quality of WB may extend beyond current transfusion practices. If confirmed clinically, this would increase availability and extend benefits of reduced donor exposure and transfusion requirements.
doi:10.1111/j.1537-2995.2010.02772.x
PMCID: PMC3821701  PMID: 20663116
17.  Amiodarone-Associated Optic Neuropathy: A Critical Review 
The American Journal of Medicine  2012;125(5):447-453.
Although amiodarone is the most commonly prescribed antiarrhythmic drug, its use is limited by serious toxicities, including optic neuropathy. Current reports of amiodarone associated optic neuropathy identified from the Food and Drug Administration's Adverse Event Reporting System (FDA-AERS) and published case reports were reviewed. A total of 296 reports were identified: 214 from AERS, 59 from published case reports, and 23 from adverse events reports for patients enrolled in clinical trials. Mean duration of amiodarone therapy before vision loss was 9 months (range 1-84 months). Insidious onset of amiodarone associated optic neuropathy (44%) was the most common presentation, and nearly one-third were asymptomatic. Optic disc edema was present in 85% of cases. Following drug cessation, 58% had improved visual acuity, 21% were unchanged, and 21% had further decreased visual acuity. Legal blindness (< 20/200) was noted in at least one eye in 20% of cases. Close ophthalmologic surveillance of patients during the tenure of amiodarone administration is warranted.
doi:10.1016/j.amjmed.2011.09.020
PMCID: PMC3322295  PMID: 22385784
amiodarone; vision loss; optic neuropathy
18.  Genome Wide Linkage Analysis of 972 Bipolar Pedigrees Using Single Nucleotide Polymorphisms 
Molecular Psychiatry  2011;17(8):818-826.
Because of the high costs associated with ascertainment of families most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. While microsatellite markers spaced every 10 centimorgans typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carry out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 SNPs. Of the ~1100 families, 972 were informative for further analyses and mean information content was 0.86 after pruning for LD. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with Bipolar II disorder (BPII) and 702 subjects with Recurrent Major Depression. Three affection status models were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus Recurrent Major Depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (Nonparametric Pairs Lod 3.4 for rs1046943 at 119 cM) and 9q21 (Nonparametric Pairs Lod 3.4 for rs722642 at 78 cM) using only BPI and SA, BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis we observed 59 parametric lods of 2 or greater, many of which are likely to be close to maximum possible scores. While some linkage findings may be false positives the results could help prioritize the search for rare variants using whole exome or genome sequencing.
doi:10.1038/mp.2011.89
PMCID: PMC3204161  PMID: 21769101
Bipolar disorder; Whole genome linkage; Single Nucleotide Polymorphisms; 6q21; 9q21; 2q12
19.  Genome Wide Linkage Analysis of 972 Bipolar Pedigrees Using Single Nucleotide Polymorphisms 
Molecular psychiatry  2011;17(8):818-826.
Because of the high costs associated with ascertainment of families most linkage studies of Bipolar I disorder (BPI) have used relatively small samples. Moreover, the genetic information content reported in most studies has been less than 0.6. While microsatellite markers spaced every 10 centimorgans typically extract most of the genetic information content for larger multiplex families, they can be less informative for smaller pedigrees especially for affected sib pair kindreds. For these reasons we collaborated to pool family resources and carry out higher density genotyping. Approximately 1100 pedigrees of European ancestry were initially selected for study and were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel 12 set of 6090 SNPs. Of the ~1100 families, 972 were informative for further analyses and mean information content was 0.86 after pruning for LD. The 972 kindreds include 2284 cases of BPI disorder, 498 individuals with Bipolar II disorder (BPII) and 702 subjects with Recurrent Major Depression. Three affection status models were considered: ASM1 (BPI and schizoaffective disorder, BP cases (SABP) only), ASM2 (ASM1 cases plus BPII) and ASM3 (ASM2 cases plus Recurrent Major Depression). Both parametric and non-parametric linkage methods were carried out. The strongest findings occurred at 6q21 (Nonparametric Pairs Lod 3.4 for rs1046943 at 119 cM) and 9q21 (Nonparametric Pairs Lod 3.4 for rs722642 at 78 cM) using only BPI and SA, BP cases. Both results met genome-wide significant criteria, although neither was significant after correction for multiple analyses. We also inspected parametric scores for the larger multiplex families to identify possible rare susceptibility loci. In this analysis we observed 59 parametric lods of 2 or greater, many of which are likely to be close to maximum possible scores. While some linkage findings may be false positives the results could help prioritize the search for rare variants using whole exome or genome sequencing.
doi:10.1038/mp.2011.89
PMCID: PMC3204161  PMID: 21769101
Bipolar disorder; Whole genome linkage; Single Nucleotide Polymorphisms; 6q21; 9q21; 2q12
20.  Fast Photochemical Oxidation of Proteins (FPOP) for Epitope Mapping 
Analytical chemistry  2011;83(20):7657-7661.
The growing use of monoclonal antibodies as therapeutics underscores the importance of epitope mapping as an essential step in characterizing antibody-antigen complexes. The use of protein footprinting coupled with mass spectrometry, which is emerging as a tool in structural biology, offers opportunities to map antibody-binding regions of antigens. We report here the use of footprinting via fast photochemical oxidation of proteins (FPOP) with OH radicals to characterize the epitope of the serine-protease thrombin. The data correlate well with previously published results that determined the epitope of thrombin. This study marks the first time oxidative labeling has been used for epitope mapping.
doi:10.1021/ac2007366
PMCID: PMC3193551  PMID: 21894996
Mass spectrometry; oxidation; epitope mapping; protein footprinting
21.  Functional neuroimaging of the baboon during concurrent image-guided transcranial magnetic stimulation 
NeuroImage  2011;57(4):1393-1401.
Transcranial magnetic stimulation (TMS) has well-established applications in basic neuroscience and promising applications in neurological and psychiatric disorders. However the underlying mechanisms of TMS-induced alterations in brain function are not well understood. As a result, treatment design parameters are determined ad hoc and not informed by any coherent theory or model. Once the mechanisms underlying TMS’s modulatory effects on brain systems are better understood and modeled, TMS’s potential as a therapeutic and/or investigative tool will be more readily explored and exploited. An animal model is better suited to study different TMS variables, therefore we developed a baboon model to facilitate testing of some of the current theoretical models of TMS interactions with brain regions. We have demonstrated the feasibility of this approach by successfully imaging cerebral blood flow (CBF) changes with H215O positron emission tomography imaging during high-frequency, suprathreshold repetitive TMS in the primary motor cortex of five healthy, adult baboons.
doi:10.1016/j.neuroimage.2011.05.065
PMCID: PMC3139451  PMID: 21664276
TMS; fMRI; PET; animal models; motor cortex
22.  Echocardiographic Findings and Their Impact on Outcomes of Critically Ill Patients with AIDS in the Era of HAART 
Pulmonary Medicine  2012;2012:575793.
Objective. To describe the echocardiographic findings in critically ill patients with AIDS and their impact on clinical outcome. Design. A retrospective chart review of consecutive AIDS patients over 18 years of age, who had a trans-thoracic echocardiogram performed during the course of intensive care unit stay over the course of 2 years at a tertiary care hospital. Main outcome measures. The prevalence of echocardiogram abnormalities in this population and its impact on ICU mortality, ICU length of stay, hospital mortality, hospital length of stay and 60 day survival. Results. Among 107 patients who met the inclusion criteria, an admission echocardiogram was performed in 62 (58%). The prevalence of cardiac abnormalities was 60%. The most common admission diagnosis was respiratory failure n = 27 (43%). The most common finding on echocardiogram was left ventricular (LV) dysfunction n = 31 (50%) followed by pulmonary hypertension n = 25 (40%). None of these findings had a significant impact on clinical outcomes. There was trend toward reduced 60 day survival among patients with depressed LV function. Conclusions. Although echocardiogram abnormalities were prevalent among this population none of these findings had a significant impact on ICU mortality or hospital mortality and ICU length of stay or hospital length of stay.
doi:10.1155/2012/575793
PMCID: PMC3337497  PMID: 22567277
23.  Stressful life events and the serotonin transporter gene (5-HTT) in recurrent clinical depression. 
Journal of affective disorders  2011;136(1-2):189-193.
Background
An interaction between recent stressful life events (SLEs) and a serotonin transporter promoter polymorphism (5-HTTLPR) in depression has been inconsistently reported. Some of this variability may be due to a previous focus on sub-clinical depression, inclusion of individuals at the lower or upper ends of the age-span, or assumptions concerning the degree of dominance of the low expressing allele. Therefore, a large sample of patients with recurrent clinically diagnosed depression and controls screened for absence of depression was utilised to examine the moderating effect of each 5-HTTLPR genetic model on the association between SLEs and severe depressive episodes.
Method
A sample of 1236 recurrent unipolar depression cases and 598 age-matched, never psychiatrically ill controls completed the List of Threatening Experiences Questionnaire to assess the number of SLEs experienced in the 6 months prior to the most severe depressive episode (cases) or interview (controls). DNA extracted from blood or cheek swabs was genotyped for the short (s) and long (l) alleles of 5-HTTLPR.
Results
A greater number of SLEs were reported by cases than controls and this held across all genotypic groups. There was no main effect of 5-HTTLPR on depression and no evidence of interaction between total SLEs and any of the 5-HTTLPR genetic models. The results were the same for men and women.
Limitations
Utilisation of retrospective self-reported SLEs may have reduced the accuracy of the findings and the cross-sectional design prevents causal inference.
Conclusions
This study failed to find evidence of gene-environment interplay in recurrent clinical depression.
doi:10.1016/j.jad.2011.09.016
PMCID: PMC3272366  PMID: 21982504
Stressful life events; unipolar depression; recurrent; serotonin transporter gene; gene-environment interaction; 5-HTTLPR
25.  Fast Photochemical Oxidation of Proteins (FPOP) for Comparing Structures of Protein/Ligand Complexes: The Calmodulin-peptide Model System 
Analytical chemistry  2010;83(1):311-318.
Fast Photochemical Oxidation of Proteins (FPOP) is a mass-spectrometry-based protein footprinting method that modifies proteins on the microsecond time scale. Highly reactive •OH, produced by laser photolysis of hydrogen peroxide, oxidatively modifies the side chains of approximately one half the common amino acids on this time scale. Owing to the short labeling exposure, only solvent-accessible residues are sampled. Quantification of the modification extent for the apo and holo states of a protein-ligand complex should provide structurally sensitive information at the amino-acid level to compare the structures of unknown protein complexes with known ones. We report here the use of FPOP to monitor the structural changes of calmodulin in its established binding to M13 of the skeletal muscle myosin light chain kinase. We use the outcome to establish the unknown structures resulting from binding with melittin and mastoparan. The structural comparison follows from a comprehensive examination of the extent of FPOP modifications as measured by proteolysis and LC-MS/MS for each protein-ligand equilibrium. The results not only show that the three calmodulin-peptide complexes have similar structures but also reveal those regions of the protein that became more or less solvent-accessible upon binding. This approach has the potential for relatively high throughput, information-dense characterization of a series of protein-ligand complexes in biochemistry and drug discovery when the structure of one reference complex is known, as is the case for calmodulin and M13 of the skeletal muscle myosin light chain kinase, and the structures of related complexes are not,.
doi:10.1021/ac102426d
PMCID: PMC3078576  PMID: 21142124

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