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1.  The zebrafish reference genome sequence and its relationship to the human genome 
Howe, Kerstin | Clark, Matthew D. | Torroja, Carlos F. | Torrance, James | Berthelot, Camille | Muffato, Matthieu | Collins, John E. | Humphray, Sean | McLaren, Karen | Matthews, Lucy | McLaren, Stuart | Sealy, Ian | Caccamo, Mario | Churcher, Carol | Scott, Carol | Barrett, Jeffrey C. | Koch, Romke | Rauch, Gerd-Jörg | White, Simon | Chow, William | Kilian, Britt | Quintais, Leonor T. | Guerra-Assunção, José A. | Zhou, Yi | Gu, Yong | Yen, Jennifer | Vogel, Jan-Hinnerk | Eyre, Tina | Redmond, Seth | Banerjee, Ruby | Chi, Jianxiang | Fu, Beiyuan | Langley, Elizabeth | Maguire, Sean F. | Laird, Gavin K. | Lloyd, David | Kenyon, Emma | Donaldson, Sarah | Sehra, Harminder | Almeida-King, Jeff | Loveland, Jane | Trevanion, Stephen | Jones, Matt | Quail, Mike | Willey, Dave | Hunt, Adrienne | Burton, John | Sims, Sarah | McLay, Kirsten | Plumb, Bob | Davis, Joy | Clee, Chris | Oliver, Karen | Clark, Richard | Riddle, Clare | Eliott, David | Threadgold, Glen | Harden, Glenn | Ware, Darren | Mortimer, Beverly | Kerry, Giselle | Heath, Paul | Phillimore, Benjamin | Tracey, Alan | Corby, Nicole | Dunn, Matthew | Johnson, Christopher | Wood, Jonathan | Clark, Susan | Pelan, Sarah | Griffiths, Guy | Smith, Michelle | Glithero, Rebecca | Howden, Philip | Barker, Nicholas | Stevens, Christopher | Harley, Joanna | Holt, Karen | Panagiotidis, Georgios | Lovell, Jamieson | Beasley, Helen | Henderson, Carl | Gordon, Daria | Auger, Katherine | Wright, Deborah | Collins, Joanna | Raisen, Claire | Dyer, Lauren | Leung, Kenric | Robertson, Lauren | Ambridge, Kirsty | Leongamornlert, Daniel | McGuire, Sarah | Gilderthorp, Ruth | Griffiths, Coline | Manthravadi, Deepa | Nichol, Sarah | Barker, Gary | Whitehead, Siobhan | Kay, Michael | Brown, Jacqueline | Murnane, Clare | Gray, Emma | Humphries, Matthew | Sycamore, Neil | Barker, Darren | Saunders, David | Wallis, Justene | Babbage, Anne | Hammond, Sian | Mashreghi-Mohammadi, Maryam | Barr, Lucy | Martin, Sancha | Wray, Paul | Ellington, Andrew | Matthews, Nicholas | Ellwood, Matthew | Woodmansey, Rebecca | Clark, Graham | Cooper, James | Tromans, Anthony | Grafham, Darren | Skuce, Carl | Pandian, Richard | Andrews, Robert | Harrison, Elliot | Kimberley, Andrew | Garnett, Jane | Fosker, Nigel | Hall, Rebekah | Garner, Patrick | Kelly, Daniel | Bird, Christine | Palmer, Sophie | Gehring, Ines | Berger, Andrea | Dooley, Christopher M. | Ersan-Ürün, Zübeyde | Eser, Cigdem | Geiger, Horst | Geisler, Maria | Karotki, Lena | Kirn, Anette | Konantz, Judith | Konantz, Martina | Oberländer, Martina | Rudolph-Geiger, Silke | Teucke, Mathias | Osoegawa, Kazutoyo | Zhu, Baoli | Rapp, Amanda | Widaa, Sara | Langford, Cordelia | Yang, Fengtang | Carter, Nigel P. | Harrow, Jennifer | Ning, Zemin | Herrero, Javier | Searle, Steve M. J. | Enright, Anton | Geisler, Robert | Plasterk, Ronald H. A. | Lee, Charles | Westerfield, Monte | de Jong, Pieter J. | Zon, Leonard I. | Postlethwait, John H. | Nüsslein-Volhard, Christiane | Hubbard, Tim J. P. | Crollius, Hugues Roest | Rogers, Jane | Stemple, Derek L.
Nature  2013;496(7446):498-503.
Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3–5. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
PMCID: PMC3703927  PMID: 23594743
2.  Targeting Cattle-Borne Zoonoses and Cattle Pathogens Using a Novel Trypanosomatid-Based Delivery System 
PLoS Pathogens  2011;7(10):e1002340.
Trypanosomatid parasites are notorious for the human diseases they cause throughout Africa and South America. However, non-pathogenic trypanosomatids are also found worldwide, infecting a wide range of hosts. One example is Trypanosoma (Megatrypanum) theileri, a ubiquitous protozoan commensal of bovids, which is distributed globally. Exploiting knowledge of pathogenic trypanosomatids, we have developed Trypanosoma theileri as a novel vehicle to deliver vaccine antigens and other proteins to cattle. Conditions for the growth and transfection of T. theileri have been optimised and expressed heterologous proteins targeted for secretion or specific localisation at the cell interior or surface using trafficking signals from Trypanosoma brucei. In cattle, the engineered vehicle could establish in the context of a pre-existing natural T. theileri population, was maintained long-term and generated specific immune responses to an expressed Babesia antigen at protective levels. Building on several decades of basic research into trypanosomatid pathogens, Trypanosoma theileri offers significant potential to target multiple infections, including major cattle-borne zoonoses such as Escherichia coli, Salmonella spp., Brucella abortus and Mycobacterium spp. It also has the potential to deliver therapeutics to cattle, including the lytic factor that protects humans from cattle trypanosomiasis. This could alleviate poverty by protecting indigenous African cattle from African trypanosomiasis.
Author Summary
Single-celled parasites of the order Kinetoplastida are responsible for devastating diseases of humans and animals, including African trypanosomiasis, Chagas' disease and leishmaniasis. However, there are also many species of trypanosomatids that do not cause disease and are distributed globally. One example is Trypanosoma (Megatrypanum) theileri, which is restricted to bovids and ubiquitous in cattle herds worldwide. This organism is maintained extracellularly in the blood and tissues long-term without any observed ill effects on host health or productivity. Using knowledge of gene expression and protein trafficking in pathogenic trypanosomatids, we have successfully developed, from first principles, Trypanosoma theileri as a delivery system for vaccine antigens and therapeutics. Procedures for the growth, transfection and heterologous gene expression of T. theileri have been developed, and the delivery of a vaccine antigen derived from Babesia divergens evaluated in vivo. Our results demonstrate the ability of T. theileri to be used as a flexible and easily manipulated protein delivery system suitable for the control of cattle pathogens and cattle-borne zoonoses. In one notable application, we propose that the system could allow the expression of serum trypanolytic factors in cattle, with the potential to alleviate poverty in Africa through the killing of pathogenic trypanosomatids in livestock.
PMCID: PMC3203185  PMID: 22046137
3.  Interspecific Nest Parasitism by Pseudabispa paragioides, a Solitary Australian Wasp 
In morphology, coloration, and size, Pseudabispa wasps (Hymenoptera: Vespidae: Eumeninae) closely resemble mason wasps in the genus Abispa, and their distributions overlap. Although these two genera are among the largest solitary wasps in Australia, the biology of Pseudabispa was not previously known. Field observations from near Katherine, Northern Territory, strongly suggest that P. paragioides (Meade-Waldo) females attack and kill female A. ephippium (Fabricius) and usurp their nests, then appropriate cells, mass provision them with caterpillars acquired by theft from still other nests, and close them with mud taken from the host nest. Despite an abundance of potentially available cells in nests of three other large solitary wasps common at the same site, P. paragioides was found associated only with nests of A. ephippium. This unusual report of apparently forcible and lethal interspecific nest takeover for a non-social wasp parallels behaviors previously known only from socially parasitic eusocial Hymenoptera. Exploitation by P. paragioides may help explain why its host displays some of the most highly developed parental care known in any solitary eumenid, and why its nests are spaced widely from one another.
PMCID: PMC3016984  PMID: 21067418
exploitation; interspecific competition; kleptoparasitism; lethal fighting; prey theft; provisioning; social parasitism; usurpation
4.  Cohort differences in disease and disability in the young-old: findings from the MRC Cognitive Function and Ageing Study (MRC-CFAS) 
BMC Public Health  2007;7:156.
Projections of health and social care need are highly sensitive to assumptions about cohort trends in health and disability. We use a repeated population-based cross-sectional study from the Cambridgeshire centre of the UK Medical Research Council Cognitive Function and Ageing Study to investigate trends in the health of the young-old UK population
Non-overlapping cohorts of men and women aged 65–69 years in 1991/2 (n = 689) and 1996/7 (n = 687) were compared on: self-reported diseases and conditions; self-rated health; mobility limitation; disability by logistic regression and four-year survival by Cox Proportional Hazards Regression models, with adjustments for differences in socio-economic and lifestyle factors.
Survival was similar between cohorts (HR: 0.91, 95% CI: 0.62 to 1.32). There was a significant increase in the number of conditions reported between cohorts, with more participants reporting 3 or more conditions in the new cohort (14.2% vs. 10.1%). When individual conditions were considered, there was a 10% increase in the reporting of arthritis and a significant increase in the reporting of chronic airways obstruction (OR: 1.36, 95% CI: 1.04 to 1.78).
This study provides evidence of rising levels of ill-health, as measured by the prevalence of self-reported chronic conditions, in the newer cohorts of the young-old. Though changes in diagnosis or reporting of disease cannot, as yet, be excluded, to better understand whether our findings reflect real increases in ill-health, investment should be made into improved population-based databases, linking self-report and objective measures of health and function, and including those in long-term care.
PMCID: PMC1947964  PMID: 17629910
6.  FlyBase: a Drosophila database. The FlyBase consortium. 
Nucleic Acids Research  1997;25(1):63-66.
FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, transposons, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. The Encyclopedia of Drosophila is a joint effort between FlyBase and the Berkeley Drosophila Genome Project which integrates FlyBase data with those from the BDGP.
PMCID: PMC146418  PMID: 9045212
7.  Changes in cerebral oxygen consumption are independent of changes in body oxygen consumption after severe head injury in childhood. 
This study examines the relation between cerebral O2 consumption (CMRO2) and the O2 consumption of the rest of the body (BVO2) after severe head injury. Seventy nine serial measurements of whole body O2 consumption, CMRO2, plasma adrenaline, T3, and glucagon concentrations were made in 15 children with severe head injuries receiving neurointensive care. Body O2 consumption was measured with indirect calorimetry and CMRO2 with the Kety-Schmidt technique. There was no evidence of a significant relation between CMRO2 and BVO2. Within each child there were statistically significant positive relations between BVO2 and adrenaline, T3, and glucagon. By contrast, there was only a weak significant positive relation between CMRO2 and T3. In conclusion, CMRO2 and BVO2 seem to be determined independently after severe head injury. Thus therapeutic measures aiming to reduce CMRO2 need to be specific to the brain and it should not be assumed that measures which decrease whole body energy expenditure will necessarily have the same effect on CMRO2.
PMCID: PMC486069  PMID: 7561912
8.  Temperature response to severe head injury and the effect on body energy expenditure and cerebral oxygen consumption. 
Archives of Disease in Childhood  1995;72(6):507-515.
This study examines the relationship between core temperature and whole body energy expenditure, cerebral oxygen consumption (CMRO2), cerebral blood flow (CBF), and intracranial pressure (ICP) in severely head injured children. A total of 107 serial measurements of temperature, energy expenditure, CMRO2, CBF, and ICP were made in 18 head injured children receiving neurointensive care. Energy expenditure was measured using indirect calorimetry, and CMRO2 and CBF using the Kety-Schmidt technique. The mean rectal temperature was 37.8 degrees C (34-39.1 degrees C) despite modification with paracetamol. Within each child there was a positive relationship between rectal temperature and energy expenditure, energy expenditure increasing by a mean of 7.4% per degree C. There was no evidence of significant relationships between rectal temperature and CMRO2, CBF, or ICP. Mild induced hypothermia in two children did not result in decreased CMRO2 or CBF measurements. The efficacy of interventions aiming to modify cerebral energy metabolism by changing core temperature cannot be readily assessed by the response of the whole body.
PMCID: PMC1511122  PMID: 7618935
10.  Colitis: an unusual presentation of Wegener's granulomatosis 
BMJ Case Reports  2013;2013:bcr2012007566.
Wegener's granulomatosis (WG) also known as granulomatosis with polyangiitis (GPA) is an anti-neutrophil cytoplasmic antibody-positive (ANCA) vasculitis which most commonly affects the upper respiratory tract, lungs and kidneys. It is uncommon for colitis to be the primary reason for the first hospital admission related to WG. This case represents one of the few in the literature where colitis is associated with WG and in particular, where colonic involvement was the presenting symptom. The patient presented to hospital with a 3-day history of bloody diarrhoea and was treated for colitis. The disease progressed and during the second admission renal and pulmonary involvement was found. A renal biopsy showed a crescentic change and a CT-confirmed inflammatory changes in the caecum and ascending colon. A diagnosis of WG was made and appropriate treatment initiated. The patient is now in remission.
PMCID: PMC3604320  PMID: 23436885
11.  Chemical Atherogenesis: Role of Endogenous and Exogenous Poisons in Disease Development 
Toxics  2014;2(1):17-34.
Chemical atherogenesis is an emerging field that describes how environmental pollutants and endogenous toxins perturb critical pathways that regulate lipid metabolism and inflammation, thus injuring cells found within the vessel wall. Despite growing awareness of the role of environmental pollutants in the development of cardiovascular disease, the field of chemical atherogenesis can broadly include both exogenous and endogenous poisons and the study of molecular, biochemical, and cellular pathways that become dysregulated during atherosclerosis. This integrated approach is logical because exogenous and endogenous toxins often share the same mechanism of toxicity. Chemical atherogenesis is a truly integrative discipline because it incorporates concepts from several different fields, including biochemistry, chemical biology, pharmacology, and toxicology. This review will provide an overview of this emerging research area, focusing on cellular and animal models of disease.
PMCID: PMC4333738
chemical atherogenesis; endogenous toxins; environmental pollutants; atherosclerosis; carboxylesterases; inflammation; oxidative stress
12.  Deficiency of Melanoma Differentiation–associated Protein 5 Results in Exacerbated Chronic Postviral Lung Inflammation 
Rationale: Respiratory viral infections can result in the establishment of chronic lung diseases. Understanding the early innate immune mechanisms that participate in the development of chronic postviral lung disease may reveal new targets for therapeutic intervention. The intracellular viral sensor protein melanoma differentiation–associated protein 5 (MDA5) sustains the acute immune response to Sendai virus, a mouse pathogen that causes chronic lung inflammation, but its role in the development of postviral chronic lung disease is unknown.
Objectives: To establish the role of MDA5 in the development of chronic lung disease.
Methods: MDA5-deficient or control mice were infected with Sendai virus. The acute inflammatory response was evaluated by profiling chemokine and cytokine expression and by characterizing the composition of the cellular infiltrate. The impact of MDA5 on chronic lung pathology and function was evaluated through histological studies, degree of oxygen saturation, and responsiveness to carbachol.
Measurements and Main Results: MDA5 deficiency resulted in normal virus replication and in a distinct profile of chemokines and cytokines that associated with acute lung neutropenia and enhanced accumulation of alternatively activated macrophages. Diminished expression of neutrophil-recruiting chemokines was also observed in cells infected with influenza virus, suggesting a key role of MDA5 in driving the early accumulation of neutrophils at the infection site. The biased acute inflammatory response of MDA5-deficient mice led to an enhanced chronic lung inflammation, epithelial cell hyperplasia, airway hyperreactivity, and diminished blood oxygen saturation.
Conclusions: MDA5 modulates the development of chronic lung inflammation by regulating the early inflammatory response in the lung.
PMCID: PMC3977719  PMID: 24417465
respiratory virus; chronic lung disease; innate immunity; paramyxovirus
13.  Molecular Mechanism of Activation of Transforming Growth Factor Beta/Smads Signaling Pathway in Ets Related Gene-Positive Prostate Cancers 
Transforming growth factor beta (TGF-β) signaling pathway is involved in diverse cellular processes, including cell proliferation, differentiation, adhesion, apoptosis, and some human diseases including cancer. Smad proteins function as mediators of intracellular signal transduction of TGF-β. Following their phosphorylation by TGF-β receptor I, Smad2 and Smad3 form a heteromeric complex with Smad4 and then are translocated into the nucleus where they bind to other co-factors and regulate the expression of target genes. ERG (Ets Related Gene) belongs to the ETS family of transcriptional factors. Chromosomal rearrangement of TMPRSS2 gene and ERG gene has been found in the majority of prostate cancers. Over-expression of full length or truncated ERG proteins is associated with a higher rate of recurrence and unfavorable prognosis. In this review, we focus on recent understanding of regulation of TGF-β/Smads signaling pathway by ERG proteins in prostate cancer.
PMCID: PMC4322943
TGF-β; Smad3; Phosphorylation; ERG; TMPRSS2-ERG
14.  A community-based pilot randomised controlled study of life skills classes for individuals with low mood and depression 
BMC Psychiatry  2015;15:17.
Cognitive behavioural therapy (CBT) is recommended for the treatment of depression and anxiety. However, access is limited. Low-intensity approaches such as guided CBT self-help (bibliotherapy) can increase access to treatment and is recommended by UK guidelines. No previous research has explored the provision of group-based guidance/support for a bibliotherapy approach for depression and anxiety in community settings. The objective was to carry out a pilot study of a group guided self-help intervention, using community based recruitment methods.
A randomised controlled trial comparing an 8 week CBT group guided self-help intervention to usual care. Recruitment and the delivery of the intervention were carried out in Glasgow and Derry/Londonderry in partnership with national depression charities. Fifty-three people were randomised, however we refer only to the forty-six participants who provided baseline data: 16 males and 30 females, aged 16 or over, with a PHQ-9 score of ≥ 5, were recruited from the community. The mean age of the sample was 43.7 (sd = 13) and 93.5% of participants had suffered from low mood for a year or more.
There was effective recruitment, randomisation, uptake and adherence with 21 Immediate Access (IA) and 25 Delayed Access Control (DAC) participants. The intervention was highly acceptable to participants attending on average 4.46 of the 8 sessions (sd 3.06), 65.2% attended more than half of all sessions. The mean satisfaction on the Client Satisfaction Questionnaire was 28 out of 32 (sd 4.8). The provisional results in the pilot suggest the intervention may improve both anxiety and depression. At three months, data collection was achieved from 74% of participants. The trial successfully provided estimates of the sample size needed for the future planned trial.
Low-intensity group-based classes may offer an alternative method of managing depression and anxiety and warrant further research.
Trial registration
Current Controlled Trials ISRCTN84893887. Registered 3 November 2011.
PMCID: PMC4331464
Depression; Guided self-help; Cognitive behavioural therapy; Low intensity; Living life to the full classes
15.  Linked Clinical Trials – The Development of New Clinical Learning Studies in Parkinson’s Disease Using Screening of Multiple Prospective New Treatments 
Journal of Parkinson's disease  2013;3(3):231-239.
Finding new therapies for Parkinson’s disease (PD) is a slow process. We assembled an international committee of experts to examine drugs potentially suitable for repurposing to modify PD progression. This committee evaluated multiple drugs currently used, or being developed, in other therapeutic areas, as well as considering several natural, non-pharmaceutical compounds. The committee prioritized which of these putative treatments were most suited to move immediately into pilot clinical trials. Aspects considered included known modes of action, safety, blood-brain-barrier penetration, preclinical data in animal models of PD and the possibility to monitor target engagement in the brain. Of the 26 potential interventions, 10 were considered worth moving forward into small, parallel ‘learning’ clinical trials in PD patients. These trials could be funded in a multitude of ways through support from industry, research grants and directed philanthropic donations. The committee-based approach to select the candidate compounds might help rapidly identify new potential PD treatment strategies for use in clinical trials.
PMCID: PMC4318242  PMID: 24018336
Drug repositioning; disease modification; neuroprotection
20.  An epithelial circadian clock controls pulmonary inflammation and glucocorticoid action 
Nature medicine  2014;20(8):919-926.
The circadian system is as an important regulator of immune function. Human inflammatory lung diseases frequently show time-of-day variation in symptom severity and lung function, but the mechanisms and cell types that are underlying these effects remain unclear. We show that pulmonary antibacterial responses are modulated by a circadian clock within epithelial club (Clara) cells. These drive circadian neutrophil recruitment to the lung via the chemokine CXCL5. Genetic ablation of the clock gene Bmal1 (also called Arntl or MOP3) in bronchiolar cells disrupts rhythmic Cxcl5 expression, resulting in exaggerated inflammatory responses to lipopolysaccharide and bacterial infection. Adrenalectomy blocks rhythmic inflammatory responses and the circadian regulation of CXCL5, suggesting a key role for the adrenal axis in driving CXCL5 expression and pulmonary neutrophil recruitment. Glucocorticoid receptor occupancy at the Cxcl5 locus shows circadian oscillations, but this is disrupted in mice with bronchiole-specific ablation of Bmal1, leading to enhanced CXCL5 expression despite normal corticosteroid secretion. In clock-gene disrupted mice the synthetic glucocorticoid dexamethasone loses anti-inflammatory efficacy. We now define a regulatory mechanism that links the circadian clock and glucocorticoid hormones to control both time-of-day variation and also the magnitude of pulmonary inflammation and responses to bacterial infection.
PMCID: PMC4268501  PMID: 25064128
21.  Lipidomic Analyses, Breast- and Formula-Feeding, and Growth in Infants 
The Journal of Pediatrics  2015;166(2):276-281.e6.
To evaluate lipidomic differences between breast- and formula-fed infants.
Study design
We utilized high-resolution mass-spectrometry methods to analyze 3.2 mm dried blood spot samples collected at ages 3 months (n = 241) and 12 months (n = 144) from a representative birth cohort study. Lipidomic profiles were compared between infants exclusively breast-fed, formula-fed, or mixed-fed, and related to 12-month infancy weight. Data analysis included supervised multivariate statistics (partial least squares discriminant analysis), and univariate analysis with correction for multiple testing.
Distinct differences in 3-month lipidomic profiles were observed between exclusively breast-fed and formula-fed infants; mixed-fed infants showed intermediate profiles. Principle lipidomic characteristics of breast-fed infants were lower total phosphatidylcholines (PCs), with specifically lower short chain unsaturated PC but higher long chain polyunsaturated PC; higher cholesterol esters; and variable differences in sphingomyelins. At 12 months, lipidomic profiles were markedly different to those at 3 months, and differences between the earlier breast/formula/mixed-feeding groups were no longer evident. However, several specific lipid species, associated with breast-feeding at 3 months, also correlated with differences in 3- to 12-month weight.
State-of-the-art dried blood spot sample lipidomic profiling demonstrated striking differences between breast-fed and formula-fed infants. Although these changes diminished with age, breast-fed lipidomic profiles at 3 months were associated with infancy weight and could potentially represent biomarkers of infant nutrition.
PMCID: PMC4302220  PMID: 25454937
CBGS, Cambridge Baby Growth Study; CE, Cholesterol ester; DBS, Dried blood spot; LC-PUFA, Long chain polyunsaturated fatty acid; PC, Phosphatidylcholine; PC-O, 1-alkyl,2-acylglycerophosphocholine; PC-P, 1-(alkenyl),2-acylglycerophosphocholin; PLS-DA, Partial least squares-discriminant analysis; SM, Sphingomyelin; TG, Triglyceride
22.  Depressive symptoms in Chinese Americans with Cognitive Impairment 
To assess the prevalence of geriatric depression in Chinese American patients with cognitive impairment and to compare the prevalence to that of cognitively normal elderly Chinese Americans and Caucasians.
We compared rates of depressive symptomatology in elderly Chinese Americans to a matched group of Caucasians, with and without dementia, and assessed rates of treatment for depression across all groups.
Academic subspecialty referral clinic.
Participants included a total of 137 elderly, cognitively impaired and cognitively normal Chinese Americans and 140 Caucasians with and without cognitive impairment.
Demographic (e.g. age, education, race, language ability), cognitive (MMSE score), medical (e.g. cardiovascular morbidity) and functional (Clinical Dementia Rating Scale) risk factors were assessed for association with depressive symptomatology as measured by the Geriatric Depression Scale (GDS).
Depression (GDS score ≥ 6 out of 15) was significantly more common in cognitively impaired Chinese Americans (35%) versus cognitively impaired Caucasians (15%, χ2 = 33.8, p<0.05), and Chinese Americans were less likely to be on treatment for depression (12%) than Caucasians (37%, χ2 = 41, p<0.05). Cognitive and functional impairment, age and education were all independent predictors of GDS score. Rates of depression were not significantly different in cognitively normal Chinese American (6%) and Caucasian (0%) groups.
These findings indicate that elderly Chinese Americans with cognitive impairment are at significantly increased risk for unrecognized depression and that education, and/or other cultural factors associated with education may contribute to this risk.
PMCID: PMC4309267  PMID: 24021225
geriatric depression; dementia; Chinese American
23.  Genetics of ecological divergence during speciation 
Nature  2014;511(7509):307-311.
Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Though this process is a major generator of biodiversity, its genetic basis remains poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but that depend on the ecological context.
PMCID: PMC4149549  PMID: 24909991
24.  Expression of the CHOP-inducible carbonic anhydrase CAVI-b is required for BDNF-mediated protection from hypoxia 
Brain research  2013;1543:28-37.
Carbonic anhydrases (CAs) comprise a family of zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide. CAs contribute to a myriad of physiological processes, including pH regulation, anion transport and water balance. To date, 16 known members of the mammalian alpha-CA family have been identified. Given that the catalytic family members share identical reaction chemistry, their physiologic roles are influenced greatly by their tissue and sub-cellular locations. CAVI is the lone secreted CA and exists in both saliva and the gastrointestinal mucosa. An alternative, stress-inducible isoform of CAVI (CAVI-b) has been shown to be expressed from a cryptic promoter that is activated by the CCAAT/Enhancer-Binding Protein Homologous Protein (CHOP). The CAVI-b isoform is not secreted and is currently of unknown physiological function. Here we use neuronal models, including a model derived using Car6 and CHOP gene ablations, to delineate a role for CAVI-b in ischemic protection. Our results demonstrate that CAVI-b expression, which is increased through CHOP-signaling in response to unfolded protein stress, is also increased by oxygen-glucose deprivation (OGD). While enforced expression of CAVI-b is not sufficient to protect against ischemia, CHOP regulation of CAVI-b is necessary for adaptive changes mediated by BDNF that reduce subsequent ischemic damage. These results suggest that CAVI-b comprises a necessary component of a larger adaptive signaling pathway downstream of CHOP.
PMCID: PMC3888505  PMID: 24275196
carbonic anhydrase; ischemia; neurosphere; unfolded protein response (UPR); oxygen glucose deprivation (OGD); brain-derived neurotrophic factor (BDNF)
25.  Cytotoxic Mediators in Paradoxical HIV–Tuberculosis Immune Reconstitution Inflammatory Syndrome 
Tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) frequently complicates combined antiretroviral therapy and antituberculosis therapy in HIV-1–coinfected tuberculosis patients. The immunopathological mechanisms underlying TB-IRIS are incompletely defined, and improved understanding is required to derive new treatments and to reduce associated morbidity and mortality. We performed longitudinal and cross-sectional analyses of human PBMCs from paradoxical TB-IRIS patients and non-IRIS controls (HIV-TB–coinfected patients commencing antiretroviral therapy who did not develop TB-IRIS). Freshly isolated PBMC stimulated with heat-killed Mycobacterium tuberculosis H37Rv (hkH37Rv) were used for IFN-γ ELISPOT and RNA extraction. Stored RNA was used for microarray and RT-PCR, whereas corresponding stored culture supernatants were used for ELISA. Stored PBMC were used for perforin and granzyme B ELISPOT and flow cytometry. There were significantly increased IFN-γ responses to hkH37Rv in TB-IRIS, compared with non-IRIS PBMC (p = 0.035). Microarray analysis of hkH37Rv-stimulated PBMC indicated that perforin 1 was the most significantly upregulated gene, with granzyme B among the top five (log2 fold difference 3.587 and 2.828, respectively), in TB-IRIS. Downstream experiments using RT-PCR, ELISA, and ELISPOT confirmed the increased expression and secretion of perforin and granzyme B. Moreover, granzyme B secretion reduced in PBMC from TB-IRIS patients during corticosteroid treatment. Invariant NKT cell (CD3+Vα24+) proportions were higher in TB-IRIS patients (p = 0.004) and were a source of perforin. Our data implicate the granule exocytosis pathway in TB-IRIS pathophysiology. Further understanding of the immunopathogenesis of this condition will facilitate development of specific diagnostic and improved therapeutic options.
PMCID: PMC4319311  PMID: 25589068

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