Note: the “Life in the Lab” series features interviews of interns and visitors. This post is by our second 2016 OMA Visiting Fellow Tunca Doğan, who spent a month with us earlier this year. You can follow Tunca on Twitter at @tuncadogan. —Christophe
Please introduce yourself in a few sentences.
My name is Tunca Doğan. I received my PhD in 2013 with a thesis study in the fields of bioinformatics and computational biology where we developed methods for the clustering........ Read more »
Doğan T, & Karaçalı B. (2013) Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences. PloS one, 8(9). PMID: 24069417
Doğan T, MacDougall A, Saidi R, Poggioli D, Bateman A, O'Donovan C, & Martin MJ. (2016) UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. Bioinformatics (Oxford, England), 32(15), 2264-71. PMID: 27153729
The paper by Wenjie Sun and colleagues  (open-access) provides the blogging fodder for today's post and although based on the science of epigenetics, the usual suspect - DNA methylation - gives way to another concept: histone acetylation with autism in mind. Before heading into the paper myself, I'll draw your attention to some other write-ups of the study including a hat-tip to Jeff Craig and his piece on the topic (see here).So histone acetylation... I've covered the subject ........ Read more »
Sun, W., Poschmann, J., Cruz-Herrera del Rosario, R., Parikshak, N., Hajan, H., Kumar, V., Ramasamy, R., Belgard, T., Elanggovan, B., Wong, C.... (2016) Histone Acetylome-wide Association Study of Autism Spectrum Disorder. Cell, 167(5), 1385-2147483647. DOI: 10.1016/j.cell.2016.10.031
Last week I returned from the 6th annual IMO Workshop at the Moffitt Cancer Center in Tampa, Florida. As I’ve sketched in an earlier post, my team worked on understanding ruxolitinib resistance in chronic myelomonocytic leukemia (CMML). We developed a suite of integrated multi-scale models for uncovering how resistance arises in CMML with no apparent […]... Read more »
Merlevede, J., Droin, N., Qin, T., Meldi, K., Yoshida, K., Morabito, M., Chautard, E., Auboeuf, D., Fenaux, P., Braun, T.... (2016) Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Nature Communications, 10767. PMID: 26908133
In the forests of West Africa, bands of handsome primates called Diana monkeys roam the tree branches. Each group has just one male and several females with their babies. The tradeoff for his apparently cushy living situation is that the male has to chase off predators. His female companions use specific calls to tell him what kinds of threats are nearby. And he responds to whatever they tell him—even if it goes against his own judgment.
Diana monkeys (Cercopithecus diana) of both sex... Read more »
Stephan, C., & Zuberbühler, K. (2016) Persistent Females and Compliant Males Coordinate Alarm Calling in Diana Monkeys. Current Biology, 26(21), 2907-2912. DOI: 10.1016/j.cub.2016.08.033
Birt–Hogg–Dubé syndrome (BHD) is caused by germline mutations in the FLCN gene and characterized by fibrofolliculomas, lung cysts, spontaneous pneumothorax and renal tumours. The stretch hypothesis for pulmonary cyst formation proposes that cysts in BHD arise from defects in cell–cell adhesion, leading to repeated respiration-induced physical stretch-induced stress and, over time, expansion of alveolar spaces particularly in vulnerable regions of lung (Kennedy et al., 20........ Read more »
Hoshika, Y., Takahashi, F., Togo, S., Hashimoto, M., Nara, T., Kobayashi, T., Nurwidya, F., Kataoka, H., Kurihara, M., Kobayashi, E.... (2016) Haploinsufficiency of the gene leads to impaired functions of lung fibroblasts in patients with Birt–Hogg–Dubé syndrome . Physiological Reports, 4(21). DOI: 10.14814/phy2.13025
by Piter Kehoma Boll A flatworm again, at last! Not a land planarian, but a flatworm nonetheless. If there is a group of flatworms that may put land planarians in second plan regarding beauty, those are the polyclads. Living in … Continue reading →... Read more »
"The overall CD [coeliac disease or celiac disease depending on where you live] prevalence was 2.62%, which is statistically significant higher to that reported in the Italian paediatric population... If replicated, these data suggest the importance of regular screening for CD in young patients with ASD [autism spectrum disorder]."Those were some of the findings/conclusions reported in the paper by Sara Calderoni and colleagues  (open-access) and with them, some ........ Read more »
Calderoni, S., Santocchi, E., Del Bianco, T., Brunori, E., Caponi, L., Paolicchi, A., Fulceri, F., Prosperi, M., Narzisi, A., Cosenza, A.... (2016) Serological screening for Celiac Disease in 382 pre-schoolers with Autism Spectrum Disorder. Italian Journal of Pediatrics, 42(1). DOI: 10.1186/s13052-016-0308-x
"After adjustment for several confounders, longer duration of breastfeeding was independently associated with better cognitive development and with fewer autistic traits."So said the paper by Olivier Boucher and colleagues  communicating findings based on the examination of data from "the INMA Project, a Spanish multicenter birth-cohort study" (an initiative that has cropped up on this blog before).Including over 1300 children who were subject to a battery of psychometric and behavioural asse........ Read more »
Boucher O, Julvez J, Guxens M, Arranz E, Ibarluzea J, Sánchez de Miguel M, Fernández-Somoano A, Tardon A, Rebagliato M, Garcia-Esteban R.... (2016) Association between breastfeeding duration and cognitive development, autistic traits and ADHD symptoms: a multicenter study in Spain. Pediatric research. PMID: 27846197
Apolipoprotein A5 gene (APOA5) is one of the genes implicated in contributing to a predisposition for hypertriacylglycerolaemia (HTG), a complex polygenic pathology that is highly influenced by environment. Hypertriacylglycerolaemia is characterized by having high circulating triacylglycerol levels and is a significant risk factor for cardiovascular disease and atherosclerosis. This genetic predisposition has an inherited component (based on polymorphisms) as well as an acquired component regu........ Read more »
Oliva, I., Guardiola, M., Vallve, J., Ibarretxe, D., Plana, N., Masana, L., Monk, D., & Ribalta, J. (2016) APOA5 genetic and epigenetic variability jointly regulate circulating triacylglycerol levels. Clinical Science, 130(22), 2053-2059. DOI: 10.1042/CS20160433
"This study does not support the hypothesis that MPH [methylphenidate] increases risk of incident psychotic events. It does indicate an increased risk of psychotic events before the first prescription of MPH, which may be because of an association between psychotic events and the behavioural and attentional symptoms that led to psychiatric assessment and initiation of MPH treatment."The results published by Man and colleagues  (open-access) sit right with me. I say that on the basis........ Read more »
Man, K., Coghill, D., Chan, E., Lau, W., Hollis, C., Liddle, E., Banaschewski, T., McCarthy, S., Neubert, A., Sayal, K.... (2016) Methylphenidate and the risk of psychotic disorders and hallucinations in children and adolescents in a large health system. Translational Psychiatry, 6(11). DOI: 10.1038/tp.2016.216
Note: We are rebooting our “Life in the Lab” series, which features interviews of interns and visitors. This post is by our inaugural OMA Visiting Fellow Rosa Fernández García, who spent a month with us earlier this year. You can follow Rosa on Twitter at @Rosamygale. —Christophe
Please introduce yourself and your research interests.
I received my bachelor’s degree in Biology (major in Zoology) at Complutense University in Madrid, Spain. I got my master’s and PhD at the s........ Read more »
Fernández R, Laumer CE, Vahtera V, Libro S, Kaluziak S, Sharma PP, Pérez-Porro AR, Edgecombe GD, & Giribet G. (2014) Evaluating topological conflict in centipede phylogeny using transcriptomic data sets. Molecular biology and evolution, 31(6), 1500-13. PMID: 24674821
Fernández, R., Hormiga, G., & Giribet, G. (2014) Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers. Current Biology, 24(15), 1772-1777. DOI: 10.1016/j.cub.2014.06.035
Fernández R, & Giribet G. (2015) Unnoticed in the tropics: phylogenomic resolution of the poorly known arachnid order Ricinulei (Arachnida). Royal Society open science, 2(6), 150065. PMID: 26543583
Novo M, Fernández R, Andrade SC, Marchán DF, Cunha L, & Díaz Cosín DJ. (2016) Phylogenomic analyses of a Mediterranean earthworm family (Annelida: Hormogastridae). Molecular phylogenetics and evolution, 94(Pt B), 473-8. PMID: 26522608
Fernández R, Edgecombe GD, & Giribet G. (2016) Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. Systematic biology, 65(5), 871-89. PMID: 27162151
Sharma, P., Fernandez, R., Esposito, L., Gonzalez-Santillan, E., & Monod, L. (2015) Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. Proceedings of the Royal Society B: Biological Sciences, 282(1804), 20142953-20142953. DOI: 10.1098/rspb.2014.2953
Rosa Fernandez, Prashant Sharma, Ana LM Tourinho, & Gonzalo Giribet. (2016) The Opiliones Tree of Life: shedding light on harvestmen relationships through transcriptomics. BioRxiv. DOI: 10.1101/077594
I'm gonna be fairly brief today and draw your attention to yet another systematic review and meta-analysis this time looking at how "probiotic supplementation can have a positive effect on mood and psychological symptoms such as depression and anxiety."  Probiotics by the way, include a variety of bacteria and related lifeforms that are thought to confer some health advantage.The review/re-analysis by Jennifer McKean and colleagues found 7 studies on this topic in the peer-reviewed resea........ Read more »
McKean J, Naug H, Nikbakht E, Amiet B, & Colson N. (2016) Probiotics and Subclinical Psychological Symptoms in Healthy Participants: A Systematic Review and Meta-Analysis. Journal of alternative and complementary medicine (New York, N.Y.). PMID: 27841940
"CRP [C-reactive protein] concentrations are increased in bipolar disorder regardless of mood state, but are higher during mania than in depression and euthymia, suggesting an increased inflammatory burden in mania."So said the systematic review and meta-analysis published by Brisa Fernandes and colleagues  who surveyed the peer-reviewed literature on the topic of "measured serum and plasma CRP concentrations in adult patients with bipolar disorder (as defined by DSM-IV-TR) and........ Read more »
Fernandes BS, Steiner J, Molendijk ML, Dodd S, Nardin P, Gonçalves CA, Jacka F, Köhler CA, Karmakar C, Carvalho AF.... (2016) C-reactive protein concentrations across the mood spectrum in bipolar disorder: a systematic review and meta-analysis. The lancet. Psychiatry. PMID: 27838212
The results published by Robert Joseph and colleagues  provide some blogging fodder today, observing that as part of the ELGAN (Extremely Low Gestational Age Newborns) Research Study, gestational age might matter when it comes to offspring risk of autism spectrum disorder (ASD).Gestational age is a measure of how far along a pregnancy is but in the context of the Joseph study refers to premature birth or those "born at least 3 months early." Researchers included data for nearly 1000........ Read more »
Joseph, R., Korzeniewski, S., Allred, E., O’Shea, T., Heeren, T., Frazier, J., Ware, J., Hirtz, D., Leviton, A., & Kuban, K. (2016) Extremely low gestational age and very low birth weight for gestational age are risk factors for ASD in a large cohort study of 10-year-old children born at 23-27 weeks gestation. American Journal of Obstetrics and Gynecology. DOI: 10.1016/j.ajog.2016.11.1009
I don’t mean to brag, but I’ve got irritable bowel syndrome, says a character of a sitcom.
Irritable bowel syndrome used to be a rare condition, but became a problem of epidemic proportions, until the disease "came out of the closet". Then Internet searches and doctor visits started to dwindle down and less than halved compared to earlier decades.
Is IBS no longer a problem? [...]... Read more »
Camilleri M, Oduyebo I, & Halawi H. (2016) Chemical and molecular factors in irritable bowel syndrome: current knowledge, challenges, and unanswered questions. American journal of physiology. Gastrointestinal and liver physiology, 311(5). PMID: 27609770
Lacy BE, Patel H, Guérin A, Dea K, Scopel JL, Alaghband R, Wu EQ, & Mody R. (2016) Variation in Care for Patients with Irritable Bowel Syndrome in the United States. PloS one, 11(4). PMID: 27116612
Dorn, S., & Meek, P. (2013) Su1024 Ambulatory Care for Irritable Bowel Syndrome in the United States, 1993-2010. Gastroenterology, 144(5). DOI: 10.1016/S0016-5085(13)61392-X
Lackner, J., Brasel, A., Quigley, B., Keefer, L., Krasner, S., Powell, C., Katz, L., & Sitrin, M. (2010) The ties that bind: perceived social support, stress, and IBS in severely affected patients. Neurogastroenterology , 22(8), 893-900. DOI: 10.1111/j.1365-2982.2010.01516.x
The Zoo Hypothesis Hello? Anybody out there in the starry skies? If there are extra-terrestrial civilizations, why haven’t we heard from them yet? The sheer magnitude of the universe with its billions upon billions of stars has led many to suggest that life must have arisen more than once in the cosmos. Some have gone […]... Read more »
de Magalhães, J. (2016) A direct communication proposal to test the Zoo Hypothesis. Space Policy. DOI: 10.1016/j.spacepol.2016.06.001
Follicular lymphoma is a B-cell lymphoma that remains incurable with conventional therapies. Ying et al. (2016) present a new study exploring the biological and genetic features of follicular lymphoma and identifying potential new therapeutic targets. The authors identified recurrent mutations in the mTOR regulator RRAGC, a small G-protein, in approximately 10% of follicular lymphoma cases. Mutations in RRAGC localized to one protein surface area surrounding the GTP/GDP–binding sites. In s........ Read more »
Ying ZX, Jin M, Peterson LF, Bernard D, Saiya-Cork K, Yildiz M, Wang S, Kaminski MS, Chang AE, Klionsky DJ.... (2016) Recurrent Mutations in the MTOR Regulator RRAGC in Follicular Lymphoma. Clinical cancer research : an official journal of the American Association for Cancer Research, 22(21), 5383-5393. PMID: 27267853
Consider this short blog post an extension of some previous discussions (see here and see here) on a rather peculiar 'association' between urinary tract infections (UTIs) and psychosis. UTIs basically refer to an infection in any part of the urinary system (kidneys, bladder, etc) typically treated with antibiotics. Psychosis is a state that causes a person to perceive or interpret things around them in an atypical way, usually accompanied by delusions or hallucinations. For a while now........ Read more »
Carson, C., Phillip, N., & Miller, B. (2016) Urinary tract infections in children and adolescents with acute psychosis. Schizophrenia Research. DOI: 10.1016/j.schres.2016.11.004
Is your dog a natural athlete or a couch pup-tato? The answer might depend on how far removed it is from its wild ancestors. Dogs that are more similar to wolves have kept more of their natural athleticism, while breeding has rendered other types of dogs a little...less impressive.
Caleb Bryce, a PhD candidate at UC Santa Cruz, says his study of canine athletes came about serendipitously. "We were just hoping to calibrate a new wildlife collar we’ve developed," he says; he planned to te........ Read more »
Bryce CM, & Williams TM. (2016) Comparative locomotor costs of domestic dogs reveal energetic economy of wolf-like breeds. The Journal of experimental biology. PMID: 27811300
DNA methylation is a biological clock that ticks with age, and numerous studies have been able to construct age-prediction models based on methylation status. However in somatic cells, DNA methylation is highly polymorphic – though this is not always appreciated in genome wide studies because coverage is often limited and variants below 10% usually escape detection. In an effort to clarify the origin of somatic DNA methylation heterogeneity and the impact it has on chromatin domains and ge........ Read more »
Russo, G., Landi, R., Pezone, A., Morano, A., Zuchegna, C., Romano, A., Muller, M., Gottesman, M., Porcellini, A., & Avvedimento, E. (2016) DNA damage and Repair Modify DNA methylation and Chromatin Domain of the Targeted Locus: Mechanism of allele methylation polymorphism. Scientific Reports, 33222. DOI: 10.1038/srep33222
Cuozzo, C., Porcellini, A., Angrisano, T., Morano, A., Lee, B., Pardo, A., Messina, S., Iuliano, R., Fusco, A., Santillo, M.... (2007) DNA Damage, Homology-Directed Repair, and DNA Methylation. PLoS Genetics, 3(7). DOI: 10.1371/journal.pgen.0030110
Morano, A., Angrisano, T., Russo, G., Landi, R., Pezone, A., Bartollino, S., Zuchegna, C., Babbio, F., Bonapace, I., Allen, B.... (2013) Targeted DNA methylation by homology-directed repair in mammalian cells. Transcription reshapes methylation on the repaired gene. Nucleic Acids Research, 42(2), 804-821. DOI: 10.1093/nar/gkt920
Landan, G., Cohen, N., Mukamel, Z., Bar, A., Molchadsky, A., Brosh, R., Horn-Saban, S., Zalcenstein, D., Goldfinger, N., Zundelevich, A.... (2012) Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nature Genetics, 44(11), 1207-1214. DOI: 10.1038/ng.2442
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