It would be great if, before starting a therapy, it was possible to test small doses of several drugs, at the same time, in a patient and compare their effects on the tumor, so to identify the one that works best.
The study of Yaari and colleagues from the Israel Institute of Technology in Haifa, published in Nature Communication, opens a way to this achievement.... Read more »
Yaari, Z., da Silva, D., Zinger, A., Goldman, E., Kajal, A., Tshuva, R., Barak, E., Dahan, N., Hershkovitz, D., Goldfeder, M.... (2016) Theranostic barcoded nanoparticles for personalized cancer medicine. Nature Communications, 13325. DOI: 10.1038/ncomms13325
Identify everyone born in Denmark between 1985-2002. Identify those treated "in the primary care setting" for an infection. Identify those diagnosed with schizophrenia and affective disorders. Look-see whether there is an overlap between infection or treated infection and schizophrenia / affective disorders. Report results.That's basically the study published by Köhler and colleagues  (a name that has appeared on this blog before) who concluded that: "Infections treated with anti-infect........ Read more »
Köhler O, Petersen L, Mors O, Mortensen PB, Yolken RH, Gasse C, & Benros ME. (2016) Infections and exposure to anti-infective agents and the risk of severe mental disorders: a nationwide study. Acta psychiatrica Scandinavica. PMID: 27870529
It was inevitable ("it is your destiny") that I would formulate a post about the paper published by Khaled Saad and colleagues  reporting results based on "a double-blinded, randomized clinical trial (RCT)" looking at the potential usefulness of a vitamin D supplement on "the core symptoms of autism in children." Inevitable because the peer-reviewed research literature looking at the sunshine vitamin/hormone in relation to autism is getting rather voluminous (see here and see here f........ Read more »
Saad K, Abdel-Rahman AA, Elserogy YM, Al-Atram AA, El-Houfey AA, Othman HA, Bjørklund G, Jia F, Urbina MA, Abo-Elela MG.... (2016) Randomized controlled trial of vitamin D supplementation in children with autism spectrum disorder. Journal of child psychology and psychiatry, and allied disciplines. PMID: 27868194
Most neuroscientists will tell you that long-term memories are stored in the brain in the form of synapses, the connections between neurons. On this view, memory formation occurs when synaptic connections are strengthened, or entirely new synapses are formed.
However, in a new piece in Frontiers in Systems Neuroscience, Austrian researcher Patrick C. Trettenbrein critiques the synapse-memory theory: The Demise of the Synapse As the Locus of Memory.
Trettenbrein acknowledges that "t... Read more »
Trettenbrein, P. (2016) The Demise of the Synapse As the Locus of Memory: A Looming Paradigm Shift?. Frontiers in Systems Neuroscience. DOI: 10.3389/fnsys.2016.00088
Do not mess with Lois.Today I'm posting on the topic of the paper by Rose Nevill and colleagues  concluding: "that while most outcome domains of parent-delivered intervention are associated with small effects, the quality of research is improving."Parent-mediated interventions in relation to autism have been covered on this blog quite recently (see here) accompanied by that 'super-parenting' headline fail. Such approaches work on the idea that helping parents to "develop strategies........ Read more »
Nevill, R., Lecavalier, L., & Stratis, E. (2016) Meta-analysis of parent-mediated interventions for young children with autism spectrum disorder. Autism. DOI: 10.1177/1362361316677838
Lab protocols on Blastocystis culture, cryopreservation, and subtyping are now available in Wiley Online Library.... Read more »
Stensvold CR, & Clark CG. (2016) Molecular Identification and Subtype Analysis of Blastocystis. Current Protocols in Microbiology. PMID: 27858971
Clark CG, & Stensvold CR. (2016) Blastocystis: Isolation, Xenic Cultivation, and Cryopreservation. Current protocols in microbiology. PMID: 27858970
"I was at a conference, and a colleague was talking about the locomotion of great apes in the trees," says Lewis Halsey, a physiologist at the University of Roehampton in London. The colleague mentioned that it's tough to measure how these animals use energy. That's when Halsey had an epiphany. "I was working with parkour athletes on another project," he says, studying how much energy the athletes used while jumping and climbing around a city. Why not use these human athletes to stand in........ Read more »
Halsey LG, Coward SR, & Thorpe SK. (2016) Bridging the gap: parkour athletes provide new insights into locomotion energetics of arboreal apes. Biology letters, 12(11). PMID: 27881766
Matsutani et al. (2016) reported for the first time BHD syndrome accompanied by pulmonary arteriovenous malformation. The patient, a young male with no significant medical history, presented with chest pain. Chest X-ray and CT revealed emphysematous changes in both lungs and a tumour with pleural fluid. A thoracoscopy revealed dark red pleural fluid and multiple cysts in the lung. The tumour lesion was resected and identified as a non-malignant intrapulmonary hematoma caused by a significant hae........ Read more »
Matsutani, N., Dejima, H., Takahashi, Y., Uehara, H., Iinuma, H., Tanaka, F., & Kawamura, M. (2016) Birt-Hogg-Dube syndrome accompanied by pulmonary arteriovenous malformation. Journal of Thoracic Disease, 8(10). DOI: 10.21037/jtd.2016.09.68
Gunji-Niitsu, Y., Kumasaka, T., Kitamura, S., Hoshika, Y., Hayashi, T., Tokuda, H., Morita, R., Kobayashi, E., Mitani, K., Kikkawa, M.... (2016) Benign clear cell “sugar” tumor of the lung in a patient with Birt-Hogg-Dubé syndrome: a case report. BMC Medical Genetics, 17(1). DOI: 10.1186/s12881-016-0350-y
by Piter Kehoma Boll Today’s Friday Fellow may not seem to be such an astonishing plant, but it has its peculiarities, some of them quite interesting. Commonly known as Indian shot, African arrowroot, purple arrowroot, and many other names, it … Continue reading →... Read more »
Cui, L., Ouyang, Y., Lou, Q., Yang, F., Chen, Y., Zhu, W., & Luo, S. (2010) Removal of nutrients from wastewater with Canna indica L. under different vertical-flow constructed wetland conditions. Ecological Engineering, 36(8), 1083-1088. DOI: 10.1016/j.ecoleng.2010.04.026
Woradulayapinij, W., Soonthornchareonnon, N., & Wiwat, C. (2005) In vitro HIV type 1 reverse transcriptase inhibitory activities of Thai medicinal plants and Canna indica L. rhizomes. Journal of Ethnopharmacology, 101(1-3), 84-89. DOI: 10.1016/j.jep.2005.03.030
Yes, it is childish but...With all the continued chatter on a possible role for the collected gut microbiota - those wee beasties that inhabit our deepest, darkest recesses - in relation to some autism (see here for example), the paper by Roberta Grimaldi and colleagues  (open-access available here) provides yet more potentially important information.So, poo(p) samples were the starring material in the paper - "obtained from three non-autistic children and three autistic child donors"- and sp........ Read more »
Grimaldi R, Cela D, Swann JR, Vulevic J, Gibson GR, Tzortzis G, & Costabile A. (2016) In vitro fermentation of B-GOS: Impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children. FEMS microbiology ecology. PMID: 27856622
"Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium."So said the findings reported by Mahesh Desai and colleagues  meriting an editorial in the publishing journal  as the sentiments of 'eating your greens' applies to some rather interesting [mouse] findings.Fibre (UK spelling) comes in various different forms typically categorised as soluble and insoluble d........ Read more »
Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A.... (2016) A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell, 167(5), 1339-2147483647. PMID: 27863247
Ovarian cancer is the most lethal gynecologic malignancy. After epigenomic analysis of patient tumors, aberrant DNA methylation patterns are universally observed in the most abundant histological subtype of ovarian cancer, high-grade serous ovarian cancer (HGSOC). These epigenetic modifications like DNA methylation are known to frequently affect gene regulation involved in cancer-related processes. Since epigenetic alterations are reversible in nature, these changes have emerged as attractive ta........ Read more »
Tomar T, de Jong S, Alkema NG, Hoekman RL, Meersma GJ, Klip HG, van der Zee AG, & Wisman GB. (2016) Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways. Genome medicine, 8(1), 107. PMID: 27765068
Alkema NG, Wisman GB, van der Zee AG, van Vugt MA, & de Jong S. (2016) Studying platinum sensitivity and resistance in high-grade serous ovarian cancer: Different models for different questions. Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy, 55-69. PMID: 26830315
Hidalgo M, Amant F, Biankin AV, Budinská E, Byrne AT, Caldas C, Clarke RB, de Jong S, Jonkers J, Mælandsmo GM.... (2014) Patient-derived xenograft models: an emerging platform for translational cancer research. Cancer discovery, 4(9), 998-1013. PMID: 25185190
Alkema NG, Tomar T, Duiker EW, Jan Meersma G, Klip H, van der Zee AG, Wisman GB, & de Jong S. (2015) Biobanking of patient and patient-derived xenograft ovarian tumour tissue: efficient preservation with low and high fetal calf serum based methods. Scientific reports, 14495. PMID: 26440065
The findings reported by Maureen Russell and colleagues  provide some blogging fodder today and the observation that: "Biological caregivers of children with ASD [autism spectrum disorder] demonstrated a high prevalence of RLS [Restless Legs Syndrome] symptoms and poorer mental health."OK, I know some people might be asking 'just what is Restless Legs Syndrome'? It is a recognised condition complete with 'disease' title (Willis-Ekbom disease). Symptoms, as the name suggests, centre ........ Read more »
Russell M, Baldwin C, McClain D, Matthews N, Smith C, & Quan SF. (2016) Symptoms of Restless Legs Syndrome in Biological Caregivers of Children with Autism Spectrum Disorders. Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine. PMID: 27855729
From bacteria to vertebrates, life — as we know it today — relies on complex molecular interactions, the intricacies of which science has not fully untangled. But for all its complexity, life always requires two essential abilities. Organisms need to preserve their genetic information and reproduce. In our own cells, these tasks are assigned to […]... Read more »
Yeates JA, Hilbe C, Zwick M, Nowak MA, & Lehman N. (2016) Dynamics of prebiotic RNA reproduction illuminated by chemical game theory. Proceedings of the National Academy of Sciences of the United States of America, 113(18), 5030-5. PMID: 27091972
The title of the paper by Konstantin Mechler and colleagues - "Defining the hidden evidence in autism research. Forty per cent of rigorously designed clinical trials remain unpublished - a cross-sectional analysis"  - provides some discussion today. Drawing on the ideas that publication bias and/or the so-called 'file-drawer problem' - terms that refer to the non-publication of study results potentially skewing the collected scientific opinion in a particular area - might also exten........ Read more »
Mechler K, Hoffmann GF, Dittmann RW, & Ries M. (2016) Defining the hidden evidence in autism research. Forty per cent of rigorously designed clinical trials remain unpublished - a cross-sectional analysis. International journal of methods in psychiatric research. PMID: 27862603
Researchers recently announced the discovery of a frog whose groin flashes orange to scare away predators! The species was discovered in Australia.
When biologist Simon Clulow spotted a frog with an unusual marble pattern on its belly, he knew it could be a new species. If that turned to be true, it would be very surprising as the sighting took place on land close to an airport and not some ... Read more »
CLULOW, S., ANSTIS, M., KEOGH, J., & CATULLO, R. (2016) A new species of Australian frog (Myobatrachidae: Uperoleia) from the New South Wales mid-north coast sandplains. Zootaxa, 4184(2), 285. DOI: 10.11646/zootaxa.4184.2.3
The paper by Nahit Motavalli Mukaddes and colleagues  provides some important, if small-scale, information when it comes to that still controversial term - optimal outcome - with the diagnosis of autism in mind. Optimal outcome basically refers to a particular 'type' of autism whereby following a definite diagnosis of autism or autism spectrum disorder (ASD), a later re-evaluation of signs and symptoms reveals that diagnostic thresholds are subsequently not reached and/or exceeded a........ Read more »
Motavalli Mukaddes, N., Mutluer, T., Ayik, B., & Umut, A. (2016) What Happens to Children Who Move off the Autism Spectrum? A Clinical Follow-Up Study. Pediatrics International. DOI: 10.1111/ped.13202
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
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