by Christian de Guttry in genome ecology evolution etc
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons About 450 mya bony vertebrates radiated into Lobe-finned fish, from which tetrapods appeared later, and Ray-finned fish, which include Teleost (Fig.1). Nowadays they make up to 96 percent of … Continue reading →... Read more »
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J.... (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature genetics, 48(4), 427-37. PMID: 26950095
"The tryptophan metabolic pathway collectively displays the largest perturbations in ASD [autism spectrum disorder]."So said the findings reported by Federica Gevi and colleagues  (open-access) who provide yet more 'metabolomic' data when it comes to autism to add to the already quite voluminous peer-reviewed matter on this topic (see here for example).Just in case you aren't analytical chemistry-saavy, metabolomics is basically the study of the various chemical fingerprints that th........ Read more »
Gevi, F., Zolla, L., Gabriele, S., & Persico, A. (2016) Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism. Molecular Autism, 7(1). DOI: 10.1186/s13229-016-0109-5
"Online communities are used as platforms by parents to verify developmental and health concerns related to their child."That was the starting point for the study results reported by Ben-Sasson & Yom-Tov  (open-access available here) who approached an increasingly important issue related to how the Internet and social media in particular, is fast becoming one of the 'go-to' options when it comes to parental concerns about their child's development and the question: could it be autism........ Read more »
Ben-Sasson A, & Yom-Tov E. (2016) Online Concerns of Parents Suspecting Autism Spectrum Disorder in Their Child: Content Analysis of Signs and Automated Prediction of Risk. Journal of medical Internet research, 18(11). PMID: 27876688
Pity the insect that tumbles into a pitcher plant's trap. The slippery walls and waiting pool of water ensure it won't clamber back out. There's nothing left to do but wait to be digested.
The California pitcher plant (Darlingtonia californica) is also called the cobra lily for its curled-over shape that hides its exit from its victims. Unlike other pitcher plants, it doesn't fill its trap from above with rainwater but from below, drawing water up with its roots. But like others, it seems... Read more »
Armitage DW. (2016) Bacteria facilitate prey retention by the pitcher plant Darlingtonia californica. Biology letters, 12(11). PMID: 27881762
A scrappy mammal that lived alongside dinosaurs 66 million years ago may not have been huge, but it packed the most powerful bite ever recorded in any mammal, living or extinct, scientists say.... Read more »
Wilson, G., Ekdale, E., Hoganson, J., Calede, J., & Vander Linden, A. (2016) A large carnivorous mammal from the Late Cretaceous and the North American origin of marsupials. Nature Communications, 13734. DOI: 10.1038/ncomms13734
Old World monkeys detailed in the title of this post, specifically refers to a type of animal called a rhesus macaque who were the 'participants' of choice as detailed in a recent study by Destanie Rose and colleagues  looking at a concept called maternal immune activation (MIA).Those who followed this blog down the years will no doubt have seen me discuss MIA before in the context of autism and/or schizophrenia (see here for example). The basic theory is that whilst in-utero a........ Read more »
Rose, D., Careaga, M., Van de Water, J., McAllister, K., Bauman, M., & Ashwood, P. (2016) Long-term altered immune responses following fetal priming in a non-human primate model of maternal immune activation. Brain, Behavior, and Immunity. DOI: 10.1016/j.bbi.2016.11.020
Previously, on the story of MS2 in yeast: Last year, Roy Parker published a short article, in which he claimed that using the MS2 system in yeast causes the accumulation of 3′ RNA fragments, probably due to inhibition of mRNA … Continue reading →... Read more »
Heinrich, S., Sidler, C., Azzalin, C., & Weis, K. (2016) Stem loop RNA labeling can affect nuclear and cytoplasmic mRNA processing. RNA. DOI: 10.1261/rna.057786.116
The title of this post reflects the commentary published by Andrew Whitehouse  (open-access) discussing the meaning of the findings reported by Kung and colleagues  who quite categorically stated that there was: "No relationship between prenatal androgen exposure and autistic traits" in their study.OK, androgen exposure and psychology basically refers to the extreme male brain theory and autism which suggests that the so-called over-representation of autism in males is potentiall........ Read more »
Whitehouse AJ. (2016) Commentary: Are we expecting too much from the extreme male brain theory of autism? A reflection on Kung et al. (2016). Journal of child psychology and psychiatry, and allied disciplines, 57(12), 1463-1464. PMID: 27859346
Today I bring the findings reported by Chou and colleagues  (open-access available here) to the blogging table and how the research might of the Taiwan National Health Insurance Database (NHIRD) brought it's 'big data' ("n = 23 422 955") to bear on the question: what is the risk of developing schizophrenia where one or more first-degree or other relatives are affected?The answer: "Having an affected co-twin, first-degree relative, second-degree relative, or spouse was associate........ Read more »
Chou IJ, Kuo CF, Huang YS, Grainge MJ, Valdes AM, See LC, Yu KH, Luo SF, Huang LS, Tseng WY.... (2016) Familial Aggregation and Heritability of Schizophrenia and Co-aggregation of Psychiatric Illnesses in Affected Families. Schizophrenia bulletin. PMID: 27872260
When you're doing two things at once - like listening to the radio while driving - your brain organizes itself into two, functionally independent networks, almost as if you temporarily have two brains. That's according to a fascinating new study from University of Wisconsin-Madison neuroscientists Shuntaro Sasai and colleagues. It's called Functional split brain in a driving/listening paradigm
In referring to 'split brains' in their title, Sasai et al. are linking their work to the litera... Read more »
Sasai, S., Boly, M., Mensen, A., & Tononi, G. (2016) Functional split brain in a driving/listening paradigm. Proceedings of the National Academy of Sciences, 201613200. DOI: 10.1073/pnas.1613200113
by Kamil S. Jaron in genome ecology evolution etc
Exploration of variability of human genomes represents a key step in the holy grail of human genetics – to link genotypes with phenotypes, it also provides insights to human evolution and history. For this purpose Exome Aggregation Consortium (ExAC) have … Continue reading →... Read more »
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB.... (2016) Analysis of protein-coding genetic variation in 60,706 humans. Nature, 536(7616), 285-91. PMID: 27535533
One central concept in the OMA project and other
work we do to infer relationships between genes is that of Hierarchical
Orthologous Groups, or “HOGs” for the initiated.
We’ve written several papers on aspects pertaining to HOGs—how to infer
how to evaluate them, they being
increasingly adopted by orthology
resources, etc.—but there is
still a great deal of confusion as to what HOGs are and why they matter.
Natasha Glover, talented postdoc in the lab,........ Read more »
Altenhoff, A., Gil, M., Gonnet, G., & Dessimoz, C. (2013) Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs. PLoS ONE, 8(1). DOI: 10.1371/journal.pone.0053786
Boeckmann, B., Robinson-Rechavi, M., Xenarios, I., & Dessimoz, C. (2011) Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings in Bioinformatics, 12(5), 423-435. DOI: 10.1093/bib/bbr034
Sonnhammer, E., Gabaldon, T., Sousa da Silva, A., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P., Dessimoz, C., & , . (2014) Big data and other challenges in the quest for orthologs. Bioinformatics, 30(21), 2993-2998. DOI: 10.1093/bioinformatics/btu492
Where is the septum?
The term septum, when used in reference to the brain (it is a common anatomical term used to refer to a partition), indicates a subcortical structure in the forebrain that is found near the midline of the brain. The septum in humans can be separated into two structures: the septum pellucidum and septum verum. Each of these is sometimes........ Read more »
Sheehan, T., Chambers, R., & Russell, D. (2004) Regulation of affect by the lateral septum: implications for neuropsychiatry. Brain Research Reviews, 46(1), 71-117. DOI: 10.1016/j.brainresrev.2004.04.009
"Prescription drug use and polypharmacy rates among adults with ASD [autism spectrum disorder] are substantially higher than those in an age-, sex-, and race-matched cohort of adults without ASD."That sentence taken from the paper by Rini Vohra and colleagues  (open-access available here) is probably not likely to win any 'novel findings of the year' awards given the already quite voluminous data published on the medication use and autism (see here for example). What gives the ........ Read more »
Vohra R, Madhavan S, Sambamoorthi U, StPeter C, Poe S, Dwibedi N, & Ajmera M. (2016) Prescription Drug Use and Polypharmacy Among Medicaid-Enrolled Adults with Autism: A Retrospective Cross-Sectional Analysis. Drugs - real world outcomes. PMID: 27873285
"A total of 22 original papers that examined the association between folic acid supplementation in human pregnancy and neurodevelopment/autism were identified after the screening, with 15 studies showing a beneficial effect of folic acid supplementation on neurodevelopment/autism, 6 studies showed no statistically significant difference, while one study showed a harmful effect in > 5 mg folic acid supplementation/day during pregnancy."That rather long quote taken from the paper published by Y........ Read more »
Gao Y, Sheng C, Xie RH, Sun W, Asztalos E, Moddemann D, Zwaigenbaum L, Walker M, & Wen SW. (2016) New Perspective on Impact of Folic Acid Supplementation during Pregnancy on Neurodevelopment/Autism in the Offspring Children - A Systematic Review. PloS one, 11(11). PMID: 27875541
MicroRNAs (miRNAs) are non-coding RNAs, roughly 22 nucleotides in size that are central and negative regulators of gene expression. They exert their functions through base-pairing with the 3’UTR of mRNAs and block expression at the transcriptional and post-transcriptional levels, depending on the perfect or imperfect match in sequences between miRNAs and their target genes. miRNAs are central nodes in a variety of biological processes like cell proliferation, apoptosis, migration and dif........ Read more »
Parodi F, Carosio R, Ragusa M, Di Pietro C, Maugeri M, Barbagallo D, Sallustio F, Allemanni G, Pistillo MP, Casciano I.... (2016) Epigenetic dysregulation in neuroblastoma: A tale of miRNAs and DNA methylation. Biochimica et biophysica acta, 1859(12), 1502-1514. PMID: 27751904
Does non-ionizing radiation pose a health risk? Everyone knows that ionizing radiation, like gamma rays, can cause cancer by damaging DNA. But the scientific consensus is that there is no such risk from non-ionizing radiation such as radiowaves or Wi-Fi.
Yet according to a remarkable new paper from Magda Havas, the risk is real: it's called When theory and observation collide: Can non-ionizing radiation cause cancer?
There are a few remarkable things about this paper but chief among th... Read more »
Havas, M. (2016) When theory and observation collide: Can non-ionizing radiation cause cancer?. Environmental Pollution. DOI: 10.1016/j.envpol.2016.10.018
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
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