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  • December 8, 2016
  • 09:14 AM
  • 20 views

What are Hierarchical Orthologous Groups (HOGs)?

by Christophe Dessimoz in Open Reading Frame


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
them,
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 »

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  

  • December 8, 2016
  • 05:59 AM
  • 17 views

Know your brain: Septum

by neurosci in Neuroscientifically Challenged

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 »

  • December 8, 2016
  • 04:51 AM
  • 25 views

Prescription medication use and autism: good medicines management required

by Paul Whiteley in Questioning Answers

"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 [1] (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 »

  • December 7, 2016
  • 12:36 PM
  • 36 views

Pregnancy folic acid and offspring autism systematically reviewed

by Paul Whiteley in Questioning Answers

"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 »

  • December 7, 2016
  • 08:00 AM
  • 28 views

MicroRNA expression is regulated by DNA methylation: a complex cascade of gene regulation events

by Barbara Banelli in EpiBeat

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  

  • December 6, 2016
  • 02:29 PM
  • 33 views

Fun With Non-Ionizing Radiation

by Neuroskeptic in Neuroskeptic_Discover

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 »

  • December 6, 2016
  • 12:20 PM
  • 64 views

Finding the Best Personalized Cancer Therapy

by Agnese Mariotti in United Academics

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  

  • December 6, 2016
  • 03:05 AM
  • 64 views

Infections treated with anti-infective agents linked to schizophrenia?

by Paul Whiteley in Questioning Answers

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 [1] (a name that has appeared on this blog before) who concluded that: "Infections treated with anti-infect........ Read more »

  • December 5, 2016
  • 02:58 AM
  • 89 views

Double-blind randomised, placebo-controlled trial of vitamin D in autism

by Paul Whiteley in Questioning Answers

It was inevitable ("it is your destiny") that I would formulate a post about the paper published by Khaled Saad and colleagues [1] 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  

  • December 4, 2016
  • 03:34 PM
  • 119 views

Do Synapses Really Store Memories?

by Neuroskeptic in Neuroskeptic_Discover

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 »

  • December 3, 2016
  • 04:23 AM
  • 118 views

Parent-mediated interventions for young children with autism meta-analysed

by Paul Whiteley in Questioning Answers

Do not mess with  Lois.Today I'm posting on the topic of the paper by Rose Nevill and colleagues [1] 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 »

  • December 2, 2016
  • 08:30 PM
  • 70 views

This Month in Blastocystis Research (NOV 2016)

by Christen Rune Stensvold in Blastocystis Parasite Blog

Lab protocols on Blastocystis culture, cryopreservation, and subtyping are now available in Wiley Online Library.... Read more »

  • December 2, 2016
  • 01:40 PM
  • 122 views

Parkour Athletes Teach Scientists about Swinging Apes

by Elizabeth Preston in Inkfish



"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 »

  • December 2, 2016
  • 07:48 AM
  • 117 views

Case studies: BHD syndrome associated with pulmonary malformation and with lung neoplasm

by Joana Guedes in BHD Research Blog

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  

  • December 2, 2016
  • 06:18 AM
  • 108 views

Friday Fellow: Indian shot

by Piter Boll in Earthling Nature

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 »

  • December 2, 2016
  • 03:18 AM
  • 143 views

The prebiotic galactooligosaccharide (B-GOS) and autism: just add to poo(p)

by Paul Whiteley in Questioning Answers

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 [1] (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 »

  • December 1, 2016
  • 02:57 AM
  • 135 views

Dietary fibre deficiency and gut barrier integrity

by Paul Whiteley in Questioning Answers

"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 [1] meriting an editorial in the publishing journal [2] 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  

  • November 30, 2016
  • 07:00 AM
  • 107 views

A Better Model System for Ovarian Cancer: Patient-derived tumor xenografts (PDXs) are suitable for epigenetic methylome-based cancer research

by Tushar Tomar in EpiBeat

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 »

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  

  • November 30, 2016
  • 03:10 AM
  • 118 views

Restless leg syndrome in parents of children with autism

by Paul Whiteley in Questioning Answers

The findings reported by Maureen Russell and colleagues [1] 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  

  • November 30, 2016
  • 02:00 AM
  • 112 views

Chemical games and the origin of life from prebiotic RNA

by Eric Bolo in Evolutionary Games Group

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  

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