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  • January 21, 2016
  • 08:25 AM

A 5,300 Year Old Stomach Ache

by Bill Sullivan in The 'Scope

The fascinating history of the stomach ulcer bacteria H. pylori, which was recently found in Otzi, the 5,300 year old iceman.... Read more »

Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S.... (2012) Insights from characterizing extinct human gut microbiomes. PloS one, 7(12). PMID: 23251439  

Maixner, F., Krause-Kyora, B., Turaev, D., Herbig, A., Hoopmann, M., Hallows, J., Kusebauch, U., Vigl, E., Malfertheiner, P., Megraud, F.... (2016) The 5300-year-old Helicobacter pylori genome of the Iceman. Science, 351(6269), 162-165. DOI: 10.1126/science.aad2545  

  • January 21, 2016
  • 07:49 AM

A sewage-loving, foam-making, spaghetti-resembling bacterium

by Rosin Cerate in Rosin Cerate

While working on my doctorate, I lived for a time in an apartment just down the street from a small wastewater treatment facility. I never noticed a bad smell, but if I stayed up too late I'd end up having to fall asleep to the very low pitched rumble of gallons upon gallons of poop water being pumped into and out of large tanks. I tried not to think too hard about this, which tends to be difficult when you're, y'know, trying to fall asleep.Wastewater treatment facilities, or sewage treatment plants if you're old school and talking specifically about municipal (read: lots of poop) as opposed to industrial wastewater, are interesting places. Physical, chemical, and biological processes are put to work to clean up dirty water by removing particulate matter and harmful (or at least unpleasant) microbes and chemical compounds. As it works its way around a facility, wastewater typically experiences the thrills of sedimentation (essentially, grease floats and solids sink), filtration, chemical oxidation (breaking down organic compounds and killing microbes) by adding chlorine/ozone/bleach, and microbial growth (which removes organic compounds and inorganic nutrients).Wastewater as it progresses through a treatment facility (Source)One of the more interesting microscopic inhabitants of your typical sewage treatment plant is a bacterium called "Microthrix parvicella". The quotation marks are necessary because its status as a proper taxonomic name remains in flux. Nevertheless, this name is commonly used by those in the wastewater treatment industry. Getting the name thing sorted out requires the collection of sufficient information about the biochemical pathways utilized by the bacterium, which is difficult since it doesn't like living alone under controlled conditions in a laboratory (it grows very slowly and doesn't appear healthy). In sewage, "M. parvicella" usually appears as long, thin, and unbranched cell-filled threads with a propensity to coil up into tangles (it is often likened to cooked spaghetti), making it easy to spot under a microscope. When grown on its own in flasks on a lab bench, the threads often contain swollen and dying cells, indicating the bacterium is under considerable stress."M. parvicella" belongs to the phylum Actinobacteria, which includes a bunch of other rad thread-forming bacteria (e.g. Streptomyces). Remarkably, as far as we know, it's only found in wastewater treatment facilities. Where the heck did it live before these were invented? Folks in the wastewater treatment industry are interested in "M. parvicella" because of its contributions to bulking and foaming at treatment facilities all over the world. These physical changes to wastewater make it more difficult to separate out its solid and liquid components, which happens to be a key part of the whole treatment thing. Thus, facility operators are very interested in ways to control the growth of the bacterium.There's probably a bunch of  "M. parvicella" in this foam (Source)Unfortunately for them, "M. parvicella" is a resilient bit of microbial spaghetti. It's a chemoorganotroph, meaning it can extract energy and carbon building blocks from organic compounds (which just happen to be plentiful in sewage). Further, it's able to utilize both simple and complex forms of such compounds, helping it to compete with other microbes. Unlike many of its sewage neighbours, "M. parvicella" is okay with growing at low temperatures and under low oxygen concentrations. Due to its cold tolerance, it tends to be a major member of wintertime microbial communities inhabiting treatment facilities in temperate parts of the world. It's able to survive for months without access to oxygen (such conditions are known to develop in municipal treatment facilities), bouncing back quickly once a supply of the gas (in dissolved form) is restored. Aiding its survival, the bacterium is able to store lipids inside its cells as food for a rainy day.ReferencesMcIlroy SJ, Kristiansen R, Albertsen M, Karst SM, Rossetti S, Nielsen JL, Tandoi V, Seviour RJ, Nielsen PH. 2013. Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. ISME Journal 7(6):1161-1172. [Full text]Rossetti S, Tomei MC, Nielsen PH, Tandoi V. 2005. "Microthrix parvicella", a filamentous bacterium causing bulking and foaming in activated sludge systems: A review of current knowledge. FEMS Microbiology Reviews 29(1):49-64. [Full text]... Read more »

  • January 21, 2016
  • 02:51 AM

Pendulum swings... prenatal antidepressant exposure not linked to autism or ADHD

by Paul Whiteley in Questioning Answers

"Multiple studies have examined the risk of prenatal antidepressant exposure and risk for autism spectrum disorder (ASD) or attention-deficit hyperactivity disorder (ADHD), with inconsistent results."And..."These results suggest that prior reports of association between prenatal antidepressant exposure and neurodevelopmental disease are likely to represent a false-positive finding, which may arise in part through confounding by indication."'These results' refers to the findings reported by Castro and colleagues [1] (open-access available here) who looked at the records of over 1200 children diagnosed with ASD and ~1700 children diagnosed with ADHD compared with over 3400 and 3700 controls respectively with regards to antidepressant exposure during pregnancy and maternal antidepressant use before pregnancy. Based on exposures identified "using e-prescribing data in the EHR [electronic health records], both inpatient and outpatient, which record number of pills, frequency and refill number, allowing calculation of exposure period" researchers were, with reasonable confidence, able to test the idea that a diagnosis of ASD or ADHD might be elevated following prenatal exposure to said pharmaceutics.The headline that most media discussing this study picked up on was the lack of any significant association between antidepressant use during pregnancy and risk of offspring autism or ADHD. This finding kinda contrasts with other recent independent reports that have been covered on this blog (see here). Indeed the authors - including one Isaac Kohane (see here) - suggest that their results, bearing in mind certain limitations, highlight how 'false-positive' might indeed be a good description of some of the previous data in this area.But just before any sweeping generalisations are made about this class of pharmaceutic being 'off the hook' there were some other potentially important findings also reported by Castro et al. To quote once again: "For both ASD and ADHD, pre-pregnancy antidepressant use was associated with greater risk, even after adjustment for maternal major depression." The risk reported was significant insofar as what it might mean for offspring autism and/or ADHD and also how "the requirement for maternal antidepressant treatment, rather than the medication itself, may be associated with risk for neurodevelopmental disorders in offspring".As I've discussed before, the idea that antidepressant use during pregnancy might be linked to offspring developmental outcomes is a complicated area. That such medicines use is not generally entered into lightly is something to bear in mind given what depression can do to a person and those around them. I cannot readily account for the discrepancy between these and other reports on this topic outside of the idea that the question of a connection or not may not be as simple as 'yes' or 'no' but rather a slightly more convoluted story where genetics and other more 'environmental' factors might play some role. The idea that there may be specific phenotypes of autism associated with such medication use has received a boost in other independent studies [2] looking at other medicines. I suppose such confusion kinda sums up autism research when it comes to questions of such exposure and the range of pharmaceutics that have been correlated with offspring risk (see here and see here).Music: Björk - It's Oh So Quiet. Shhh.----------[1] Castro VM. et al. Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. Transl Psychiatry. 2016 Jan 5;6:e708.----------Castro VM, Kong SW, Clements CC, Brady R, Kaimal AJ, Doyle AE, Robinson EB, Churchill SE, Kohane IS, & Perlis RH (2016). Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. Translational psychiatry, 6 PMID: 26731445... Read more »

  • January 20, 2016
  • 02:29 PM

Overwhelmed and depressed? Well, there may be a connection

by Dr. Jekyll in Lunatic Laboratories

Ever feel overwhelmed when you are depressed, well the good news is it isn't just you, the bad news is it's probably your brain. Regions of the brain that normally work together to process emotion become decoupled in people who experience multiple episodes of depression, neuroscientists report. The findings may help identify which patients will benefit from long term antidepressant treatment to prevent the recurrence of depressive episodes.

... Read more »

Jacobs, R., Barba, A., Gowins, J., Klumpp, H., Jenkins, L., Mickey, B., Ajilore, O., Peciña, M., Sikora, M., Ryan, K.... (2016) Decoupling of the amygdala to other salience network regions in adolescent-onset recurrent major depressive disorder. Psychological Medicine, 1-13. DOI: 10.1017/S0033291715002615  

  • January 20, 2016
  • 11:00 AM

WATCH: Persistence Pays Off For Squirrels

by Jenny Ludmer in Rooster's Report

Surely you can expect that the ubiquitous furry creature — a regular at your public park — is a master problem-solver. After all, squirrels must continuously stockpile acorns and occasionally raid bird feeders, all while playing in traffic and dodging hairy little beasts on leashes. But what personality characteristic most drives these exceptional abilities: persistence or flexibility? ... Read more »

  • January 20, 2016
  • 09:36 AM

Video Tip of the Week: LilBUBome sequencing project

by Mary in OpenHelix

Ok, the phrase “Lil Bub is an American celebrity cat….” is not the way I start a lot of blog posts. I enjoy cats on the internet as much as anyone–but their relevance to science is not one of the reasons, usually. But the Lil Bub genome project changes that. A popular, crowd-funded, genome sequencing project […]... Read more »

  • January 20, 2016
  • 06:55 AM

Pump Up Your Brain

by Mark Lasbury in As Many Exceptions As Rules

Exercising makes you smarter! Preadolescents who begin exercising score better on a cognitive assessment not unlike an IQ test. They also perform better on a math test, even though no additional math instruction was given. But to maximize the increase in neural plasticity, you have to exercise several times a week for months. The weirdest part – different types of exercise alter different neurotrophins, so to be your smartest, you need to do aerobic training and resistance training. ... Read more »

  • January 20, 2016
  • 06:06 AM

Dear kids, don't eat that falling snow...

by Usman Paracha in SayPeople

Main Point:

Snow falling in urban areas could be toxic for human beings due to the presence of dangerous chemicals and pollutants coming from cars and industries.

Published in:

Environmental Science: Processes & Impacts

Study Further:

Beauty can be dangerous and recent research is showing the same, i.e. beautiful and pure snowflakes can be dangerous. Researchers have found that snowflakes are not as clean as they may appear. They reported that snow falling, especially in cities, has the ability to absorb toxic as well as carcinogenic chemicals and pollutants released from car exhausts. Moreover, the interaction between those dangerous chemicals and snows can also produce new types of toxic chemicals.

Snowflakes have different types of surfaces, some of which are able to absorb particulate pollutants and gaseous materials. Researchers simulated the research in a “snow chamber”, and found that snow can absorb pollutant particles in the air surrounding the snow. This research shows two important points; One is that it is better for people living in snowy environment as it could help in purification of environment, and the other is that the level of pollutants can rise, when snow melts. So, researchers and experts of climate have to consider this public health threat.

“The alteration of exhaust aerosol size distributions at freezing temperatures and in the presence of snow, accompanied by changes of the organic pollutant content in snow, has potential to alter health effects of human exposure to vehicle exhaust” researchers wrote in the paper.

This research also shows that you have to forbid your kids from eating snowflakes falling in urban areas.


Nazarenko, Y., Kurien, U., Nepotchatykh, O., Rangel-Alvarado, R., & Ariya, P. (2016). Role of snow and cold environment in the fate and effects of nanoparticles and select organic pollutants from gasoline engine exhaust Environ. Sci.: Processes Impacts DOI: 10.1039/C5EM00616C... Read more »

  • January 20, 2016
  • 03:11 AM

Middle ear infections and autism

by Paul Whiteley in Questioning Answers

I'm gonna be fairly brief today in drawing your attention to the paper published by Daniel Adams and colleagues [1] reporting that: "Children with ASD [autism spectrum disorders] are more likely to have middle ear infections and otitis-related complications."The results, which we've known were coming (see here), detail findings based on a retrospective case-cohort study where the health insurance records of children of US military families were initially screened for the presence of autism or an ASD and then further screened for ICD-9-CM diagnostic codes relevant to acute otitis media and related diagnoses. The supplementary material provided alongside the article gives further details (see here).Alongside the findings of an elevated rate of acute otitis media (AOM) among children diagnosed with autism were various other details including a higher rate of complications following AOM such as mastoiditis - affecting the mastoid bone behind the ear - and the requirement for a mastoidectomy. The surgical reconstruction of the eardrum (tympanoplasty) was also more frequently noted for the autism group versus the non-autism controls. The authors conclude that quite a bit more research is required in this area alongside "highlighting the importance of routine middle ear examinations and close attention to hearing impairment in this population."This is interesting work. For many years I've heard about how quite a few children on the autism spectrum had a history of early ear infections that were typically followed by quite an aggressive schedule of antibiotic use. Indeed, on one of the previous blogging occasions when I've mentioned ear infections and autism it was to speculate on the double-edged sword that might be the [early repeated] use of antibiotics with [some] autism in mind (see here). That 'association' remains as relevant today as it did during earlier descriptions [2] playing into the various emerging gut bacteria studies of autism.I have only a few more things to add. First is the idea that screening for middle ear infections might be an important issue for children on the autism spectrum. I can't argue with that; and indeed added to the requirement for screening other sensory gateways such as the eyes (see here), the evidence is accumulating for preferential services to be offered. Second is the idea that recurrent otitis media might show some connection with aspects of sleep too [3] such that issues such as sleep apnoea occurring alongside autism (see here) might also be something to look out for. Finally is the need for quite a bit more research on what happens to autistic symptoms when ear infections are finally diagnosed and treated. Take for example the case report detailed by Kazuhiro Tajima-Pozo and colleagues [4] and the suggestion that surgical correction of the "middle ear for repetitive otitis" correlated with "an improvement in autistic behaviours". One wonders how many other children have shown or might show similar effects and what the possible mechanism(s) could be...Music: Alanis Morissette - Ironic.----------[1] Adams DJ. et al. Otitis Media and Related Complications Among Children with Autism Spectrum Disorders. J Autism Dev Disorders. 2016. Jan 6.[2] Bolte ER. Autism and Clostridium tetani. Med Hypotheses. 1998 Aug;51(2):133-44.[3] Gozal D. et al. Prevalence of Recurrent Otitis Media in Habitually Snoring School-Aged Children. Sleep medicine. 2008;9(5):549-554.[4] Tajima-Pozo K. et al. Otitis and autism spectrum disorders. BMJ Case Rep. 2010 May 6;2010. pii: bcr1020092351.----------Adams, D., Susi, A., Erdie-Lalena, C., Gorman, G., Hisle-Gorman, E., Rajnik, M., Elrod, M., & Nylund, C. (2016). Otitis Media and Related Complications Among Children with Autism Spectrum Disorders Journal of Autism and Developmental Disorders DOI: 10.1007/s10803-015-2689-x... Read more »

Adams, D., Susi, A., Erdie-Lalena, C., Gorman, G., Hisle-Gorman, E., Rajnik, M., Elrod, M., & Nylund, C. (2016) Otitis Media and Related Complications Among Children with Autism Spectrum Disorders. Journal of Autism and Developmental Disorders. DOI: 10.1007/s10803-015-2689-x  

  • January 19, 2016
  • 11:45 PM

A year in books: Neanderthals to the National Cancer Act to now

by Artem Kaznatcheev in Evolutionary Games Group

A tradition I started a couple of years ago is to read at least one non-fiction book per month and then to share my thoughts on the reading at the start of the following year. Last year, my dozen books were mostly on philosophy, psychology, and political economy. My brief comments on them ended up […]... Read more »

Monge, J., Kricun, M., Radovčić, J., Radovčić, D., Mann, A., & Frayer, D. (2013) Fibrous Dysplasia in a 120,000 Year Old Neandertal from Krapina, Croatia. PLoS ONE, 8(6). DOI: 10.1371/journal.pone.0064539  

  • January 19, 2016
  • 02:14 PM

Can you trust your gut when public speaking?

by Dr. Jekyll in Lunatic Laboratories

There is good news for frequent public speakers. New research shows that individuals have the ability to quickly and accurately identify a crowd's general emotion as focused or distracted, suggesting that we can trust our first impression of a crowd's mood.

... Read more »

  • January 19, 2016
  • 12:20 PM

What Is Citizen Science Good For? Birds, Butterflies, Big Data

by Elizabeth Preston in Inkfish

No matter how unhip you feel wearing waders or hauling a butterfly net, citizen science is cool. That's obvious from the boom in online projects that let you count penguins, hunt planets, or identify animals in the Serengeti, as well as the scientific papers using these data. Now researchers in Sweden have looked into the science of citizen science itself. How much of this volunteer research is really happening, they asked—and what is it producing?

Christopher Kullenberg and Dick Kasperow... Read more »

  • January 19, 2016
  • 04:29 AM

Get your (autism genetics) kicks on root 66?

by Paul Whiteley in Questioning Answers

With the ever-increasing volumes of research being published in the peer-reviewed domain these days, one sometimes has to be a little creative to ensure that your research paper stands out and is not lost in the scientific noise. Quite a good way of getting noticed is to make sure that your paper catches the attention of your reader base. Y'know, give it a snappy title; something that social media might pick up on...So it was that my attention was taken when coming across the paper by Diaz-Beltran and colleagues [1] (open-access) titled: 'A common molecular signature in ASD gene expression: following Root 66 to autism'. Root 66 and Route 66 eh?The 'root 66' appearing in the title of the Diaz-Beltran paper actually refers to the results of an "integrated systems biology analysis of 9 independent gene expression experiments covering 657 autism, 9 mental retardation and developmental delay and 566 control samples to determine if a common signature exists and to test whether regulatory patterns in the brain relevant to autism can also be detected in blood." I might add that those are the authors words and not my own.Including a familiar name on the authorship list - one Dennis Wall, he of 'boiling down ADOS' and 'screening triage by YouTube' fame - researchers used various automated statistical methods to see whether "a signature of autism can be found in the blood that might be a molecular echo of autism-related regulatory impairment in the brain." The identified signature included a collection of 66 genes based on their examination of "27 case–control biosets of 9 independent experiments" - the root 66 cluster.That root 66 cluster was subsequently tested to see what genes might be connected and some data about "related biological functions" across various conditions including autism. I really can't provide anything more detailed about the hows and whys of this process as I am fast approaching the limits of my knowledge in this area. Suffice to say that there was some previous work on some of the root 66 genes with autism in mind (4 genes) and quite a few others "have been shown to interact directly with known autism candidates or have been implicated in other autism-related neurological disorders."When it came to looking at what those root 66 genes might be doing (functionally), the authors reported that quite a few of the genes were involved in one of three processes: (1) brain growth and development with a side-order of "neuroendocrine activity", (2) nervous system inflammation and loss of neurological functions, and (3) neurodegeneration "and damage of the nervous system." In that last category the authors made an important point that genes thought to be connected with cases of autism are generally not 'autism-specific' in terms of their possible connections with other conditions and labels. Without scaremongering or wishing to equate autism with cancer, some of the root 66 genes have been mentioned with various cancers in mind; something that might be important for at least some people on the autism spectrum (see here). On the basis of their collected studies, they concluded that: "the Root 66 cluster is non-random and likely plays a role unique to autism."It is important to understand that whilst this is an important piece of research, further independent validation of the root 66 cluster is required before anyone gets ahead of themselves. As per other examples where genetic 'markers' have been talked about (see here), replication is the name of the scientific game bearing in mind how wide the autism spectrum is (the autisms) and the important idea that the label rarely appears in some sort of diagnostic vacuum (see here). I don't believe that we are witnessing a genetic profile for [all] autism just yet...Before I go, I do also want to comment on at least one area where the genetics of autism seems to be heading: inflammation. As per other research occasions, inflammation and immune function seem to be quite a regular feature of autism genetics studies (see here and see here) and the analysis of more functional biological processes (see here for example). Added to some interesting data on a possible role for those chemical messengers called cytokines with autism in mind (see here) and it looks to me like we have further evidence for how immune function and behaviour might have some interesting connections pertinent to at least some autism (see here).Music: Amy Winehouse - Back To Black.----------[1] Diaz-Beltran L. et al. A common molecular signature in ASD gene expression: following Root 66 to autism. Translational Psychiatry. 2016. 6, e705.----------Diaz-Beltran L, Esteban FJ, & Wall DP (2016). A common molecular signature in ASD gene expression: following Root 66 to autism. Translational psychiatry, 6 PMID: 26731442... Read more »

  • January 18, 2016
  • 04:07 PM

Thwarting abnormal neural development with a new mutation

by Dr. Jekyll in Lunatic Laboratories

Researchers at the RIKEN Brain Science Institute in Japan have discovered how to reverse the abnormal axonal development characteristic of CFEOM3, a congenital disease that affects the muscles that control eye movements. The work shows how creating a specific mutation rescued abnormal axonal growth in the developing mouse brain.

... Read more »

Minoura, I., Takazaki, H., Ayukawa, R., Saruta, C., Hachikubo, Y., Uchimura, S., Hida, T., Kamiguchi, H., Shimogori, T., & Muto, E. (2016) Reversal of axonal growth defects in an extraocular fibrosis model by engineering the kinesin–microtubule interface. Nature Communications, 10058. DOI: 10.1038/ncomms10058  

  • January 18, 2016
  • 11:29 AM

Catch Him If You Can

by Miss Behavior in The Scorpion and the Frog

By Caitlin LockardWhen playing Frisbee with your dog, do you ever wonder how they have the ability to catch it so effortlessly? The art of being able to figure out where something like a Frisbee is headed requires some crazy math skills. Ostracods are one kind of animal that puts their wicked math skills to the test while finding a mate.The image above of a female ostracod was provided by Trevor Rivers.You’ve never heard of an ostracod you say? Ostracods are small crustaceans, which basically means they have lots of legs and are covered by a hard shell. Male ostracods can be seen roaming throughout the ocean trying to enchant females with light displays. Typically, just after sunset, males begin their light displays, which consist of two phases. The first phase is the bright phase, which is short. The goal here is to signal to the female that “I’m here, single (except all my buddies that I brought with me of course) and ready to mingle”. The second phase is where males spiral up in a helix while pulsing repeatedly. This phase is much dimmer and is used by females to choose a mate. But exactly how do female ostracods go about catching the moving and light-pulsing man of her dreams? Scientists, Trevor Rivers of the University of Kansas and Jim Morin of Cornell University, set off to explore if female ostracods try to intercept the moving and pulsing males or if they just chase them. In order to conduct this experiment, immature female ostracods were collected off the shore of Southwater Caye in Belize. After catching the ostracods, females were put into tanks and raised to maturity, ensuring that all the females were sexually mature virgins. Rivers and Morin put an LED light behind the different tanks in order to mimic an actual mating display. The LED light looked like a string of Christmas lights pulsing from bottom to top, mimicking the males’ helical light display. In the control group, there was an LED light placed behind the tank, however it was turned off. The duo questioned whether or not the LED light show was able to mimic the display put on by male ostracods. Also, they questioned how females respond to the males’ display by measuring the height at which females intercepted the LED light, how straight of a line the female swam in, if the female swam at an angle, and what direction the female swam in. Check out a video here.The scientists found that the LED light was able to mimic the helical phase that male ostracods put on well enough for the females to respond. Females in the control group merely swam at the same height, as there was no reason for her to waste her energy with no “male” around. However, females in the experimental group had to think on their feet to figure out where their male crush was heading. They swam directly toward but slightly above the “male” than when there was no “mate” around. If the female merely headed to the same spot where her “male” previously was, she would miss him. Instead, she had to anticipate where he was going next and head that direction. What’s the moral of the story here? If you’re a female ostracod, your man will always be on the move, so you better have some gnarly geometry skills in order to track him down.Work Cited: Rivers, T., & Morin, J. (2013). Female ostracods respond to and intercept artificial conspecific male luminescent courtship displays Behavioral Ecology, 24 (4), 877-887 DOI: 10.1093/beheco/art022... Read more »

  • January 18, 2016
  • 09:00 AM
  • 1 view

Introduction to CellMiner and rcellminer

by Augustin Luna in Lunean

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others. The purpose of the CellMiner project has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

The CellMiner project makes much of its work transparent in the community by providing data downloads for the datasets used by the project. The rcellminer R package adds to this effort by providing additional functionality to help R users access the CellMiner data, including both NCI-60 molecular profiling and drug response data. The package allows programmatic access to CellMiner's gene and protein expression, copy number, whole exome mutations, as well as activity data for ∼21K compounds, with information on their structure, mechanism of action and repeat screens. In addition to the provided data, R functions simplify the visualization of compound structures, drug compound activity patterns and molecular feature profile. Lastly, several web applications have been embedded into the rcellminer R package that allow interactive data exploration. ... Read more »

Luna A, Rajapakse VN, Sousa FG, Gao J, Schultz N, Varma S, Reinhold W, Sander C, & Pommier Y. (2015) rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. Bioinformatics (Oxford, England). PMID: 26635141  

  • January 18, 2016
  • 04:29 AM

Supporting siblings of children with autism too

by Paul Whiteley in Questioning Answers

A weekend not wasted...The idea that a diagnosis/label of autism may have repercussions for quite a few more people than just the person diagnosed is not a new one.Without trying to generalise nor stigmatise, the process of working up to and receiving a diagnosis on the autism spectrum can often have profound consequences for family life. Parents typically shoulder quite a lot of the additional duties that follow from a diagnosis (and indeed before diagnosis) but other family members also have to play their part. When it comes to the possible 'impact' of receipt of an autism diagnosis on some of those other family member, science is starting to come around to the idea that siblings in particular, might need a little more support.So it was found in the paper by Brian Lovell & Mark Wetherell [1] who reported findings based on the examination of "the psychophysiological impact of childhood ASD [autism spectrum disorder] on siblings." Looking at a variety of measures including those measuring depressive symptoms and cortisol levels, researchers compared values for "25 siblings of children with ASD (and their mothers) and a control group of 20 siblings of neuro-typical children (and their mothers)." They found that depressive symptoms were elevated for the ASD sibling group but when it came to cortisol measurements "groups were comparable on all cortisol indices." They concluded by suggesting that more needs to be done to tackle the "greater emotional problems and overall depressive symptoms" noted in the ASD sibling group. Cortisol, I might add, has been talked about with autism in mind before (see here) bearing in mind 'issues' emerging as to when the best time for collection should be with autism in mind [2].There are a couple of ways that such results can be interpreted. One could argue that the increased frequency of 'emotional issues' and depressive symptoms noted in the ASD sibling group might well be associated with their sibling ASD label and much of what comes with it. Again avoiding any sweeping stigmatisation of autism, this is a serious matter and reiterates how the impact of autism goes well beyond that of personal experience when it comes to affecting family and other loved ones.The other way one could interpret this data is by suggesting that within the scope of the broader autism phenotype (BAP) - that is, the idea that around the diagnostic edges of autism there may be a spectrum of more subtle presentations (see here) - [some] siblings may already be more prone to emotional and/or depressive issues on the basis of how depression for example, shows some pretty strong links to autism (see here for example). Without any psycho-babble explanations, one could foresee how an increased tendency towards depressive symptoms or depression might be to some degree compounded by the lived experience of having a sibling diagnosed with ASD; particularly if and when there is significant disruption to typical family life. I might also acknowledge that autism does not normally reside in some sort of diagnostic vacuum (see here) so one has to be mindful that other behaviours outside of autism might also be contributory to any additional family stress.Irrespective of the whys and wherefores, the idea that other family members may require additional support as well as children/adults diagnosed with an ASD is paramount. As I've previously discussed on this blog, support can take many guises (see here) as this authorship team have previously discussed [3]; some of which could be transferable to siblings too. Other research has looked at issues such as family adaptation [4] and I'm minded to bring in the concept of resilience too. That also having a sibling diagnosed with ASD may be a significant influence on career choices of unaffected siblings (unaffected in terms of symptom presentation) is an additional variable to take into account, save any charges of me painting a too one-sided, negative picture of the possible familial effects of autism.The picture included in this post by the way, represents a nearly full weekend attempt by some of my brood to muster enough 'snow' to put together this marvellous fellow. Don't you just love winter?----------[1] Lovell B. & Wetherell MA. The psychophysiological impact of childhood autism spectrum disorder on siblings. Res Dev Disabil. 2015 Dec 22;49-50:226-234.[2] Sharpley CF. et al. Is afternoon cortisol more reliable than waking cortisol in association studies of children with an ASD? Physiol Behav. 2015 Dec 21. pii: S0031-9384(15)30217-1.[3] Lovell B. et al. With a little help from my friends: psychological, endocrine and health corollaries of social support in parental caregivers of children with autism or ADHD. Res Dev Disabil. 2012 Mar-Apr;33(2):682-7.[4] O'Brien S. Families of Adolescents with Autism: Facing the Future. J Pediatr Nurs. 2015 Dec 19. pii: S0882-5963(15)00352-8.----------Lovell B, & Wetherell MA (2015). The psychophysiological impact of childhood autism spectrum disorder on siblings. Research in developmental disabilities, 49-50, 226-234 PMID: 26720849... Read more »

  • January 17, 2016
  • 10:11 PM

A Primer on Linear Regression and its Associated Misconceptions

by Geoffrey Hannigan in Prophage

I wanted to start the year off with post about math. I know, I know, math is an intimidating way to start the year, but don't run off yet! I swear that this will be painless and we will even learn something new! We are going to keep things simple and focus on an elegant paper that presents some misconceptions about a complicated topic. This topic is multiple linear regression...... Read more »

  • January 17, 2016
  • 02:37 PM

Little Brown Bat

by Jason Organ in Eatlemania!

The Eatles have recently polished off the soft tissue remains of a little brown bat. Come read about this fascinating animal.... Read more »

Dzal YA, & Brigham RM. (2013) The tradeoff between torpor use and reproduction in little brown bats (Myotis lucifugus). Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology, 183(2), 279-88. PMID: 22972361  

Fenton, M., & Barclay, R. (1980) Myotis lucifugus. Mammalian Species, 1. DOI: 10.2307/3503792  

Veselka, N., McGuire, L., Dzal, Y., Hooton, L., & Fenton, M. (2013) Spatial variation in the echolocation calls of the little brown bat ( ) . Canadian Journal of Zoology, 91(11), 795-801. DOI: 10.1139/cjz-2013-0094  

  • January 17, 2016
  • 02:31 PM

Nanodevice, build thyself

by Dr. Jekyll in Lunatic Laboratories

As we continue to shrink electronic components, top-down manufacturing methods begin to approach a physical limit at the nanoscale. Rather than continue to chip away at this limit, one solution of interest involves using the bottom-up self-assembly of molecular building blocks to build nanoscale devices.

... Read more »

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