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  • September 11, 2015
  • 03:16 PM

An antibody that can attack HIV in new ways

by Dr. Jekyll in Lunatic Laboratories

Proteins called broadly neutralizing antibodies (bNAbs) are a promising key to the prevention of infection by HIV, the virus that causes AIDS. bNAbs have been found in blood samples from some HIV patients whose immune systems can naturally control the infection. These antibodies may protect a patient’s healthy cells by recognizing a protein called the envelope spike, present on the surface of all HIV strains and inhibiting, or neutralizing, the effects of the virus. Now Caltech researchers have discovered that one particular bNAb may be able to recognize this signature protein, even as it takes on different conformations during infection–making it easier to detect and neutralize the viruses in an infected patient.... Read more »

  • September 11, 2015
  • 12:34 PM

Perfect Pitch: Is this for real?

by Henkjan Honing in Music Matters

Absolute Pitch (AP) or Perfect Pitch, as some prefer to call it, is common throughout the animal world, and dogs are no exception (Levitin & Rogers, 2005).*... Read more »

Levitin, D., & Rogers, S. (2005) Absolute pitch: perception, coding, and controversies. Trends in Cognitive Sciences, 9(1), 26-33. DOI: 10.1016/j.tics.2004.11.007  

  • September 11, 2015
  • 10:04 AM

You Are an Expert Tweeter

by Elizabeth Preston in Inkfish

Do you tweet formally for a wide audience (and use abbrevs 4 ur peeps)? You may not realize you're doing it. But a study of  hundreds of thousands of tweets showed that Twitter users subtly tailor their language based on who's reading.

Twitter "is a single platform that serves a huge range of communicative functions," says Jacob Eisenstein, who leads a computational linguistics lab at Georgia Tech. With the same 140-character messages, a user can participate in a mass social movement or g... Read more »

Pavalanathan, U., & Eisenstein, J. (2015) AUDIENCE-MODULATED VARIATION IN ONLINE SOCIAL MEDIA. American Speech, 90(2), 187-213. DOI: 10.1215/00031283-3130324  

  • September 11, 2015
  • 09:00 AM

Upcoming BHD and Upstate Kidney Cancer Symposium

by Danielle Stevenson in BHD Research Blog

On September 23-26th the Sixth BHD and First Upstate Kidney Cancer Symposium will be taking place in Syracuse, New York. Hosted by Dr Medhi Mollapour and Professor Gennady Bratslavsky of the Upstate Medical University (both also presenting), it will focus on scientific and clinical developments in BHD and renal cell cancer.... Read more »

  • September 11, 2015
  • 02:38 AM

School and autism: anxiety, aggression and making things easier

by Paul Whiteley in Questioning Answers

Today's post is a bit of a mash-up insofar as including two papers into (brief) discussions. The first paper is from Pamela Gaye Ambler and colleagues [1] who bring in a number of important issues associated with quite a bit of autism: anxiety and aggression during adolescence and how this can manifest during school time. The second paper from Will Mandy and colleagues [2] (open-access available here) provides some interesting discussion on a "manualised intervention" called STEP-ASD designed to "facilitate successful school transition for people with ASD via intervention on the child’s educational environment."The Ambler paper details results for just over 100 high-school students (here in Blighty we might call them secondary school pupils) aged between 12-18 years of age. Half (n=52) were "students with ASDs [autism spectrum disorders], without intellectual disability" and the others were asymptomatic controls (from an autism point of view). Self- and teacher-reported measures of anxiety and anger were completed to investigate any link between the two concepts.The results suggested that: "Students with ASDs who attend mainstream high schools reported higher levels of anxiety and reactive anger than their peers, were reported by their teachers to engage in more aggressive behaviours, and were at higher risk of being suspended from school." Further that: "social anxiety is a significant moderator of the relationship between autism and physical aggression." In other words, elevated levels of anxiety seemed to be associated with higher levels of physical aggression.The Mandy paper looked at the "feasibility and efficacy" of STEP-ASD for a sample of children with ASD (N=37) transitioning from primary school to secondary school. The study design took the form of a "non-randomised (quasi-experimental) controlled trial" where compared with a management as usual control group (20/37), STEP-ASD was delivered to 17 students and before and after measures of emotional and behavioural problems analysed.The results suggested that there may indeed be more to see when it comes to STEP-ASD insofar as: "Children receiving STEP-ASD (n = 17) showed a large... reduction in school-reported emotional and behavioural difficulties, whereas controls (n = 20) showed a slight increase." Authors also noted that when it came to a measure of hyperactivity on one of the outcome measures used (the SDQ) "the STEP-ASD group, but not the control group, showed a large reduction in symptoms across the transition." Ergo: "These encouraging findings suggest the value of STEP-ASD as a low-intensity intervention for reducing problem behaviours and distress in children with autism spectrum disorder as they transition to mainstream secondary school."There are several features of these two studies that perhaps unite them. First is the realisation that school can be a significant source of stress and distress for young people on the autism spectrum. I don't want to get too heavily involved in any debates about the rights and wrongs of mainstream vs. specialised provision (or even home schooling) when it comes to education and autism, but the various moves to make 'inclusion' a universal feature of education do not always solve all of the issues that they are meant to tackle.Second, is the idea that the core features of autism - the dyad as it is now known in some diagnostic circles - might not always be the the core issues when it comes to schooling and autism. I refer of course to the growing interest in the concept of anxiety comorbid to many cases of autism and the often profound 'disability' that it can cause within settings like school. The Ambler paper highlights how anxiety might correlate with issues such as aggression (bearing in mind that much more work needs to be done on how this relationship manifests). In previous posts, I've talked about how aggression when present alongside autism in the school setting tends to be more 'reactive' and spontaneous than anything else (see here) so this would perhaps tally with the idea of a connection with anxiety in the here-and-now.Finally, as per the Mandy report, is the idea that there may be strategies that can be put in place to help students during important times like school transition where anxiety levels can increase as a result of things like a change of school environment and perhaps a fear of the unknown (an intolerance of uncertainty?). The onus in that case is on both providing information (to all parties concerned) and to some extent, tailoring the school experience to that of the student's individual needs. I'd also like to think that there are other ways and means that the transition stage and indeed, day-to-day schooling can be adapted to individuals (buddy systems, time-out and/or quiet zones, flexibility in curriculum delivery, targeting bullying, effective use of classroom assistants, see here for more.) to further improve outcomes and importantly, make school work for those on the spectrum as it is supposed to for those not on the autism spectrum. This includes the idea that 'choice-making' could also be incorporated [3] into proceedings.Music: FFS - Johnny Delusional.----------[1] Ambler PG. et al. Anxiety and aggression in adolescents with autism spectrum disorders attending mainstream schools. Research in Autism Spectrum Disorders. 2015; 18: 97-109.[2] Mandy W. et al. Easing the transition to secondary education for children with autism spectrum disorder: An evaluation of the Systemic Transition in Education Programme for Autism Spectrum Disorder (STEP-ASD). Autism. 2015 Aug 24. pii: 1362361315598892.[3] Reutebuch CK. et al. A systematic review of the effects of choice on academic outcomes for students with autism spectrum disorder. Research in Autism Spectrum Disorders. 2015; 20: 1-16.----------Ambler, P., Eidels, A., & Gregory, C. (2015). Anxiety and aggression in adolescents with autism spectrum disorders attending mainstream schools Research in Autism Spectrum Disorders, 18, 97-109 DOI: 10.1016/j.rasd.2015.07.005... Read more »

  • September 10, 2015
  • 04:52 PM

Xanthophyllomyces dendrorhous brightens up lobsters and leaking trees

by Rosin Cerate in Rosin Cerate

Like people, trees can bleed. Unlike people, this bleeding occurs mostly in the spring, at least in temperate parts of the world. As winter subsides and temperatures rise, deciduous trees begin to move sap (a dilute sugar solution) from their roots up to their branches to fuel the growth of leaves and flowers. Where a tree has been wounded (e.g. by a rutting deer or logging corporation), they will often bleed sap. This stuff makes great food for yeasts. Being ubiquitous in outdoor air, these fungi inevitably end up landing on a sap-soaked tree wound. They grow rapidly, producing a pungent sludge that appears to be oozing from a wound but in fact is just following the trail of its leaking sap. The yeasts inhabiting these tree slimes are eaten by nematodes and fruit flies, which in turn are eaten by larger organisms, and the circle of life moves ever forward.The pretty colours of tree slimes are the result of yeast-made pigments. One of the pigment makers is Xanthophyllomyces dendrorhous (aka Phaffia rhodozyma). In the northern hemisphere, X. dendrorhous is typically found on sap oozing from birch trees (genus Betula) in temperate forests, turning them a vibrant pink to orange colour. However, down in Patagonia, X. dendrorhous hangs out on southern beech trees (genus Nothofagus). More precisely, the yeast inhabits the fruiting bodies (mushrooms) of Cyttaria hariotii, a parasitic fungus capable of taping into a southern beech tree's sap ducts and growing clumps of what appear to be spongy yellow golf balls every spring. These balls are rich in sap-derived sugars, presumably making them very attractive to X. dendrorhous.Xanthophyllomyces dendrorhous pizza, kinda! (Source)Unlike any other fungus we know of, X. dendrorhous is able to produce a reddish orange pigment called astaxanthin. A derivative of beta-carotene, astaxanthin can function as an antioxidant and is thought to protect yeast cells from oxidative stress caused by their exposure to sunlight. It's also what gives certain shrimp, and consequently flamingos and the scarlet ibis, their pink colour. Astaxanthin is highly valued for its ability to help ensure salmon, lobsters, chicken breasts, and egg yolks have the appealing colours we enjoy and have grown to expect when we purchase them. The pigment is added to animal feeds (e.g. for salmon farming), leading to its uptake and incorporation by those who ingest it. It's fairy expensive, and there is a big market for it, so there has been a lot of research into how to reduce the cost to produce it. In particular, efforts have been made to coax X. dendrorhous, which can be fairly easily grown in giant tanks, into making more astaxanthin. Thanks to this, we now know quite a bit about how the pigment is put together by the yeast and what environmental factors influence its synthesis. Beyond its use as an antioxidant and feed additive, there is some evidence that astaxanthin can reduce inflammation and protect the brain from damage.X. dendrorhous also produces β-fructofuranosidase, an enzyme capable of catalyzing the synthesis of fructooligosaccharides. These short chains of fructose molecules are of interest due to their ability to function as prebiotics, selectively enhancing the growth of health-promoting bacteria in the gastrointestinal tract. The yeast may provide a means of producing these beneficial compounds on a large scale.ReferencesDavid-Palma M, Libkind D, Sampaio JP. 2014. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Molecular Ecology 23(4):921-932.Gimeno-Pérez M, Linde D, Fernández-Arrojo L, Plou FJ, Fernández-Lobato M. 2015. Heterologous overproduction of β-fructofuranosidase from yeast Xanthophyllomyces dendrorhous, an enzyme producing prebiotic sugars. Applied Microbiology and Biotechnology 99(8):3459-3467. [First two pages]Johnson EA. 2003. Phaffia rhodozyma: Colorful odyssey. International Microbiology 6(3):169-174. [First two pages]Sharma R, Gassel S, Steiger S, Xia X, Bauer R, Sandmann G, Thines M. 2015. The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. BMC Genomics 16:233. [Full text]Verwaal R, Wang J, Meijnen JP, Visser H, Sandmann G, van den Berg JA, van Ooyen AJ. 2007. High-level production of beta-carotene in Saccharomyces cerevisiae by successive transformation with carotenogenic genes from Xanthophyllomyces dendrorhous. Applied and Environmental Microbiology 73(13):4342-4350. [Full text]Weber RWS. 2006. On the ecology of fungal consortia of spring sap-flows. Mycologist 20(4): 140-143.Weber RWS, Davoli P, Anke H. 2006. A microbial consortium involving the astaxanthin producer Xanthophyllomyces dendrorhous on freshly cut birch stumps in Germany. Mycologist 20(2):57-61. Read more »

  • September 10, 2015
  • 04:50 AM

The digit ratio and autism: ALSPAC says no

by Paul Whiteley in Questioning Answers

"In this population-based study, there was no strong evidence of an association between 2D:4D [second-to-fourth digit ratio] and ASD [autism spectrum disorder] diagnosis or traits, although the CIs [confidence intervals] were wide. These results are not consistent with the extreme male brain theory."So said the study results from Anna Louise Guyatt and colleagues [1] (open-access) who investigated the 2D:4D ratio as part of the ALSPAC (Avon Longitudinal Study of Parents and Children) initiative. The 2D:4D ratio in case you didn't know, is the idea that the subtle difference in the length of the index finger and ring finger might be a marker for androgen exposure during the nine months that made you/us."The index to ring finger ratio (second-to-fourth digit ratio, 2D:4D) has been widely used as a proxy for fetal testosterone exposure in autism research" is the link back to autism and onwards the idea that testosterone exposure might be part and parcel of the extreme male brain (EMB) hypothesis ("that children with ASD exhibit an exaggerated form of the male cognitive profile... and proposes that prenatal androgens are plausible biological candidates.")ALSPAC data was used to "examine the association between 2D:4D and ASD and various autistic trait measures in a population-based cohort in the UK." Further: "The primary hypothesis being tested was that lower 2D:4D would be associated with ASDs and ASD traits."Analysis of the 2D:4D ratio was undertaken in 56 ASD cases, 616 "high risk trait group" participants and some 5300 other children who were part of ALSPAC. Aside from an autism diagnosis (or not) and various other measures looking at ASD traits, other data were also collected on things like socio-economic status (SES) as possible confounders. An IQ measure was also included for "44/56 of included participants with ASDs."As per the opening statement, the results were not exactly convincing that the 2D:4D is associated with an increased risk for ASD. There was some weak evidence that 2D:4D ratios might be linked to autistic traits but, and it is an important point: "These associations were mostly directionally discordant with the extreme male theory of autism, and given the number of comparisons made, and the lack of consistent association between ASD diagnosis and 2D:4D in this study, we consider that they were due to chance."ALSPAC as an initiative, carries some significant methodological strengths insofar of the hows and whys of data collected. I've mentioned previous results from the cohort on this blog before (see here and see here for example). Obviously ALSPAC is not perfect (no cohort ever is) and pertinent to the Guyatt results, the authors acknowledge that there may have been a bias towards the applicability of their results "being weighted towards Asperger syndrome and other high-functioning ASD cases" in light of their participant group.That being said, I do think these results add to other research suggesting that once again, we should be guarded against making too many sweeping generalisations when it comes to the autism spectrum. In a previous post on the finger length ratio (see here) some of the other 'correlates' of the 2D:4D ratio were mentioned, excluding the 'specificity' of any findings to just autism. Other research on cord blood testosterone levels and autistic traits (see here) has been similarly critical of the EMB hypothesis.But that might not mean that is all bunk though [2]...Music: Phats & Small - Turn Around.----------[1] Guyatt AL. et al. Digit ratio and autism spectrum disorders in the Avon Longitudinal Study of Parents and Children: a birth cohort study. BMJ Open. 2015; 5: e007433.[2] Baron-Cohen S. et al. The “Reading the Mind in the Eyes” Test: Complete Absence of Typical Sex Difference in ~400 Men and Women with Autism. PLoS ONE. 2015; 10(8): e0136521.----------Guyatt, A., Heron, J., Knight, B., Golding, J., & Rai, D. (2015). Digit ratio and autism spectrum disorders in the Avon Longitudinal Study of Parents and Children: a birth cohort study BMJ Open, 5 (8) DOI: 10.1136/bmjopen-2014-007433... Read more »

  • September 9, 2015
  • 03:12 PM

Cells from human umbilical cord blood improve cognition in Alzheimer’s disease model mice

by Dr. Jekyll in Lunatic Laboratories

Alzheimer’s disease (AD), which affects an estimated 26 million people worldwide, is the fourth leading cause of death among the elderly and the leading cause of dementia. Predictions are that the number of AD cases will quadruple by 2050. Although pharmacological methods for treating AD have been discovered, none significantly delay the progression of the disease.... Read more »

Donna Darlington, Song Li2, Huayan Hou, Ahsan Habib, Jun Tian, Yang Gao, Jared Ehrhart, Paul R Sanberg, Darrell Sawmiller, Brian Giunta.... (2015) Human umbilical cord blood-derived monocytes improve cognitive deficits and reduce ß-amyloid pathology in PSAPP mice. Cell Transplantation. DOI:  

  • September 9, 2015
  • 09:36 AM

Video Tip of the Week: UCSC features for ENCODE data utilization

by Mary in OpenHelix

As noted in last week’s tip about the ENCODE DCC at Stanford, there was a workshop recently for the ENCODE project. There were a lot of folks speaking and a big room full of attendees. You should check out the full agenda and the playlist at the NHGRI site for all the videos, slides, and […]... Read more »

Mangan ME, Williams JM, Kuhn RM, & Lathe WC. (2014) The UCSC Genome Browser: What Every Molecular Biologist Should Know. Current Protocols in Molecular Biology., 107(19.9), 199-199. DOI: 10.1002/0471142727.mb1909s107  

Rosenbloom, K., Armstrong, J., Barber, G., Casper, J., Clawson, H., Diekhans, M., Dreszer, T., Fujita, P., Guruvadoo, L., Haeussler, M.... (2014) The UCSC Genome Browser database: 2015 update. Nucleic Acids Research, 43(D1). DOI: 10.1093/nar/gku1177  

Raney, B., Dreszer, T., Barber, G., Clawson, H., Fujita, P., Wang, T., Nguyen, N., Paten, B., Zweig, A., Karolchik, D.... (2013) Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics, 30(7), 1003-1005. DOI: 10.1093/bioinformatics/btt637  

  • September 9, 2015
  • 08:15 AM

When You’re Not Just Yourself

by Mark Lasbury in As Many Exceptions As Rules

How would you react if you were told that the DNA testing shows that you are not your child’s parent or your parents’ child? Demand another test? – you bet. But wait, you or your parent might be a tetragametic chimeric, carrying around DNA from another person in your body. You might have had a dizygotic twin that you didn’t know about!... Read more »

Yu, N., Kruskall, M., Yunis, J., Knoll, J., Uhl, L., Alosco, S., Ohashi, M., Clavijo, O., Husain, Z., Yunis, E.... (2002) Disputed Maternity Leading to Identification of Tetragametic Chimerism. New England Journal of Medicine, 346(20), 1545-1552. DOI: 10.1056/NEJMoa013452  

Lee, H., Yoon, S., Ko, J., Seong, M., Park, S., Choi, J., & Oh, S. (2014) Monochorionic dizygotic twins with discordant sex and confined blood chimerism. European Journal of Pediatrics, 173(9), 1249-1252. DOI: 10.1007/s00431-014-2312-8  

  • September 9, 2015
  • 02:51 AM

SCQ vs. M-CHAT for autism screening: no winner

by Paul Whiteley in Questioning Answers

"While screening tests may provide useful information, their accuracy is moderate. Screening information in isolation should not be used to make referral decisions regarding specialized ASD [autism spectrum disorder] assessment."That was the findings of the study published by Tony Charman and colleagues [1] who sought to "test the accuracy of two screening instruments in UK Community health services: Modified Checklist for Autism in Toddlers (M-CHAT) and Social Communication Questionnaire (SCQ) for autism spectrum disorder (ASD)."Looking at referrals to "speech and language therapy services in two London districts over a 12-month period between September 2004 and September 2005" researchers initially had screen data for over 540 children (aged between 18 and 48 months) which was subsequently whittled down to a "stratified subsample of 120 children" who then  received an in-depth assessment for possible ASD based on ICD-10 criteria. We are also told that: "Community clinician judgement of likely ASD was available for 98 out of the 120 children."Based on that in-depth assessment for ASD, data is presented on the performance of the SCQ and/or M-CHAT as part of the instigator of said assessment. The data don't read particularly well. Measures of sensitivity and specificity (also called the 'true positive' and 'true negative' rate) were mediocre at best; for example, the specificity of the M-CHAT came in at 50% (33-64%). The SCQ did slightly better on that particular parameter but it has to be said, still not great. The authors conclude: "The screening tests did not perform well to confirm preliminary clinical judgement to refer (in series), nor as an alternative indicator for referral (in parallel)."I've been interested in autism screening (early autism screening) for quite a while on this blog. The peaks and troughs of autism research in this area are quite evident (see here) and have perhaps been contributory to recent going-ons in the United States for example, with the Preventive Services Task Force asking for more evidence to support universal screening for autism in young children who show no developmental issues.There are issues to iron out here, based on what questions to ask (see here) when considering screening as well as understanding that variables such as regression can influence age of onset (see here); particularly relevant to the removal of specific age of onset limits with the latest manifestation of DSM (see here). One factor that I would also perhaps like to see more attention given to is parents as agents of screening and referral (see here). That and further consideration of the how good/bad (delete as appropriate) the pre-diagnostic experience might be (see here) and lots more questions need to be answered.And as I write, lo and behold a possible new player in the autism screening stakes [2]?Music: Robert Palmer - Addicted To Love.-----------[1] Charman T. et al. Testing two screening instruments for autism spectrum disorder in UK community child health services. Dev Med Child Neurol. 2015 Aug 25.[2] Grodberg D. et al. A Simplified Diagnostic Observational Assessment of Autism Spectrum Disorder in Early Childhood. Autism Res. 2015 Aug 25.----------Charman T, Baird G, Simonoff E, Chandler S, Davison-Jenkins A, Sharma A, O'Sullivan T, & Pickles A (2015). Testing two screening instruments for autism spectrum disorder in UK community child health services. Developmental medicine and child neurology PMID: 26303216... Read more »

Charman T, Baird G, Simonoff E, Chandler S, Davison-Jenkins A, Sharma A, O'Sullivan T, & Pickles A. (2015) Testing two screening instruments for autism spectrum disorder in UK community child health services. Developmental medicine and child neurology. PMID: 26303216  

  • September 8, 2015
  • 04:51 PM

A tale of leeches and imminent nuclear war

by Rosin Cerate in Rosin Cerate

The human experience with leeches typically centers around the unpleasantness of being fed upon, with perhaps a dash of they make good fishing bait or we sometimes use them for medical purposes. Oh, and jokes about medieval doctors being mostly useless. Notably, most leeches don't feed on people, opting instead to harvest the fluids of birds, turtles, fishes, frogs, salamanders, snails, and/or insect larvae. They've definitely found a niche, and boy is it an annoying one.The truth is substantially less cute (Source)Leeches can also be used to determine if freshwater environments have been contaminated with harmful chlorinated aromatic organics such as polychlorinated biphenyls (PCBs). Since they are hella difficult to break down, these pollutants tend to accumulate within aquatic organisms as they go about their business (e.g. consuming water containing tiny particles to which PCBs have become attached). Many creatures end up with way higher concentrations of pollutants in their guts than those found in their water and sediment surroundings. This is useful because it allows the quantification of pollutants (by mashing up an organism and analyzing the resulting slurry) otherwise present in a freshwater system at concentrations too low to be easily measured. Aquatic organisms also provide an indication of pollutant levels over time, since they essentially continually sample their surrounding environment over the course of their lives.For some reason, leeches in particular are known to concentrate chlorinated aromatic pollutants to super high levels compared to their crustacean and fish neighbours. Since they are eaten by fish, measuring pollutant concentrations in leeches informs how much of a pollutant is being transferred up the food chain. Leeches are also particularly useful as pollution indicators because they are ubiquitous and abundant in freshwater rivers and lakes, including shallow waters where fish (another commonly used indicator) might not be present. Furthermore, while many fish tend to migrate, leeches tend to be homebodies and so are generally more representative of the area where they are collected.Not all leeches like human blood, but this one appears to (Source)Way up in northern Ontario, which really is most of Ontario, lies a former military installation by the name of site 050 (map). It was part of a coast-to-coast chain of radar antennae built as an early warning system by Canada during the 1950s when everyone was freaking out about the potential for a Soviet nuclear attack (i.e. bombers, and later ballistic missiles, being launched across the Arctic at the USA). All told, the Mid-Canada Radar Line (MCRL) was made up of 98 sites installed along the 55th parallel. After operating for less than a decade, the MCRL was shuttered (having been supplanted by the DEW Line) and more or less left to rot.Unfortunately, the presence of PCBs (e.g. transformer oil) and other nasty pollutants at MCRL sites resulted in contamination of the surrounding environment. In particular, at site 050, nearby inhabitants of Fort Albany First Nation were found to have elevated levels of PCBs in their blood. The site underwent remediation in 2001 and subsequently was studied using leeches to assess the effectiveness of this effort. Members of the genus Haemopis from a section of the Albany River near the site unwillingly gave their lives to establish that PCB levels had decreased in the years following remediation, indicating it was at least somewhat successful. Thanks, leeches.ReferencesGrzelak B, Michałowicz J, Dukowska M. 2012. Bioaccumulation of phenol, guaiacol and some chlorophenols by selected freshwater species of leeches. Bulletin of Environmental Contamination and Toxicology 88(6):976-984. [First two pages]Macova S et al. 2009. Leeches as sensor-bioindicators of river contamination by PCBs. Sensors 9(3):1807-1820. [Full text]Prahacs SM, Hall KJ, Duncan W. 1996. Leeches as in situ biomonitors of chlorinated phenolic compounds. Part 2: Pulp mill investigations. Water Research 30(10):2301-2308.Tsuji LJS, Martin ID. 2009. The use of leeches to monitor aquatic PCB contamination at Mid-Canada radar line site 050: Four years post-remediation. Environmental Monitoring and Assessment 153(1-4):1-7. [First two pages]... Read more »

  • September 8, 2015
  • 03:12 PM

Artificial ‘plants’ could fuel the future

by Dr. Jekyll in Lunatic Laboratories

Imagine creating artificial plants that make gasoline and natural gas using only sunlight. And imagine using those fuels to heat our homes or run our cars without adding any greenhouse gases to the atmosphere. By combining nanoscience and biology, researchers led by scientists at University of California, Berkeley, have taken a big step in that direction.... Read more »

  • September 8, 2015
  • 10:40 AM

Spiders Sailing The Seven Seas

by Gunnar De Winter in United Academics

Spiders Sailing The Seven Seas
Discovery of a new type of behaviour shows that some spiders are really good sailors.
With the exception of the coldest places on our planet, spiders are almost everywhere. From giant bird-eating tarantulas to pin-prick-sized web-builders, from solitary hunters to social colonies, spiders are versatile in more ways than one.
Some of our eight-legged friends on the smaller side of the size/weight scale even know how to fly! ... Read more »

  • September 8, 2015
  • 06:14 AM

Psychiatric history infection during pregnancy increases the risk of psychosis in offspring

by Paul Whiteley in Questioning Answers

The title of this (hopefully) brief post mirrors the conclusion reached by Åsa Blomström and colleagues [1] who analysed data pertinent to all children "born in Sweden 1978-1997" to calculate hazard ratios (HRs) of nonaffective psychosis "in relation to maternal infection during pregnancy." Also detailing RERI - relative excess risk due to interaction - bringing in factors such as maternal history of psychiatric disorder as part and parcel of any effect, and authors reported that: "Among mothers with a history of psychiatric disease, infection during pregnancy increases the risk of psychosis in offspring." The authors further speculate that: "Maternal infections during pregnancy appear to contribute to the risk of childhood infections, which together render the child more vulnerable to psychosis development."I've covered research on the potential effects of maternal infection during pregnancy for offspring child and adult outcomes before on this blog (see here for example). Names like Alan Brown and the late Paul Patterson have done much to put some scientific flesh on the bones of this hypothesis particularly with schizophrenia in mind [2].The Blomström findings add a new layer to the idea of a connection between viral exposure, immune function during pregnancy and 'programming' for offspring psychiatric risk insofar as the idea that elements of familial psychiatric history might also play something of a synergistic role in this relationship. You might well say that parental psychiatric history already puts offspring at greater risk and perhaps represents the larger factor here. Bear in mind however the observation that maternal infection correlated with childhood infection and that this might also play a hand in the development of psychosis and one could speculate that the genetics of psychiatric illness might also overlay with the genetics of infection susceptibility for example. Add in the idea that immune function seems to be more readily accepted as a feature of psychiatric presentation [3] alongside the concept of inflammation being potentially relevant (see here) and voilà, lots of ideas for further study.Music: Sigma ft. Ella Henderson - Glitterball.----------[1] Blomström Å. et al. Associations Between Maternal Infection During Pregnancy, Childhood Infections and the Risk of Subsequent Psychotic Disorder-A Swedish Cohort Study of Nearly 2 Million Individuals. Schizophr Bull. 2015 Aug 24. pii: sbv112.[2] Brown AS. & Patterson PH. Maternal Infection and Schizophrenia: Implications for Prevention. Schizophrenia Bulletin. 2011;37(2):284-290.[3] Gibney SM. & Drexhage HA. Evidence for a dysregulated immune system in the etiology of psychiatric disorders. J Neuroimmune Pharmacol. 2013 Sep;8(4):900-20.----------Blomström Å, Karlsson H, Gardner R, Jörgensen L, Magnusson C, & Dalman C (2015). Associations Between Maternal Infection During Pregnancy, Childhood Infections and the Risk of Subsequent Psychotic Disorder-A Swedish Cohort Study of Nearly 2 Million Individuals. Schizophrenia bulletin PMID: 26303935... Read more »

  • September 7, 2015
  • 03:42 PM

Tree of life study unveils inner workings of a cell

by Dr. Jekyll in Lunatic Laboratories

A multinational team of scientists have sifted through cells of vastly different organisms, from amoebae to worms to mice to humans, to reveal how proteins fit together to build different cells and bodies. This tour de force of protein science, a result of a collaboration between seven research groups from three countries, led by Professor Andrew Emili from the University of Toronto’s Donnelly Centre, uncovered tens of thousands of new protein interactions, accounting for about a quarter of all estimated protein contacts in a cell.... Read more »

Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan, O., Kwan, J., Bezginov, A.... (2015) Panorama of ancient metazoan macromolecular complexes. Nature. DOI: 10.1038/nature14877  

  • September 7, 2015
  • 03:07 AM

Gluten- and casein-free diets and autism: the Hyman results (at last)

by Paul Whiteley in Questioning Answers

"Although these findings must be interpreted with caution because of the small sample size, the study does not provide evidence to support general use of the GFCF [gluten-free/casein-free] diet."So said the results of the study finally published by Susan Hyman and colleagues [1] detailing the effects (or not) of a small (n=14) "double-blind, placebo-controlled challenge study" of the use of a diet devoid of gluten and casein for young children diagnosed with an autism spectrum disorder (ASD). If you really want some background history to this often controversial area of autism research, look no further than some of my past musings on this blog (see here and see here) or if you wish, in peer-reviewed form [2].I say 'finally' in that previous sentence about publication because there has been a considerable degree of waiting for these results to appear in complete peer-reviewed form given that the trial was initially registered in 2004 and things were all supposed to have been wrapped up in 2009 (see here for the entry). Some people with their eyes and ears to the autism research grapevine will have probably heard about some of the whys and wherefores of the delay in publishing these results, but I'm not going to get too involved in that here.Unfortunately the paper is not open-access at the present time but I'll give you a summary of some of the mechanics and findings:Some 66 children were initially assessed for eligibility. This was whittled down to 22 kids taking into account those who declined to participate and those who "did not meet inclusion criteria." That inclusion criteria by the way "required children to be enrolled in a comprehensive applied behavior analysis (ABA) intervention program from one of two community agencies" as well as excluding those where seizures were part of clinical presentation and/or the "presence of a chronic illness in addition to ASD that required medical management, celiac disease, documented food allergy to wheat or milk, nutritional compromise such as iron deficiency that required treatment, and family inability to complete rating scales and assessments in English."The study design was interesting. It included an implementation phase whereby a GFCF was put in place over the course of 2 weeks (baseline) and maintained for at least 4 weeks. Then came the challenge phase which consisted of weekly challenges to the diet for 12 weeks including one of the following: "foods that contained gluten only, casein only, both gluten and casein, or neither (placebo)." Finally, there was a maintenance period where families were free to "maintain, modify, or abandon the GFCF diet in this phase."Various assessments were carried out throughout the study phases covering areas of "physiologic functioning, challenging behaviors (not specific to ASD), and behaviors associated with ASD."Results: well, data for 14 of the 22 children were analysed as a function of attrition and or other factors such as "laboratory exclusion criteria." First and foremost we are told: "No serious adverse events were reported during the trial." First, do no harm and all that. When looking at sleep quality and quantity, stool frequency and type, a measure of ADHD (attention-deficit hyperactivity disorder) and a measure of behaviours associated with autism (the Ritvo-Freeman Real Life Rating Scales), authors reported no significant effect following dietary challenges. In other words: "experimental challenges [to the GFCF diet] were not reliably associated with more frequent ASD behaviors." That being said: "All of the families elected to continue the diet for the 12 weeks after completion of the challenges."There are some significant strengths to this data based on close monitoring of adherence to the diet, controlling the consumption of gluten and casein levels in challenge snacks and the use of ABA in terms of "stable, consistent educational and behavioral services."Likewise however, there are some notable issues associated with the study and the findings outside of the small participant group, not least the emphasis on 'dietary challenge' and importantly the fact that researchers "excluded children who had known gastrointestinal disorders, who might have been more likely to respond positively to dietary restriction." This last point ties in well with other literature in this area [3]. I might add that "individualized supplementation was added for a few participants when deemed necessary by the study dietitian to address low intake of iron, calcium, or vitamin D." Interesting (see here).The authors conclude that their study "does not provide evidence to support general use of the GFCF diet" with caveats. I can imagine that the Hyman results are probably going to generate some interesting discussions depending on your view of a GFCF diet for autism. I have a professional interest in this topic given some of my research history in this small part of the autism research arena [4] but have tried to stay as objective as possible as per other entries on this topic (see here).Despite any potential bias I might have, I do still think there is more to see in this area of diet and autism. I've talked before about the idea that the diagnosis of autism is by no means protective against other conditions/labels appearing including those related to issues with gluten for example (see here). This similarly applied to milk also (see here). Some of other peer-reviewed research that I've also been a part of has hinted that there may be 'best responders' to this type of intervention [5] (see here for more discussion); something which ties in well with the concept of plurality and autism (see here).That caveat about the Hyman study excluding children with known gastrointestinal (GI) disease is also worth re-iterating. Again, this takes autism research into some controversial areas (see here) but as per recent data, both functional (see here) and pathological bowel disorders (see here) do seem to over-represented in cases of autism, so one might see this as an area ripe for further dietary investigations. Indeed, one assumes we might see if there is anything in such an association as and when the Harland Winter trial sees the peer-reviewed light of day (hopefully quite soon).----------[1] Hyman SL. et al. The Gluten-Free/Casein-Free Diet: A Double-Blind Challenge Trial in Children with Autism. Journal of Autism and Developmental Disorders. 2015. Sept 5.[2] Whiteley P. e... Read more »

Hyman, S., Stewart, P., Foley, J., Cain, U., Peck, R., Morris, D., Wang, H., & Smith, T. (2015) The Gluten-Free/Casein-Free Diet: A Double-Blind Challenge Trial in Children with Autism. Journal of Autism and Developmental Disorders. DOI: 10.1007/s10803-015-2564-9  

  • September 6, 2015
  • 09:28 PM

Do Lyme disease spirochetes produce a toxin?

by Microbe Fan in Spirochetes Unwound

According to the current view of Lyme disease pathogenesis, tissue damage is caused by the inflammatory response to the spirochetes.  Borrelia species do not produce toxins that injure the host directly.  A new study published in BMC Microbiology may force us to modify our view.The study shows that some Borrelia strains carry a set of genes with the potential to generate a peptide resembling streptolysin S (SLS), a potent toxin produced by the pathogen Streptococcus pyogenes.  The enzymes that produce SLS in S. pyogenes are expressed from a cluster of genes surrounding sagA, a tiny gene encoding the SLS precursor.  The peptide produced from sagA is nontoxic; it has to undergo several alterations to its structure to become toxic.  A critical modification is carried out by the SagBCD protein complex, which converts the side chains of cysteine, serine, and threonine into ring structures.Figure 2 from Molloy et al., 2011Other genes surrounding sagA encode a peptidase that is thought to trim the leader peptide from the amino terminus of the SLS precursor and an ABC transporter that may be responsible for expelling SLS from the cytoplasm.Figure 1A from Molloy et al., 2011SLS targets neutrophils and possibly other immune cells during S. pyogenes infection.  SLS-like toxins are also produced by other Gram-positive pathogens, including Staphylococcus aureus, Listeria monocytogenes and Clostridium botulinum.The investigators mined the genomes of other bacteria in search for genes encoding the machinery that generates SLS-like toxins.  They found SLS-like gene clusters in various Firmicutes and Actinobacteria, both Gram-positive groups of bacteria.The researchers also found the gene cluster in the genomes of Borrelia afzelii strain PKo, Borrelia valaisiana strain VS116, and Borrelia spielmanii strain A14S.  B. afzelii is a major cause of Lyme disease in Europe and Asia.  B. valaisiana and B. spielmanii are responsible for occasional cases of Lyme disease.Figure 4 from Molloy et al., 2015.  Top: organization of SLS-like gene cluster in S. pyogenes and three Borrelia strains. Bottom: sequence of the SLS precursor (SagA) and the borrelial SLS-like precursors.They also used PCR to screen the DNA of 140 patient and tick isolates of Lyme Borrelia for the genes encoding the SLS-like biosynthetic machinery.  Most of the isolates were obtained from Europe and the U.S., with a few coming from Asia.  Design of the PCR primers was based on the sequence of the B. valaisiana bvalB, bvalC, and bvalD genes, which encode homologs of the S. pyogenes sagB, sagC, and sagD gene products.  Most of the B. garinii, B. afzelii, B. valaisiana, B. spielmanii, and B. lusitaniae isolates that were examined tested positive.  On the other hand, none of the 22 isolates of B. burgdorferi or 13 isolates of B. bavariensis were PCR positive.  These results indicate that SLS-like sequences are widespread among Lyme disease spirochetes (though not in B. burgdorferi).The next step was to show that the borrelial gene believed to encode the SLS-like toxin actually expressed a peptide that damages mammalian cells.  A simple assay based on the ability of many toxins to rupture (hemolyze) red blood cell in vitro is available.  Hemolysis is measured easily by mixing the toxin with sheep red blood cells.  Hemoglobin released from the ruptured cells is quantified with a spectrophotometer.They decided to test the SLS-like peptide encoded by B. valaisiana, BvalA, for hemolytic activity.  The researchers succeeded in expressing and purifying a recombinant form of BvalA.  Not surprisingly,  BvalA was not hemolytic because its amino acid side chains had to be converted into ring structures necessary for the peptide to injure red blood cells.  They wanted to mix BvalA with the BvalBCD protein complex so that the peptide would be modified, but they could not generate the protein complex.  Instead, they used the SagBCD complex from S. pyogenes to modify the BvalA peptide.  When they did this, they finally observed hemolytic activity.Red blood cells are unlikely to be a major target of borrelial SLS-like peptides during infection.  So what is the real target?  More studies are needed to answer this question, but we should consider the possibility that the toxin has nothing to do with Lyme disease.  Instead, it may help the spirochete to survive during its residence within the tick vector.  A number of nonpathogenic bacteria carry gene clusters distantly related to the ones that produce SLS.  Several peptide toxins produced by these bacteria are known to kill competing microbes.  Like us humans, ticks have a microbiome inhabiting their gut.  Some Lyme spirochetes may need to secrete the toxin to ward off their microbial neighbors.ReferencesMolloy EM, Casjens SR, Cox CL, Maxson T, Ethridge NA, Margos G, Fingerle V, & Mitchell DA (2015). Identification of the minimal cytolytic unit for streptolysin S and an expansion of the toxin family. BMC Microbiology, 15 PMID: 26204951Molloy EM, Cotter PD, Hill C, Mitchell DA, & Ross RP (2011). Streptolysin S-like virulence factors: the continuing sagA. Nature Reviews Microbiology, 9 (9), 670-81 PMID: 21822292... Read more »

Molloy EM, Cotter PD, Hill C, Mitchell DA, & Ross RP. (2011) Streptolysin S-like virulence factors: the continuing sagA. Nature Reviews Microbiology, 9(9), 670-81. PMID: 21822292  

  • September 6, 2015
  • 03:35 PM

Guilting teens into exercise won’t increase activity

by Dr. Jekyll in Lunatic Laboratories

Just like attempts at influencing hairstyles or clothing can backfire, adults who try to guilt middle-schoolers into exercising won’t get them to be any more active. The study found students who don’t feel in control of their exercise choices or who feel pressured by adults to be more active typically aren’t.... Read more »

  • September 5, 2015
  • 05:10 AM

Vitamin D fortified mozzarella topped pizzas. Yum!

by Paul Whiteley in Questioning Answers

A slightly more light-hearted but nevertheless important post for you today as I bring to your attention the paper by Banaz Al-Khalidi and colleagues [1] and their conclusion that: "Vitamin D3 is safe and bioavailable from fortified mozzarella cheese baked on pizza."Adding vitamin D3 - cholecalciferol - to mozzarella cheese, researchers assessed what happened to serum levels of 25-hydroxyvitamin D in a high (28,000 international units, IU) and low (200 IU) dose group of "96 apparently healthy, ethnically diverse adults" randomly assigned to one or other group. The results suggested that combined with pizza consumption "once weekly for 8 weeks" measurable levels of vitamin D did increase in both groups compared with baseline alongside the important finding that: "None of the subjects in either group developed any adverse events during the supplementation protocol."Understanding that not everyone might be as enthusiastic about pizza (proper pizza!) and vitamin D as myself, the Al-Khalidi results might be something quite important. Calls for supplementing vitamin D grow louder in recent times (see here) following quite a bit of research linking vitamin D deficiency to various potential issues outside of just the 'English disease'. Although many health professionals might be a little reluctant to suggest that fortified pizza might be a route to increasing vitamin D levels as a function of society's tendency to go a little overboard when it comes to foods like pizza, I'd tend to favour such a model. If we further assume that vitamin D deficiency might stretch to a relationship with obesity and its partners for example [2], one can perhaps see how the risks attached to food fortification with vitamin D in such a manner might be outweighed by the potential population benefits.Music: Lost Frequencies - Are You With Me.----------[1] Al-Khalidi B. et al. Bioavailability and Safety of Vitamin D3 from Pizza Baked with Fortified Mozzarella Cheese: A Randomized Controlled Trial. Can J Diet Pract Res. 2015 Sep;76(3):109-116.[2] Awad AB. et al. Vitamin d and metabolic syndrome risk factors: evidence and mechanisms. Crit Rev Food Sci Nutr. 2012;52(2):103-12.----------Al-Khalidi B MSc, Chiu W MSc, Rousseau D PhD, & Vieth R PhD (2015). Bioavailability and Safety of Vitamin D3 from Pizza Baked with Fortified Mozzarella Cheese: A Randomized Controlled Trial. Canadian journal of dietetic practice and research : a publication of Dietitians of Canada = Revue canadienne de la pratique et de la recherche en dietetique : une publication des Dietetistes du Canada, 76 (3), 109-116 PMID: 26280790... Read more »

Al-Khalidi B MSc, Chiu W MSc, Rousseau D PhD, & Vieth R PhD. (2015) Bioavailability and Safety of Vitamin D3 from Pizza Baked with Fortified Mozzarella Cheese: A Randomized Controlled Trial. Canadian journal of dietetic practice and research : a publication of Dietitians of Canada , 76(3), 109-116. PMID: 26280790  

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