Biology

Daddy's girl. Photo from freedigitalphotos.net.Let’s take a moment to appreciate just how special dads are. Across the animal kingdom, fathers caring for their young is the exception, not the rule. Paternal care is most often seen in species in which males can be pretty sure that they are indeed the father (for example, in species that fertilize eggs outside of the mothers’ bodies or in socially monogamous species). Mammals rarely act fatherly - Only 10% of mammalian species show paternal care at all. But among mammals, primates (including ourselves) are more likely to do so.Dads do a number of things to care for their young: Depending on the species (and the individual), they may incubate them, provide them with food, groom them, keep them close to home, guard and protect them, and help them gain survival and mate-attraction skills. These behaviors are costly to a male, who could often be reproductively more successful by spending his time and resources courting more females. But they do it nonetheless.Regardless of whether a dad is behaviorally involved with his offspring, he contributes a fair amount to the individuals we grow up to be. Dads provide nearly half of our genes, which are the instructions for the production of all of our bodies’ tissues and chemicals. These tissues and chemicals don’t just make up our physical bodies, they underlie much of our physical abilities, susceptibilities to disease, and behavior patterns (including personalities).Just because about half of your genes are from dad and about half of your genes are from mom, doesn’t mean that you are strictly half-your-dad and half-your-mom. Imagine you are given two books of Thanksgiving Day recipes: Both books have the same recipe for turkey, so that is the one you are going to follow. But one book has a recipe for garlic mashed potatoes and the other has a recipe for plain mashed potatoes. If no one in your family likes garlic, you will likely follow the recipe for plain potatoes. In addition to choosing between recipes, you can also combine them: If one book has a recipe for stuffing with lots of garlic and onions and the other has a recipe for stuffing without garlic or onions, you could make stuffing with onions and no garlic. Your pairs of genes work in similar ways: if the two copies of a gene are different, you may get the trait of one of them or they could combine to give you an intermediate trait. If the versions of the gene are the same, you will likely just get that trait.When something is made by following the instructions in a gene, this process is called gene expression. Not all genes are expressed equally everywhere: All of the cells of our body have the same genes, but the way they express in a particular cell determines whether that cell is part of a lung, a heart, a brain or something else. If for a particular gene the instructions in the gene from one parent are followed and the gene from the other parent is ignored, this is called parent-specific gene expression. We have several traits that occur as a result of dad-specific gene expression.Your genes are lined up on doubled-stranded DNA, which is tightly coiled around proteins called histones. The DNA is then wrapped even more and packed into chromosomes. You have 23 different pairs of chromosomes in each cell, where one of each pair came from mom and the other came from dad. Figure adapted from an image by KES47 at Wikimedia.More variation is caused by the fact that two individuals with identical genes may not have identical traits. Our genes are encoded in strings of DNA, which are coiled around proteins called histones and then packed into chromosomes. Biological factors can cause the string of DNA to coil tightly around these histones, hindering access to any genes in that section of DNA. This reduces or even prevents gene expression from happening (Imagine what would happen if two pages of your Thanksgiving Day recipe book stuck together). Alternatively, other biological fa

“ Hunting and gathering was humanity’s first and most successful adaptation, occupying at least 90 percent of human history. Until 12,000 years ago, all humans lived this way. ” [The Cambridge Encyclopedia of Hunters and Gatherers. Richard B. Lee and … Continue reading →... Lachance J, Vernot B, Elbers CC, Ferwerda B, Froment A, Bodo JM, Lema G, Fu W, Nyambo TB, Rebbeck TR.... (2012) Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell, 150(3), 457-69. PMID: 22840920 Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers.

The Genomics Law Report has provided ample coverage throughout the litigation over Myriad Genetics’ BRCA1/2 patents. The saga had a rather lengthy procedural history, so a timeline of key landmarks with hyperlinks to GLR coverage as appropriate (in the “where” column) may be useful. When Where Action Citation 1997 USPTO US Patent 5693473 issued to Myriad Genetics Inc.   March 2010 SDNY US Patent 5693473 invalidated AMP v. USPTO, 702 F.Supp.2d 181 July 2011 Fed Cir NY SDNY decision affirmed in part, reversed in part AMP v. USPTO, 653 F.3d 1329. March 2010 SCOTUS Certiorari granted, Fed Cir NY judgment vacated, case remanded to Fed Cir NY AMP v. Myriad, 132 S.Ct. 1794 August 2012 FedCir NY Subsequent determination made (in light of Mayo v. Prometheus) AMP v. USPTO, 689 F.3d 1303 November 2012 SCOTUS Certiorari granted AMP v. Myriad, 133 S.Ct. 694 April 2013 SCOTUS Heard oral arguments   June 2013 SCOTUS Fed Cir decision affirmed in part, reversed in part AMP v. Myriad, 569 US – To understand the Supreme Court’s decision in AMP v. Myriad, announced on June 13, 2013, it’s important to keep in mind what question was before the Court. For a valid patent to issue, the following requirements must be met: • 35 USCA §101 – patentable subject matter • 35 USCA §102 – novelty • 35 USCA §103 – non-obviousness • 35 USCA §112 – adequate, explicit description The only question before the Supreme Court was whether human genes are patentable. (The Court left the methods patent decisions of the Federal Circuit unaffected. In other words, Myriad’s diagnostic method patents are invalid but its therapeutic screening method patent is valid.) Basically, in answering this question, the Supreme Court would decide whether the patents held by Myriad met the first requirement of patentable subject matter (35 USCA §101). The SCOTUS decision The Court unanimously (9-0) answered that isolated DNA is not patentable subject matter but cDNA is patentable subject matter. Justice Thomas wrote the opinion. Justice Scalia wrote a succinct concurring opinion indicating he joined the judgment and all Parts except Part I-A (the scientific discussion). Justice Thomas wrote: …In this case, by contrast [to the facts of Diamond v. Chakrabarty, 447 US 303], Myriad did not create anything. To be sure, it found an important and useful gene, but separating that gene from its surrounding genetic material is not an act of invention. ¶Groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry. The Court rejected the idea that a products patent (like the isolated DNA patent issued to Myriad) meets §101 by virtue of the extensive research efforts required to isolate the DNA of BRCA1 and BRCA2, that bonds are severed in the process of isolating the DNA from the surrounding genetic material, and of necessary deference to the USPTO practice of granting gene patents of this sort in the past. This last argument was rejected primarily because Congress had not endorsed the USPTO’s practice (in contrast to the example provided by Myriad, i.e., new plant breeds were held patentable as Congress endorsed the practice via its Patent Act amendment). Justice Thomas continued: …the lab technician unquestionably creates something new when cDNA is made. cDNA retains the naturally occurring exons of DNA, but it is distinct from the DNA from which it was derived. As a result, cDNA is not a ‘product of nature’ and is patent eligible under §101, except insofar as very short series of DNA may have no intervening introns to remove when creating cDNA. In that situation, a short strand of cDNA may be indistinguishable from natural DNA. What does the SCOTUS decision mean? John Conley provided analysis of the decision for the GLR here. Robert Cook-Deegan called the recent ruling a “sensible decision” and explained the case highlights Myriad’s mismanagement of its patent portfolio, because cDNAs are useless for diagnostics but invaluable fo

In browsing the GBIF classification in BioNames I keep coming across cases of wholesale duplication of taxa. I recently blogged about a single example, the White-browed Gibbon, but here's a larger example involving frogs.Consider the frog genera Philautus and Raorchestes. The latter was described in 2010:A ground-dwelling rhacophorid frog from the highest mountain peak of the Western Ghats of India (2010)Current Science (Bangalore) 98(8): 1119–1125. http://bionames.org/references/e0ab13cbb8bc8b3627bb53e88e7641a9and contains a number of species previously in Philautus. The GBIF classification for Philautus still has these species, which means that these taxa appear twice in the GBIF data portal (associated with different occurrences).To gauge the scale of the problem I've done a crude pairwise plot of species names in the two genera. In the diagram below a dot(?) appears if the species name in the corresponding row and column is identical. The diagonal corresponds to comparisons of a species name with itself.Note the ?'s that appear off the diagonal. These are species in Philautus and Raorchestes that have the same species name (e.g., Philautus glandulosus and Raorchestes glandulosus. The off-diagonal dots indicate taxa that are duplicated.? ? Raorchestes anili ? ? Raorchestes annandalii ? ? Raorchestes beddomii ? ? Raorchestes bobingeri ? ? Raorchestes bombayensis ? ? Raorchestes chalazodes ? ? Raorchestes charius ? ? Raorchestes dubois ? ? Raorchestes flaviventris ? ? Raorchestes glandulosus ? ? Raorchestes graminirupes ? ? Raorchestes griet ? ?

If Mayor Bloomberg's wildest decay-related fantasies are realized, New Yorkers will soon be sparing their food scraps from the garbage. A new composting program would encourage (or possibly require) people in the city to collect their food waste in a separate container. Yet Bloomberg may want to consider whether a Manhattan apartment has the square footage to fit both its residents and their potentially harmful compost fungi. The New York City recycling plan, as described in the New York Times this week, would start out on a voluntary basis. Participants would gather their food waste in "containers the size of picnic baskets in their homes," then dump the compost in curbside bins for regular collection. Instead of going into landfills, that waste might be turned into biogas for electricity. Eventually, the program could become mandatory. Vidya De Gannes, a graduate student at the University of the West Indies, St. Augustine campus, in Trinidad and Tobago, has been composting too. She made three kinds of compost, each based on one type of dried plant material (agricultural wastes from the processing of rice, sugar cane, or coffee) mixed with cow or sheep manure. De Gannes and William Hickey, a soil microbiologist at the University of Wisconsin, Madison, who's the senior author of the new study, say these composts are most similar to a homeowner's compost mix of grass and yard waste. To study the biodiversity of species living in compost, De Gannes collected fungal DNA from her compost containers and sequenced it. In total, she found 120 different species of fungus. Each kind of compost had a unique mix of species living inside it. She also turned up 15 fungus species that can cause disease in humans. These were present in every kind of compost and ranged from Aspergillus fumigatus, a common fungus that can cause lung infections in people with compromised immune systems, to other species that can infect the skin or eyes. Although the composts De Gannes studied weren't quite what New Yorkers would be collecting in their kitchens—unless they're keeping pet sheep too—some of the potentially dangerous fungi she found have also turned up in studies of all-plant compost. Keeping a compost bucket in an enclosed space is "potentially risky," Hickey and De Gannes wrote in an email. Fungal spores floating on the air can cause infections, especially in people with weakened immune systems. "Compost kept in an enclosed area like a small apartment would probably not have adequate ventilation." To get some fresh air, composters might have to leave their apartments and go around the corner for an extra-extra-large soda. Image: Waldo Jaquith (not, as far as I know, a dangerous fungus) De Gannes, V., Eudoxie, G., & Hickey, W. (2013). Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety Frontiers in Microbiology, 4 DOI: 10.3389/fmicb.2013.00164... De Gannes, V., Eudoxie, G., & Hickey, W. (2013) Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety. Frontiers in Microbiology. DOI: 10.3389/fmicb.2013.00164 Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety

UK legal experts are querying the 2011 Court of Justice of the European Union (CJEU)ruling that the products of research using stem cells derived from human embryos are not patentable (see previous news). ? The UK High Court has itself requested clarification from the CJEU in Luxembourg; depu ...

Researchers at the University of Wisconsin-Madison Department of Bacteriology are studying the colonies of leaf-cutter ants as they cultivate thriving communities of fungi and bacteria using freshly cut plant material. While these fungi provide nutrients for the ants, researchers are hoping to replicate the process and apply it for better biofuel production.... Aylward, F., Burnum-Johnson, K., Tringe, S., Teiling, C., Tremmel, D., Moeller, J., Scott, J., Barry, K., Piehowski, P., Nicora, C.... (2013) Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens. Applied and Environmental Microbiology, 79(12), 3770-3778. DOI: 10.1128/AEM.03833-12 Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens

We’ve been doing training and workshops on the UCSC Genome Browser for 10 years now. It’s a tremendous tool that has to be a foundational item in your toolkit in genomics. But–there may be times when you want to examine some of the data that you can find there in another way, with a different [...]... Auerbach, R., Chen, B., & Butte, A. (2013) Relating Genes to Function: Identifying Enriched Transcription Factors using the ENCODE ChIP-Seq Significance Tool. Bioinformatics. DOI: 10.1093/bioinformatics/btt316 Relating Genes to Function: Identifying Enriched Transcription Factors using the ENCODE ChIP-Seq Significance Tool

Research continues on what is the most basal animal on Earth and if that animal is representative of the earliest metazoaon. A 2013 report says that it isn’t time to rewrite the books, but even if we tried to do just that, what would we place at the bottom of the tree? Recent studies argue for different groups. A 2009 study says it is the placozoans. A 2012 study gives the award to the sponges. And several studies in the 2000’s wanted to nominate the comb jellies. The biggest difference in these studies – the 2013 report makes the porifera different from all the other animals, while the 2009 study says the lower metazoans all diverged from the bilaterians at the same time and then evolved in parallel.... Dohrmann, M., & Worheide, G. (2013) Novel Scenarios of Early Animal Evolution--Is It Time to Rewrite Textbooks?. Integrative and Comparative Biology. DOI: 10.1093/icb/ict008 Novel Scenarios of Early Animal Evolution--Is It Time to Rewrite Textbooks? Schierwater, B., Eitel, M., Jakob, W., Osigus, H., Hadrys, H., Dellaporta, S., Kolokotronis, S., & DeSalle, R. (2009) Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis. PLoS Biology, 7(1). DOI: 10.1371/journal.pbio.1000020 Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

When I first saw the paper from Nga Lau and colleagues* (open-access) looking for markers of gluten sensitivity and/or coeliac (celiac) disease in children with autism I have to admit to raising a smile. I smiled because in a previous post on this blog I talked about a 'wish-list' for autism research specifically focused on the gluten and casein-free dietary intervention**. Part of that wish list was some further inquiry into why, biochemically, some people on the autism spectrum might benefit from dietary intervention. My prayers it seems have started to be answered.Smiler @ Wikipedia When it comes to the area of dietary intervention for conditions like schizophrenia (no really), there seemed to be a lot more enthusiasm for looking at why some cases of schizophrenia might overlap with dietary issues over investigations into autism. I can't pretend to know why schizophrenia research took the lead; maybe something to do with Dohan and his original discussions on diet and schizophrenia or that schizophrenia research has some very talented people like Emily Severance and colleagues (see here and here and here) taking an interest. One might also speculate that some of the politics of autism - diet, gastrointestinal (GI) issues = (see here) - might also creep into this lack of autism research interest too? Who knows.No mind, Lau et al did look at immune reactivity to gluten (or rather a fraction of gluten called gliadin) in a group of children with autism (n=37) compared with their asymptomatic siblings (n=27) and typically developing controls (n=76). They looked for anti-gliadin antibodies (IgA and IgG). They looked for antibodies to deamidated gliadin (that is where gliadin has already been subjected to some kind of enzymatic modification). They looked at antibodies to tissue transglutaminase (tTG). They even examined HLA genotype for the DQ2 and DQ8 haplotypes (linked to the genetics of coeliac disease). All in all, the primary bases were covered.Results: well, the serum samples all came from AGRE - the Autism Genetic Resource Exchange - so no quibbling about the diagnosis of autism. They also subdivided the autism group up into those with GI symptoms and those without and remarked on those who were following a gluten-free diet too.The authors report that levels of IgG anti-gliadin antibody were elevated in the autism group compared to siblings and controls. This differences lasted even when certain confounders such as age, gender and race were taken into account and the calculated odds ratio of an having an elevated IgG antibody levels to gliadin was not to be sniffed at either (OR 4.97; CI 1.39 - 17.8). That being said, there was cross-over between the relatively small participant groups and levels of IgA antibody to gliadin were not significantly different between the groups. Very interestingly, the presence of comorbid GI symptoms appearing alongside autism seemed to be linked to that elevated IgG antibody response to gliadin compared with no comorbid GI symptoms.Just short of 50% of the children with autism were "positive for HLA-DQ2 and/or -DQ8 (6 DQ2, 12 DQ8)". I probably didn't explain this well, but a significant proportion of people with coeliac disease carry these haplotypes which all relates back to the almighty MHC and antigen presentation (see here for explanation).Insofar as the other parameters on antibodies to deamidated gliadin and tTG, there was little difference to write home about. Although not wholly relevant, I'll refer you back to some interesting work down on tTG with autism in mind from a while back (see here).A few choice quotes from the authors: "The findings indicate that the observed anti-gliadin immune response in patients with autism is likely to involve a mechanism that is distinct from celiac disease, without the requirement for TG2 activity or antigen presentation through DQ2/DQ8 MHC molecules". Well, we know that coeliac disease, when it is tested for in cases of autism, is probably not great