The genome of the model beetle and pest Tribolium castaneum.

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

The routinization of lay expertise: A diachronic account of the invention and stabilization of an open-source artificial pancreas.

Embodied health movements (EHMs) advance their agendas by mediating the production, circulation, and revision of biomedical knowledge. To do this, their constituents become lay experts by blending their embodied experience of illness with self-taught technical knowledge. However, it is unclear how lay expertise is routinized within EHMs, and consequently, to what extent it can be made durable in long-term partnerships with credentialed experts. I follow the OpenAPS community-a group of people with type one diabetes who engineered an open-source 'artificial pancreas'-from their inception in the transient #WeAreNotWaiting movement to their research collaborations with endocrinologists and detente with the FDA. I argue that OpenAPS user-contributors formalized their expertise in three steps: First, they broke the OpenAPS algorithm into modules so that prospective users must become experts to assemble it. Second, they lowered this barrier to entry by facilitating the socialization of new user-contributors with a training ritual. And third, they intervened in the strained endocrinologist-patient relationship. These tactics-restricting membership, reproducing expertise, and realigning interests-won the respect of credentialled experts who saw themselves in the OpenAPS community's image. While not all EHMs follow this trajectory, this case demonstrates that lay expertise can mature and assume new institutional forms without relying on commercialization or patronage.

The finished DNA sequence of human chromosome 12.

Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12, which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents.

The DNA sequence, annotation and analysis of human chromosome 3.

After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

Evaluation of hexavalent chromium extraction method EPA method 3060A for soils using XANES spectroscopy.

Hexavalent chromium (Cr(VI)) occurrence in soils is generally determined using an extraction step to transfer it to the liquid phase where it is more easily detected and quantified. In this work, the performance of the most common extraction procedure (EPA Method 3060A) using NaOH-Na(2)CO(3) solutions is evaluated using X-ray absorption near edge structure spectroscopy (XANES), which enables the quantification of Cr(VI) directly in the solid state. Results obtained with both methods were compared for three solid samples with different matrices: a soil containing chromite ore processing residue (COPR), a loamy soil, and a paint sludge. Results showed that Cr(VI) contents determined by the two methods differ significantly, and that the EPA Method 3060A procedure underestimated the Cr(VI) content in all studied samples. The underestimation is particularly pronounced for COPR. Low extraction yield for EPA Method 3060A was found to be the main reason. The Cr(VI) present in COPR was found to be more concentrated in magnetic phases. This work provides new XANES analyses of SRM 2701 and its extraction residues for the purpose of benchmarking EPA 3060A performance.

Homo adhaerens: Risk and adherence in biomedical HIV prevention research.

After the turn of the millennium, HIV clinical researchers pivoted from developing and testing new antiretrovirals (ARVs) for treatment, to reconfiguring the same molecules for pre-exposure prophylaxis (PrEP). In 2012, Truvada became the first HIV therapy to also be approved by the FDA for PrEP, regarded as a magic bullet that promised to end the epidemic. However, six years after its approval, it continues to be inaccessible to those who are most vulnerable. In this article, I critically analyze HIV PrEP clinical trials, dissecting the novel techniques researchers use to demonstrate efficacy. I argue that in making sense of the interplay between adherence to a prophylactic regimen and risk for HIV, biomedical HIV prevention research has revealed a new subject of biopolitics, Homo adhaerens. In the early 2000s, clinical researchers operating in the Global South identified Homo adhaerens as the ideal subject, one who embodies both high-risk behavior and diligent adherence to a daily oral regimen. I trace the construction of Homo adhaerens to the United States, where I listen closely to activists engaged with the ongoing DISCOVER trial of PrEP. Activists either aspire for Homo adhaerens as a standard, making the liberal argument that expanding access could make PrEP successful, or they rebuke the framework of clinical research that produces narrow understandings of adherence, efficacy, and universality. Ultimately, I argue that by failing to grapple with the social realities that underlie poor adherence, PrEP clinical trials produce knowledge that is not useful for those who are most vulnerable.

Evolutionary and biomedical insights from the rhesus macaque genome.

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.