The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Transforming growth factor β neutralization ameliorates pre-existing hepatic fibrosis and reduces cholangiocarcinoma in thioacetamide-treated rats.

Considerable evidence has demonstrated that transforming growth factor β (TGF-β) plays a key role in hepatic fibrosis, the final common pathway for a variety of chronic liver diseases leading to liver insufficiency. Although a few studies have reported that blocking TGF-β with soluble receptors or siRNA can prevent the progression of hepatic fibrosis, as yet no evidence has been provided that TGF-β antagonism can improve pre-existing hepatic fibrosis. The aim of this study was to examine the effects of a murine neutralizing TGF-β monoclonal antibody (1D11), in a rat model of thioacetamide (TAA)-induced hepatic fibrosis. TAA administration for 8 weeks induced extensive hepatic fibrosis, whereupon 1D11 dosing was initiated and maintained for 8 additional weeks. Comparing the extent of fibrosis at two time points, pre- and post-1D11 dosing, we observed a profound regression of tissue injury and fibrosis upon treatment, as reflected by a reduction of collagen deposition to a level significantly less than that observed before 1D11 dosing. Hepatic TGF-β1 mRNA, tissue hydroxyproline, and plasminogen activator inhibitor 1 (PAI-1) levels were significantly elevated at the end of the 8 week TAA treatment. Vehicle and antibody control groups demonstrated progressive injury through 16 weeks, whereas those animals treated for 8 weeks with 1D11 showed striking improvement in histologic and molecular endpoints. During the course of tissue injury, TAA also induced cholangiocarcinomas. At the end of study, the number and area of cholangiocarcinomas were significantly diminished in rats receiving 1D11 as compared to control groups, presumably by the marked reduction of supporting fibrosis/stroma. The present study demonstrates that 1D11 can reverse pre-existing hepatic fibrosis induced by extended dosing of TAA. The regression of fibrosis was accompanied by a marked reduction in concomitantly developed cholangiocarcinomas. These data provide evidence that therapeutic dosing of a TGF-β antagonist can diminish and potentially reverse hepatic fibrosis and also reduce the number and size of attendant cholangiocarcinomas

Increased PAI-1 protein in fibrotic liver was reduced in rats dosed with 1D11.

<p><b>A</b>. A representative Western blot of pooled samples (n = 3) showed marked increase in PAI-1 expression before the start of therapeutic dosing at week 8. Levels were maintained in both PBS and 13C4 groups at the end of study at week 16. Levels of PAI-1 were normalized in livers treated with 1D11. <b>B and C</b>. Hepatic PAI-1 protein was also analyzed by ELISA. At the end of TAA administration, total (B) and active PAI-1 (C) were markedly elevated in fibrotic livers, with a further increase by week 16 in rats treated with PBS or 13C4. After 8 weeks of 1D11 dosing, total PAI-1 and active PAI-1 had returned to normal levels, confirming the immunoblotting data. Values are expressed as mean ± SE, n = 8; * p<0.01 vs. normal controls at week 8; ** p<0.01 vs. PBS or 13C4 group at week 16.</p

1D11decreased TGF-β1 mRNA.

<p>mRNA expression of TGF-β1 was analyzed by quantitative real-time RT-PCR for livers harvested at baseline (prior to treatment) and at week 16 (after treatment). TAA caused a sustained overexpression of TGF-β1 (>6 fold) throughout the study and treatment with 1D11 significantly reduced mRNA levels compared to baseline levels and in both PBS and 13C4 groups at end of study (week 16). Data at week 16 with 1D11 treatment suggest a reversal of fibrosis. Values are expressed as means ± SE, n = 8 per group; * p<0.01 vs. normal controls at week 8; ** p<0.05 vs. PBS or 13C4 group at week 16.</p

1D11 reversed pre-existing hepatic fibrosis.

<p><b>A</b>. Representative photomicrographs of picrosirius red stained liver sections following treatment with TAA for 8 weeks (“baseline”; TAA-8W), or an additional 8 weeks with 13C4 (13C4–16W) or 1D11 (1D11–16W) after cessation of TAA administration. A normal rat liver is also shown (Normal). Livers of rats dosed with TAA for 8 weeks (TAA-8W) had substantial lesions with widely spread fibrous bands (septa), originating from portal areas and extending into the parenchyma. 8 weeks after stopping TAA dosing, fibrotic areas were further expanded, with extensive architectural disorganization and more fibrosis covering a greater percentage of the livers (13C4–16W). Treatment with 1D11 for 8 weeks significantly ameliorated the TAA-mediated histopathological lesions, as shown by an overall improvement in hepatic morphology (1D11–16W). Liver collagen deposition in rats treated with 1D11 was noticeably much reduced than the pre-established fibrosis seen at baseline (TAA-W8), shown in rats that were examined at baseline. Magnification: 40x. <b>B</b>. Morphometric analysis of picrosirius red stained sections. Significantly less collagen was deposited in livers treated with 1D11 (▴) for 4 weeks or 8 weeks, when compared to the PBS (•, * p<0.01) or 13C4 (▪, * p<0.01) treatment groups. Moreover, comparison of 1D11 treated livers to those at week 8 before therapeutic treatment started, showed significantly less collagen deposition (treatment for 4 weeks: 9.61%; 8 weeks: 7.53%, * p<0.05) than that harvested at baseline (week 8∶12.7%). Morphometric quantification further supports the histology of a reversal of pre-existing hepatic fibrosis when TGF-β was neutralized by 1D11. Values represent the percentage of collagen deposition in the total liver section and are expressed as mean ± SE (n = 8, except n = 4 for normal controls at week 0).</p

1D11 reduced cholangiocarcinomas induced by TAA.

<p><b>A</b>. TAA induced profound neoplastic changes in biliary ductules (cholangiocarcinoma) at week 16. As visualized by CK staining, these neoplastic cells extended into the parenchyma, as fibrosis evolved (arrow heads). The neoplasia displayed a typical “intestinal metaplasia”-like appearance (arrows). The number of neoplastic biliary ductules or cells was much lower with 1D11 treatment, compared to the PBS or 13C4 groups. For comparison, a normal liver stained for CK is shown. Magnification: x100 <b>B</b>. CK staining was quantitated. The TAA-induced neoplasia was significantly reduced in rats treated with 1D11 for 8 weeks. In contrast, the neoplasia showed no reduction in rats dosed with PBS or 13C4. Values are expressed as mean ± SE of percentage of CK staining of the entire area of liver section. n = 8; * p<0.01 vs. normal controls; ** p<0.01 vs. PBS, 13C4 and normal control groups. <b>C</b>. To quantify the areas of cholangiocarcinoma, liver sections from the 16 time point were scanned by ChromaVision Imaging Analysis System. The area of the cholangiocarcinomas defined as neoplastic biliary epithelial cells plus stromal fibrotic tissue and infiltrated cells, was measured and expressed as a percentage of the total area of the liver section. Data revealed a striking reduction with 1D11 treatment, as compared to the PBS and 13C4 groups, reflecting a diminishment of cholangiocarcinoma by TGF-β neutralization. n = 8, * p<0.01 vs. normal controls; ** p<0.01 vs. PBS, 13C4 and normal control groups. Values represent mean ± SE.</p

Experimental protocol of TAA induced liver fibrosis.

<p>Fischer rats were dosed with TAA intraperitoneally for 8 weeks (300 mg/kg for 6 weeks, three times weekly, then two times weekly for 2 weeks). A cohort of rats received PBS as normal controls. At the end of 8 weeks, TAA was withdrawn and rats were divided into three cohorts that were given PBS, 13C4 or 1D11 for 8 weeks. 13C4 and 1D11 were dosed at a concentration of 5 mg/kg, intraperitoneally, three times per week.</p

Disassembling Actor-network Theory

The final published version of this paper can be found at: http://dx.doi.org/10.1177/0048393114525858One of the strikingly iconoclastic features of actor-network theory is its juxtaposition of the claim to be a realist perspective with denials that supposedly natural phenomena existed before scientists “made them up”. This paper explains and criticises such arguments in the work of Bruno Latour. By combining referent and reference in the concept of assemblages, Latour provides a superficially viable way to reconcile these apparently incompatible claims. This paper will argue, however, that this conflation of referent and reference leads Latour’s ontology into difficulties that can only be resolved by abandoning it in favour of a more conventional – critical – realism

The Genomics of Arthrogryposis, a Complex Trait: Candidate Genes and Further Evidence for Oligogenic Inheritance

Arthrogryposis is a clinical finding that is present either as a feature of a neuromuscular condition or as part of a systemic disease in over 400 Mendelian conditions. The underlying molecular etiology remains largely unknown because of genetic and phenotypic heterogeneity. We applied exome sequencing (ES) in a cohort of 89 families with the clinical sign of arthrogryposis. Additional molecular techniques including array comparative genomic hybridization (aCGH) and Droplet Digital PCR (ddPCR) were performed on individuals who were found to have pathogenic copy number variants (CNVs) and mosaicism, respectively. A molecular diagnosis was established in 65.2% (58/89) of families. Eleven out of 58 families (19.0%) showed evidence for potential involvement of pathogenic variation at more than one locus, probably driven by absence of heterozygosity (AOH) burden due to identity-by-descent (IBD). RYR3, MYOM2, ERGIC1, SPTBN4, and ABCA7 represent genes, identified in two or more families, for which mutations are probably causative for arthrogryposis. We also provide evidence for the involvement of CNVs in the etiology of arthrogryposis and for the idea that both mono-allelic and bi-allelic variants in the same gene cause either similar or distinct syndromes. We were able to identify the molecular etiology in nine out of 20 families who underwent reanalysis. In summary, our data from family-based ES further delineate the molecular etiology of arthrogryposis, yielded several candidate disease-associated genes, and provide evidence for mutational burden in a biological pathway or network. Our study also highlights the importance of reanalysis of individuals with unsolved diagnoses in conjunction with sequencing extended family members