An Efficient and Reliable DNA-based Sex Identification Method for Archaeological Pacific Salmonid (Oncorhynchus spp.) Remains

Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region\u27s Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay coamplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method\u27s reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method\u27s reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method\u27s sensitivity. The method\u27s reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

Ancient DNA reveals northwest range extension of Richardson’s ground squirrel (Urocitellus richardsonii) into northeastern British Columbia, Canada, during the Late Pleistocene

Ancient DNA was extracted from 12 500 to 10 500 year old ground squirrel bones from Tse’K’wa, an archaeological site in the Peace River region of northeastern British Columbia, Canada. Analysis of mitochondrial DNA from seven individuals demonstrates that all are Urocitellus richardsonii (Richardson’s ground squirrel), a species not found in the region today. Phylogenetic and sequence analyses indicate these individuals share a previously undocumented mitochondrial control region haplotype that is most closely related to haplotypes observed in modern specimens from Saskatchewan and Montana. At the end of the Pleistocene these ground squirrels extended their range north and west into open vegetation communities that developed when ice sheets melted and glacial lakes drained. They were subsequently extirpated from the Peace River region when forests replaced earlier pioneering vegetation communities.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Colorectal Endoscopic Stenting Trial (CReST) for obstructing left-sided colorectal cancer: randomized clinical trial

Background Colorectal cancer often presents with obstruction needing urgent, potentially life-saving decompression. The comparative efficacy and safety of endoluminal stenting versus emergency surgery as initial treatment for such patients is uncertain. Methods Patients with left-sided colonic obstruction and radiological features of carcinoma were randomized to endoluminal stenting using a combined endoscopic/fluoroscopic technique followed by elective surgery 1–4 weeks later, or surgical decompression with or without tumour resection. Treatment allocation was via a central randomization service using a minimization procedure stratified by curative intent, primary tumour site, and severity score (Acute Physiology And Chronic Health Evaluation). Co-primary outcome measures were duration of hospital stay and 30-day mortality. Secondary outcomes were stoma formation, stenting completion and complication rates, perioperative morbidity, 6-month survival, 3-year recurrence, resource use, adherence to chemotherapy, and quality of life. Analyses were undertaken by intention to treat. Results Between 23 April 2009 and 22 December 2014, 245 patients from 39 hospitals were randomized. Stenting was attempted in 119 of 123 allocated patients (96.7 per cent), achieving relief of obstruction in 98 of 119 (82.4 per cent). For the 89 per cent treated with curative intent, there were no significant differences in 30-day postoperative mortality (3.6 per cent (4 of 110) versus 5.6 per cent (6 of 107); P = 0.48), or duration of hospital stay (median 19 (i.q.r. 11–34) versus 18 (10–28) days; P = 0.94) between stenting followed by delayed elective surgery and emergency surgery. Among patients undergoing potentially curative treatment, stoma formation occurred less frequently in those allocated to stenting than those allocated to immediate surgery (47 of 99 (47.5 per cent) versus 72 of 106 (67.9 per cent); P = 0.003). There were no significant differences in perioperative morbidity, critical care use, quality of life, 3-year recurrence or mortality between treatment groups. Conclusion Stenting as a bridge to surgery reduces stoma formation without detrimental effects. Registration number: ISRCTN13846816 (http://www.controlled-trials.com)