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We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth ≥3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbour-joining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution., Competing Interests: The authors have declared that no competing interests exist.

There is face validity to the expectation that adults with level 3 autism spectrum disorder (ASD-3) will benefit from a range of psychoeducational interventions. This paper reviews the empirical evidence supporting the effectiveness of these interventions, many of which are currently used in clinical settings. We reviewed 56 peer-reviewed studies of psychoeducational interventions for adults with ASD-3, written in English and since 1968, that met our criteria. The reviewing team included educators, clinicians, researchers, and a biostatistician. The available literature was limited, and most, if not all, of the studies presented some significant methodological limitations. When using Cochrane's criteria to assess seven key outcome domains-activities of daily living, aggressive/destructive behaviors, emotional functioning, language/communication skills, self-injurious behaviors, stereotypy/mannerisms, and vocational skills-we found only moderately reliable evidence to support the effectiveness of interventions designed to improve emotional functioning in adults with ASD-3. The reliability of evidence relevant to the six other outcome domains was rated as low or very low. Based on this review, we suggest directions for future study of interventions for adults with ASD-3, including topics, subpopulations, and approaches that should be explored. We also propose some crucial changes in how future studies regarding this population should be designed, analyzed, and documented, while balancing clinical considerations with scientific/educational utility.

The rodent malaria parasite Plasmodium berghei is an excellent model organism for laboratory-based experimental evaluation of anti-malarial therapeutics prior to studies with human malaria parasites. The rodent model is especially important for evaluation of pre-erythrocytic (PE) stage therapies, especially as current efforts to develop new PE vaccines and drugs is limited by access to P. falciparum and P. vivax sporozoites. Developing a more effective method for cryopreservation of sporozoites would help improve access to sporozoites for laboratories lacking suitable insectary facilities. In this study, P. berghei GFP-expressing sporozoites were purified from infected mosquitoes by manual dissection of salivary glands and different commercially-available, serum-free cryopreservative solutions were evaluated for efficient cryopreservation of the sporozoites. The cryopreservative solutions evaluated included CryoStor CS2, CryoSolutions DX5, CryoSolutions MC, Hestar 200, Voluven, Hetastarch, and Glycerolyte 57. The viability of fresh and post-thaw cryopreserved sporozoites was determined as a function of the relative sporozoite infectivity by infecting HC-04 cells in vitro, monitoring invasion and growth and development of liver stage parasites. Flow cytometer-based counting provided unbiased and fast quantitative assessment of parasite in vitro infection in infected HC-04 and in vivo infectivity was validated by injecting sporozoites IV into mice. CryoStor CS2 delivered the highest post-thaw recovery and infectivity of cryopreserved sporozoites. Sporozoites cryopreserved in CryoStor CS2 achieved 38% complete development of hepatic stages in HC-04 and 100% infectivity in mice. The cryopreservation method described here demonstrates a viable alternative for fresh Plasmodium sporozoites. The use of cryopreserved sporozoites should facilitate greater access to sporozoites for chemotherapeutic and vaccine research.

The Duffy binding protein (DBP) of Plasmodium vivax is vital for host erythrocyte invasion. DBP region II (DBPII) contains critical residues for receptor recognition and anti-DBPII antibodies have been shown to inhibit erythrocyte binding and invasion, thereby making the molecule an attractive vaccine candidate against P. vivax blood stages. Similar to other blood-stage antigens, allelic variation within the DBPII and associated strain-specific immunity is a major challenge for development of a broadly effective vaccine against P. vivax malaria. We hypothesized that immunization with a vaccine composed of multiple DBP alleles or a modified epitope DBP (DEKnull) will be more effective in producing a broadly reactive and inhibitory antibody response to diverse DBPII alleles than a single allele vaccine. In this study, we compared single, naturally occurring DBPII allele immunizations (Sal1, 7.18, P) and DEKnull with a combination of (Sal1, 7.18, P) alleles. Quantitative analysis by ELISA demonstrated that the multiple allele vaccine tend to be more immunogenic than any of the single allele vaccines when tested for reactivity against a panel of DBPII allelic variants whereas DEKnull was less immunogenic than the mixed-allele vaccine but similar in reactivity to the single allele vaccines. Further analysis for functional efficacy by in vitro erythrocyte-binding inhibition assays demonstrated that the multiple allele immunization produced a stronger strain-neutralizing response than the other vaccination strategies even though inhibition remained biased toward some alleles. Overall, there was no correlation between antibody titer and functional inhibition. These data suggest that a multiple allele vaccine may enhance immunogenicity of a DBPII vaccine but further investigation is required to optimize this vaccine strategy to achieve broader coverage against global P. vivax strains., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.

The use of ancient DNA in paleopathological studies of tuberculosis has largely been restricted to confirmation of disease identifications made by skeletal analysis; few attempts at obtaining genotype data from archaeological samples have been made because of the need to perform different PCRs for each genetic locus being studied in an ancient DNA extract. We used a next generation sequencing approach involving hybridization capture directed at specific polymorphic regions of the Mycobacterium tuberculosis genome to identify a detailed genotype for a historic strain of M. tuberculosis from an individual buried in the 19th century St. George's Crypt, Leeds, West Yorkshire, England. We obtained 664,500 sequencing by oligonucleotide ligation and detection (SOLiD) reads that mapped to the targeted regions of the M. tuberculosis genome; the coverage included 218 of 247 SNPs, 10 of 11 insertion/deletion regions, and the repeat elements IS1081 and IS6110. The accuracy of the SOLiD data was checked by conventional PCRs directed at 11 SNPs and two insertion/deletions. The data placed the historic strain of M. tuberculosis in a group that is uncommon today, but it is known to have been present in North America in the early 20th century. Our results show the use of hybridization capture followed by next generation sequencing as a means of obtaining detailed genotypes of ancient varieties of M. tuberculosis, potentially enabling meaningful comparisons between strains from different geographic locations and different periods in the past.

The physical impact of in vitro fertilisation (IVF) is not well explored. The aim of this prospective controlled longitudinal study was to examine the impact of 11 symptoms during an entire long down regulation (LDR) cycle and to determine the effect of the mean recombinant follicle stimulating hormone (RecFSH) dose and ovarian responsiveness of patients and outcome had on reported symptoms. The severity of symptoms was measured using a daily questionnaire to determine a total summary score (TSS) for each symptom, a summary symptom score (SSS) based on all TSS and a mean daily severity for each symptom. Outcome was determined by beta human chorionic gonadotrophin (β-hCG) test result. 79.1% of women undertaking LDR IVF cycles had significant physical symptoms. Treatment symptom severity peaked at oocyte retrieval, with prominent symptoms including bloating, abdominal pain/cramps and fatigue. No relationship was found between outcome, RecFSH dose and ovarian responsiveness with reported symptoms. In conclusion, IVF places a real physical burden on women should be encouraged to reduce undertaking LDR cycles. The impact of the symptoms, particularly the increase in severity leading up to day of oocyte retrieval suggests that women may be warned to reduce stress and activities during this time.