$1 DNA barcodes for reconstructing complex phenomes and finding rare species in specimen‐rich samples

Several of the biggest challenges in taxonomy and systematics are related to a toxic mixture of small size, abundance, and rarity. There are too many species in groups with too few taxonomists and many of these species are very rare and hard to find because they are hidden in mass samples. To make matters worse, these species often have life‐history stages that are morphologically so different that it is difficult to identify them as semaphoronts of the same species. We demonstrate that these biodiversity challenges can be addressed with cost‐effective molecular markers. Here, we describe a next‐generation‐sequencing protocol that can yield barcodes at a chemical cost of < 0.40 USD per specimen. We use this protocol to generate molecular markers for 1015 specimens of tropical midges (Diptera: Chironomidae). The barcodes cluster into 52–61 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering (OC), Generalized Mixed Yule Coalescent (GMYC), or Poisson Tree Process (PTP) is used. More than half of the putative species are rare (< 10 specimens) and we are able to match larvae and adults for 24 of these OTUs. We argue that the proposed protocol will help with processing specimen‐rich biodiversity samples at low cost.     

Continuing to Confront COPD International Patient Survey: Economic Impact of COPD in 12 Countries

BackgroundThe Continuing to Confront COPD International Patient Survey estimated the prevalence and burden of COPD across 12 countries. Using data from this survey we evaluated the economic impact of COPD.MethodsThis cross-sectional, population-based survey questioned 4,343 subjects aged 40 years and older, fulfilling a case definition of COPD based on self-reported physician diagnosis or symptomatology. Direct cost measures were based on exacerbations of COPD (treated and those requiring emergency department visits and/or hospitalisation), contacts with healthcare professionals, and COPD medications. Indirect costs were calculated from work loss values using the Work Productivity and Activity Impairment scale. Combined direct and indirect costs estimated the total societal costs per patient.ResultsThe annual direct costs of COPD ranged from $504 (South Korea) to $9,981 (USA), with inpatient hospitalisations (5 countries) and home oxygen therapy (3 countries) being the key drivers of direct costs. The proportion of patients completely prevented from working due to their COPD ranged from 6% (Italy) to 52% (USA and UK) with 8 countries reporting this to be ≥20%. Total societal costs per patient varied widely from $1,721 (Russia) to $30,826 (USA) but a consistent pattern across countries showed greater costs among those with increased burden of COPD (symptoms, health status and more severe disease) and a greater number of comorbidities.ConclusionsThe economic burden of COPD is considerable across countries, and requires targeted resources to optimise COPD management encompassing the control of symptoms, prevention of exacerbations and effective treatment of comorbidities. Strategies to allow COPD patients to remain in work are important for addressing the substantial wider societal costs.     

Analysis of hybrid H-2D and L antigens with reciprocally mismatched aminoterminal domains: functional T cell recognition requires preservation of fine structural determinants

Studies of immune recognition of hybrid class I antigens expressed on transfected cells have revealed an apparent general requirement that the N(alpha 1) and C1(alpha 2) domains be derived from the same gene in order to preserve recognition by virus-specific H-2-restricted and allospecific T cells. One exception has been the hybrid DL antigen in which the N domain of H-2Ld has been replaced by that of H-2Dd. Cells bearing this molecule serve as targets for some virus and allospecific CTL. Because cells expressing the reciprocal hybrid LD (N domain of H-2Dd replaced by that of H-2Ld) antigen have not been available, it has not been possible to evaluate whether this exception stemmed from the relatedness of H-2Ld and H-2Dd or whether the DL antigen fortuitously preserved some function of the parent molecule as a rare exception. To assess this question, and to evaluate the contribution of the N and C1 domains of H-2Ld and H-2Dd to serologic and T cell recognition, we have constructed the reciprocal chimeric gene pLD (the N exon of H-2Ld substituted for that of H-2Dd), introduced this into mouse L cells by DNA-mediated gene transfer, and analyzed the expressed product biochemically, serologically, and functionally. Transformant L cells expressing either LD or DL antigens were both reactive with a number of anti-H-2Ld or anti-H-2Dd N/C1-specific monoclonal antibodies, indicating the preservation in the hybrid molecules of determinants controlled by discrete domains. Mab binding was generally greater with cells expressing hybrid DL antigen than with those transformants expressing LD molecules. Moreover, the amount of beta 2M associated with DL antigens was more than that associated with LD. Cells expressing hybrid DL antigens were recognized as targets by bulk and cloned allospecific anti-H-2Dd and anti-H-2Ld CTL, whereas cells expressing LD molecules were not recognized by any of the T cells tested. VSV-specific H-2Ld-restricted CTL failed to lyse VSV-infected targets expressing either DL or LD. These results indicate that T cell reactivity of cells expressing the DL hybrid antigen is an exception to the observed general requirement for class I antigens to possess matched N and C1 domains for functional T cell recognition by T cells restricted to parental antigens.(ABSTRACT TRUNCATED AT 400 WORDS)     

Leucocyanidin: Synthesis and properties of (2R,3S,4R)-(+)-3,4,5,7,3′,4′-hexahydroxyflavan

An isomer of leucocyanidin, (2R,3S,4R)-(+)-3,4,5,7,3′,4′-hexahydroxyflavan has been synthesized from (+)-taxifolin, isolated in its phe     

Proanthocyanidins of barley and sorghum; composition as a function of maturity of barley ears

Sorghum vulgare seeds contain a proanthocyanidin polymer consisting largely of 2,3-cis procyanidin units with M?_n, 2500. Hordeum vulgare ears contain low levels of proanthocyanidin oligomers containing 2–4 units, and composed largely of 2,3-trans procyanidin and prodelphinidin units with catechin as the terminal unit. The concentration of the oligomers in barley ears was virtually constant throughout the 33 day growth and ripening period.     

The phytochemistry of proanthocyanidin polymers

The structures of 38 proanthocyanidin polymers (condensed tannins) from 14 widely distributed families of plants are described. The polymers have been isolated from a wide variety of tissues including fruit (ripe and unripe), leaves, bark and phloem. They are all based on a common 4-8 (or 6) linked polyflavan-3-ol structure, analogous to B-type proanthocyanidin dimers.     

Tumor rejection mediated by transfection with allogeneic class I histocompatibility gene

Non-self class I histocompatibility Ag can act as strong alloantigens and be recognized as distinct targets by CTL. To study the possibility of using allograft rejection to generate tumor-specific immunity, we have introduced an allogeneic class I histocompatibility gene, the H-2Kb gene, into a k haplotype tumor, K36.16, by DNA-mediated gene transfer. The K36.16 tumor grows readily and does not confer protective immunity in AKR mice. A total of 37 H-2Kb-transfected K36.16 clones (Kb/K36.16) was isolated and studied individually. The Kb/K36.16 clones were found to differ significantly in the amount of the exogenous H-2Kb antigens expressed on their cell surface. Moreover, as a result of the transfection, the level of expression of the endogenous H-2Dk Ag was also altered when compared to that of the parental K36.16 tumor cells. All the Kb/K36.16 clones that were positive for the H-2Kb Ag were rejected by the semisyngeneic AKR mice. Moreover, some of these Kb/K36.16 clones were also rejected by syngeneic (AKR x C57BL/10)F1 mice. In consequence of immunization with the Kb/K36.16 clones, the AKR and F1 mice were able to survive a subsequent challenge of the wild-type, unmodified, parental K36.16 tumor cells. More importantly, some of these Kb/K36.16 clones demonstrated an active and specific immunotherapeutic effect, and they were able to eradicate the growth of the parental K36.16 tumor cells in AKR mice. This observation therefore reinforces the feasibility of using DNA-mediated gene transfer as a molecular approach to abrogate tumor growth.     

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer

The traditional view of cancer as a genetic disease that can successfully be treated with drugs targeting mutant onco-proteins has motivated whole-genome sequencing efforts in many human cancer types. However, only a subset of mutations found within the genomic landscape of cancer is likely to provide a fitness advantage to the cell. Distinguishing such “driver” mutations from innocuous “passenger” events is critical for prioritizing the validation of candidate mutations in disease-relevant models. We design a novel statistical index, called the Hitchhiking Index, which reflects the probability that any observed candidate gene is a passenger alteration, given the frequency of alterations in a cross-sectional cancer sample set, and apply it to a mutational data set in colorectal cancer. Our methodology is based upon a population dynamics model of mutation accumulation and selection in colorectal tissue prior to cancer initiation as well as during tumorigenesis. This methodology can be used to aid in the prioritization of candidate mutations for functional validation and contributes to the process of drug discovery.