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\"James D. Watson, the Nobel laureate whose pioneering work helped unlock the mystery of DNA's structure, charts the greatest scientific journey of our time, from the discovery of the double helix to today's controversies to what the future may hold. [This edition has been] updated to include new findings in gene editing, epigenetics, agricultural chemistry, as well as two entirely new chapters on personal genomics and cancer research\"--Provided by publisher.

When DNA profiling was first introduced into the American legal system in 1987, it was heralded as a technology that would revolutionize law enforcement. As an investigative tool, it has lived up to much of this hype-it is regularly used to track down unknown criminals, put murderers and rapists behind bars, and exonerate the innocent.Yet, this promise took ten turbulent years to be fulfilled. In Genetic Witness, Jay D. Aronson uncovers the dramatic early history of DNA profiling that has been obscured by the technique's recent success. He demonstrates that robust quality control and quality assurance measures were initially nonexistent, interpretation of test results was based more on assumption than empirical evidence, and the technique was susceptible to error at every stage. Most of these issues came to light only through defense challenges to what prosecutors claimed to be an infallible technology. Although this process was fraught with controversy, inefficiency, and personal antagonism, the quality of DNA evidence improved dramatically as a result. Aronson argues, however, that the dream of a perfect identification technology remains unrealized.

The human reference genome represents only a small number of individuals, which limits its usefulness for genotyping. We present a method named HISAT2 (hierarchical indexing for spliced alignment of transcripts 2) that can align both DNA and RNA sequences using a graph Ferragina Manzini index. We use HISAT2 to represent and search an expanded model of the human reference genome in which over 14.5 million genomic variants in combination with haplotypes are incorporated into the data structure used for searching and alignment. We benchmark HISAT2 using simulated and real datasets to demonstrate that our strategy of representing a population of genomes, together with a fast, memory-efficient search algorithm, provides more detailed and accurate variant analyses than other methods. We apply HISAT2 for HLA typing and DNA fingerprinting; both applications form part of the HISAT-genotype software that enables analysis of haplotype-resolved genes or genomic regions. HISAT-genotype outperforms other computational methods and matches or exceeds the performance of laboratory-based assays.

The present study demonstrates the plant growth promoting (PGP) potential of a bacterial isolate CDP-13 isolated from 'Capparis decidua' plant, and its ability to protect plants from the deleterious effect of biotic and abiotic stressors. Based on 16S rRNA gene sequence analysis, the isolate was identified as Serratia marcescens. Among the PGP traits, the isolate was found to be positive for ACC deaminase activity, phosphate solubilization, production of siderophore, indole acetic acid production, nitrogen fixation, and ammonia production. CDP-13 showed growth at an increased salt (NaCl) concentration of up to 6%, indicating its potential to survive and associate with plants growing in saline soil. The inoculation of S. marcescens enhanced the growth of wheat plant under salinity stress (150-200 mM). It significantly reduced inhibition of plant growth (15 to 85%) caused by salt stressors. Application of CDP-13 also modulated concentration (20 to 75%) of different osmoprotectants (proline, malondialdehyde, total soluble sugar, total protein content, and indole acetic acid) in plants suggesting its role in enabling plants to tolerate salt stressors. In addition, bacterial inoculation also reduced the disease severity caused by fungal infection, which illustrated its ability to confer induced systemic resistance (ISR) in host plants. Treatment of wheat plants with the test organism caused alteration in anti-oxidative enzymes activities (Superoxide dismutase, Catalase, and Peroxidase) under various salinity levels, and therefore minimizes the salinity-induced oxidative damages to the plants. Colonization efficiency of strain CDP-13 was confirmed by CFU count, epi-fluorescence microscopy, and ERIC-PCR-based DNA fingerprinting approach. Hence, the study indicates that bacterium CDP-13 enhances plant growth, and has potential for the amelioration of salinity stress in wheat plants. Likewise, the results also provide insights into biotechnological approaches to using PGPR as an alternative to chemicals and pesticides.

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean ( Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro’s expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe. Common bean has two distinct domestication centers in Mesoamerica and in the Andes. The authors show that the Andean is the first gene pool successfully introduced in Europe and identify signature of pervasive introgression among gene pools and of selection for flowering underlying adaptation.

Background Wheat is a major cereal that can narrow the gap between the increasing human population and food production. In this connection, assessing genetic diversity and conserving wheat genetic resources for future exploitation is very important for breeding new cultivars that may withstand the expected climate change. The current study evaluates the genetic diversity in selected wheat cultivars using ISSR and SCoT markers, the rbc L and mat K chloroplast DNA barcoding, and grain surface sculpture characteristics. We anticipate that these objectives may prioritize using the selected cultivars to improve wheat production. The selected collection of cultivars may lead to the identification of cultivars adapted to a broad spectrum of climatic environments. Results Multivariate clustering analyses of the ISSR and SCoT DNA fingerprinting polymorphism grouped three Egyptian cultivars with cultivar El-Nielain from Sudan, cultivar Aguilal from Morocco, and cultivar Attila from Mexico. In the other group, cultivar Cook from Australia and cultivar Chinese-166 were differentiated from four other cultivars: cultivar Cham-10 from Syria, cultivar Seri-82 from Mexico, cultivar Inqalab-91 from Pakistan, and cultivar Sonalika from India. In the PCA analysis, the Egyptian cultivars were distinct from the other studied cultivars. The rbc L and  mat K sequence variation analysis indicated similarities between Egyptian cultivars and cultivar Cham-10 from Syria and cultivar Inqalab-91 from Pakistan, whereas cultivar Attila from Mexico was distinguished from all other cultivars. Combining the data of ISSR and SCoT with the  rbc L and  mat K results retained the close resemblance among the two Egyptian cultivars EGY1: Gemmeiza-9 and EGY3: Sakha-93, and the Moroccan cultivar Aguilal, and the Sudanese cultivar El-Nielain and between Seri-82, Inqalab-91, and Sonalika cultivars. The analysis of all data distinguished cultivar Cham-10 from Syria from all other cultivars, and the analysis of grain traits indicated a close resemblance between cv. Cham-10 from and the two Egyptian cultivars Gemmeiza-9 and Sakha-93. Conclusions The analysis of rbc L and mat K chloroplast DNA barcoding agrees with the ISSR and the SCoT markers in supporting the close resemblance between the Egyptian cultivars, particularly Gemmeiza-9 and Sakha-93. The ISSR and SCoT data analyses significantly expressed high differentiation levels among the examined cultivars. Cultivars with closer resemblance may be recommended for breeding new wheat cultivars adapted to various climatic environments.

Background Largemouth bass ( Micropterus salmoides , LMB) is an economic fish in China, which has developed into many different cultured populations in the past decades. These populations exhibit different growth rates, morphological traits, stress resistance, and genetic diversity. Analyzing genetic diversity and molecular identification of these populations is crucial for conserving and utilizing germplasm resources, as well as for breeding new varieties. Result In this study, ten distinct LMB populations from China were collected and examined using fluorescence-labeled microsatellite markers. A total of 53 alleles were identified using seven microsatellite primer pairs, with allele counts ranging from 5 to 11 and an average of 7.571. The observed heterozygosity among the ten LMB populations varied from 0.210 to 0.967, while expected heterozygosity ranged from 0.204 to 0.651, and the polymorphism information content was between 0.175 and 0.597. Genetic distance varied from 0.019 to 0.457, the genetic differentiation index ranged from 0.013 to 0.258, and the number of effective migrants ( N m) was between 0.719 and 18.981. The genetic structure analysis indicated that the ten LMB populations could be classified into two or four groups. The analysis of molecular variance (AMOVA) revealed that 83.77% of genetic variation was found within individuals, with only 16.23% attributed to differences among populations. Through construction of DNA fingerprinting, we discovered unique fragments at several loci were detected in the populations such as the reintroduced Northern LMB population, “Youlu No.3” population, and the hybrid populations. Additionally, we also created digital DNA fingerprint maps of these LMB populations. Through analysis the digital DNA fingerprints from four candidate LMB populations, three known populations corresponded with the populations collected in this study. These results indicated high identification efficiencies of the digital DNA fingerprinting created in this study. Conclusion We established a method to distinguish 10 different LMB populations in China, which will assist in identification, traceability management, protection, and intellectual property rights of LMB in the future.

Triosteum (Caprifoliaceae) is a genus of herbaceous perennial angiosperms composed of three Asian and three North American species. The range of two similar species, T. aurantiacum and T. perfoliatum , overlap in the state of Massachusetts, USA, where the latter species is considered locally endangered and protected by regulations. The population occurring in Barnstable Co. MA, USA was morphologically atypical and had intermediate characteristics between the two taxa. Genome-wide molecular fingerprinting was used to identify this population by comparison to nearby populations with typical morphology for each of the reference species T. aurantiacum and T. perfoliatum . A set of 220,518 high quality SNPs were used to calculate expected heterozygosity, F IS , nucleotide diversity, and F ST , and to create short multi-allelic haplotype markers. Detailed population characterization was performed using Principal Component Analysis (PCA) and fastSTRUCTURE analysis on SNPs, and the haplotype markers were used to create a NJ phylogenetic tree, and pairwise comparisons of the genetic distance (Jaccard Inverse Distance) between individual plants within and between subpopulations, populations, and species. Furthermore, complete chloroplast genome sequences were created, and structural polymorphisms characterized and compared to a range of closely related species. Taken together, the data reveals a fine subpopulation structure within the morphologically atypical population at Barnstable Co. MA, that are more closely related to T. perfoliatum than to T. aurantiacum.

Broccoli ( Brassica oleracea var. italica ) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.

We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.