Next-generation sequencing (NGS) platforms: An exciting era of genome sequence analysis

© Springer Nature Singapore Pte Ltd. 2019. DNA referred to as blueprint of life codes for the diversity and function of all the living organisms. Determining DNA sequences of the living organisms not only gives an overview of their genetic makeup, but also provides information about their function. Nonetheless it was not easy to determine the genome sequencing of all the diversity around us especially with the technologies available before 2010. Therefore, determining the sequence of humans and some other organisms only was prioritized. Pioneering methods for DNA sequencing given discovered by Maxam and Gilbert, and Sanger although were very powerful and popular but were not high throughput and economic. Therefore, it was necessary to develop new economic and high-throughput methods that can sequence the biodiversity consequently providing better insights of their possible function. New methods were developed and commercialized by Roche Life Sciences, Thermo Fisher Scientific, Illumina, and Applied Biosystems. These methods generally referred to as next-generation sequencing methods have revolutionized the DNA sequencing. Many sequencing platforms employing NGS have been developed including pyrosequencing, Ion Torrent technology, Illumina/Solexa platform, and SOLiD (Sequencing by Oligonucleotide Ligation and Detection). Further optimization has led to innovative third and fourth-generation platforms as single molecule real-time (SMRT) sequencing by PacBio, nanopore sequencing, etc. As a consequence there is a sharp increase in the number of genomes being published and other genome-based studies since 2012. This has made it easy even to imagine of sequencing the genomes of individuals. Furthermore, scientists are now looking for third-generation sequencers that may be significantly different from the sequencers that are currently available

Chiral perturbation theory with Wilson-type fermions including a2a^2 effects: Nf=2N_f=2 degenerate case

We have derived the quark mass dependence of $m_{\pi}^2$, $m_{\rm AWI}$ and $f_{\pi}$, using the chiral perturbation theory which includes the $a^2$ effect associated with the explicit chiral symmetry breaking of the Wilson-type fermions, in the case of the $N_f=2$ degenerate quarks. Distinct features of the results are (1) the additive renormalization for the mass parameter $m_q$ in the Lagrangian, (2) $O(a)$ corrections to the chiral log ($m_q\log m_q$) term, (3) the existence of more singular term, $\log m_q$, generated by $a^2$ contributions, and (4) the existence of both $m_q\log m_q$ and $\log m_q$ terms in the quark mass from the axial Ward-Takahashi identity, $m_{\rm AWI}$. By fitting the mass dependence of $m_\pi^2$ and $m_{\rm AWI}$, obtained by the CP-PACS collaboration for $N_f=2$ full QCD simulations, we have found that the data are consistently described by the derived formulae. Resumming the most singular terms $\log m_q$, we have also derived the modified formulae, which show a better control over the next-to-leading order correction.Comment: 21 pages, 4 figures (10 eps files), Revtex4, some discussions and references added, the final version to appear in PR

Two flavors of dynamical quarks on anisotropic lattices

We report on our study of two-flavor full QCD on anisotropic lattices using $O(a)$-improved Wilson quarks coupled with an RG-improved glue. The bare gauge and quark anisotropies corresponding to the renormalized anisotropy $\xi=a_s/a_t = 2$ are determined as functions of $\beta$ and $\kappa$, which covers the region of spatial lattice spacings $a_s\approx 0.28$--0.16 fm and $m_{PS}/m_V\approx 0.6$--0.9. The calibrations of the bare anisotropies are performed with the Wilson loop and the meson dispersion relation at 4 lattice cutoffs and 5--6 quark masses. Using the calibration results we calculate the meson mass spectrum and the Sommer scale $r_0$. We confirm that the values of $r_0$ calculated for the calibration using pseudo scalar and vector meson energy momentum dispersion relation coincide in the continuum limit within errors. This work serves to lay ground toward studies of heavy quark systems and thermodynamics of QCD including the extraction of the equation of state in the continuum limit using Wilson-type quark actions.Comment: 16 pages, 23 figures, Version accepted for publication in Physical Review

Development of an indigenous screening instrument in Pakistan: the Aga Khan University Anxiety and Depression Scale

The use of translations of instruments for detecting anxiety and depression continues to be debated. An indigenous screening instrument has been developed in Urdu for anxiety-depression syndromes at the Aga Khan University. It has been developed from the complaints of 150 anxious and depressed patients presenting to a non-speciality clinic and has been validated in 53 patients in a psychiatry clinic. The questionnaire has 25 items, 13 psychlogical and 12 somatic. At a score of 20 it has a sensitivity of 66%, a specificity of 79%, a positive predictive value of 83 and a negative predictive value of 60. In comparison with available instruments in Urdu, comprising of either psychological or somatic items, this scale includes both, which increases its reliability for use as a screening instrument by Community Health Workers in a primary health care setting, in epidemiologic work in Pakistan and in transcultural psychiatric research

Physicians’ and nurses’ perspectives on the importance of advance directives in tertiary care hospitals

Objective: This study aimed to explore and identify the nurses’ and physicians’ views about Advance Directives and identified their perspectives on its importance, in the context of Pakistan.Methodology: Using a purposive sample, six physicians and seven nurses from two tertiary care hospitals in Karachi participated in the study. Data was collected using semi structured interviews that were transcribed verbatim. The interviews were coded and categorized manually. Analysis of the data drew four categories: roles of physicians and nurses in the End of life care, challenges they faced while taking end of life care decisions; their perspectives about Advance Directives, and the scope of acceptability of Advance Directives in the context of a Pakistani society.Results: This study revealed that patients’ families and physicians usually take decisions for patients’ End of Life care. Although majority of participants acknowledged the usefulness of Advance Directives, they explicated several issues that may be encountered in implementing it. The issues included non-disclosure of diagnosis to the patient in Pakistani culture, the tedious legalization process involved, and the potential problem of forged documents.Conclusion: Participants recommended establishment of Palliative Care services before execution of Advance Directives. This study indicated viability of Advance Directives; however, a wider exploration would be required in terms of study population. Reforms to support this concept would be required in systems, structure, legal policy, and training of Health care professionals. Besides these transformations, promotion of public education about the advantages of Advance Directives could enhance their acceptability among the general population

Canine plasma and tissue fatty acid profiles and their correlation with hair coat conditions

This study was initiated to study the probable relationships between the fatty acid profiles of the plasma, skin, liver and brain and to determine their correlations with hair coat conditions in owned and stray dogs. A total of35 dogs were used in this study. Twenty-three owned dogs obtained from the University Veterinary Hospital (UVH dogs) were subjected to blood sampling and hair coat scoring only. Twelve euthanized dogs were sourced from a local animal shelter (LAS dogs) and blood, brain, liver and skin samples were obtained. Hair coat scores were performed under standardized conditions and was found that the UVH dogs (median score = 4.1) had significantly better scores compared to LAS dogs (median score = 3.1, P<0.05). The UVH dogs had significantly lower (P<0.05) n-6:n-3 ratios and lower plasma arachidonate content. The skin and plasma fatty acid profiles correlated well with each other but no correlation was evident between the brain and plasma fatty acid profiles. Increased amounts of plasma and skin n-3 and n-6 polyunsaturated fatty acids were associated with better hair coat conditions. However, plasma n-6 fatty acids seemed to .have a stronger positive correlation to hair coat scores in dogs (p = 0.683, P<0.05) compared to plasma n-3 fatty acids (p = 0.512, P<0.05) and fatty acid profiles from other tissues. In summary, this report underscores the importance of n-3 and n-6 fatty acids to the hair coat condition of dogs kept under humid tropical conditions

Study on genetic diversity in Pakistani wheat varieties using simple sequence repeat (SSR) markers

Common wheat ( Triticum aestivum L.) is a grass species, cultivated world wide. Globally, it is the most important human food grain and ranks second in total production as a cereal crop behind maize. Genetic diversity evaluation of germplasm is the basis of improvement in wheat. In the present study genetic diversity of 10 varieties of wheat (T. aestivum) were analyzed using 14 simple sequence repeat (SSR) primer sets. To estimate the genetic diversity among the genotypes, bivariate data matrix was generated and genetic distances were calculated using unweighted pair group of arithmetic mean (UPGMA) procedure. A high degree of genetic polymorphism was observed among the wheat varieties with average genetic distances ranged from 16 to 67%. SSR primer gdm-3, gdm-19, gdm-61, gdm-62, gdm-64, gdm-86, gdm-88, gdm 93-2a, 93-4b, gdm-13 and gdm-115 amplified 3, 2.9, 4.1, 4.7, 3, 1.7, 2.7, 3.7, 5.8, 4.1 and 1.4 loci per variety, respectively. Most diverse varieties of wheat were identified (Punjab-81 and Indus-79) and recommendations were made to utilize these varieties in future breeding program