Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags

<p>Abstract</p> <p>Background</p> <p>Pearl millet [<it>Pennisetum glaucum </it>(L.) R. Br.] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent. It is also a summer forage crop in the southern USA, Australia and Latin America, and is the preferred mulch in Brazilian no-till soybean production systems. Use of molecular marker technology for pearl millet genetic improvement has been limited. Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes. Therefore, we sought to develop additional SSR markers for the pearl millet research community.</p> <p>Results</p> <p>A set of new pearl millet SSR markers were developed using available sequence information from 3520 expressed sequence tags (ESTs). After clustering, unigene sequences (2175 singlets and 317 contigs) were searched for the presence of SSRs. We detected 164 sequences containing SSRs (at least 14 bases in length), with a density of one per 1.75 kb of EST sequence. Di-nucleotide repeats were the most abundant followed by tri-nucleotide repeats. Ninety primer pairs were designed and tested for their ability to detect polymorphism across a panel of 11 pairs of pearl millet mapping population parental lines. Clear amplification products were obtained for 58 primer pairs. Of these, 15 were monomorphic across the panel. A subset of 21 polymorphic EST-SSRs and 6 recently developed genomic SSR markers were mapped using existing mapping populations. Linkage map positions of these EST-SSR were compared by homology search with mapped rice genomic sequences on the basis of pearl millet-rice synteny. Most new EST-SSR markers mapped to distal regions of linkage groups, often to previous gaps in these linkage maps. These new EST-SSRs are now are used by ICRISAT in pearl millet diversity assessment and marker-aided breeding programs.</p> <p>Conclusion</p> <p>This study has demonstrated the potential of EST-derived SSR primer pairs in pearl millet. As reported for other crops, EST-derived SSRs provide a cost-saving marker development option in pearl millet. Resources developed in this study have added a sizeable number of useful SSRs to the existing repertoire of circa 100 genomic SSRs that were previously available to pearl millet researchers.</p

A Multi-centre Study to Evaluate the Long-Term Efficacy and Safety of Biosimilar Infliximab (Infimab™) in Ankylosing Spondylitis in Real-world Clinical Settings - A perspective from Eastern India

Introduction: Owing to dearth of data on infliximab biosimilars in Indian patients, a pan-India case database-based study with infliximab biosimilar BOW015 (Infimab™) was carried out to capture its efficacy and safety in real world clinical settings in India. Here, we assessed its efficacy and safety in ankylosing spondylitis (AS) among patients in the East India cohort. Materials and methods: Data were collected from multiple centers across the eastern region of India. Patients diagnosed with AS, within the preceding 4-6 months during the preceding one year were included in the study. Patients who were given BOW015 for other indications, prior innovator infliximab or other biologics were excluded from the study. Primary variable was Ankylosing Spondylitis Disease Activity Scale (ASDAS) response defined as change of &gt; 2 in the ASDAS score from the baseline by 4-6 months of follow up. Results: The cohort consisted of 149 patients, predominantly male (69.8%), with mean (±SD) age of 36.75 (±11.11) years and mean (±SD) body weight of 58.26 (±15.4) kgs. Of the treated patients, 91 (61.1%) patients were administered four doses, 10 (6.7%) patients were administered three doses, 37 (24.8%) patients were administered two doses and 11 (7.4%) patients were administered only a single dose of BOW015. In the final analysis set, 81 patients had data at baseline and 4th visit. Among the 81 patients, 74 (91%) patients achieved major improvement, 5 (6%) patients achieved clinically important improvement and 2 (3%) were non-responders at 4th visit. Secondarily, cross categorization of the cohort into disease activity categories by number of infusions administered from baseline to 4th visit and assessment of trends in Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) scores were also carried out and these too confirmed the efficacy of BOW015. Conclusion: Infimab™ (BOW015) showed significant improvement in ASDAS and BASDAI in patients with AS at the end of 4-6 months of follow up with its clinical benefits being apparent as early as first dose of BOW015

Ego-Splitting and the Transcendental Subject. Kant’s Original Insight and Husserl’s Reappraisal

In this paper, I contend that there are at least two essential traits that commonly define being an I: self-identity and self-consciousness. I argue that they bear quite an odd relation to each other in the sense that self-consciousness seems to jeopardize self-identity. My main concern is to elucidate this issue within the range of the transcendental philosophies of Immanuel Kant and Edmund Husserl. In the first section, I shall briefly consider Kant’s own rendition of the problem of the Egosplitting. My reading of the Kantian texts reveals that Kant himself was aware of this phenomenon but eventually deems it an unexplainable fact. The second part of the paper tackles the same problematic from the standpoint of Husserlian phenomenology. What Husserl’s extensive analyses on this topic bring to light is that the phenomenon of the Ego-splitting constitutes the bedrock not only of his thought but also of every philosophy that works within the framework of transcendental thinking

Machine-Part cell formation through visual decipherable clustering of Self Organizing Map

Machine-part cell formation is used in cellular manufacturing in order to process a large variety, quality, lower work in process levels, reducing manufacturing lead-time and customer response time while retaining flexibility for new products. This paper presents a new and novel approach for obtaining machine cells and part families. In the cellular manufacturing the fundamental problem is the formation of part families and machine cells. The present paper deals with the Self Organising Map (SOM) method an unsupervised learning algorithm in Artificial Intelligence, and has been used as a visually decipherable clustering tool of machine-part cell formation. The objective of the paper is to cluster the binary machine-part matrix through visually decipherable cluster of SOM color-coding and labelling via the SOM map nodes in such a way that the part families are processed in that machine cells. The Umatrix, component plane, principal component projection, scatter plot and histogram of SOM have been reported in the present work for the successful visualization of the machine-part cell formation. Computational result with the proposed algorithm on a set of group technology problems available in the literature is also presented. The proposed SOM approach produced solutions with a grouping efficacy that is at least as good as any results earlier reported in the literature and improved the grouping efficacy for 70% of the problems and found immensely useful to both industry practitioners and researchers.Comment: 18 pages,3 table, 4 figure

Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia

Recent advances in DNA sequencing have enabled mapping of genes for monogenic traits in families with small pedigrees and even in unrelated cases. We report the identification of disease-causing mutations in a rare, severe, skeletal dysplasia, studying a family of two healthy unrelated parents and two affected children using whole-exome sequencing. The two affected daughters have clinical and radiographic features suggestive of anauxetic dysplasia (OMIM 607095), a rare form of dwarfism caused by mutations of RMRP. However, mutations of RMRP were excluded in this family by direct sequencing. Our studies identified two novel compound heterozygous loss-of-function mutations in POP1, which encodes a core component of the RNase mitochondrial RNA processing (RNase MRP) complex that directly interacts with the RMRP RNA domains that are affected in anauxetic dysplasia. We demonstrate that these mutations impair the integrity and activity of this complex and that they impair cell proliferation, providing likely molecular and cellular mechanisms by which POP1 mutations cause this severe skeletal dysplasia

Poly-Thymidine Oligonucleotides Mediate Activation of Murine Glial Cells Primarily Through TLR7, Not TLR8

The functional role of murine TLR8 in the inflammatory response of the central nervous system (CNS) remains unclear. Murine TLR8 does not appear to respond to human TLR7/8 agonists, due to a five amino acid deletion in the ectodomain. However, recent studies have suggested that murine TLR8 may be stimulated by alternate ligands, which include vaccinia virus DNA, phosphothioate oligodeoxynucleotides (ODNs) or the combination of phosphothioate poly-thymidine oligonucleotides (pT-ODNs) with TLR7/8 agonists. In the current study, we analyzed the ability of pT-ODNs to induce activation of murine glial cells in the presence or absence of TLR7/8 agonists. We found that TLR7/8 agonists induced the expression of glial cell activation markers and induced the production of multiple proinflammatory cytokines and chemokines in mixed glial cultures. In contrast, pT-ODNs alone induced only low level expression of two cytokines, CCL2 and CXCL10. The combination of pT-ODNs along with TLR7/8 agonists induced a synergistic response with substantially higher levels of proinflammatory cytokines and chemokines compared to CL075. This enhancement was not due to cellular uptake of the agonist, indicating that the pT-ODN enhancement of cytokine responses was due to effects on an intracellular process. Interestingly, this response was also not due to synergistic stimulation of both TLR7 and TLR8, as the loss of TLR7 abolished the activation of glial cells and cytokine production. Thus, pT-ODNs act in synergy with TLR7/8 agonists to induce strong TLR7-dependent cytokine production in glial cells, suggesting that the combination of pT-ODNs with TLR7 agonists may be a useful mechanism to induce pronounced glial activation in the CNS

On measurement of top polarization as a probe of ttˉt \bar t production mechanisms at the LHC

In this note we demonstrate the use of top polarization in the study of $t \bar t$ resonances at the LHC, in the possible case where the dynamics implies a non-zero top polarization. As a probe of top polarization we construct an asymmetry in the decay-lepton azimuthal angle distribution (corresponding to the sign of $\cos\phi_\ell$) in the laboratory. The asymmetry is non-vanishing even for a symmetric collider like the LHC, where a positive $z$ axis is not uniquely defined. The angular distribution of the leptons has the advantage of being a faithful top-spin analyzer, unaffected by possible anomalous $tbW$ couplings, to linear order. We study, for purposes of demonstration, the case of a $Z'$ as might exist in the little Higgs models. We identify kinematic cuts which ensure that our asymmetry reflects the polarization in sign and magnitude. We investigate possibilities at the LHC with two energy options: $\sqrt{s} = 14$ TeV and $\sqrt{s} = 7$ TeV, as well as at the Tevatron. At the LHC the model predicts net top quark polarization of the order of a few per cent for $M_{Z'} \simeq 1200$ GeV, being as high as $10$ for a smaller mass of the $Z'$ of $700$ GeV and for the largest allowed coupling in the model, the values being higher for the $7$ TeV option. These polarizations translate to a deviation from the standard-model value of azimuthal asymmetry of up to about $4$ ($7$) for $14$ ($7$) TeV LHC, whereas for the Tevatron, values as high as $12$ are attained. For the $14$ TeV LHC with an integrated luminosity of 10 fb$^{-1}$, these numbers translate into a $3 \sigma$ sensitivity over a large part of the range $500 \lesssim M_{Z'} \lesssim 1500$ GeV.Comment: 28 page, LaTeX, requires JHEP style file, 12 figures. Typos corrected and references adde

Universal corrections to entanglement entropy of local quantum quenches

We study the time evolution of single interval Renyi and entanglement entropies following local quantum quenches in two dimensional conformal field theories at finite temperature for which the locally excited states have a finite temporal width, \epsilon. We show that, for local quenches produced by the action of a conformal primary field, the time dependence of Renyi and entanglement entropies at order \epsilon^2 is universal. It is determined by the expectation value of the stress tensor in the replica geometry and proportional to the conformal dimension of the primary field generating the local excitation. We also show that in CFTs with a gravity dual, the \epsilon^2 correction to the holographic entanglement entropy following a local quench precisely agrees with the CFT prediction. We then consider CFTs admitting a higher spin symmetry and turn on a higher spin chemical potential \mu. We calculate the time dependence of the order \epsilon^2 correction to the entanglement entropy for small \mu, and show that the contribution at order \mu^2 is universal. We verify our arguments against exact results for minimal models and the free fermion theory