The transcriptomic and genomic architecture of acrididae grasshoppers

Genetic polymorphism is described as the variation in DNA sequence between distinct individuals of a given species or population. This polymorphism is reflected from individuals to entire populations, and from single nucleotides to the entire genome spanning billions of base pairs. A fundamental aim of functional genomics is to establish links between genetic polymorphism and phenotypic variation, to explain this observed variation. Recent developments in high throughput sequencing have made it possible to adequately explore this link. My dissertation explores genetic and genomic polymorphism in Gomphocerine grasshoppers, an insect group with unusually large and complex genomes using novel and contemporary transcriptomic and genomic methods.Genetische Polymorphismen beschreiben die Variation in DNS-Sequenzen zwischen Individuen einer Art oder zwischen Populationen. Die genetischen Polymorphismen zwischen Individuen bis zu ganzen Population und von Punktmutationen zu ganzen Genomen umfassen Milliarden von Basenpaaren. Ein fundamentales Ziel funktioneller Genomik ist es, den Zusammenhang von genetischen Polymorphismen und phänotypischer Variation zu verstehen. Neuste Entwicklungen in der Hochdurchsatzsequenzierung haben es möglich gemacht, diesen Zusammenhang umfassend zu explorieren. Meine Dissertation ergründet genetische und genomische Polymorphismen in Heuschrecken der Unterfamilie Gomphocerinae, einer Insektengruppe mit ungewöhnlich großen und komplexen Genomen, mittels moderner transkriptomischer und genomischer Methoden

Outcomes of Cement in Cement revision, in Revision Total Hip Arthroplasty

BACKGROUND: The cement-in-cement femoral revision technique involves removing a femoral component from a well-fixed femoral cement mantle and cementing a new stem into the original mantle. This technique, when carried out for the correct indications, is fast, relatively inexpensive and carries a reduced short-term risk for the patient compared with conventional way of removing well-fixed cement. AIM: To analyze the effectiveness of cement in cement revision of the femoral stem while performing a revision Total Hip Arthroplasty (THA). METHODS: We analyzed a consecutive series of 79 patients who underwent a cement in cement revision THA between June-2015 to June-2018. All the patients were retrospectively analysed for operative time, complications, clinical and radiological outcomes. RESULTS: Average age was 76 years (49-86). The mean follow-up was 16.2 months (12-45). The average operative time was 184.6 (90-290) minutes. Most common indication was cup loosening in 28 patients (42.4%), dislocation in 14 patients (21.2%) and stem loosening in 12 patients (18.2%) Nine patients (11%) had one or more complications. Pre-operatively, 10 patients (13%) had lucency at the cement bone interface. Recent review has shown that 8 of these patients’ radiographs have remained unchanged, and in 2 of them there is a slight progression of lucency. Common post op clinical complaintswere persistent pain and abductor weakness. Five (6.3%) patients required a re-revision. Most of the patients had a good or satisfactory outcome.No stems showed radiological loosening. CONCLUSION: The cement-in-cement technique for revision of the femoral component gave promising results and had the advantages of speed, less blood or bone stock loss, less risk of femoral perforation or fracture, decreased financial costs and reduced post op morbidity

Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size

Shah A, Hoffman J, Schielzeth H. Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size. BMC genomics. 2019;20(1): 370.BACKGROUND: The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering. We then combined the best-assembled contigs from three different de novo transcriptome assemblers (Trinity, SOAPdenovo-trans and Oases/Velvet) into a single assembly.; RESULTS: This resulted in 82,251 contigs with a N50 of 1357 and a TransRate assembly score of 0.325, which compares favourably with other orthopteran transcriptome assemblies. Around 87% of the transcripts could be annotated using InterProScan 5, BLASTx and the dammit! annotation pipeline. We identified a number of genes involved in pigmentation and green pigment metabolism pathways. Furthermore, we identified 76,221 putative single nucleotide polymorphisms residing in 8400 contigs. We also assembled the mitochondrial genome and investigated levels of sequence divergence with other species from the genus Gomphocerus. Finally, we detected and assembled Wolbachia sequences, which revealed close sequence similarity to the strain pel wPip.; CONCLUSIONS: Our study has generated a significant resource for uncovering genotype-phenotype associations in a species with an extraordinarily large genome, while also providing mitochondrial and Wolbachia sequences that will be useful for comparative studies

Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size

Shah A, Hoffman J, Schielzeth H. Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size. BMC genomics. 2019;20(1): 370.BACKGROUND: The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering. We then combined the best-assembled contigs from three different de novo transcriptome assemblers (Trinity, SOAPdenovo-trans and Oases/Velvet) into a single assembly.; RESULTS: This resulted in 82,251 contigs with a N50 of 1357 and a TransRate assembly score of 0.325, which compares favourably with other orthopteran transcriptome assemblies. Around 87% of the transcripts could be annotated using InterProScan 5, BLASTx and the dammit! annotation pipeline. We identified a number of genes involved in pigmentation and green pigment metabolism pathways. Furthermore, we identified 76,221 putative single nucleotide polymorphisms residing in 8400 contigs. We also assembled the mitochondrial genome and investigated levels of sequence divergence with other species from the genus Gomphocerus. Finally, we detected and assembled Wolbachia sequences, which revealed close sequence similarity to the strain pel wPip.; CONCLUSIONS: Our study has generated a significant resource for uncovering genotype-phenotype associations in a species with an extraordinarily large genome, while also providing mitochondrial and Wolbachia sequences that will be useful for comparative studies

Functional outcome of Schatzker type V and VI tibial plateau fractures managed with open reduction internal fixation using dual plates

Background: Complex tibial plateau fractures remain a challenge to even the most experienced surgeons. These injuries usually affect the young population in their productive years thereby causing socioeconomic impact. We performed a retrospective study to evaluate the functional outcome of of Schatzker type V and VI managed through open reduction and internal fixation.Methods: 26 patients with Schatzker type V and type VI tibial plateau fractures treated with open reduction and internal fixation using plates were included in the study. Three patients were lost to follow up, 23 patients were evaluated in the final analysis. The preoperative, intraoperative data was noted from the indoor files.The final evaluation was done using Oxford knee score and VAS score.Results: There were nine Schatzker type V fractures and 14 patients with Schatzker type VI fractures. The mean duration of follow-up was 68.32 months ranging from 41 months to 126 months. The mean Oxford knee score was 39.78. Patients with Schatzker type VI had mean OKS of 37.7.The mean MPTA and mean PPTA were 88.75 degrees and 7.35 degrees respectively. Average VAS Score was 2.8 ranging from 1 to 3.9. All patients returned to their pre-injury level of activity and employment. There were no patients of deep infection. Conclusions: We conclude that open reduction and internal fixation of high-energy tibial plateau fractures gives excellent to good functional outcome with minimal soft tissue complications. The complications can be minimized with proper patient selection and soft tissue dissection

Algorithms for merging tick data and data analysis for Indian financial market

This paper discusses the problem of ‘merging’ financial tick data available from data sources such as Bloomberg, NSE, and Thomson Reuters etc. Different derivative securities are traded on the exchange with different frequencies in each unit of time such as second or minute in intraday trading , therefore, it is difficult to form ‘ordered pairs’, which are essential for any financial analysis, of tick data representing the simultaneous trades of the different derivative securities. Merging refers to the conversion of intraday tick data of different securities of varying frequencies, as provided by data sources, into the form in which the tick data of all traded derivative securities have same frequency, so that it is possible to form ordered pairs of data (in every unit time period) in such a way that the original nature of the data is preserved. The four merging algorithms: Truncation, Weighted mean, median and all-combinations algorithm are compared with Dropdown algorithm, which is being used widely by the trading firms. Using NSE intraday tick data for various trading days, it is found that ‘Truncation’ and ‘Weighted Mean’ algorithms are more efficient merging algorithms

High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome

Shah A, Schielzeth H, Albersmeier A, Kalinowski J, Hoffman J. High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome. Ecology and Evolution. 2016;16(6):5718-5727.Despite recent advances in high-throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club-legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired-end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild-caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high-throughput sequencing and graph-based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes

High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome

Shah A, Schielzeth H, Albersmeier A, Kalinowski J, Hoffman J. High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome. Ecology and Evolution. 2016;16(6):5718-5727.Despite recent advances in high-throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club-legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired-end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild-caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high-throughput sequencing and graph-based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes

Outcomes of Transcatheter Aortic Valve Replacement in Patients With Cardiogenic Shock

AIMS: The safety and efficacy of transcatheter aortic valve replacement (TAVR) with contemporary balloon expandable transcatheter valves in patients with cardiogenic shock (CS) remain largely unknown. In this study, the TAVRs performed for CS between June 2015 and September 2022 using SAPIEN 3 and SAPIEN 3 Ultra bioprosthesis from the Society of Thoracic Surgeons/American College of Cardiology Transcatheter Valve Therapy Registry were analysed. METHODS AND RESULTS: CS was defined as: (i) coding of CS within 24 h on Transcatheter Valve Therapy Registry form; and/or (ii) pre-procedural use of inotropes or mechanical circulatory support devices and/or (iii) cardiac arrest within 24 h prior to TAVR. The control group was comprised of all the other patients undergoing TAVR. Baseline characteristics, all-cause mortality, and major complications at 30-day and 1-year outcomes were reported. Landmark analysis was performed at 30 days post-TAVR. Cox-proportional multivariable analysis was performed to determine the predictors of all-cause mortality at 1 year. A total of 309 505 patients underwent TAVR with balloon-expandable valves during the study period. Of these, 5006 patients presented with CS prior to TAVR (1.6%). The mean Society of Thoracic Surgeons score was 10.76 ± 10.4. The valve was successfully implanted in 97.9% of patients. Technical success according to Valve Academic Research Consortium-3 criteria was 94.5%. In a propensity-matched analysis, CS was associated with higher in-hospital (9.9% vs. 2.7%), 30-day (12.9% vs. 4.9%), and 1-year (29.7% vs. 22.6%) mortality compared to the patients undergoing TAVR without CS. In the landmark analysis after 30 days, the risk of 1-year mortality was similar between the two groups [hazard ratio (HR) 1.07, 95% confidence interval (CI) 0.95-1.21]. Patients who were alive at 1 year noted significant improvements in functional class (Class I/II 89%) and quality of life (ΔKCCQ score +50). In the multivariable analysis, older age (HR 1.02, 95% CI 1.02-1.03), peripheral artery disease (HR 1.25, 95% CI 1.06-1.47), prior implantation of an implantable cardioverter-defibrillator (HR 1.37, 95% CI 1.07-1.77), patients on dialysis (HR 2.07, 95% CI 1.69-2.53), immunocompromised status (HR 1.33, 95% CI 1.05-1.69), New York Heart Association class III/IV symptoms (HR 1.50, 95% CI 1.06-2.12), lower aortic valve mean gradient, lower albumin levels, lower haemoglobin levels, and lower Kansas City Cardiomyopathy Questionnaire scores were independently associated with 1-year mortality. CONCLUSION: This large observational real-world study demonstrates that the TAVR is a safe and effective treatment for aortic stenosis patients presenting with CS. Patients who survived the first 30 days after TAVR had similar mortality rates to those who were not in CS

Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases

Wollenberg Valero KC, Garcia-Porta J, Rodriguez A, et al. Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. Nature Communications. 2017;8(1): 15213.Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying expression of genes related to morphological feature formation. We test these predictions by combining evidence from gene expression in two distantly related frogs, Xenopus laevis and Mantidactylus betsi-leanus, with patterns of morphological evolution in the entire radiation of Madagascan mantellid frogs. Genes linked to morphological structure formation are expressed in a highly phase-specific pattern, suggesting uncoupling of phenotypic evolution across life-history phases. This gene expression pattern agrees with uncoupled rates of trait evolution among life-history phases in the mantellids, which we show to have undergone an adaptive radiation. Our results validate a prevalence of uncoupling in the evolution of tadpole and adult phenotypes of frogs