scholarly journals Genetic insights into the globally invasive and taxonomically problematic tree genus Prosopis

AoB Plants ◽  
2020 ◽  
Author(s):  
María L Castillo ◽  
Urs Schaffner ◽  
Brian W van Wilgen ◽  
Noé Manuel Montaño ◽  
Ramiro O Bustamante ◽  
...  
Keyword(s):  
Diploid Species ◽  
Eastern Africa ◽  
Special Focus ◽  
Sequencing Data ◽  
Management Options ◽  
Multiple Introductions ◽  
Non Invasive ◽  
Chloroplast Markers ◽  
Allopatric Species ◽  
Native Populations

Abstract Accurate taxonomic identification of alien species is crucial to detect new incursions, prevent or reduce the arrival of new invaders and implement management options such as biological control. Globally, the taxonomy of non-native Prosopis species is problematic due to misidentification and extensive hybridization. We performed a genetic analysis on several Prosopis species, and their putative hybrids, including both native and non-native populations, with a special focus on Prosopis invasions in Eastern Africa (Ethiopia, Kenya and Tanzania). We aimed to clarify the taxonomic placement of non-native populations and to infer the introduction histories of Prosopis in Eastern Africa. DNA sequencing data from nuclear and chloroplast markers showed high homology (almost 100%) between most species analysed. Analyses based on seven nuclear microsatellites confirmed weak population genetic structure among Prosopis species. Hybrids and polyploid individuals were recorded in both native and non-native populations. Invasive genotypes of P. juliflora in Kenya and Ethiopia could have a similar native Mexican origin, while Tanzanian genotypes likely are from a different source. Native Peruvian Prosopis pallida genotypes showed high similarity with non-invasive genotypes from Kenya. Levels of introduced genetic diversity, relative to native populations, suggest that multiple introductions of P. juliflora and P. pallida occurred to Eastern Africa. Polyploidy may explain the successful invasion of P. juliflora in Eastern Africa. The polyploid Prosopis juliflora was highly differentiated from the rest of the (diploid) species within the genus. The lack of genetic differentiation between most diploid species in their native ranges supports the notion that hybridization between allopatric species may occur frequently when they are co-introduced into non-native areas. For regulatory purposes, we propose to treat diploid Prosopis taxa from the Americas as a single taxonomic unit in non-native ranges.

Wound With Diabetes: Present Scenario And Future

2020 ◽  
Vol 16 ◽  
Author(s):  
Kuldeep B. Pawar ◽  
Shivani Desai ◽  
Ramesh R. Bhonde ◽  
Ritesh P. Bhole ◽  
Atul A. Deshmukh
Keyword(s):  
Wound Healing ◽  
Blood Flow ◽  
Healing Process ◽  
Endocrine System ◽  
Healing Time ◽  
Special Focus ◽  
Diabetic Wound ◽  
Management Options ◽  
And Migration ◽  
Proliferation And Migration

: Diabetes is a chronic metabolic disorder of endocrine system characterized by increase in blood glucose level. Several factors such as pancreatic damage, oxidative stress, infection, genetic factor, obesity, liver dysfunction play a vital role in pathogenesis of diabetes which further lead to serious diabetic complications. Diabetic wound is one such complication where the wound formation occurs, especially due to pressure and its healing process is disrupted due to factors such as hyperglycemia, neuropathy, nephropathy, peripheral vascular disease, reduction of blood flow, atherosclerosis, impaired fibroblast. Process of wound healing is delayed due to different abnormalities like alteration in nitric oxide level, increase in aldose reductase, sorbitol and fructose. Therefore, diabetic wound requires more time to heal as compare to normal wound. Healing time is delayed in diabetic wound due to many factors such as stress, decreased oxygenation supply, infection, decreased blood flow, impaired proliferation and migration rate, impaired growth factor production, impaired keratinocytes proliferation and migration, and altered vascular endothelial mediators. The current treatment for diabetic wound includes wound patches, oxygenation therapy, hydrogel patches, gene therapy, laser therapy, and stem cell therapy. Medications with phytoconstituents is also one way to manage diabetic wound, but it is not more effective for quick healing. The objective of this review is to understand the potential of various management options which are available for diabetic wound, with a special focus on biological cells.

scholarly journals recoup: flexible and versatile signal visualization from next generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Panagiotis Moulos
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Special Focus ◽  
Next Generation ◽  
Sequencing Data ◽  
User Friendliness ◽  
Computational Environment ◽  
Level Data ◽  
Data Signal ◽  
Generation Sequencing

Abstract Background The relentless continuing emergence of new genomic sequencing protocols and the resulting generation of ever larger datasets continue to challenge the meaningful summarization and visualization of the underlying signal generated to answer important qualitative and quantitative biological questions. As a result, the need for novel software able to reliably produce quick, comprehensive, and easily repeatable genomic signal visualizations in a user-friendly manner is rapidly re-emerging. Results recoup is a Bioconductor package for quick, flexible, versatile, and accurate visualization of genomic coverage profiles generated from Next Generation Sequencing data. Coupled with a database of precalculated genomic regions for multiple organisms, recoup offers processing mechanisms for quick, efficient, and multi-level data interrogation with minimal effort, while at the same time creating publication-quality visualizations. Special focus is given on plot reusability, reproducibility, and real-time exploration and formatting options, operations rarely supported in similar visualization tools in a profound way. recoup was assessed using several qualitative user metrics and found to balance the tradeoff between important package features, including speed, visualization quality, overall friendliness, and the reusability of the results with minimal additional calculations. Conclusion While some existing solutions for the comprehensive visualization of NGS data signal offer satisfying results, they are often compromised regarding issues such as effortless tracking of processing and preparation steps under a common computational environment, visualization quality and user friendliness. recoup is a unique package presenting a balanced tradeoff for a combination of assessment criteria while remaining fast and friendly.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals In Vivo Imaging of Biodegradable Implants and Related Tissue Biomarkers

Polymers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 2348
Author(s):  
Leon Riehakainen ◽  
Chiara Cavallini ◽  
Paolo Armanetti ◽  
Daniele Panetta ◽  
Davide Caramella ◽  
...  
Keyword(s):  
Imaging Modality ◽  
Imaging Techniques ◽  
Special Focus ◽  
Tissue Remodelling ◽  
Biodegradable Implant ◽  
Advantages And Disadvantages ◽  
Non Invasive ◽  
Positron Emission ◽  
Longitudinal Imaging

Non-invasive longitudinal imaging of osseointegration of bone implants is essential to ensure a comprehensive, physical and biochemical understanding of the processes related to a successful implant integration and its long-term clinical outcome. This study critically reviews the present imaging techniques that may play a role to assess the initial stability, bone quality and quantity, associated tissue remodelling dependent on implanted material, implantation site (surrounding tissues and placement depth), and biomarkers that may be targeted. An updated list of biodegradable implant materials that have been reported in the literature, from metal, polymer and ceramic categories, is provided with reference to the use of specific imaging modalities (computed tomography, positron emission tomography, ultrasound, photoacoustic and magnetic resonance imaging) suitable for longitudinal and non-invasive imaging in humans. The advantages and disadvantages of the single imaging modality are discussed with a special focus on preclinical imaging for biodegradable implant research. Indeed, the investigation of a new implant commonly requires histological examination, which is invasive and does not allow longitudinal studies, thus requiring a large number of animals for preclinical testing. For this reason, an update of the multimodal and multi-parametric imaging capabilities will be here presented with a specific focus on modern biomaterial research.

scholarly journals Molecular Tools for the Detection and Deduction of Azole Antifungal Drug Resistance Phenotypes in Aspergillus Species

2017 ◽  
Vol 30 (4) ◽  
pp. 1065-1091 ◽  
Author(s):  
Anna Dudakova ◽  
Birgit Spiess ◽  
Marut Tangwattanachuleeporn ◽  
Christoph Sasse ◽  
Dieter Buchheidt ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Invasive Aspergillosis ◽  
Initial Therapy ◽  
Resistance Testing ◽  
Sequencing Data ◽  
Management Options ◽  
Secondary Resistance ◽  
Content Type ◽  
Antifungal Drug Resistance ◽  
Geographical Regions

SUMMARY The incidence of azole resistance in Aspergillus species has increased over the past years, most importantly for Aspergillus fumigatus. This is partially attributable to the global spread of only a few resistance alleles through the environment. Secondary resistance is a significant clinical concern, as invasive aspergillosis with drug-susceptible strains is already difficult to treat, and exclusion of azole-based antifungals from prophylaxis or first-line treatment of invasive aspergillosis in high-risk patients would dramatically limit drug choices, thus increasing mortality rates for immunocompromised patients. Management options for invasive aspergillosis caused by azole-resistant A. fumigatus strains were recently reevaluated by an international expert panel, which concluded that drug resistance testing of cultured isolates is highly indicated when antifungal therapy is intended. In geographical regions with a high environmental prevalence of azole-resistant strains, initial therapy should be guided by such analyses. More environmental and clinical screening studies are therefore needed to generate the local epidemiologic data if such measures are to be implemented on a sound basis. Here we propose a first workflow for evaluating isolates from screening studies, and we compile the MIC values correlating with individual amino acid substitutions in the products of cyp51 genes for interpretation of DNA sequencing data, especially in the absence of cultured isolates.

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Liping Guan ◽  
Ke Cao ◽  
Yong Li ◽  
Jian Guo ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

scholarly journals Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex

BioTech ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 19
Author(s):  
Emily Amor Stander ◽  
Wesley Williams ◽  
Yamkela Mgwatyu ◽  
Peter van Heusden ◽  
Fanie Rautenbach ◽  
...  
Keyword(s):  
Plant Material ◽  
Transcriptome Assembly ◽  
Cape Floristic Region ◽  
Growth Forms ◽  
Sequencing Data ◽  
Non Invasive ◽  
Aspalathus Linearis ◽  
Wide Range ◽  
Health Promoting ◽  
Biochemical Profiles

Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.

scholarly journals ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA

2020 ◽  
Vol 36 (9) ◽  
pp. 2665-2674
Author(s):  
Nicola Casiraghi ◽  
Francesco Orlando ◽  
Yari Ciani ◽  
Jenny Xiang ◽  
Andrea Sboner ◽  
...  
Keyword(s):  
Cancer Patients ◽  
R Package ◽  
Circulating Tumor Dna ◽  
Supplementary Information ◽  
Sequencing Error ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
Liquid Biopsies ◽  
Non Invasive ◽  
Cross Platform

Abstract Motivation The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next-generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single-nucleotide variants (SNVs) in circulating cell-free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs. Results We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples. Availability and implementation ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http://github.com/cibiobcg/abemus, and it is also available at CRAN official R repository. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Afirma Genomic Sequencing Classifier & Xpression Atlas Molecular Findings in Consecutive Bethesda III-VI Thyroid Nodules

2021 ◽  
Author(s):  
Mimi I Hu ◽  
Steven G Waguespack ◽  
Chrysoula Dosiou ◽  
Paul W Ladenson ◽  
Masha J Livhits ◽  
...  
Keyword(s):  
Needle Aspiration ◽  
Braf V600e ◽  
Genomic Alteration ◽  
Genomic Sequencing ◽  
Test Results ◽  
Sequencing Data ◽  
Non Invasive ◽  
Thyroid Fine Needle Aspiration ◽  
Data Files ◽  
Genomic Variant

Abstract Context Broad genomic analyses among thyroid histologies have been described from relatively small cohorts. Objective Investigate the molecular findings across a large, real-world cohort of thyroid fine needle aspiration (FNA) samples. Design Retrospective analysis of RNA sequencing data files. Setting CLIA laboratory performing Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas (XA) testing. Participants 50,644 consecutive Bethesda III-VI nodules. Intervention none. Main Outcome Measures Molecular test results. Results Of 48,952 Bethesda III/IV FNAs studied, 66% were benign by Afirma GSC. The prevalence of BRAF V600E was 2% among all Bethesda III/IV FNAs and 76% among Bethesda VI FNAs. Fusions involving NTRK, RET, BRAF, and ALK were most prevalent in Bethesda V (10%), and 130 different gene partners were identified. Among small consecutive Bethesda III/IV sample cohorts with one of these fusions and available surgical pathology excision data, the positive predictive value of an NTRK or RET fusion for carcinoma or non-invasive follicular thyroid neoplasm with papillary-like nuclear features was >95%, while for BRAF and ALK fusions it was 81% and 67%, respectively. At least one genomic alteration was identified by the expanded Afirma XA panel in 70% of Medullary Thyroid Carcinoma Classifier positive FNAs, 44% of Bethesda III or IV Afirma GSC suspicious FNAs, 64% of Bethesda V FNAs, and 87% of Bethesda VI FNAs. Conclusions This large study demonstrates that almost half of Bethesda III/IV Afirma GSC suspicious and most Bethesda V/VI nodules had at least 1 genomic variant or fusion identified, which may optimize personalized treatment decisions.

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