scholarly journals The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations

2020 ◽  
Author(s):  
Jessica Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Travis Wheeler ◽  
Arian F.A. Smit
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Consensus Sequence ◽  
Model Organisms ◽  
Community Resource ◽  
Genome Annotations ◽  
Protein Alignments ◽  
Insight Into ◽  
Proof Of Principle

Abstract The 3.0-3.2 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

scholarly journals The Dfam community resource of transposable element families, sequence models, and genome annotations

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jessica Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Travis J. Wheeler ◽  
Arian F. Smit
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Consensus Sequence ◽  
Model Organisms ◽  
Community Resource ◽  
Open Access Database ◽  
Genome Annotations ◽  
Protein Alignments ◽  
Insight Into

AbstractDfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

scholarly journals Comparative analysis of whole flower transcriptomes in the Zingiberales

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5490 ◽  
Author(s):  
Ana Maria R. Almeida ◽  
Alma Piñeyro-Nelson ◽  
Roxana B. Yockteng ◽  
Chelsea D. Specht
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Model Organisms ◽  
Comparative Approach ◽  
Careful Study ◽  
Sequencing Technologies ◽  
Outgroup Species ◽  
Floral Diversification ◽  
Genomic Scale ◽  
Insight Into

The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.

Turkish Muslims in a German city: Entrepreneurial and residential self-determination

2015 ◽  
Vol 12 (1) ◽  
pp. 1-12
Author(s):  
Sarah Hackett
Keyword(s):  
Residential Patterns ◽  
Academic Literature ◽  
Self Employment ◽  
German City ◽  
Post War ◽  
Oral History Interviews ◽  
The City ◽  
Insight Into ◽  
Term Objective

Drawing upon a collection of oral history interviews, this paper offers an insight into entrepreneurial and residential patterns and behaviour amongst Turkish Muslims in the German city of Bremen. The academic literature has traditionally argued that Turkish migrants in Germany have been pushed into self-employment, low-quality housing and segregated neighbourhoods as a result of discrimination, and poor employment and housing opportunities. Yet the interviews reveal the extent to which Bremen’s Turkish Muslims’ performances and experiences have overwhelmingly been the consequences of personal choices and ambitions. For many of the city’s Turkish Muslim entrepreneurs, self-employment had been a long-term objective, and they have succeeded in establishing and running their businesses in the manner they choose with regards to location and clientele, for example. Similarly, interviewees stressed the way in which they were able to shape their housing experiences by opting which districts of the city to live in and by purchasing property. On the whole, they perceive their entrepreneurial and residential practices as both consequences and mediums of success, integration and a loyalty to the city of Bremen. The findings are contextualised within the wider debate regarding the long-term legacy of Germany’s post-war guest-worker system and its position as a “country of immigration”.

Is 3 years adequate for tracking completely occluded coiled aneurysms?

2020 ◽  
Vol 133 (3) ◽  
pp. 758-764
Author(s):  
Eung Koo Yeon ◽  
Young Dae Cho ◽  
Dong Hyun Yoo ◽  
Su Hwan Lee ◽  
Hyun-Seung Kang ◽  
...  
Keyword(s):  
De Novo ◽  
Careful Monitoring ◽  
Surveillance Period ◽  
Radiological Data ◽  
De Novo Aneurysm ◽  
Low Probability ◽  
Almost All ◽  
Annual Risk

OBJECTIVEThe authors conducted a study to ascertain the long-term durability of coiled aneurysms completely occluded at 36 months’ follow-up given the potential for delayed recanalization.METHODSIn this retrospective review, the authors examined 299 patients with 339 aneurysms, all shown to be completely occluded at 36 months on follow-up images obtained between 2011 and 2013. Medical records and radiological data acquired during the extended monitoring period (mean 74.3 ± 22.5 months) were retrieved, and the authors analyzed the incidence of (including mean annual risk) and risk factors for delayed recanalization.RESULTSA total of 5 coiled aneurysms (1.5%) occluded completely at 36 months showed recanalization (0.46% per aneurysm-year) during the long-term surveillance period (1081.9 aneurysm-years), 2 surfacing within 60 months and 3 developing thereafter. Four showed minor recanalization, with only one instance of major recanalization. The latter involved the posterior communicating artery as an apparent de novo lesion, arising at the neck of a firmly coiled sac, and was unrelated to coil compaction or growth. Additional embolization was undertaken. In a multivariate analysis, a second embolization for a recurrent aneurysm (HR = 22.088, p = 0.003) independently correlated with delayed recanalization.CONCLUSIONSAlmost all coiled aneurysms (98.5%) showing complete occlusion at 36 months postembolization proved to be stable during extended observation. However, recurrent aneurysms were predisposed to delayed recanalization. Given the low probability yet seriousness of delayed recanalization and the possibility of de novo aneurysm formation, careful monitoring may be still considered in this setting but at less frequent intervals beyond 36 months.

Moving Songs

2019 ◽  
pp. 590-606
Author(s):  
Sally Treloyn ◽  
Matthew Dembal Martin ◽  
Rona Goonginda Charles
Keyword(s):  
Cultural Heritage ◽  
Knowledge Transmission ◽  
Intercultural Relationships ◽  
Cultural Negotiation ◽  
Intercultural Collaboration ◽  
Present Collection ◽  
Intergenerational Knowledge ◽  
Early Phases ◽  
Insight Into

Repatriation has become almost ubiquitous in ethnomusicological research on Australian Indigenous song. This article provides insights into processes of a repatriation-centered song revitalization project in the Kimberley, northwest Australia. Authored by an ethnomusicologist and two members of the Ngarinyin cultural heritage community, the article provides firsthand accounts of the early phases of a long-term repatriation-centered project referred to locally as the Junba Project. The authors provide a sample of narratives and dialogues that deliver insight into experiences of the work of identifying recordings “in the archive” and cultural negotiation and use of recordings “on Country.” The entanglement of local epistemological frameworks with past and present collection, archival research, repatriation, and dissemination for intergenerational knowledge transmission between spirits, Country, and the living, is explored, showing how recordings move song knowledge from community to archive to community and from generation to generation, and move people in present-day communities. The chapter considers how these “moving songs” allow an interrogation of the fraught endeavor of intercultural collaboration in the pursuit of revitalizing Indigenous song traditions. It positions repatriation as a method that can support intergenerational knowledge transmission and as a method to consider past and present intercultural relationships within research projects and between cultural heritage communities and collecting institutions.

scholarly journals Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

2021 ◽  
Author(s):  
José Cerca ◽  
Marius F. Maurstad ◽  
Nicolas C. Rochette ◽  
Angel G. Rivera‐Colón ◽  
Niraj Rayamajhi ◽  
...  
Keyword(s):  
De Novo ◽  
Model Organisms

scholarly journals Long-term outcomes of fully covered self-expandable metal stents versus plastic stents in chronic pancreatitis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sang Hoon Lee ◽  
Yeon Suk Kim ◽  
Eui Joo Kim ◽  
Hee Seung Lee ◽  
Jeong Youp Park ◽  
...  
Keyword(s):  
Chronic Pancreatitis ◽  
Clinical Efficacy ◽  
De Novo ◽  
Plastic Stents ◽  
Metal Stents ◽  
Plastic Stent ◽  
Sems Group ◽  
Spontaneous Migration

AbstractChronic pancreatitis (CP) related main pancreatic duct (MPD) stricture has been a challenge for endoscopists. Fully covered self-expandable metal stents (FC-SEMS) has been tried in CP patients, but the efficacy and safety are still controversial. Thus, we aim to compare the long-term clinical efficacy of FC-SEMS vs. plastic stent placement in persistent MPD strictures secondary to CP. Between 2007 and 2018, 80 chronic pancreatitis patients (58 males, median age 49 years), who underwent endoscopic placement of FC-SEMS (n = 26) and plastic stent (n = 54) for persistent MPD strictures after at least 3 months of initial single plastic stenting, were retrospectively analyzed during a median follow-up duration of 33.7 months. As a result, MPD stricture resolution rate was statistically higher in FC-SEMS group (87.0% vs. 42.0%, p < 0.001). Although immediate complications occurred similarly (38.5% vs. 37.0%, p = 0.902), spontaneous migration (26.9%) and de novo strictures (23.1%) were pronounced delayed complications in FC-SEMS group. Pain relief during follow-up was significantly higher in FC-SEMS group (76.9% vs. 53.7%, p = 0.046). The total procedure cost was similar in both groups ($1,455.6 vs. $1,596.9, p = 0.486). In comparison with plastic stent, FC-SEMS placement for persistent MPD strictures had favorable long-term clinical efficacy, with its typical complications like spontaneous migration and de novo strictures.

scholarly journals Clinical benefit of glasdegib plus low-dose cytarabine in patients with de novo and secondary acute myeloid leukemia: long-term analysis of a phase II randomized trial

2021 ◽  
Author(s):  
Michael Heuser ◽  
B. Douglas Smith ◽  
Walter Fiedler ◽  
Mikkael A. Sekeres ◽  
Pau Montesinos ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Phase Ii ◽  
Clinical Benefit ◽  
Myeloid Leukemia ◽  
Low Dose ◽  
De Novo ◽  
Secondary Acute Myeloid Leukemia ◽  
Low Dose Cytarabine ◽  
Acute Myeloid

AbstractThis analysis from the phase II BRIGHT AML 1003 trial reports the long-term efficacy and safety of glasdegib + low-dose cytarabine (LDAC) in patients with acute myeloid leukemia ineligible for intensive chemotherapy. The multicenter, open-label study randomized (2:1) patients to receive glasdegib + LDAC (de novo, n = 38; secondary acute myeloid leukemia, n = 40) or LDAC alone (de novo, n = 18; secondary acute myeloid leukemia, n = 20). At the time of analysis, 90% of patients had died, with the longest follow-up since randomization 36 months. The combination of glasdegib and LDAC conferred superior overall survival (OS) versus LDAC alone; hazard ratio (HR) 0.495; (95% confidence interval [CI] 0.325–0.752); p = 0.0004; median OS was 8.3 versus 4.3 months. Improvement in OS was consistent across cytogenetic risk groups. In a post-hoc subgroup analysis, a survival trend with glasdegib + LDAC was observed in patients with de novo acute myeloid leukemia (HR 0.720; 95% CI 0.395–1.312; p = 0.14; median OS 6.6 vs 4.3 months) and secondary acute myeloid leukemia (HR 0.287; 95% CI 0.151–0.548; p < 0.0001; median OS 9.1 vs 4.1 months). The incidence of adverse events in the glasdegib + LDAC arm decreased after 90 days’ therapy: 83.7% versus 98.7% during the first 90 days. Glasdegib + LDAC versus LDAC alone continued to demonstrate superior OS in patients with acute myeloid leukemia; the clinical benefit with glasdegib + LDAC was particularly prominent in patients with secondary acute myeloid leukemia. ClinicalTrials.gov identifier: NCT01546038.

scholarly journals Genomic Characterization Provides an Insight into the Pathogenicity of the Poplar Canker Bacterium Lonsdalea populi

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 246
Author(s):  
Xiaomeng Chen ◽  
Rui Li ◽  
Yonglin Wang ◽  
Aining Li
Keyword(s):  
Genome Sequence ◽  
Extracellular Enzymes ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Hybrid Poplars ◽  
A Genome ◽  
Conserved Genes ◽  
Genomic Characterization ◽  
Molecular Bases ◽  
Insight Into

An emerging poplar canker caused by the gram-negative bacterium, Lonsdalea populi, has led to high mortality of hybrid poplars Populus × euramericana in China and Europe. The molecular bases of pathogenicity and bark adaptation of L. populi have become a focus of recent research. This study revealed the whole genome sequence and identified putative virulence factors of L. populi. A high-quality L. populi genome sequence was assembled de novo, with a genome size of 3,859,707 bp, containing approximately 3434 genes and 107 RNAs (75 tRNA, 22 rRNA, and 10 ncRNA). The L. populi genome contained 380 virulence-associated genes, mainly encoding for adhesion, extracellular enzymes, secretory systems, and two-component transduction systems. The genome had 110 carbohydrate-active enzyme (CAZy)-coding genes and putative secreted proteins. The antibiotic-resistance database annotation listed that L. populi was resistant to penicillin, fluoroquinolone, and kasugamycin. Analysis of comparative genomics found that L. populi exhibited the highest homology with the L. britannica genome and L. populi encompassed 1905 specific genes, 1769 dispensable genes, and 1381 conserved genes, suggesting high evolutionary diversity and genomic plasticity. Moreover, the pan genome analysis revealed that the N-5-1 genome is an open genome. These findings provide important resources for understanding the molecular basis of the pathogenicity and biology of L. populi and the poplar-bacterium interaction.

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