scholarly journals Genus-Wide Characterization of Nuclear Mitochondrial DNAs in Bumblebee (Hymenoptera: Apidae) Genomes

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 963
Author(s):  
Lele Ding ◽  
Huiling Sang ◽  
Cheng Sun
Keyword(s):  
De Novo ◽  
Nuclear Genome ◽  
Cox1 Gene ◽  
Bumblebee Species ◽  
Molecular Features ◽  
Mitochondrial Dnas ◽  
Intergenic Regions ◽  
Numt Sequence ◽  
Shed Light

In eukaryotes, DNA of mitochondria is transferred into the nucleus and forms nuclear mitochondrial DNAs (NUMTs). Taking advantage of the abundant genomic resources for bumblebees, in this study, we de novo generated mitochondrial genomes (mitogenomes) for 11 bumblebee species. Then, we identified and characterized NUMTs in genus-wide bumblebee species. The number of identified NUMTs varies across those species, with numbers ranging from 32 to 72, and nuclear genome size is not positively related to NUMT number. The insertion sites of NUMTs in the nuclear genome are not random, with AT-rich regions harboring more NUMTs. In addition, our results suggest that NUMTs derived from the mitochondrial COX1 gene are most abundant in the bumblebee nuclear genome. Although the majority of NUMTs are found within intergenic regions, some NUMTs do reside within genic regions. Transcripts that contain both the NUMT sequence and its flanking non-NUMT sequences could be found in the bumblebee transcriptome, suggesting a potential domestication of NUMTs in the bumblebee. Taken together, our results shed light on the molecular features of NUMTs in the bumblebee and uncover their contribution to genome innovation.

scholarly journals Integrative Molecular Characterization of Sarcomatoid and Rhabdoid Renal Cell Carcinoma Reveals Determinants of Poor Prognosis and Response to Immune Checkpoint Inhibitors

2020 ◽  
Author(s):  
Ziad Bakouny ◽  
David A. Braun ◽  
Sachet A. Shukla ◽  
Wenting Pan ◽  
Xin Gao ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Immune Checkpoint ◽  
Renal Cell ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Molecular Features ◽  
Aggressive Tumors ◽  
Shed Light

AbstractSarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors1–3, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, including BAP1 mutations, CDKN2A deletions, and increased expression of MYC transcriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings shed light on the molecular drivers of aggressivity and responsiveness to immune checkpoint inhibitors of S/R RCC tumors.

scholarly journals Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina

2015 ◽  
Vol 28 (11) ◽  
pp. 1198-1215 ◽  
Author(s):  
Lida Derevnina ◽  
Sebastian Chin-Wo-Reyes ◽  
Frank Martin ◽  
Kelsey Wood ◽  
Lutz Froenicke ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Nuclear Genome ◽  
Peronospora Tabacina ◽  
Protein Coding ◽  
Rxlr Effectors ◽  
Intergenic Regions ◽  
High Level ◽  
Genomic Regions ◽  
Hyaloperonospora Arabidopsidis

Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain–containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.

scholarly journals Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ziad Bakouny ◽  
David A. Braun ◽  
Sachet A. Shukla ◽  
Wenting Pan ◽  
Xin Gao ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Prior Work ◽  
Molecular Features ◽  
Aggressive Tumors ◽  
Shed Light

AbstractSarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, including BAP1 mutations, CDKN2A deletions, and increased expression of MYC transcriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings build on prior work and shed light on the molecular drivers of aggressivity and responsiveness to ICI of S/R RCC.

scholarly journals Characterization of De Novo Synthesized GPCRs Supported in Nanolipoprotein Discs

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44911 ◽  
Author(s):  
Tingjuan Gao ◽  
Jitka Petrlova ◽  
Wei He ◽  
Thomas Huser ◽  
Wieslaw Kudlick ◽  
...  
Keyword(s):  
De Novo

scholarly journals Ni Oxidation State and Ligand Saturation Impact on the Capability of Octaazamacrocyclic Complexes to Bind and Reduce CO2

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4139
Author(s):  
Barbora Vénosová ◽  
Ingrid Jelemenská ◽  
Jozef Kožíšek ◽  
Peter Rapta ◽  
Michal Zalibera ◽  
...  
Keyword(s):  
Quantum Theory ◽  
Oxidation State ◽  
Central Atom ◽  
Population Analysis ◽  
Mulliken Population Analysis ◽  
Mulliken Population ◽  
Theoretical Methods ◽  
Ni Oxidation ◽  
Shed Light

Two 15-membered octaazamacrocyclic nickel(II) complexes are investigated by theoretical methods to shed light on their affinity forwards binding and reducing CO2. In the first complex 1[NiIIL]0, the octaazamacrocyclic ligand is grossly unsaturated (π-conjugated), while in the second 1[NiIILH]2+ one, the macrocycle is saturated with hydrogens. One and two-electron reductions are described using Mulliken population analysis, quantum theory of atoms in molecules, localized orbitals, and domain averaged fermi holes, including the characterization of the Ni-CCO2 bond and the oxidation state of the central Ni atom. It was found that in the [NiLH] complex, the central atom is reduced to Ni0 and/or NiI and is thus able to bind CO2 via a single σ bond. In addition, the two-electron reduced 3[NiL]2− species also shows an affinity forwards CO2.

scholarly journals De Novo Assembly and Characterization of the Xenocatantops brachycerus Transcriptome

2018 ◽  
Vol 19 (2) ◽  
pp. 520 ◽  
Author(s):  
Le Zhao ◽  
Xinmei Zhang ◽  
Zhongying Qiu ◽  
Yuan Huang
Keyword(s):  
De Novo Assembly ◽  
De Novo

scholarly journals Prenatal diagnosis and molecular cytogenetic characterization of a de novo duplication of 15q24.3-q26.1

2018 ◽  
Vol Volume 11 ◽  
pp. 77-80 ◽  
Author(s):  
Isabel Ochando ◽  
Melanie Cristine Alonzo Martínez ◽  
Ana María Serrano ◽  
Antonio Urbano ◽  
Eduardo Cazorla ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
De Novo ◽  
Molecular Cytogenetic ◽  
Cytogenetic Characterization

scholarly journals Ultrasound evaluation of access complications: Thrombosis, aneurysms, pseudoaneurysms and infections

2021 ◽  
pp. 112972982110180
Author(s):  
Mario Meola ◽  
Antonio Marciello ◽  
Gianfranco Di Salle ◽  
Ilaria Petrucci
Keyword(s):  
Vascular Access ◽  
Pulse Wave ◽  
De Novo ◽  
Late Complications ◽  
Prosthesis Infection ◽  
Ultrasound Evaluation ◽  
Access Complications ◽  
Vein Stenosis ◽  
Post Implantation

Arteriovenous fistula (AVF) complications are classified based on fistula outcomes. This review aims to update colour Doppler (CD) and pulse wave Doppler (PWD) roles in managing early and late complications of the native and prosthetic AVF. Vascular access (VA) failure occurs because inflow or outflow stenosis activates Wirchow’s triad inducing thrombosis. Therefore, the diagnosis of the tributary artery and outgoing vein stenosis will be the first topic considered. Post-implantation complications occur from the inability to achieve AVF maturation and dialysis suitability due to inflow/outflow stenosis. Late stenosis is usually a sequence of early defects repaired to maintain patency. Less frequently, in the mature AVF or graft, complications are acquired ‘de novo’. They derive either from incorrect management of vascular access (haematoma, pseudoaneurysm, prosthesis infection) or wall pathologies (aneurysm, myxoid valve degeneration, kinking, coiling, abnormal dilation from defects of elastic structures). High-resolution transducers (10–20 MHz) allow the characterization of the wall damage, haemodynamic dysfunctions, early and late complications even if phlebography remains the gold standard for the diagnosis for its sensitivity and specificity.

Sign in / Sign up

Export Citation Format

Share Document