scholarly journals Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 604
Author(s):  
Mohd Faiz Mat Saad ◽  
Aziz Ramlee Sau ◽  
Muhamad Afiq Akbar ◽  
Syarul Nataqain Baharum ◽  
Ahmad Bazli Ramzi ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Potential Threat ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Agriculture Sector ◽  
Infectious Clones ◽  
And Function ◽  
Virus Genomes ◽  
Considerable Loss

Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.

Functional characterization of human brown adipose tissue metabolism

2020 ◽  
Vol 477 (7) ◽  
pp. 1261-1286 ◽  
Author(s):  
Marie Anne Richard ◽  
Hannah Pallubinsky ◽  
Denis P. Blondin
Keyword(s):  
Adipose Tissue ◽  
Brown Adipose Tissue ◽  
Functional Characterization ◽  
Human Infants ◽  
Positron Emission ◽  
Brown Adipose ◽  
Treatment Of Obesity ◽  
And Function

Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) with the glucose tracer [18F]fluorodeoxyglucose ([18F]FDG) made it possible to begin characterizing the possible function of BAT in adult humans, and whether it could play a role in the prevention or treatment of obesity and type 2 diabetes (T2D). This review focuses on the in vivo functional characterization of human BAT, the methodological approaches applied to examine these features and addresses critical gaps that remain in moving the field forward. Specifically, we describe the anatomical and biomolecular features of human BAT, the modalities and applications of non-invasive tools such as PET and magnetic resonance imaging coupled with spectroscopy (MRI/MRS) to study BAT morphology and function in vivo, and finally describe the functional characteristics of human BAT that have only been possible through the development and application of such tools.

Functional characterization of the trypanosome translational repressor SCD6

2013 ◽  
Vol 457 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Marina Cristodero ◽  
Bernd Schimanski ◽  
Manfred Heller ◽  
Isabel Roditi
Keyword(s):  
Functional Characterization ◽  
Stress Granule ◽  
Granule Formation ◽  
Translational Repressor ◽  
And Function

Trypanosomal SCD6 is a general repressor of translation. It is not required for stress granule formation and, unusually, does not interact with the helicase DHH1. We analysed domains involved in the localization and function of TbSCD6 and identified interacting partners.

scholarly journals Unique structure and function of viral rhodopsins

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Dmitry Bratanov ◽  
Kirill Kovalev ◽  
Jan-Philipp Machtens ◽  
Roman Astashkin ◽  
Igor Chizhov ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Structure And Function ◽  
Proton Donor ◽  
Dna Viruses ◽  
Host Interactions ◽  
Hydrophobic Barrier ◽  
High Resolution Structure ◽  
Group 2 ◽  
Marine Protists ◽  
And Function

Abstract Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists.

scholarly journals The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

2021 ◽  
Vol 12 ◽  
Author(s):  
Danijela Miljanovic ◽  
Ognjen Milicevic ◽  
Ana Loncar ◽  
Dzihan Abazovic ◽  
Dragana Despot ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Early Summer ◽  
Future Research ◽  
Viral Genomes ◽  
Rare Mutations ◽  
Second Wave ◽  
Genome Variants ◽  
Local Transmission

March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.

scholarly journals Ontogenic, phenotypic, and functional characterization of XCR1+ dendritic cells leads to a consistent classification of intestinal dendritic cells based on the expression of XCR1 and SIRPα

2014 ◽  
Author(s):  
Martina Becker ◽  
Steffen Güttler ◽  
Annabell Bachem ◽  
Evelyn Hartung ◽  
Ahmed Mora ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
T Cell ◽  
Functional Characterization ◽  
Cross Presentation ◽  
Intestinal Immune System ◽  
Lineage Marker ◽  
And Function ◽  
First Time

In the past, lack of lineage markers confounded the classification of dendritic cells (DC) in the intestine and impeded a full understanding of their location and function. We have recently shown that the chemokine receptor XCR1 is a lineage marker for cross-presenting DC in the spleen. Now we provide evidence that intestinal XCR1+ DC largely, but not fully, overlap with CD103+ CD11b- DC, the hypothesized correlate of “cross-presenting DC” in the intestine, and are selectively dependent in their development on the transcription factor Batf3. XCR1+ DC are located in the villi and epithelial crypts of the lamina propria of the small intestine, the T cell zones of Peyer’s Patches, and in the T cell zones and sinuses of the draining mesenteric lymph node. Functionally, we could demonstrate for the first time that XCR1+ / CD103+ CD11b- DC excel in the cross-presentation of orally applied antigen. Together, our data show that XCR1 is a lineage marker for cross-presenting DC also in the intestinal immune system. Further, extensive phenotypic analyses reveal that expression of the integrin SIRPα consistently demarcates the XCR1- DC population. We propose a simplified and consistent classification system for intestinal DC based on the expression of XCR1 and SIRPα.

Functional characterization of long-chain prenyl diphosphate synthases from tomato

2013 ◽  
Vol 449 (3) ◽  
pp. 729-740 ◽  
Author(s):  
Matthew O. Jones ◽  
Laura Perez-Fons ◽  
Francesca P. Robertson ◽  
Peter M. Bramley ◽  
Paul D. Fraser
Keyword(s):  
Functional Characterization ◽  
Primary Metabolism ◽  
Virus Induced Gene Silencing ◽  
In Planta ◽  
Constitutive Overexpression ◽  
Prenyl Diphosphate ◽  
And Function ◽  
Leaf Appearance ◽  
Long Chain

The electron transfer molecules plastoquinone and ubiquinone are formed by the condensation of aromatic head groups with long-chain prenyl diphosphates. In the present paper we report the cloning and characterization of two genes from tomato (Solanum lycopersicum) responsible for the production of solanesyl and decaprenyl diphosphates. SlSPS (S. lycopersicum solanesyl diphosphate synthase) is targeted to the plastid and both solanesol and plastoquinone are associated with thylakoid membranes. A second gene [SlDPS (S. lycopersicum solanesyl decaprenyl diphosphate synthase)], encodes a long-chain prenyl diphosphate synthase with a different subcellular localization from SlSPS and can utilize geranyl, farnesyl or geranylgeranyl diphosphates in the synthesis of C45 and C50 prenyl diphosphates. When expressed in Escherichia coli, SlSPS and SlDPS extend the prenyl chain length of the endogenous ubiquinone to nine and ten isoprene units respectively. In planta, constitutive overexpression of SlSPS elevated the plastoquinone content of immature tobacco leaves. Virus-induced gene silencing showed that SlSPS is necessary for normal chloroplast structure and function. Plants silenced for SlSPS were photobleached and accumulated phytoene, whereas silencing SlDPS did not affect leaf appearance, but impacted on primary metabolism. The two genes were not able to complement silencing of each other. These findings indicate a requirement for two long-chain prenyl diphosphate synthases in the tomato.

The quest to achieve the detailed structural and functional characterization of CymA

2012 ◽  
Vol 40 (6) ◽  
pp. 1291-1294 ◽  
Author(s):  
Ricardo O. Louro ◽  
Catarina M. Paquete
Keyword(s):  
Microbial Fuel Cells ◽  
Critical Role ◽  
Functional Characterization ◽  
Shewanella Oneidensis ◽  
Model Organism ◽  
Structural Behaviour ◽  
Metal Compounds ◽  
Potential Applications ◽  
And Function

Shewanella oneidensis MR-1 is a sediment organism capable of dissimilatory reduction of insoluble metal compounds such as those of Fe(II) and Mn(IV). This bacterium has been used as a model organism for potential applications in bioremediation of contaminated environments and in the production of energy in microbial fuel cells. The capacity of Shewanella to perform extracellular reduction of metals is linked to the action of several multihaem cytochromes that may be periplasmic or can be associated with the inner or outer membrane. One of these cytochromes is CymA, a membrane-bound tetrahaem cytochrome localized in the periplasm that mediates the electron transfer between the quinone pool in the cytoplasmic membrane and several periplasmic proteins. Although CymA has the capacity to regulate multiple anaerobic respiratory pathways, little is known about the structure and functional mechanisms of this focal protein. Understanding the structure and function of membrane proteins is hampered by inherent difficulties associated with their purification since the choice of the detergents play a critical role in the protein structure and stability. In the present mini-review, we detail the current state of the art in the characterization of CymA, and add recent information on haem structural behaviour for CymA solubilized in different detergents. These structural differences are deduced from NMR spectroscopy data that provide information on the geometry of the haem axial ligands. At least two different conformational forms of CymA are observed for different detergents, which seem to be related to the micelle size. These results provide guidance for the discovery of the most promising detergent that mimics the native lipid bilayer and is compatible with biochemical and structural studies.

Inflammation of conduction tissue in patients with arrhythmic phenotype of myocarditis

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
A Frustaci ◽  
R Verardo ◽  
M Alfarano ◽  
G Agnes ◽  
C Chimenti
Keyword(s):  
Influenza A ◽  
Left Ventricular ◽  
Funding Source ◽  
Viral Genomes ◽  
Immune Mediated ◽  
Positive Immunostaining ◽  
Ectopic Beats ◽  
Public Grant ◽  
And Function

Abstract Background Manifestation of arrhythmias in otherwise normal heart suggests a possible compromise of conduction tissue. It, however, remains, usually, a supposition with limited therapeutical implications. Purpose Reporting histology of inflammation/infection of conduction tissue as a cause of arrhythmic phenotype of myocarditis. Material and methods Among 420 patients with a biopsy proven myocarditis diagnosed from 2009 to 2019, 42 presented with an arrhythmic phenotype and normal cardiac anatomy and function (LVEF >50%). Of the latter, 12 subjects (28.5%; M 9; F 3; mean age 44,75±14.9 years) had included in a left ventricular endomyocardial biopsy sections of conduction tissue (CT). CT was identified by recognition of morphological Aschoff and Monckeberg criteria and positive immunostaining for HCN4. CT inflammation was defined by ≥7 CD3+ T lymphocytes with focal necrosis of adjacent cells. Cause of CT inflammation was investigated by polymerase chain reaction (PCR) of 2 frozen endomyocardial samples, immunohistochemistry for the identified viral antigens and for Tall like receptor 4 (TLR4). Results Four pts presented with non-sustained ventricular tachycardia (nsVT), seven pts with sustained (S) VT, 1 died during hospitalization because of ventricular fibrillation (VF). Inflammatory involvement of CT was documented in all 12 pts. PCR was positive for Influenza A virus in 2 pts and HHV2 in 1 with positive CT immunostaining for related antigens. In the remaining 8 pts negative PCR for viral genomes and overexpression of TLR4 suggested an immune-mediated pathway of CT inflammation. Pts with Influenza A myocarditis and CT infection responded to tamiflu (1 cp bid for 5 days) with ECG normalization while the pt with HHV2 infection died. The 8 pts with virus-negative myocarditis and TLR4 overexpession were treated with steroids and azathioprine based on TIMIC protocol. Seven of them had no more repetitive ventricular ectopic beats at Holter of 2 weeks follow-up. Conclusions Arrhythmic phenotype of myocarditis is caused by elective inflammation/infection of CT. Molecular characterization of CT damage may bring to pharmacologic control of arrhythmias in up to 75% of cases. Figure 1 Funding Acknowledgement Type of funding source: Public grant(s) – EU funding. Main funding source(s): European Project ERA-CVD “Transnational Research Projects on Cardiovascular Diseases”

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