Assessing the possible maintenance of TYLCV-satellite association. [O.21]

Viruses of the genus Begomovirus (Family Geminiviridae) are frequently detected with half genome size DNA molecules, either defective DNAs or satellite DNA (? or ?). Whereas some begomoviruses, like Tomato yellow leaf curl virus (TYLCV) were never detected with satellite DNAs, other begomoviruses, like Cotton leaf curl virus (CLCuV), depend upon a betasatellite for their infectivity. Besides the CLCuV-type begomoviruses which may be considered as bipartite begomoviruses, most of the begomoviruses detected with satellites were shown to be infective without their satellites. The alphasatellite was rarely proved to have any impact on the helper virus but the betasatellite was often shown to increase the virulence of its helper virus. Although satellites were never detected with TYLCV in natural conditions, TYLCV was reported as a helper virus for both satellites in artificial conditions and its virulence was dramatically increased when co-inoculated with betasatellites. We have confirmed these results with the Cotton leaf curl Gezira betasatellite (CLCuGB) and two alphasatellites, Cotton leaf curl Gezira alphasatellite (CLCuGA) and Okra leaf curl Burkina Faso alphasatellite (OLCA). If the co-infection of TYLCV and a betasatellite would occur in natural conditions, tomato production may be severely affected. As the probability of such a scenario mainly depends on the maintenance of TYLCV-satellite associations over time, we have studied various factors potentially determining this maintenance: (i) the relative intra-plant accumulation of TYLCV and the satellites, (ii) the cellular co-infection level of TYLCV and satellites, and (iv) the transmission efficiency of satellites by the vector Bemisia tabaci. These various factors were analyzed with CLCuGB, CLCuGA and OLCA. Besides the specific question of the possible maintenance of satellites with TYLCV, the results of our study are expected to provide a new insight on begomoviruses detected in co-infection with satellites in natural conditions, but which were proved to be infectious without satellites. (Résumé d'auteur

Is the assistance of satellite by TYLCV strictly cell autonomous?

Begomoviruses are circular single stranded DNA (css) plant viruses with bipartite (A and B) or monopartite (A-like component) genomes. They are sometimes associated with satellites, cssDNA molecules, namely alphasatellites and betasatellites. Like the B component of bipartite begomoviruses, satellites depend on the A or A-like component for their replication (betasatellite) and encapsidation (alphasatellites and betasatellites). Although Tomato yellow leaf curl virus (TYLCV) was only rarely reported with satellites, alphasatellites and betasatellites of various geographic origins are readily assisted by TYLCV in experimental conditions. This result was consistent with the observation that satellite DNA contents were mostly higher than that of TYLCV (Conflon et al., 2018). The ease with which satellites can be assisted with TYLCV was supported further by FISH observations, which showed that the frequency of TYLCV-infected cells that were co-infected with a satellite exceeded 85% for an alphasatellite, and 95% for a betasatellite. Interestingly, a substantial number of cell nuclei were positive only for the satellite, suggesting that the assistance seems to be possible, even with a low amount of TYLCV DNA, and possibly no TYLCV DNA. This later possibility that need to be confirmed with further tests, is according to the “multicellular way of life” theory proposed recently for Faba bean necrotic stunt virus, a multipartite nanovirus with eight separately encapsidated components (Sicard et al.,2019)

Begomovirus disease complex: emerging threat to vegetable production systems of West and Central Africa

Vegetables play a major role in the livelihoods of the rural poor in Africa. Among major constraints to vegetable production worldwide are diseases caused by a group of viruses belonging to the genus Begomovirus, family Geminiviridae. Begomoviruses are plant-infecting viruses, which are transmitted by the whitefly vector Bemisia tabaci and have been known to cause extreme yield reduction in a number of economically important vegetables around the world. Several begomoviruses have been detected infecting vegetable crops in West and Central Africa (WCA). Small single stranded circular molecules, alphasatellites and betasatellites, which are about half the size of their helper begomovirus genome, have also been detected in plants infected by begomoviruses. In WCA, B. tabaci has been associated with suspected begomovirus infections in many vegetable crops and weed species. Sequencing of viral genomes from crops such as okra resulted in the identification of two previously known begomovirus species (Cotton leaf curl Gezira virus and Okra yellow crinkle virus) as well as a new recombinant begomovirus species (Okra leaf curl Cameroon virus), a betasatellite (Cotton leaf curl Gezira betasatellite) and new alphasatellites. Tomato and pepper plants with leaf curling were shown to contain isolates of new begomoviruses, collectively referred to as West African tomato-infecting begomoviruses (WATIBs), new alphasatellites and betasatellites. To study the potential of weeds serving as begomovirus reservoirs, begomoviruses and satellites in the weed Ageratum conyzoides were characterized. Sequence analyses showed that they were infected by isolates of a new begomovirus (Ageratum leaf curl Cameroon virus) that belong to the WATIBs group, a new betasatellite (Ageratum leaf curl Cameroon betasatellite), an alphasatellite and two types of defective recombinants between a begomovirus and an alphasatellite. Putative recombinations were detected in begomovirus genomes for all four plant species studied, indicating that recombination is an important mechanism for their evolution. A close relationship between the begomoviruses infecting pepper and tomato and A. conyzoides and the detection of the same alphasatellite in them support the idea that weeds are important reservoirs for begomoviruses and their satellites. With this high diversity, recombination potential and transmission by B. tabaci, begomoviruses and ssDNA satellites pose a serious threat to crop production in West and Central Africa

Spectral densities and frequencies in the power spectrum of higher order repeat alpha satellite in human DNA molecule

Fast Fourier transform was applied to the central segment of a fully sequenced genomic segment from the centromeric region in human chromosome 7 (GenBank/AC017075.8, 193277 bp), which is characterized by alpha satellite higher order repeats (HOR). Frequencies and spectral densities were computed for all prominent peaks in the Fourier spectrum. We have additionally introduced a peak to noise ratio as effective spectral density in order to account for frequency variations of the noise level. We have shown that a very good description of computed Fourier frequencies can be obtained by using the multiple formula with the fundamental frequency corresponding to the 2734-bp HOR sequence. The peak at f(16) corresponds to the 171-bp monomer. Above the frequency f(16), the most pronounced peaks are mostly at multiples of f(16) (monomer-multiples). The lowest sixteen monomer-multiples kf(16) are locally dominant in spectral densities. The first monomer-multiple that is not locally dominant in spectral density is at k = 17. Above k = 27, the maximum of spectral density is systematically shifted to several neighboring higher frequency multiples. On the basis of the Fourier spectrum, the 171-bp monomer unit was subdivided into three approximately 57-bp subrepeats, which were further subdivided into 12-bp, 14-bp and 17-bp basic subrepeats

Molecular diversity of Cotton leaf curl Gezira virus isolates and their satellite DNAs associated with okra leaf curl disease in Burkina Faso

Okra leaf curl disease (OLCD) is a major constraint on okra (Abelmoschus esculentus) production and is widespread in Africa. Using a large number of samples representative of the major growing regions in Burkina Faso (BF), we show that the disease is associated with a monopartite begomovirus and satellite DNA complexes. Twenty-three complete genomic sequences of Cotton leaf curl Gezira virus (CLCuGV) isolates associated with OLCD, sharing 95 to 99% nucleotide identity, were cloned and sequenced. Six betasatellite and four alphasatellite (DNA-1) molecules were also characterized. The six isolates of betasatellite associated with CLCuGV isolates correspond to Cotton leaf curl Gezira betasatellite (CLCuGB) (88 to 98% nucleotide identity). One isolate of alphasatellite is a variant of Cotton leaf curl Gezira alphasatellite (CLCuGA) (89% nucleotide identity), whereas the three others isolates appear to correspond to a new species of alphasatellite (CLCuGA most similar sequence present 52 to 60% nucleotide identity), provisionally named Okra leaf curl Burkina Faso alphasatellite (OLCBFA). Recombination analysis of the viruses demonstrated the interspecies recombinant origin of all CLCuGV isolates, with parents being close to Hollyhock leaf crumple virus (AY036009) and Tomato leaf curl Diana virus (AM701765). Combined with the presence of satellites DNA, these results highlight the complexity of begomoviruses associated with OLCD

EGFR/erB-1, HER2/erB-2, CK7, LP34, Ki67 and P53 expression in preneoplastic lesions of bronchial epithelium: an immunohistochemical and genetic study

A prognostic interpretation of preneoplastic lesions would have impact in bronchial carcinoma early diagnosis and through the study of Erb-B family receptors as they have an important role in lung carcinogenesis. The existence of drugs as tyrosine kinase inhibitors stressed the importance of studying gene alterations for selected chemoprevention schemes and characterization of carcinogenesis. Bronchial preneoplastic lesions were characterized by immunohistochemistry using the antibodies LP34 (high weigh molecular cytokeratin), CK7, chromogranin A, Ki67, p53, C-erbB-2 and EGFR. HER2 and EGFR gene copy number was also evaluated by fluorescent in situ hybridization in those lesions. The expected results defined the origin cell for basal cell hyperplasia and squamous metaplasia as adaptative lesions and dysplasia. By known experiences and published data, beyond the stem cell, the spectral evolution of bronchial preneoplastic lesions was demonstrated by characterizing basal cells (LP34) and their neoplastic potentiality. Dysplasias showed a higher expression of EGFR, Ki67 and p53 with a stepwise increase with the gravity of the respective grading. C-erbB-2 immunohistochemical overexpression was a rare event in preneoplastic lesions. Polysomy was the main mechanism for EGFR and HER2/neu higher gene copy number and together with increased proliferation index (Ki67) will account to preview bronchial carcinogenesis.info:eu-repo/semantics/publishedVersio

Intratumoral patterns of clonal evolution in gliomas

Few studies have explored the patterns of clonal evolution in gliomas. Here, we investigate the cytogenetic patterns of intratumoral clonal evolution of gliomas and their impact on tumor histopathology and patient survival. Cytogenetic analysis of 90 gliomas was performed in individual tumor cells (>200 cells/tumor) using multicolor (N = 16 probes) interphase-FISH. Overall, chromosome gains were more frequent than chromosome losses. Gains of chromosome 7 and/or EGFR amplification were detected in 91% of the cases, whereas del(9p21) (77%) and del(10q23) (78%) were the most frequent chromosome losses. Virtually, all cases (99%) showed >/=2 tumor cell clones, with higher numbers among high- versus low-grade gliomas (p = 0.001). Nine different cytogenetic patterns were found in the ancestral tumor clones. In most gliomas, ancestral clones showed abnormalities of chromosome 7, 9p, and/or 10q and cytogenetic evolution consisted of acquisition of additional abnormalities followed by tetraploidization. Conversely, early tetraploidization was associated with low-grade astrocytomas-2/3 pilocytic and 3/6 grade II diffuse astrocytomas-and combined loss of 1p36/19q13 with oligodendrogliomas, respectively; both aberrations were associated with a better patient outcome (p = 0.03). Overall, our results support the existence of different pathways of intratumoral evolution in gliomas

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus

Background: The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3–16); hence, the mechanisms responsible for changes in copy number at this locus are unclear. Results: In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure. Conclusions: Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear

Begomovirus and DNA satellites diversity in Bemisia tabaci from cotton growing areas of Pakistan

Cotton leaf curl disease (CLCuD), a major threat to cotton production in Pakistan and northwestern India, is caused by a complex of begomoviruses transmitted by the whitefly Bemisia tabaci. These begomoviruses are typically associated with Cotton leaf curl Multan betasatellite (CLCuMuB) and often alphasatellites. Historically, the Burewala strain of Cotton leaf curl Kokhran virus (CLCuKoV-Bur) with the Burewala strain of CLCuMuB (CLCuMuBBur) was the dominant CLCuD strain in Pakistan. This study investigates the diversity and distribution of begomoviruses and their associated satellites in B. tabaci populations across major cotton-growing district of Punjab (including Faisalabad, Burewala, Vehari, and Rahim Yar Khan) and Sindh (Tando Allah Yar, Dadu, Moro, and Sakarand) of Pakistan, providing critical insights into their role in CLCuD epidemiology. The full-length begomoviruses (n = 41), betasatellites (n = 20), and alphasatellites (n = 24) were amplified, cloned and sequenced from B. tabaci (n = 56) collected during 2012-2014. Phylogenetic analyses were performed for isolates classification, and recombination events were investigated using Recombination Detection Program (RDP) and SimPlot. Phylogenetic analyses revealed a complex landscape of viral diversity, with Cotton leaf curl Kokhran virus - Burewala strain (CLCuKoV-Bur) (28/41 isolates, 68%) and its cognate betasatellite, Cotton leaf curl Multan betasatellite - Burewala strain (CLCuMuBBur) (18/20 isolates, 90%), as the dominant species.  Cotton leaf curl Multan alphasatellite (14/24 isolates, 58%) was the most prevalent satellite. The predominant B. tabaci cryptic species, Asia II 1 (or Asia–Pacific Islands–Australia, (ASIA) putative cryptic species), harbored a greater diversity of viruses and satellites compared to the less prevalent MEAM 1 (or North Africa–Middle East (NAFME) putative cryptic species). Recombination events were observed in 34% of begomovirus isolates and 40% of satellite sequences, underscoring the rapid evolutionary adaptation of these pathogens. The predominant B. tabaci cryptic species, Asia II 1 (or Asia–Pacific Islands–Australia, (ASIA) putative cryptic species), harbored a greater diversity of viruses and satellites compared to the less prevalent MEAM 1 (or North Africa–Middle East NAFME putative species). Unlike prior studies, this work is the first to identify full-length genome sequencing of begomoviruses and their associated satellites, isolated directly from B. tabaci populations, with cryptic species identification, providing a comprehensive analysis of virus-vector associations. These findings enhance our understanding of CLCuD’s molecular epidemiology and inform targeted management strategies