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PubMed2026

OsCLSY4 modulates epigenomic patterns and grain size in rice.

De novo DNA methylation, orchestrated by the RNA-directed DNA methylation (RdDM) pathway, is essential for gene regulation and transposon silencing. While CLASSY (CLSY) proteins facilitate RNA POLYMERASE IV (Pol IV) recruitment to initiate the RdDM pathway in plants, their roles in crops are incompletely explored. Here, we report OsCLSY4 as the dominant regulator within the OsCLSY family, driving Pol IV-mediated epigenomic patterns and influencing diverse agricultural traits. Epigenomics analyses reveal that OsCLSY4 controls over 95% of Pol IV-dependent 24-nucleotide small interfering RNA (24-nt siRNA) clusters and more than 70% of Pol IV-dependent hypomethylated CHH differentially methylated regions (DMRs), predominantly at miniature inverted-repeat transposable elements (MITEs). Loss of OsCLSY4 leads to dysregulation of MADS22 and GA20ox1 in a DNA methylation-dependent manner. SunTag-mediated targeted demethylation confirms that reduced DNA methylation in promoter regions leads to MADS22 activation and GA20ox1 repression to influence grain size, linking epigenetic changes to phenotypic outcomes of osclsy4. Moreover, OsCLSY4 governs tissue-specific methylation patterns in panicle and seedling. Mechanistically, OsCLSY4 is the predominantly expressed OsCLSY family member and interacts with Pol IV. Collectively, our findings position OsCLSY4 as a central hub for Pol IV-mediated epigenomic regulation in rice and suggest its potential utility in epigenetic breeding strategies.

Oryza↗
PubMed2026

Mutation in THO2, a component of THO/TREX complex, causes transcriptional gene silencing and genome-wide DNA methylation changes.

DNA methylation plays important roles in silencing of transgenes, endogenous genes, and transposable elements (TEs). To identify genes involved in antagonizing transcriptional or DNA hypermethylation-induced gene silencing, a genetic screening was conducted and thus a tho2-8 mutant was recovered. THO2 is a major component of the THO/TREX (Transcription-Export) complex, which plays essential roles in mRNA export. The tho2-8 mutation caused overaccumulation of DNA methylation on a d35S promoter ahead of LUC, suggesting its roles in antisilencing of transgenes. This mutation also resulted in significant genome-wide alterations in DNA methylation in a locus-specific manner, including 2513 hyper-DMRs and 1717 hypo-DMRs. The hyper-DMRs in the tho2-8 mutant not only exhibited a considerable overlap with those in DNA demethylation mutants (like ros1-7), but also with hypo-DMRs from nrpd1-3 and nrpe1-11 mutants, demonstrating that THO2 is able to protect those loci targeted by DNA demethylation and/or RdDM pathways from hypermethylation. The tho2-8 mutant also contained a plethora of CHH hypo-DMRs, which overlapped in large numbers with those from the nrpd1-3 and nrpe1-11 mutants, indicating that THO2 is required for the establishment/maintenance of DNA methylation at many loci. Additionally, the tho2-8 mutation caused an increase in overall 24-nt siRNA levels and many upregulated and downregulated DEGs/DETEs. The effects of THO2 on DNA methylation patterns appeared to be associated with the functioning of Pol IV and Pol V because THO2 physically interacted with NRPD7 and was necessary for normal accumulation levels of several Pol V-dependent IGNs' transcripts. Thus, this study provided valuable insights into new roles of THO2 in DNA methylation patterning.

DNA Methylation↗
PubMed1992

In vitro characterization of repair synthesis initiated by T4 endonuclease V on a synthetic DNA substrate.

The size of the repair patch produced by E. coli DNA polymerase (Pol I) following the removal of a pyrimidine dimer from DNA in response to the nicking activity of T4 endonuclease (T4 endo V) was determined. A 48-bp DNA containing a pyrimidine dimer at a defined location was labelled in the damaged strand and incubated with T4 endo V and E. coli endonuclease IV. Subsequently, DNA synthesis by DNA Pol I was carried out in the presence of four dNTPs, ATP and DNA ligase. Analysis of the reaction products on a sequencing gel revealed a ladder of only 4-oligonucleotides, 1-4 nucleotides greater in length than the fragment generated by the combined nicking activities of T4 endo V and E. coli endonuclease IV. Thus we conclude that the in vitro repair patch size of T4 endo V is 4 nucleotides and that in some cases the repaired DNA is not ligated.

Base Sequence↗
PubMed1976

Mapping oligonucleotides of Rous sarcoma virus RNA that segregate with polymerase and group-specific antigen markers in recombinants.

The RNase-T1-resistant oligonucleotides of two Prague Rous sarcoma viruses with temperature-sensitive (ts) DNA polymerases (DNA nucleotidyltransferases), termed ts LA 337 and 335 of one leukosis virus, RAV-6, and 20 of their recombinant progeny have been mapped relative to the 3' poly (A) terminus of the viral RNA. The resulting oligonucleotide maps have been ocrrelated with markers of the four known viral genetic elements encoded in the RNA of 10,000 nucleotides. In accord with previous results recombinant RNAs contained (i) oligonucleotides characteristic of the src gene, coding for sarcoma formation, between the poly(A) end and 2000 nucleotides and (ii) olignucleotides characteristic of the env gene, coding for the envelope glycoprotein, between 2500 and 5000 nucleo tides from the poly(A) end. (iii) A cluster of four oligonucleotides that mapped between 6000 and 8000 nucleotides from the 3' poly(A) end of each RNA was shared by both parental viruses and all recombinants. Since all other map segments of our recombinants failed to segregate with the ts- or wild-type markers of the parental DNA polymerase gene (pol), it was concluded that the ts pol lesion maps in this RNA segment. (iv) The 5' segment of each recombinant RNA contained a cluster of four to five oligonucleotides whose parental origin correlated with an electrophoretic marker of one of the parental virion proteins, p27, a major product of the viral gag gene. The gene order 5'-gag-pol-env-src-poly(A) is consistent with our data.

Antigens, Viral↗
PubMed2026

Interfering with DNA repair pathways to enhance CRISPR-Cas9-mediated homology-directed repair in a chelicerate genetic model.

The two-spotted spider mite, Tetranychus urticae, is a major pest and an emerging genetic model. Recent CRISPR-Cas9 advances, especially the SYNCAS method for maternal delivery of Cas9 ribonucleoproteins, have enabled precise genome editing in this and other difficult-to-transform arthropods. Yet SYNCAS-mediated knockins vary in efficiency, possibly due to competition between DNA repair pathways, whose mechanisms in T. urticae and other chelicerates remain unknown. Here, we provide the first functional analysis of double-strand break repair in a chelicerate. Loss of DNA polymerase theta (Polθ) redirects repair almost entirely toward homology-directed repair, whereas absence of Ligase IV has no detectable impact. Using a reporter assay targeting phytoene desaturase, we demonstrate that Polθ-deficient strains enhance incorporation of repair templates, even when mutations are distant from the cut site. Also, insertion of larger fragments is improved. Finally, disrupting Polθ imposes only a modest fitness cost, highlighting its value for future genome engineering in this species.

Acari↗
PubMed2026

Evaluating three alternative scenarios for the origin of a disjunct Arctium tomentosum population in the Pyrenees.

BACKGROUND: Disjunctions in species distributions offer natural experiments for investigating the mechanisms underlying distributional breaks, such as range contraction, long-distance pollen transport, or long-distance seed dispersal. Here, we document and characterise a floristic novelty in the Pyrenean and Iberian regions, and use it as a case study to investigate the processes underlying disjunct species distributions. Our analysis focuses on Arctium L. (burdocks), a genus native to Eurasia comprising several cosmopolitan weedy species. It is characterised by hooked capitula that facilitate epizoochorous dispersal. METHODS: To clarify the taxonomic identity of a previously undocumented Pyrenean population resembling A. tomentosum, we adopted an integrative approach, combining distribution information, morphology, genome size, repetitive DNA analysis and chloroplast data across the four known European species. Additionally, we conducted a comparative study of functional capitulum traits, predispersal fruit predation, and associated entomofauna for the newly discovered population and nearby A. minus populations. RESULTS: The discovered population constitutes a floristic novelty for the region and is identified as A. tomentosum, exhibiting signatures of past introgression from A. minus, as indicated by cytonuclear discordance. We evaluated three alternative scenarios to explain its origin: (i) persistence as a relict from a previously wider distribution, (ii) long-distance pollination by migrating insects, and (iii) long-distance seed dispersal from an A. tomentosum population with a history of past introgression. Of these, only the third is consistent with the available evidence. These results highlight the complexity of interpreting disjunct species distributions and underscore the value of integrative approaches for resolving population identity, origin, dispersal, and persistence across environments.

Arctium↗
PubMed1992

Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. IV. Reconstitution of an asymmetric, dimeric DNA polymerase III holoenzyme.

Individually purified subunits have been used to reconstitute the action of the Escherichia coli DNA polymerase III holoenzyme (Pol III HE) at a replication fork formed in the presence of the primosome, the single-stranded DNA binding protein, and a tailed form II DNA template. Complete activity, indistinguishable from that of the intact DNA Pol III HE, could be reproduced with a combination of the DNA polymerase III core (Pol III core), the gamma.delta complex, and the beta subunit. Experiments where the Pol III core in reaction mixtures containing active replication forks was diluted suggested that the lagging-strand Pol III core remained associated continuously with the replication fork through multiple cycles of Okazaki fragment synthesis. Since the lagging-strand Pol III core must dissociate from the 3' end of the completed Okazaki fragment, this suggests that its association with the fork is via protein-protein interactions, lending credence to the idea that it forms a dimeric complex with the leading-strand Pol III core. An asymmetry in the action of the subunits was revealed under conditions (high ionic strength) that were presumably destabilizing to the integrity of the replication fork. Under these conditions, tau acted to stimulate DNA synthesis only when the primase was present (i.e. when lagging-strand DNA synthesis was ongoing). This stimulation was reflected by an inhibition of the formation of small Okazaki fragments, suggesting that, within the context of the model developed to account for the temporal order of steps during a cycle of Okazaki fragment synthesis, the presence of tau accelerated the transit of the lagging-strand Pol III core from the 3' end of the completed Okazaki fragment to the 3' end of the new primer.

DNA↗
PubMed1976

Antigen recognition. IV. Discrimination by antigen-binding immunocompetent B cells between immunity and tolerance is determined by adherent cells.

Mouse spleen cells capable of specifically binding intrinsically tritium-labeled polymerized flagellin (POL) (labeling by biosynthesis of flagellar protein) via IgM receptors were found to comprise a distinct population of about 20-50 cells per 10(6) lymphocytes. Evidence is presented that the majority of mouse spleen cells binding tritium-labeled POL undergoes blastogenesis after antigen capping, antigen shedding, and receptor reformation. Under conditions of tolerance induction in vitro, however, loss of antigen from the cell surface was inhibited. Such inhibition of antigen redistribution and shedding was reversed by a short pulse of colchicine and new antigen receptors were formed. In spite of this, colchicine had no effect on the tolerant state. However, tolerance could be broken, regardless of presence or absence of the alkaloid, with radioresistant theta-negative accessory (A) cells (adherent cells) from normal but not from tolerant spleen cell populations. "Tolerant" A cells, although they were incapable of cooperating in a response to POL, were capable of participating in a response to a second unrelated antigen. It is concluded that tolerance to POL in vitro is induced by mechanisms other than the physical blocking of bone marrow-derived (B) cell receptors by antigen. Most likely, the discrimination by the B cell between a tolerogenic and immunogenic signal is mediated by A cells.

Animals↗
PubMed1979

Cell fusion for genetic analysis of two nonconditional Rous sarcoma virus replication mutants.

Procedures for characterizing replication-defective viruses in nonpermissive mammalian cells were developed and applied to three nonvirogenic Rous sarcoma virus (RSV)-transformed mammalian cell lines--B4, a line of Bryan virus-transformed hamster cells, and two SRD-RSV transformed rat cell lines, LR3/1 and LR3/2. Cell fusion was used to study virus complementation. The three cell lines (i) fused with helper virus-infected chicken cells and the host range of the rescued virus examined, (ii) tested for complementation by fusion with chicken cells exhibiting various patterns of endogenous virus expression, (iii) fused with chicken cells infected with the temperature-sensitive replication mutant LA334 and assayed for complementation at permissive and nonpermissive temperatures, and (iv) tested for complementation of defective viruses in other RSV-transformed mammalian cell lines by fusing pairs of nonvirogenic cell lines and permissive chicken cells. Based upon these complementation studies, we concluded that B4 virus is defective only in the env gene, LR3/) virus is an absolute mutant in the gag and/or pol genes, and LR3/2 virus is a leaky env mutant. Clones of LR3/1 and LR3/2 virus-infected chicken cells were established, and the results obtained from the characterization of these viruses in permissive avian cells substantiates the conclusions reached in the fusion-rescue studies.

Animals↗
PubMed1979

Role of self carriers in the immune response and tolerance. IV. Active T cell suppression in the maintenance of B cell tolerance to a "T-independent" antigen.

Previous studies indicated that T cells are required for tolerance induction by hapten-modified syngeneic spleen cells (TNP-SC) in vivo. The role of T cells in the maintenance of this unresponsive state has been examined herein. By three criteria--limiting dilution precursor analysis, removal of T cells by anti-Thy-1 + C, and direct mixing experiments--we show that T cells are required for the continued suppression of the B cell response to the T-independent antigen, TNP-POL. Suppressor cells can also be induced by TNP-teratoma cells, which lack detectable H-2 antigens. Both anti-Ly-1 + C and anti-Ly-2 + C treatment reversed suppression induced by TNP-SC. These results demonstrate that normal B cell reactivity is present in the spleens of mice rendered tolerant by haptenated self, but that Ly-1,2,3 or Ly-1 + Ly-2,3 suppressor T cells prevent their responsiveness.

Animals↗
PubMedDate not supplied

Presence of erythropoiesis inhibitor in the urine of normal sheep and those with transfused polycythemia.

Presence of erythropoiesis inhibitor in the urine of normal sheep and those with transfused polycythaemia. Acta Physiol. Pol., 1978, 29 (1): 37-46. Urine from 18 ewes, normal and with transfused polycythemia, was analysed. The consequences of polycythemia were estimated in the period between 96 and 192h. The 24 h urine portions were separated on Sephadex G 100 columns, and after dialysis, tested biologically on normal mice of the BALB/c and Swiss strains. Changes of the erythropoietic activity in normal mice receiving the particular plasma fractions demonstrated that in the urine fraction IV, a factor with activity characteristic for the erythropoiesis inhibitor, is present in most normal sheep and in all those with moderate polycythemia.

Animals↗
PubMed2024

The HIV-1 Transcriptional Program: From Initiation to Elongation Control.

A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.

HIV-1↗
PubMed2026

Delphi study robot consenso: Strategies for the implementation of robotic surgery in general surgery in the Spanish hospital network.

INTRODUCTION: The implementation of robotic surgery in public hospitals presents multiple logistical, educational, and organizational challenges. In the absence of unified guidelines, a national consensus is required to optimize its safe and efficient adoption. This study aimed to establish a set of consensus-based and measurable recommendations for the implementation of robotic surgery programs in hospitals within the Spanish National Health System, based on the experience of centres with established robotic programs and intended to serve as guidance for hospitals that are initiating or planning their implementation. METHODS: A national Delphi study was conducted with the participation of robotic surgery experts from 26 public hospitals. The expert panel was composed exclusively of digestive surgeons with experience in robotic surgery. Three iterative rounds of expert panel evaluation were conducted between March 2024 and March 2025. The questions were grouped into five thematic blocks. Consensus was defined as an agreement level of ≥66.7%. Kendall's W coefficient was used to assess concordance. RESULTS: High levels of consensus were achieved on key aspects related to infrastructure, structured training, cost evaluation, and quality assurance mechanisms. Areas of disagreement were also identified, such as the need for a dedicated anaesthesiologist, purchase of accessory instruments during the initial phase, and official accreditation pathways. CONCLUSIONS: This study provides a guideline for developing a national robotic surgery strategy focused on patient safety, program sustainability, and standardized training of surgical teams. These recommendations can guide hospitals at different stages of robotic technology adoption. Given that the consensus was reached from an exclusively surgical perspective, the recommendations focus on patient safety, program sustainability, and standardized training of the surgical team, and should be interpreted in an adaptable manner according to each centre's context, case volume, and available resources.

Cirugía Asistida por Robot↗
PubMed1977

Genetic variation in the RNA transcripts of endogenous virus genes in uninfected chicken cells.

Uninfected cells from two different phenotypes of chicken embryos express significant amounts of endogenous viral information, though they do not produce virus particles. Cells of the phenotype gs(+)chf(+) are positive for both group-specific (gs) antigens and chicken helper factor (chf) activity, whereas cells of a second phenotype, gs(L)chf(+)(h(E)), demonstrate noncoordinate expression of these two viral activities (very low amounts of gs antigens, but extremely high helper activity). RNA from these cells was analyzed to determine the size, genetic content, and relative abundance of virus-specific RNAs in cells of each phenotype. Two major size classes of polyadenylic acid-containing RNA, homologous to the avian leukosis virus genome, were detectable in cells of both types. The larger RNA, which contained most of the sequences of the leukosis virus genome, was of different sizes in the two phenotypes, 31S in gs(+)chf(+) cells but 35S in the noncoordinate cell type. Analysis of the viral RNA with gene-specific complementary DNA probes revealed the following characteristics. (i) The 31S RNA appeared to lack portions of the gag and pol genes. (ii) A smaller RNA species, which sedimented at 21S in both cell types, was a transcript of the 3'-proximal portion of the viral genome, consisting of the env gene and the "common" sequences. (iii) The amount of env-specific RNA in the 21S region was more than six times higher in the noncoordinate cell type than in the gs(+)chf(+) cells; this difference was concordant with the 5- to 10-fold higher chf activity in the noncoordinate cells. (iv) The endogenous viral RNA in uninfected cells and the RNA from Rous-associated virus-0 virions hybridized only partially with DNA complementary to the common region of the Rous-associated virus-2 genome, whereas the RNA of all exogenous viruses tested hybridized almost completely to this complementary DNA. Small amounts of src-specific polyadenylated RNA were also present in uninfected chicken cells. This RNA sedimented as a single peak at 26S and was not covalently linked to any other identifiable virus-specific RNA sequences. The amount of src RNA was the same in the above two types of expression-positive cells and also in cells that were gs(-)chf(-), indicating that the transcription of the cellular sequences homologous to the src gene is independent of the transcription of the other endogenous viral genes.

Animals↗
PubMed1992

Progressive glomerulosclerosis and enhanced renal accumulation of basement membrane components in mice transgenic for human immunodeficiency virus type 1 genes.

Patients infected with human immunodeficiency virus type 1 (HIV-1) develop a renal syndrome characterized by proteinuria, renal failure, and focal segmental glomerulosclerosis. By using a noninfectious HIV-1 DNA construct lacking the gag and pol genes, three transgenic mouse lines have been generated that develop a syndrome remarkably similar to the human disease. In the present study, we have characterized in detail one of these lines, Tg26. In Tg26 mice, proteinuria was detectable at approximately 24 days of age, followed by severe nephrotic syndrome and rapid progression to end-stage renal failure. Renal histology showed focal segmental glomerulosclerosis and microcystic tubular dilatation. Indirect immunofluorescence studies demonstrated increased accumulation of the basement membrane components laminin, collagen type IV, and heparan sulfate proteoglycan. The viral protein Rev was present in sclerotic glomeruli. Northern blot analysis of total renal RNA showed expression of viral genes prior to the appearance of histologic renal disease, with greatly diminished viral gene expression late in the disease course. Kidneys from transgenic mice expressed increased steady-state levels of collagen alpha 1(IV) mRNA when glomerulosclerosis was present. We conclude that the presence of HIV-1 genes is associated with progressive renal dysfunction and glomerulosclerosis in transgenic mice.

Animals↗
PubMed1992

Analysis of HIV-1 expression in vivo with in situ hybridization and the polymerase chain reaction.

The objective of the present study was to compare the data of in situ hybridization (ISH), RNA polymerase chain reaction (PCR/RNA) and p24 core antigen (p24 Ag) enzyme immunoassay (EIA) for the detection of HIV-1 expression in peripheral blood mononuclear cells (PBMCs) and in plasma of infected patients at various CDC stages. PBMCs of 24 patients mostly of CDC stage II were obtained from heparinized blood samples, cytocentrifuged and hybridized with a (35S) labelled single-stranded RNA probe specific for gag-pol of LAVBru HIV-1 allowing the detection of genomic and/or messenger RNA. The corresponding plasma samples were used for the determination of p24 Ag by EIA and detection of HIV-1 genomic RNA by RT-PCR using specific primers in the LTR, gag and env regions. Whereas p24 was detected in only six out of 24 patients, both ISH and PCR/RNA enabled the detection of viral RNAs in more than 60% of the patients; cumulation of positive results of ISH and RT-PCR showed that 100% of patients at stage IV and 83% of patients at stages II/III have molecular signs of HIV expression therefore indicating that transcription of the provirus is a highly frequent event, even in the early stages of the disease, and, pleading for undertaking a very early antiviral chemotherapy.

CD4-Positive T-Lymphocytes↗
PubMed1992

PCR amplification of HIV-1 proteinase sequences directly from lab isolates allows determination of five conserved domains.

HIV-1 replication requires limited proteolysis of gag and gag-pol encoded precursor proteins by a specific viral proteinase (PR). Sequences of 20 different HIV-1 strains were compared in order to determine regions of conservation and variability within the PR gene. Viral strains included: (a) five new ones derived from New Orleans patient isolates, (b) four established ones grown in our laboratory, (c) eight, whose sequences were published in the Los Alamos Data Base (1990), (d) one Ugandan, and (e) two Brazilian isolates. In the first two groups, HIV proviral DNA extracted from infected lymphocytes was grown in tissue culture and directly amplified by PCR using specific primers flanking the PR gene. Amplified DNA was directly sequenced using a modified di-deoxy sequencing procedure. Sequence data showed a 25% variation among the 20 different HIV strains studied at the amino acid level, including 8% nonconservative changes and 17% conservative changes. Moreover, five noncontiguous regions were able to be delineated in which the PR showed no amino acid changes. These areas included amino acids (I) 1-9 (amino terminal sequence); (II) 21-32 (sequence around the active site); (III) 47-56 (top of the flap); (IV) 78-88; and (V) 94-99 (carboxy terminal sequence). Our results are consistent with those obtained from X-ray crystallography studies as well as single site mutational analysis.

Acquired Immunodeficiency Syndrome↗