A portrait of ribosomal DNA contacts with Hi-C reveals 5S and 45S rDNA anchoring points in the folded human genome

Ribosomal rRNAs account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, while the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. We conclude that portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase

More epigenetic hits than meets the eye: microRNAs and genes associated with the tumorigenesis of retinoblastoma

Retinoblastoma (RB), a childhood neoplasia of the retinoblasts, can occur unilaterally or bilaterally, with one or multiple foci per eye. RB is associated with somatic loss of function of both alleles of the tumor suppressor gene RB1. Hereditary forms emerge due to germline loss of function mutations in RB1 alleles. RB has long been the prototypic “model” cancer ever since Knudson's “two-hit” hypothesis. However, a simple two-hit model for RB is challenged by an increasing number of studies documenting additional hits that contribute to RB development. Here we review the genetics and epigenetics of RB with a focus on the role of small non-coding RNAs (microRNAs) and on novel findings indicating the relevance of DNA methylation in the development and prognosis of this neoplasia. Studies point to an elaborated landscape of genetic and epigenetic complexity, in which a number of events and pahtways play crucial roles in the origin and prognosis of RB. These include roles for microRNAs, inprinted loci, and parent-of-origin contributions to RB1 regulation and RB progression. This complexity is also manifested in the structure of the RB1 locus itself: it includes numerous repetitive DNA segments and retrotransposon insertion elements, some of which are actively transcribed from the RB1 locus. Altogether, we conclude that RB1 loss of function represents the tip of an iceberg of events that determine RB development, progression, severity, and disease risk. Comprehensive assessment of personalized RB risk will require genetic and epigenetic evaluations beyond RB1 protein coding sequences

Y Not a Dead End: Epistatic Interactions Between Y-Linked Regulatory Polymorphisms and Genetic Background Affect Global Gene Expression in Drosophila melanogaster

The Y chromosome, inherited without meiotic recombination from father to son, carries relatively few genes in most species. This is consistent with predictions from evolutionary theory that nonrecombining chromosomes lack variation and degenerate rapidly. However, recent work has suggested a dynamic role for the Y chromosome in gene regulation, a finding with important implications for spermatogenesis and male fitness. We studied Y chromosomes from two populations of Drosophila melanogaster that had previously been shown to have major effects on the thermal tolerance of spermatogenesis. We show that these Y chromosomes differentially modify the expression of hundreds of autosomal and X-linked genes. Genes showing Y-linked regulatory variation (YRV) also show an association with immune response and pheromone detection. Indeed, genes located proximal to the euchromatin–heterochromatin boundary of the X chromosome appear particularly responsive to Y-linked variation, including a substantial number of odorant-binding genes. Furthermore, the data show significant regulatory interactions between the Y chromosome and the genetic background of autosomes and X chromosome. Altogether, our findings support the view that interpopulation, Y-linked regulatory polymorphisms can differentially modulate the expression of many genes important to male fitness, and they also point to complex interactions between the Y chromosome and genetic background affecting global gene expression.Organismic and Evolutionary Biolog

Y Chromosome Mediates Ribosomal DNA Silencing and Modulates the Chromatin State in Drosophila

Although the Drosophila Y chromosome is degenerated, heterochromatic, and contains few genes, increasing evidence suggests that it plays an important role in regulating the expression of numerous autosomal and X-linked genes. Here we use 15 Y chromosomes originating from a single founder 550 generations ago to study the role of the Y chromosome in regulating rRNA gene transcription, position-effect variegation (PEV), and the link among rDNA copy number, global gene expression, and chromatin regulation. Based on patterns of rRNA gene transcription indicated by transcription of the retrotransposon R2 that specifically inserts into the 28S rRNA gene, we show that X-linked rDNA is silenced in males. The silencing of X-linked rDNA expression by the Y chromosome is consistent across populations and independent of genetic background. These Y chromosomes also vary more than threefold in rDNA locus size and cause dramatically different levels of PEV suppression. The degree of suppression is negatively associated with the number and fraction of rDNA units without transposon insertions, but not with total rDNA locus size. Gene expression profiling revealed hundreds of differentially expressed genes among these Y chromosome introgression lines, as well as a divergent global gene expression pattern between the low-PEV and high-PEV flies. Our findings suggest that the Y chromosome is involved in diverse phenomena related to transcriptional regulation including X-linked rDNA silencing and suppression of PEV phenotype. These results further expand our understanding of the role of the Y chromosome in modulating global gene expression, and suggest a link with modifications of the chromatin state.Organismic and Evolutionary Biolog

Seaweed extracts to control postharvest phytopathogenic fungi in Rocha pear

This study was supported by the Fundação para a Ciência e a Tecnologia (FCT) to MARE (UID/MAR/04292/2020), the Associate Laboratory ARNET (LA/P/0069/2020), through national funds, and the grants to Tânia Vicente (2020.06230.BD) and Rafael Félix (SFRH/BD/139763/2018). The authors also acknowledge the support of project ORCHESTRA—add-value to ORCHards through thE full valoriSaTion of macRoalgAe (POCI-01-0247-FEDER-070155) co-funded by FEDER—Fundo Europeu de Desenvolvimento Regional da União Europeia, Portugal 2020, through COMPETE 2020—Programa Operacional Competitividade e Internacionalização, through FCT and COSMOS: Valorização biotecnológica da alga invasora Asparagopsis armata da Costa de Peniche (MAR-04.03.01-FEAMP-0370), and MACAU: Diversidade Macroalgas da reserva natural das Berlengas e costa adjacente, do conhecimento à utilização (MAR-04.03.01-FEAMP-0128) through GAL PESCA OESTE and MAR2020 in the framework of PORTUGAL2020 and the European Maritime and Fisheries Fund. C. Félix was supported by an FCT researcher contract (2021.03113.CEECIND).Fungal infections cause losses amounting to between 20 and 25% of the fruit industry’s total outcome, with an escalating impact on agriculture in the last decades. As seaweeds have long demonstrated relevant antimicrobial properties against a wide variety of microorganisms, extracts from Asparagopsis armata, Codium sp., Fucus vesiculosus, and Sargassum muticum were used to find sustainable, ecofriendly, and safe solutions against Rocha pear postharvest fungal infections. Alternaria alternata, Botrytis cinerea, Fusarium oxysporum, and Penicillium expansum mycelial growth and spore germination inhibition activities were tested in vitro with five different extracts of each seaweed (n-hexane, ethyl acetate, aqueous, ethanolic, and hydroethanolic). An in vivo assay was then performed using the aqueous extracts against B. cinerea and F. oxysporum in Rocha pear. The n-hexane, ethyl acetate, and ethanolic extracts from A. armata showed the best in vitro inhibitory activity against B. cinerea, F. oxysporum, and P. expansum, and promising in vivo results against B. cinerea using S. muticum aqueous extract were also found. The present work highlights the contribution of seaweeds to tackle agricultural problems, namely postharvest phytopathogenic fungal diseases, contributing to a greener and more sustainable bioeconomy from the sea to the farm.info:eu-repo/semantics/publishedVersio

The contribution of somatic items

Funding Information: JO is supported by the NARSAD 2018 Young Investigator Award from the Brain & Behavior Research Foundation , (Grant ID: 27595 ). RL is supported by the 2018 Scientific Employment Stimulus from Fundação para a Ciência e Tecnologia, Portugal (CEECIND/04157/2018). DF, BS and AJO-M are supported by the BOUNCE project (grant agreement number 777167 ), and RL and AJO-M are supported by the FAITH project (grant agreement number 875358 ), both funded by the European Union's Horizon 2020 research and innovation programme. JBB-C and AJO-M are supported by grant FCT-PTDC/MEC-PSQ/30302/2017-IC&DT-LISBOA-01-0145-FEDER, funded by national funds from FCT/MCTES and co-funded by FEDER, under the Partnership Agreement Lisboa 2020 - Programa Operacional Regional de Lisboa. AJO-M is supported by grant FCT-PTDC/MED-NEU/31331/2017, funded by FCT/MCTES. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. Publisher Copyright: © 2022 The AuthorsBackground/Objective: Screening for depression in patients with cancer can be difficult due to overlap between symptoms of depression and cancer. We assessed validity of the Beck Depression Inventory (BDI-II) in this population. Method: Data was obtained in an outpatient neuropsychiatry unit treating patients with and without cancer. Psychometric properties of the BDI-II Portuguese version were assessed separately in 202 patients with cancer, and 376 outpatients with mental health complaints but without cancer. Results: Confirmatory factor analysis suggested a three-factor structure model (cognitive, affective and somatic) provided best fit to data in both samples. Criterion validity was good for detecting depression in oncological patients, with an area under the ROC curve (AUC) of 0.85 (95% confidence interval [CI], 0.76–0.91). A cut-off score of 14 had sensitivity of 87% and specificity of 73%. Excluding somatic items did not significantly change the ROC curve for BDI-II (difference AUCs = 0.002, p=0.9). A good criterion validity for BDI-II was also obtained in the non-oncological population (AUC = 0.87; 95% CI 0.81–0.91), with a cut-off of 18 (sensitivity=84%; specificity=73%). Conclusions: The BDI-II demonstrated good psychometric properties in patients with cancer, comparable to a population without cancer. Exclusion of somatic items did not affect screening accuracy.publishersversionpublishe

Splenic autoimplant and hyperbaric oxygen therapy in rats

OBJECTIVE: To study the functional and morphological features of splenic autoimplants in rats subjected, or not, to postoperative hyperbaric oxygen therapy. METHODS: One hundred and five male Wistar rats, weighing 251.6 g ± 29.5 g, were studied ot early (11th day) and late (70th day ) postoperative periods. For each period the animals were distributed in the following groups: A (n=40), splenic manipulation; B (n=65),splenic autoimplants, not treated (nt) (A11nt- n=10, B11nt- n=21, A70nt- n= 10, B70nt-n= 18) and treated with hyperbaric oxygen (t) ( A11t- n= 10, B11t- n=15, A70t - n=10, B70t- n=11). Blood was collected for measurement of lipids and immunoglobulins , platelet and Howell-Jolly body count before and after surgery. The spleen and autoimplants were removed for histologic analyses. RESULTS: There was an increase of total cholesterol (p=0.00068), LDL-cholesterol (p=0.002), VLDL-cholesterol and triglycerides (p=0.0033) in B11nt group. There was an increase of total cholesterol (p= 0.0007) and LDL-cholesterol (p=0.0000) in B70nt group, and no alterations were observed in the other groups. IgM decreased in B groups (p=0.0000) and no changes were observed in the splenic manipulation group. Number of Howell-Jolly bodies were lesser in Bt groups than in Bnt groups( p=0.03). Platelets were increased in B11t and B11nt groups (p=0.0000) and remained unchanged in the other groups. Autoimplants microscopic viability was better in Bt groups than in Bnt. CONCLUSION: The splenic autoimplants of rats treated with hyperbaric oxygen therapy showed a better functionality and viability than those subjected to other procedures.OBJETIVO: Estudar aspectos morfológicos e funcionais dos autoimplantes esplênicos de ratos submetidos ou não à oxigenioterapia hiperbárica (OHB). MÉTODOS: Foram estudados em dois períodos distintos 105 ratos Wistar. No período mediato (n= 56) os animais foram avaliados até o 11º dia de pós-operatório, e no período tardio (n= 49), até o 70º dia. Em cada período os ratos foram distribuídos nos grupos: A- Simulação, B- Autoimplante esplênico, tratados com oxigênio hiperbárico ou não. Nos animais do Grupo A realizou-se apenas manipulação do baço. Nos animais do Grupo B realizou-se esplenectomia total e a seguir quatro fragmentos do baço foram implantados no grande omento. Em todos os animais foram dosados os lípides e imunoglobulinas e contadas as plaquetas e os corpúsculos de Howell-Jolly no pré-operatório e no 11º ou 70º dia de pós-operatório. O baço dos animais do Grupo A e os autoimplantes dos animais do Grupo B foram retirados e enviados para avaliação morfológica. RESULTADOS: No grupo B11nt houve aumento do colesterol total, LDL-colesterol, VLDL-colesterol e triglicérides. No grupo B70nt houve aumento do colesterol total e LDL-colesterol. Nos grupos tratados não houve alterações lipídicas. A IgM caiu nos grupos B e não alterou nos grupos A. Os corpúsculos de Howell - Jolly foram menos freqüentes nos grupos Bt que nos grupos Bnt. As plaquetas aumentaram nos grupos B11t e B11nt e não se alteraram nos demais grupos. A viabilidade microscópica dos grupos Bt foi melhor que a dos grupos Bnt. CONCLUSÃO: Os autoimplantes esplênicos dos animais tratados com OHB apresentaram melhor função e viabilidade do que os autoimplantes dos animais não tratados.22623

Effects of Propranolol on Growth, Lipids and Energy Metabolism and Oxidative Stress Response of Phaeodactylum tricornutum

Present demographic trends suggest a rise in the contributions of human pharmaceuticals into coastal ecosystems, underpinning an increasing demand to evaluate the ecotoxicological effects and implications of drug residues in marine risk assessments. Propranolol, a non-selective β-adrenoceptor blocker, is used worldwide to treat high blood pressure conditions and other related cardiovascular conditions. Although diatoms lack β-adrenoceptors, this microalgal group presents receptor-like kinases and proteins with a functional analogy to the animal receptors and that can be targeted by propranolol. In the present work, the authors evaluated the effect of this non-selective β-adrenoceptor blocker in diatom cells using P. tricornutum as a model organism, to evaluate the potential effect of this compound in cell physiology (growth, lipids and energy metabolism and oxidative stress) and its potential relevance for marine ecosystems. Propranolol exposure leads to a significant reduction in diatom cell growth, more evident in the highest concentrations tested. This is likely due to the observed impairment of the main primary photochemistry processes and the enhancement of the mitochondrial respiratory activity. More specifically, propranolol decreased the energy transduction from photosystem II (PSII) to the electron transport chain, leading to an increase in oxidative stress levels. Cells exposed to propranolol also exhibited high-dissipated energy flux, indicating that this excessive energy is efficiently diverted, to some extent, from the photosystems, acting to prevent irreversible photoinhibition. As energy production is impaired at the PSII donor side, preventing energy production through the electron transport chain, diatoms appear to be consuming storage lipids as an energy backup system, to maintain essential cellular functions. This consumption will be attained by an increase in respiratory activity. Considering the primary oxygen production and consumption pathways, propranolol showed a significant reduction of the autotrophic O2 production and an increase in the heterotrophic mitochondrial respiration. Both mechanisms can have negative effects on marine trophic webs, due to a decrease in the energetic input from marine primary producers and a simultaneous oxygen production decrease for heterotrophic species. In ecotoxicological terms, bio-optical and fatty acid data appear as highly efficient tools for ecotoxicity assessment, with an overall high degree of classification when these traits are used to build a toxicological profile, instead of individually assessed.info:eu-repo/semantics/publishedVersio

Screening a Targeted Panel of Genes by Next-Generation Sequencing Improves Risk Stratification in Real World Patients with Acute Myeloid Leukemia

Although mutation profiling of defined genes is recommended for classification of acute myeloid leukemia (AML) patients, screening of targeted gene panels using next-generation sequencing (NGS) is not always routinely used as standard of care. The objective of this study was to prospectively assess whether extended molecular monitoring using NGS adds clinical value for risk assessment in real-world AML patients. We analyzed a cohort of 268 newly diagnosed AML patients. We compared the prognostic stratification of our study population according to the European LeukemiaNet recommendations, before and after the incorporation of the extended mutational profile information obtained by NGS. Without access to NGS data, 63 patients (23%) failed to be stratified into risk groups. After NGS data, only 27 patients (10%) failed risk stratification. Another 33 patients were re-classified as adverse-risk patients once the NGS data was incorporated. In total, access to NGS data refined risk assessment for 62 patients (23%). We further compared clinical outcomes with prognostic stratification, and observed unexpected outcomes associated with FLT3 mutations. In conclusion, this study demonstrates the prognostic utility of screening AML patients for multiple gene mutations by NGS and underscores the need for further studies to refine the current risk classification criteria.info:eu-repo/semantics/publishedVersio

ASSOCIAÇÃO DE HERBICIDAS PARA O MANEJO DE PLANTAS DANINHAS EM MILHO

Corn is an important crop for agriculture, playing a fundamental role in animal and human feed and energy production. Therefore, the purpose of this study was evaluate the effectiveness, selectivity and effects on corn physiological and productive characteristics after herbicide application either isolated or in tank mix. The procedure adopted was randomized blocks design, with four replications each. The treatments, glyphosate, [atrazine + simazine], nicosulfuron, mesotrione, tembotrione, plus a weeded control were used alone or in a tank mixture. It was evaluated the herbicide phytotoxicity in AG 9025 PRO3 hybrid corn, as well as the weed control of alexander grass and crabgrass at 7, 14, 21 and 28 days after treatment (DAT). At 50 DAT, variables related to the grain physiological characteristics were also measured. Finally, during harvest, grain yield was determined. All evaluations showed that phytotoxicity caused by herbicides was not visually perceptible in AG 9025 PRO3 corn hybrid. The control was effective in treatments that presented in tank mix treatments glyphosate with nicosulfuron and tembotrione. The physiological characteristic affected after herbicide application was photosynthesis, which, when compared to other treatments, showed better results with nicosulfuron and mesotrione. Herbicides did not interfere in corn grain yield. Glyphosate associated with other herbicides used in corn crops shows to be a valuable practice to improve and accelerate the weed control studied with selectivity to the crop.O uso de herbicidas para o controle de plantas daninhas na cultura do milho tem sido uma prática muito comum pelos produtores, sendo aplicados de modo isolado ou em mistura em tanque. Diante disso, o objetivo do trabalho foi avaliar a eficiência, a fitotoxicidade, o efeito em características fisiológicas e produtivas do milho após a aplicação de herbicidas de modo isolado ou em mistura em tanque. O experimento foi instalado a campo, no delineamento de blocos casualizados, com quatro repetições. Como tratamentos foram utilizados de forma isolada ou em mistura em tanque o glyphosate, [atrazine+simazine], nicosulfuron, mesotrione, tembotrione, mais uma testemunha capinada. Avaliou-se a fitotoxicidade dos herbicidas ao híbrido de milho AG 9025 PRO3, a eficiência no controle de papuã (Urochloa plantaginea) e milhã (Digitaria ciliaris) aos 7, 14, 21 e 28 dias após a aplicação dos tratamentos (DAT). Aos 50 DAT aferiu-se ainda as variáveis referentes às características fisiológicas do milho e na colheita determinou-se a produtividade de grãos. A fitotoxicidade ocasionada pelos herbicidas não foi perceptível ao híbrido de milho AG 9025 PRO3. O controle foi eficiente nos tratamentos que apresentaram a mistura em tanque de glyphosate com nicosulfuron e tembotrione. A taxa fotossintética aumentou com a aplicação de nicosulfuron e mesotrione ao se comparar com os demais tratamentos. A concentração interna de CO2, taxa de transpiração, condutância estomática de vapores de água, eficiência de carboxilação e uso eficiente da água não foram alteradas ao se usar os herbicidas isolados ou em mistura. A aplicação dos herbicidas não interferiu na produtividade de grãos de milho. A associação de glyphosate com outros herbicidas demonstra ser prática favorável para melhorar a eficácia de controle