Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency.

The conserved nucleic acid binding protein Translin contributes to numerous facets of mammalian biology and genetic diseases. It was first identified as a binder of cancer-associated chromosomal translocation breakpoint junctions leading to the suggestion that it was involved in genetic recombination. With a paralogous partner protein, Trax, Translin has subsequently been found to form a hetero-octomeric RNase complex that drives some of its functions, including passenger strand removal in RNA interference (RNAi). The Translin-Trax complex also degrades the precursors to tumour suppressing microRNAs in cancers deficient for the RNase III Dicer. This oncogenic activity has resulted in the Translin-Trax complex being explored as a therapeutic target. Additionally, Translin and Trax have been implicated in a wider range of biological functions ranging from sleep regulation to telomere transcript control. Here we reveal a Trax- and RNAi-independent function for Translin in dissociating RNA polymerase II from its genomic template, with loss of Translin function resulting in increased transcription-associated recombination and elevated genome instability. This provides genetic insight into the longstanding question of how Translin might influence chromosomal rearrangements in human genetic diseases and provides important functional understanding of an oncological therapeutic target.

Integrative workflows for the characterization of hydrophobin and cerato-platanin in the marine fungus Paradendryphiella salina.

Hydrophobins (HFBs) and cerato-platanins (CPs) are surface-active extracellular proteins produced by filamentous fungi. This study identified two HFB genes (pshyd1 and pshyd2) and one CP gene (pscp) in the marine fungus Paradendryphiella salina. The proteins PsCP, PsHYD2, and PsHYD1 had molecular weights of 12.70, 6.62, and 5.98 kDa, respectively, with isoelectric points below 7. PsHYD1 and PsHYD2 showed hydrophobicity (GRAVY score 0.462), while PsCP was hydrophilic (GRAVY score - 0.202). Stability indices indicated in-solution stability. Mass spectrometry identified 2,922 proteins, including CP but not HFB proteins. qPCR revealed differential gene expression influenced by developmental stage and substrate, with pshyd1 consistently expressed. These findings suggest P. salina's adaptation to marine ecosystems with fewer hydrophobin genes than other fungi but capable of producing surface-active proteins from seaweed carbohydrates. These proteins have potential applications in medical biocoatings, food industry foam stabilizers, and environmental bioremediation.

Tropical shrubs living in an extreme environment show convergent ecological strategies but divergent ecophysiological strategies.

BACKGROUND AND AIMS: Trait-based frameworks assess plant survival strategies using different approaches. Some frameworks use functional traits to assign species to a priori defined ecological strategies. Others use functional traits as the central element of a species ecophysiological strategy. We compared these two approaches by asking: (1) what is the primary ecological strategy of three dominant co-occurring shrub species from inselbergs based on the CSR scheme, and (2) what main functional traits characterize the ecophysiological strategy of the species based on their use of carbon, water and light? METHODS: We conducted our study on a Colombian inselberg. In this extreme environment with multiple stressors (high temperatures and low resource availability), we expected all species to be stress tolerant (S in the CSR scheme) and have similar ecophysiological strategies. We measured 22 anatomical, morphological and physiological leaf traits. KEY RESULTS: The three species have convergent ecological strategies as measured by CSR (S, Acanthella sprucei; and S/CS, Mandevilla lancifolia and Tabebuia orinocensis) yet divergent resource-use strategies as measured by their functional traits. A. sprucei has the most conservative carbon use, risky water use and a shade-tolerant strategy. M. lancifolia has acquisitive carbon use, safe water use and a shade-tolerant strategy. T. orinocensis has intermediate carbon use, safe water use and a light-demanding strategy. Additionally, stomatal traits that are easy to measure are valuable to describe resource-use strategies because they are highly correlated with two physiological functions that are hard to measure: stomatal conductance and maximum photosynthesis per unit mass. CONCLUSIONS: The two approaches provide complementary information on species strategies. Plant species can co-occur in extreme environments, such as inselbergs, because they exhibit convergent primary ecological strategies but divergent ecophysiological strategies, allowing them to use limiting resources differently.

Clinical and therapeutic characterisation of a multicentre cohort of patients with inflammatory bowel disease in Colombia. / Caracterización clínica y terapéutica de una cohorte multicéntrica de pacientes con enfermedad inflamatoria intestinal en Colombia.

INTRODUCTION: In Latin America and Colombia there are few studies about the clinical and therapeutic characteristics of patients with inflammatory bowel disease (IBD). The objective of this study is to obtain an approximation to these data from a sample of patients from different reference centres in Colombia. PATIENTS AND METHODS: Cross-sectional study in adult and paediatric patients, with IBD, attended ambulatory in 6 institutions in different cities, between 2017 and 2020 information was collected on different dates, about demographic, clinical, and therapeutic aspects. RESULTS: Six hundred and five subjects, 565 (93.4%) adults, mean age 43 years (SD 12.78), 64% with ulcerative colitis (UC). The age at diagnosis of UC was 41.9 years, while in Crohn's disease (CD) it was 47.9 years. In UC, there was greater left involvement (47.2%), and in CD, 42.8% ileocolonic (L3). More than 50% were in mild activity or clinical remission. In UC, the biologic requirement was 27.2%, while in CD, 78%. Overall hospitalisation requirement was 39.5%, and the need for surgery was 37.5% in UC and 62.5% in CD. Also, 40 pediatric patients, 90% female, with UC being more frequent (80%). In UC, 83.3% presented extensive colitis, and in CD, all with ileocolonic localization (L3). More than 95% were in mild activity or remission. Biologic therapy was required in 16.6% and 75% for UC and CD, respectively. The frequency of hospitalisations and surgery was 2.7%. CONCLUSIONS: This study shows some unique characteristics of patients with IBD in Colombia. An earlier diagnosis is required, with a better therapeutic approach.

Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin.

Low morphological differentiation among taxa hampers their appropriate identification, basic biological studies and promotion of any conservation effort. Aiming to provide the first insight into the evolution and speciation among north-western South American members of Pimelodus, this study tested the hypothesis that Pimelodus yuma, Pimelodus grosskopfii and Pimelodus crypticus represent three independently evolving species and explored signals of interspecific hybridisation. The outcomes based on mitochondrial (cox1) and nuclear (RADseq, microsatellites and rag2) markers combined with coalescence-based and allele-frequency methods confirmed that each studied species represents an independently evolving unit. Contrary to expectations, P. yuma was found as a sister clade of P. blochii, while P. crypticus (formerly confused with P. blochii) was phylogenetically closer to P. grosskopfii. We also found strong evidence of ancient introgression (0.66-3.32 mya) between the non-sibling species P. yuma and P. grosskopfii, breaking the absence of interbreeding and the independent evolutionary trajectory among north-western South American Pimelodus during their diversification history, a pre-requisite to define species limits. However, there were non-significant values of current gene flow between them, supporting the hypothesis of full isolation.

Virtual Reality Game for Physical and Emotional Rehabilitation of Landmine Victims.

Landmine victims require an engaging and immersive rehabilitation process to maintain motivation and therapeutic adherence, such as virtual reality games. This paper proposes a virtual reality exercise game called Exogames, which works with Nukawa, a lower limb rehabilitation robot (LLRR). Together, they constitute the general Kina system. The design and development process of Exogames is reported, as well as the evaluation of its potential for physical and emotional rehabilitation. In an initial survey designed ad-hoc, 13 health professionals evaluated compliance with various requirements. They agreed that Exogames would help the user focus on rehabilitation by providing motivation; 92.3% said that the user will feel safe in the virtual world, 66.7% of them agreed or totally agreed that it presents characteristics that may enhance the physical rehabilitation of lower limbs for amputees, 83.3% stated that it would promote the welfare of landmine victims, and 76.9% responded that the graphical interface and data report are useful for real-time assessment, and would be helpful for four interventional areas in all rehabilitation stages. In a second evaluation, using standardized surveys, five physical therapists and one lower limb amputee tried the Kina system as users. They filled out the System Usability Scale (SUS), the Physical Activity Enjoyment Scale (PACES), and the Game Experience Questionnaire (GEQ). The usability of the Kina system overall score was 69 (66, 79) out of 100, suggesting an acceptable though improvable usability. The overall PACES score of 110 (108, 112) out of 126 suggests that users enjoyed the game well. Finally, users indicated a positive effect with a good sense of immersion and smooth of gameplay during the tests, as indicated by the GEQ results. In summary, the evaluations showed that Exogames has the potential to be used as a virtual reality game for the physical and emotional rehabilitation of landmine victims.

In Vitro Anthelmintic Evaluation of Gliricidia sepium, Leucaena leucocephala, and Pithecellobium dulce: Fingerprint Analysis of Extracts by UHPLC-Orbitrap Mass Spectrometry.

In the present work, the anthelmintic activity (AA) of ethanolic extracts obtained from Gliricidia sepium, Leucaena leucocephala, and Pithecellobium dulce was evaluated using the third-stage-larval (L3) exsheathment inhibition test (LEIT) and egg hatch test (EHT) on Haemonchus contortus. Extracts were tested at concentrations of 0.3, 0.6, 1.2, 2.5, 5.0, 10, 20, and 40 mg/mL. The larval exsheathment inhibition (LEI) results showed that G. sepium achieved the highest average inhibition of 91.2%, compared with 44.6% for P. dulce and 41.0% for L. leucocephala at a concentration of 40 mg/mL; the corresponding IC50 values were 22.4, 41.7, and 43.3 mg/mL, respectively. The rates of egg hatching inhibition (EHI) at a concentration of 5 mg/mL were 99.5% for G. sepium, 64.2% for P. dulce, and 54% for L. leucocephala; the corresponding IC50 values were 1.9 mg/mL for G. sepium, 3.9 mg/mL for P. dulce, and 4.3 mg/mL for L. leucocephala. The species extracts studied here were also analyzed by ultra-high performance liquid chromatography and Orbitrap high resolution mass spectrometry (UHPLC-Q/Orbitrap/MS/MS), resulting in the compounds' identification associated with AA. Glycosylated flavonoids and methoxyphenols were observed in all three species: fatty acids in G. sepium and P. dulce; phenylpropanoids, anthraquinone glycosides, amino acids and glycosylated phenolic acids in G. sepium; and flavonoids in L. leucocephala. Comparatively, G. sepium presented a greater diversity of compounds potentially active against the control of gastrointestinal nematodes, which was associated with the results obtained in the applied tests.

Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert.

BACKGROUND: Aspergillus fumigatus is the main causative agent of aspergillosis. Infections rarely occur in immunocompetent individuals, indicating efficient clearance of conidia by pulmonary defense mechanisms. Other aspergilli like Aspergillus niger also cause infections but to a much lesser extent. Our previous studies showed that A. fumigatus and A. niger have different behavior in the presence of type II alveolar A549 epithelial cells. A. fumigatus conidia are more efficiently internalized by these cells and germination is delayed when compared to A. niger. In addition, hyphae that have escaped the epithelial cells grow parallel to the epithelium, while A. niger grows away from this cell layer. RESULTS: Here it is shown that global gene expression of A. fumigatus and A. niger is markedly different upon contact with A549 cells. A total of 545 and 473 genes of A. fumigatus and A. niger, respectively, were differentially expressed when compared to growth in the absence of A549 cells. Notably, only 53 genes (approximately 10%) were shared in these gene sets. The different response was also illustrated by the fact that only 4 out of 75 GO terms were shared that were enriched in the differentially expressed gene sets. The orthologues of A. fumigatus genes involved in hypoxia regulation and heat shock were also up-regulated in A. niger, whereas thioredoxin reductase and allergen genes were found up-regulated in A. fumigatus but down-regulated in A. niger. Infection with A. fumigatus resulted in only 62 up and 47 down-regulated genes in A549. These numbers were 17 and 34 in the case of A. niger. GO terms related with immune response were down-regulated upon exposure to A. fumigatus but not in the case of A. niger. This indicates that A. fumigatus reprograms A549 to be less immunologically alert. CONCLUSIONS: Our dual transcriptomic analysis supports earlier observations of a marked difference in life style between A. fumigatus and A. niger when grown in the presence of type II epithelial cells. The results indicate important differences in gene expression, amongst others down regulation of immune response genes in lung epithelial cells by A. fumigatus but not by A niger.

Comparative genotyping and phenotyping of Aspergillus fumigatus isolates from humans, dogs and the environment.

BACKGROUND: Aspergillus fumigatus is a ubiquitous saprotrophic fungus and an opportunistic pathogen of humans and animals. Humans and animals can inhale hundreds of A. fumigatus spores daily. Normally this is harmless for humans, but in case of immunodeficiency, invasive pulmonary aspergillosis (IPA) can develop with a high mortality rate. A. fumigatus also causes non-invasive mycoses like sino-nasal aspergillosis (SNA) in dogs. RESULTS: In this study we compared A. fumigatus isolates from humans with suspected IPA, dogs with SNA, and a set of environmental isolates. Phylogenetic inference based on calmodulin (CaM) and beta-tubulin (benA) sequences did not reveal A. fumigatus sub-groups linked to the origin of the isolates. Genotyping and microsatellite analysis showed that each dog was infected by one A. fumigatus genotype, whereas human patients had mixed infections. Azole resistance was determined by antifungal susceptibility testing and sequencing of the cyp51A gene. A total of 12 out of 29 human isolates and 1 out of 27 environmental isolates were azole resistant. Of the azole resistant strains, 11 human isolates showed TR34/L98H (n = 6) or TR46/Y121F/T289A (n = 5). Phenotypically, isolates from dogs were more variable in growth speed and morphology when compared to those isolated from human and the environment. CONCLUSIONS: 1. A. fumigatus from dogs with SNA are phenotypically very diverse in contrast to their environmental and human counterparts. 2. Phenotypic variability can be induced during the chronic infection process in the sinus of the dogs. The basis of this heterogeneity might be due to genomic differences and/or epigenetic variations. 3. Differences in dogs is a could be a result of within-host adaption and might be triggered by environmental factors in the sinus, however this hypothesis still needs to be tested.

Shell shape variation of queen conch Strombus gigas (Mesograstropoda: Strombidae) from Southwest Caribbean.

The endangered species Strombus gigas is a marine gastropod of significant economic importance through the Greater Caribbean region. In contrast to phenotypic plasticity, the role of genetics on shell variations in S. gigas has not been addressed so far, despite its importance in evolution, management and conservation of this species. This work used geometric morphometrics to investigate the phenotypic variation of 219 shells of S. gigas from eight sites of the Colombian Southwest Caribbean. Differences in mean size between sexes and among sites were contrasted by analysis of variance. Allometry was tested by multivariate regression and the hypothesis of common slope was contrasted by covariance multivariate analysis. Differences in the shell shape among sites were analyzed by principal component analysis. Sexual size dimorphism was not significant, whereas sexual shape dimorphism was significant and variable across sites. Differences in the shell shape among sites were concordant with genetic differences based on microsatellite data, supporting its genetic background. Besides, differences in the shell shape between populations genetically similar suggest a role of phenotypic plasticity in the morphometric variation of the shell shape. These outcomes evidence the role of genetic background and phenotypic plasticity in the shell shape of S. gigas. Thus, geometric morphometrics of shell shape may constitute a complementary tool to explore the genetic diversity of this species.

Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.

Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now prioritized for functional study.

The latest on positive airway pressure for pediatric obstructive sleep apnea.

INTRODUCTION: Obstructive sleep apnea (OSA) is an important and evolving area in the pediatric population, with significant sequelae when not adequately managed. The use of positive airway pressure (PAP) therapy is expanding rapidly and is being prescribed to patients with persistent OSA post adenotonsillectomy as well as those children who are not surgical candidates including those with medical complexity. AREAS DISCUSSED: This article provides a state-of-the-art review on the diagnosis of pediatric OSA and treatment with positive airway pressure (PAP). The initiation of PAP therapy, pediatric interface considerations, PAP mode selection, administration and potential complications of PAP therapy, factors influencing PAP adherence, the use of remote ventilation machine downloads, considerations surrounding follow-up of patients post PAP initiation and evaluation of weaning off PAP will be reviewed. The literature search was conducted via PubMed, Cochrane Library and Google Scholar databases through to March 2024. EXPERT OPINION: Further research is required to address barriers to adherence. Further innovation of home monitoring devices for both the diagnosis and assessment of OSA is required, given the limited pediatric sleep medicine resources in several countries worldwide.

Progesterone promotes Cxcl2-dependent vaginal neutrophil killing by activating cervical resident macrophage-neutrophil crosstalk.

Vaginal infections in women of reproductive age represent a clinical dilemma with significant socio-economic implications. The understanding of mucosal immunity failure during early pathogenic invasions that allow the pathogen to grow and thrive is far from complete. Neutrophils infiltrate most tissues following circadian patterns as part of normal repair, regulation of microbiota, or immune surveillance and become more numerous after infection. Neutrophils are responsible for maintaining vaginal immunity. Specific to the vagina, neutrophils continuously infiltrate at high levels, although during ovulation they retreat to avoid sperm damage and permit reproduction. Here we show that after ovulation, progesterone promotes resident vaginal macrophage-neutrophils crosstalk by up-regulating Yolk sac and early fetal organs (Folr2+ (folate receptor 2)) macrophage Cxcl2 expression, in a Tnfa-monocyte-derived macrophage (Cx3cr1hi MHCIIhi) mediated manner, to activate neutrophils' capacity to eliminate sex-transmitted and opportunistic microorganisms. Indeed, progesterone plays an essential role in conciliating the balance between the commensal microbiota, sperm, and the threat of pathogens: because progesterone not only promotes a flurry of neutrophils but also increases neutrophilic fury to restore immunity after ovulation to thwart pathogenic invasion post-intercourse. Therefore, modest progesterone dysregulations could lead to a suboptimal neutrophilic response, resulting in insufficient mucosal defense and recurrent unresolved infections.

Epigenetic dysregulation of virulence gene expression in severe Plasmodium falciparum malaria.

Chronic infections with the human malaria parasite Plasmodium falciparum depend on antigenic variation. P. falciparum erythrocyte membrane protein 1 (PfEMP1), the major erythrocyte surface antigen mediating parasite sequestration in the microvasculature, is encoded in parasites by a highly diverse family of var genes. Antigenic switching is mediated by clonal variation in var expression, and recent in vitro studies have demonstrated a role for epigenetic processes in var regulation. Expression of particular PfEMP1 variants may result in parasite enrichment in different tissues, a factor in the development of severe disease. Here, we study in vivo human infections and provide evidence that infection-induced stress responses in the host can modify PfEMP1 expression via the perturbation of epigenetic mechanisms. Our work suggests that severe disease may not be the direct result of an adaptive virulence strategy to maximize parasite survival but that it may indicate a loss of control of the carefully regulated process of antigenic switching that maintains chronic infections.

Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture.

We have cultured Plasmodium falciparum directly from the blood of infected individuals to examine patterns of mature-stage gene expression in patient isolates. Analysis of the transcriptome of P. falciparum is complicated by the highly periodic nature of gene expression because small variations in the stage of parasite development between samples can lead to an apparent difference in gene expression values. To address this issue, we have developed statistical likelihood-based methods to estimate cell cycle progression and commitment to asexual or sexual development lineages in our samples based on microscopy and gene expression patterns. In cases subsequently matched for temporal development, we find that transcriptional patterns in ex vivo culture display little variation across patients with diverse clinical profiles and closely resemble transcriptional profiles that occur in vitro. These statistical methods, available to the research community, assist in the design and interpretation of P. falciparum expression profiling experiments where it is difficult to separate true differential expression from cell-cycle dependent expression. We reanalyze an existing dataset of in vivo patient expression profiles and conclude that previously observed discrete variation is consistent with the commitment of a varying proportion of the parasite population to the sexual development lineage.

Distinct roles for FOXP3 and FOXP3 CD4 T cells in regulating cellular immunity to uncomplicated and severe Plasmodium falciparum malaria.

Failure to establish an appropriate balance between pro- and anti-inflammatory immune responses is believed to contribute to pathogenesis of severe malaria. To determine whether this balance is maintained by classical regulatory T cells (CD4(+) FOXP3(+) CD127(-/low); Tregs) we compared cellular responses between Gambian children (n = 124) with severe Plasmodium falciparum malaria or uncomplicated malaria infections. Although no significant differences in Treg numbers or function were observed between the groups, Treg activity during acute disease was inversely correlated with malaria-specific memory responses detectable 28 days later. Thus, while Tregs may not regulate acute malarial inflammation, they may limit memory responses to levels that subsequently facilitate parasite clearance without causing immunopathology. Importantly, we identified a population of FOXP3(-), CD45RO(+) CD4(+) T cells which coproduce IL-10 and IFN-gamma. These cells are more prevalent in children with uncomplicated malaria than in those with severe disease, suggesting that they may be the regulators of acute malarial inflammation.

Erythrocyte invasion and merozoite ligand gene expression in severe and mild Plasmodium falciparum malaria.

Erythrocyte invasion is central to malaria parasite replication and virulence. Plasmodium falciparum parasites use different alternative erythrocyte receptors and vary in expression of erythrocyte-binding antigenic (EBA) proteins and reticulocyte-binding protein homologues (Rh). Parasite invasion phenotypes and schizont-stage transcript expression profiles of the 8 eba and Rh protein-coding genes without internal stop codons were determined for 163 clinical isolates cultured ex vivo in The Gambia. There was extensive diversity in ability to invade erythrocytes treated with neuraminidase, trypsin, or chymotrypsin, and severe malaria isolates were less restricted by trypsin treatment than were mild malaria isolates (P = .015). Expression profiles of the eba and Rh genes showed distinct clusters indicating coordinated alternative transcription. The most divergent of 5 major clusters was dominated by Rh2b, with virtually no expression of eba175 or eba140 genes (which were dominant in the other 4 clusters). Particular transcripts were significantly correlated with parasitemia (Rh5 was positively correlated and eba140 negatively correlated; P < .01 for both) and age of patients (eba181 was positively correlated and eba175 negatively correlated; P < .001 for both) but not with invasion phenotypes or severity of malaria. Severe and mild malaria isolates were also evenly represented across the different expression clusters.

Gene copy number variation throughout the Plasmodium falciparum genome.

BACKGROUND: Gene copy number variation (CNV) is responsible for several important phenotypes of the malaria parasite Plasmodium falciparum, including drug resistance, loss of infected erythrocyte cytoadherence and alteration of receptor usage for erythrocyte invasion. Despite the known effects of CNV, little is known about its extent throughout the genome. RESULTS: We performed a whole-genome survey of CNV genes in P. falciparum using comparative genome hybridisation of a diverse set of 16 laboratory culture-adapted isolates to a custom designed high density Affymetrix GeneChip array. Overall, 186 genes showed hybridisation signals consistent with deletion or amplification in one or more isolate. There is a strong association of CNV with gene length, genomic location, and low orthology to genes in other Plasmodium species. Sub-telomeric regions of all chromosomes are strongly associated with CNV genes independent from members of previously described multigene families. However, approximately 40% of CNV genes were located in more central regions of the chromosomes. Among the previously undescribed CNV genes, several that are of potential phenotypic relevance are identified. CONCLUSION: CNV represents a major form of genetic variation within the P. falciparum genome; the distribution of gene features indicates the involvement of highly non-random mutational and selective processes. Additional studies should be directed at examining CNV in natural parasite populations to extend conclusions to clinical settings.

High-throughput targeted gene deletion in the model mushroom Schizophyllum commune using pre-assembled Cas9 ribonucleoproteins.

Efficient gene deletion methods are essential for the high-throughput study of gene function. Compared to most ascomycete model systems, gene deletion is more laborious in mushroom-forming basidiomycetes due to the relatively low incidence of homologous recombination (HR) and relatively high incidence of non-homologous end-joining (NHEJ). Here, we describe the use of pre-assembled Cas9-sgRNA ribonucleoproteins (RNPs) to efficiently delete the homeodomain transcription factor gene hom2 in the mushroom-forming basidiomycete Schizophyllum commune by replacing it with a selectable marker. All components (Cas9 protein, sgRNA, and repair template with selectable marker) were supplied to wild type protoplasts by PEG-mediated transformation, abolishing the need to optimize the expression of cas9 and sgRNAs. A Δku80 background further increased the efficiency of gene deletion. A repair template with homology arms of 250 bp was sufficient to efficiently induce homologous recombination. This is the first report of the use of pre-assembled Cas9 RNPs in a mushroom-forming basidiomycete and this approach may also improve the genetic accessibility of non-model species.

Course of lung function in children with cystic fibrosis in their first 3 years of life. / Evolución de la función pulmonar en niños con fibrosis quística durante los primeros 3 años de vida.

INTRODUCTION: The early prevention of respiratory complications in children with cystic fibrosis is determining for a longer survival. The implementation of lung function tests in the first months of life allows to detect respiratory involvement, even in asymptomatic children. OBJECTIVE: To assess the course of lung function in children with cystic fibrosis in their first 3 years of life and identify the factors affecting it. POPULATION AND METHODS: Observational, retrospective, analytical study. Children younger than 36 months with at least 2 lung function tests were included. RESULTS: Between 2008 and 2016, 48 patients were included; 85 % of them had been diagnosed by newborn screening. The first lung function test was done at 5 months old. The median Z-score of maximal flow at functional residual capacity was -0.05 (interquartile range: -1.09 to 1.08). The median change in the maximal flow Z-score between tests was -0.32 (interquartile range: -1.11 to 0.25), p = 0.045. Patients with Staphylococcus aureus respiratory infections, especially methicillin-resistant SA, evidenced a greater deterioration of lung function compared to those without infection. Neither sex nor the type of genetic mutation were associated with the course of lung function. Nutritional recovery throughout the study was really good. CONCLUSION: Lung function in children with cystic fibrosis worsens progressively during their first 3 years of life. These findings are associated with Staphylococcus aureus respiratory infections.

Introducción. La prevención temprana de las complicaciones respiratorias en niños con fibrosis quística determina una mayor sobrevida. La aplicación de pruebas de función pulmonar desde los primeros meses de vida permite detectar el compromiso respiratorio, inclusive en niños asintomáticos. Objetivo. Evaluar la evolución de la función pulmonar en niños con fibrosis quística durante los primeros 3 años de vida e identificar aquellos factores que la comprometen. Población y métodos. Estudio analítico, observacional, retrospectivo. Se incluyeron menores de 36 meses con, al menos, dos estudios funcionales respiratorios. Resultados. Entre 2008 y 2016, se incluyeron 48 pacientes, de los cuales el 85 % fue diagnosticado por pesquisa neonatal. La primera evaluación funcional respiratoria fue a los 5 meses. La mediana de puntaje Z de flujo máximo a nivel de la capacidad residual funcional fue de ­0,05 (intervalo intercuartil: de -1,09 a 1,08). La mediana de cambio del puntaje Z del flujo máximo entre las evaluaciones fue de -0,32 (intervalo intercuartil: de -1,11 a 0,25), p = 0,045. Los pacientes con infecciones respiratorias por Staphylococcus aureus, especialmente los resistentes a meticilina, evidenciaron una mayor declinación de la función pulmonar comparados con los no infectados. Ni el sexo ni el tipo de mutación genética se asociaron a la evolución respiratoria. Se evidenció una muy buena recuperación nutricional a lo largo del estudio. Conclusión. Los niños con fibrosis quística presentan una función pulmonar que, progresivamente, desmejora durante los primeros 3 años de vida. Estos hallazgos se asocian a las infecciones respiratorias por Staphylococcus aureus.