Miracle-dz/UniFAR-FTUs huggingface dataset:
Contribution à la caractérisation fonctionnelle de protéines de contrôle de la sécrétion d'effecteurs de type III chez la bactérie phytopathogène Ralstonia solanacearum : chaperonnes et protéine à domaine T3S4

La bacterie phytopathogene Ralstonia solanacearum est l'agent responsable du fletrissement bacterien sur plus de 200 especes vegetales, dont des especes agronomiques, faisant de cette bacteriose une des plus importantes dans le monde. Le pouvoir pathogene de la bacterie repose en grande partie sur sa capacite a injecter des proteines, appelees effecteurs de type III (ET3s), via le systeme de secretion de type III (SST3). La derniere decennie a ete notamment marquee par la decouverte chez les bacteries pathogenes de nombreuses proteines impliquees dans le controle du processus de secretion de type III. Chez R. solanacearum, ces mecanismes de controle de la secretion restent meconnus, contrairement aux mecanismes de regulation transcriptionnelle. Au cours de ces travaux, nous nous sommes attaches a caracteriser les fonctions des proteines HpaB (RSp0853), HpaD (RSp0848) et FliT-like (RSc2897) pour lesquelles plusieurs elements suggerent un potentiel role comme chaperonnes de type III (CT3s), ainsi que de la proteine HpaP (RSp0862) qui presente un domaine T3S4 (Type III Secretion Substrate Specificity Switch). Nous avons pu mettre en evidence la capacite de certaines CT3s a interagir entre elles et, pour HpaB et HpaD, a interagir avec de nombreux ET3s. De plus, les trois CT3s putatives semblent impliquees dans le pouvoir pathogene de R. solanacearum, HpaB s'averant meme indispensable a la virulence de la bacterie. D'autre part, nos travaux mettent en exergue l'importance de la proteine HpaP pour le pouvoir pathogene de la bacterie et son implication dans le controle de la secretion de substrats du SST3. Les resultats suggerent notamment que HpaP promeut la secretion de l'ET3 PopP1 en interagissant physiquement avec ce dernier. Finalement, la caracterisation de sequences conservees du domaine T3S4 revele l'importance de cette region pour la fonction de la proteine HpaP. L'ensemble de ces travaux suggere l'implication de plusieurs proteines de R. solanacearum dans le controle du processus de secretion de type III et souligne la diversite des mecanismes mis en jeu impliquant les proteines de type T3S4 chez les bacteries pathogenes.
Morphogenesis guided by 3D patterning of growth factors in biological matrices

Three-dimensional (3D) control over the placement of bioactive cues is fundamental to understand cell guidance and develop engineered tissues. Two-photon patterning (2PP) provides such placement at micro-to millimeter scale, but non-specific interactions between proteins and functionalized extracellular matrices (ECMs) restrict its use. Here we report a 2PP system based on non-fouling hydrophilic photocages and Sortase A-based enzymatic coupling offering unprecedented orthogonality and signal-to-noise ratio in both inert hydrogels and complex mammalian matrices. Improved photocaged peptide synthesis, and protein functionalization protocols with broad applicability are introduced. Importantly, the method enables 2PP in a single step and in the presence of fragile biomolecules and cells. As a corollary, we demonstrate the guidance of axons through 3D-patterned nerve growth factor (NGF) within brain-mimetic ECMs. Our approach allows for the interrogation of the role of complex signaling molecules in 3D matrices, thus helping to better understand biological guidance in tissue development and regeneration.
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
Recognition of Herpes Viruses on the Basis of a New Metric for Protein Sequences

This paper addresses the problem of intellectual human herpes viruses recognition based on the analysis of their protein sequences. To compare proteins, we use a new dissimilarity measure based on finding an optimal sequence alignment. In the previous work, we proved that the proposed way of sequence comparison generates a measure that has properties of a metric. These properties allow for more convenient and effective use of the proposed measure in further analysis in contrast to the traditional similarity measure, such as Needleman-Wunch alignment. The results of herpes viruses recognition show, that the metric properties allow to improve the classification quality. In addition, in this paper, we adduce an updated computational scheme for the proposed metric, which allows to speed up the comparison of proteins.
The influence of 2-aminoethoxydiphenyl borate on the electrical activity of the rat heart under hypoxia/reoxygenation conditions

The aim of the study was to apply the multi-electrode mapping method to investigate the effect of 2-aminoethoxydiphenyl borate (2-apb) on the electrical activity and vessels of the isolated rat heart under hypoxia/reoxygenation injury (H/R). To date, the ability to influence on the calcium currents and condition of gap junctions has been shown for 2-apb. Changes in the intracellular calcium concentration in the heart play the pivotal role in the development of H/R. As a result, it was shown that 2-apb influences on the myocardial conduction velocity, sinus rhythm and coronary blood flow in the isolated rat heart. 2-apb caused heart fibrillation during normoxia but not under hypoxia, and attenuated the effect of the H/R on heart rate and vascular function.
Alterações na resposta imune inata e desintoxicação em Melipona quadrifasciata (Apidae: Meliponini) após a exposição oral aos bioinseticidas azadiractina e espinosade

v 1. Introdução . 1 1.1. As abelhas Melipona . 1 1.2. Sistema imune em insetos . 3 1.3. Inseticidas e a defesa dos insetos . 7 2. Objetivos . 10 2.1. Objetivo geral . 10 2.2. Objetivos específicos . 10 3.0. Materiais e métodos . 10 3.1. Abelhas . 10 3.2. Bioinseticidas e concentrações para os bioinsaios . 13 3.3. Exposição aos bioinseticidas . 13 3.5. Extração do RNA e síntese do cDNA . 14 3.6. PCR em tempo real . 15 3.7. Quantificação relativa de Transcritos . 16 3.8. Ensaio com bactéria e inseticida . 16 3.9. Coleta de hemolinfa e contagem total de hemócitos . 17 3.10. Análise Estatística . 17 4.0. Resultados e Discussão . 18 5.0. Conclusões . 22 6.0. Referências Bibliográficas . 23
Alternative polyadenylation mediates genetic regulation of gene expression

With the exception of mRNA splicing, little is known about co-transcriptional or post-transcriptional regulatory mechanisms that link noncoding variation to variation in organismal traits. To begin addressing this gap, we used 3’ Seq to characterize alternative polyadenylation (APA) in the nuclear and total RNA fractions of 52 HapMap Yoruba lymphoblastoid cell lines, which we have studied extensively in the past. We identified thousands of polyadenylation sites that are differentially detected in nuclear mRNA and whole cell mRNA, and found that APA is an important mediator of genetic effects on gene regulation and complex traits. Specifically, we mapped 602 apaQTLs at 10% FDR, of which 152 were found only in the nuclear fraction. Nuclear-specific apaQTLs are highly enriched in introns and are also often associated with changes in steady-state expression levels, suggesting a widespread mechanism whereby genetic variants decrease mRNA expression levels by increasing usage of intronic PAS. We identified 24 apaQTLs associated with protein expression levels, but not mRNA expression, and found that eQTLs that are not associated with chromatin QTLs are enriched in apaQTLs. These findings support multiple independent pathways through which genetic effects on APA can impact gene regulation. Finally, we found that 19% of apaQTLs were also previously associated with disease. Thus, our work demonstrates that APA links genetic variation to variation in gene expression levels, protein expression levels, and disease risk, and reveals uncharted modes of genetic regulation.
Morphological diversity among local and introduced maize (Zea mays L.) varieties in Haiti for yield improvement

Maize, the cereal with the largest production in the world, is a staple crop in many developing countries including Haiti. Even if Haiti is the second maize consumer in the Caribbean region, its national yield is low and alleged of aflatoxin contamination. In order to increase grain yield, three introduced and two local maize varieties (these used as comparative control) were evaluated. Three field trials were carried out at Torbeck and Morne Briller (Port- Salut) during different growing seasons. Experiments were designed in a three-replicate randomized block. Each experimental plot was 3.50 m per 10.5 m with a gross area of 36.75 m2 and 40 000 plants/ha densities. The trials were carried out according to local agricultural practices. The results revealed that the introduced varieties had a smaller yield than the local ones. Moreover, all varieties showed some aflatoxin content below the European Union limit (5μg/Kg). Statistical analyses showed a strong and direct correlation between yield and ear weight and an inverse correlation between yield and male and female flowering day after sowing. The broad phenotypic diversity suggested a rich reserve of alleles to exploit in a breeding program focused to improve food security in Haiti.
Functional Diversity of Evolutionary Novelties: Insights from Waterfall-Climbing Kinematics and Performance of Juvenile Gobiid Fishes

Synopsis The evolution of novel functional traits can contribute substantially to the diversification of lineages. Older functional traits might show greater variation than more recently evolved novelties, due to the accrual of evolutionary changes through time. However, functional complexity and many-to-one mapping of structure to function could complicate such expectations. In this context, we compared kinematics and performance across juveniles from multiple species for two styles of waterfall-climbing that are novel to gobiid fishes: ancestral “powerburst” climbing, and more recently evolved “inching”, which has been confirmed only among species of a single genus that is nested within the clade of powerburst climbers. Similar net climbing speeds across inching species seem, at first, to indicate that this more recently evolved mode of climbing exhibits less functional diversity. However, these similar net speeds arise through different pathways: Sicyopterus stimpsoni from Hawai’i move more slowly than S. lagocephalus from La Réunion, but may also spend more time moving. The production of similar performance between multiple functional pathways reflects a situation that resembles the phenomenon of many-to-one mapping of structure to function. Such similarity has the potential to mask appropriate interpretations of relative functional diversity between lineages, unless the mechanisms underlying performance are explored. More specifically, similarity in net performance between “powerburst” and “inching” styles indicates that selection on climbing performance was likely a limited factor in promoting the evolution of inching as a new mode of climbing. In this context, other processes (e.g., exaptation) might be implicated in the origin of this functional novelty.
Present Status of the Management of Patients with Defective Phagocyte Function

A. Correction of the Defect 108 B. Protective Isolation 108 C. Elimination of Potentially Pathogenic M icroorganisms 108 D. Physiotherapy 109 E. Nutritional Status 109 F. Avoidance of Drugs Interfering with Phagocyte Function 109 G. Immunization 109
Leaf micromorphology of 19 Mentha taxa

Mentha (mint) is a genus in the Lamiaceae with a worldwide distribution. It has a complex classification due to frequent hybridisation at the interspecific level, variation in basic chromosome number and the occurrence of polyploidy (diploid to nonaploid). Although there have been many studies of Mentha leaf micromorphology, usually only a few taxa were described. The aim of this study was to characterise the micromorphology of Mentha leaves. Nineteen Mentha taxa, covering all four sections of the genus, were grown under controlled conditions and adaxial and abaxial leaf surfaces were examined using stereo and scanning electron microscopes. This study included examination of the previously uninvestigated Australian species, M. australis and M. diemenica. The study revealed that average lamina length varied from 3 mm (M. requienii) to 34 mm (M. × niliaca) and leaves were sessile (M. spicata) to where petiole length was 50% of total leaf length (M. requienii). Peltate and capitate glandular trichomes were found on the adaxial and abaxial leaf surfaces of almost all taxa. Most taxa were hypostomatous. A few taxa had amphistomatous leaves which was interesting given that Mentha is a mesophytic genus naturally found in moist environments beside streambanks and lake shores. Average guard cell length varied from 14 µm (M. suaveolens) to 27 µm (M. × piperita f. citrata ‘Basil’) with larger guard cell length correlated with larger DNA content and chromosome number. Two species in section Pulegium (M. requienii and M. pulegium) had small laminas, relatively long petioles and high adaxial stomatal density which distinguished them from taxa in the other three sections. Larger DNA content in plants can be associated with larger cell size. Most studies of Mentha leaf micromorphology make no mention of ploidy. The present study indicates this should be considered when comparing relative cell size between species.
Bats as predators at the nests of tropical forest birds

Nest predation is one of the main causes of bird mortality, and the development of nest anti‐predatory defenses can mold many aspects of bird evolution. Here we report that bats can attack nests in incubation and nestling stages in the Atlantic Forest, Brazil. Although other types of interactions between birds and bats have been reported, including predation of adult individuals and the co‐occurrence in cavity nests, bats may have been underestimated as nest predators. The combination of flying and olfactory skills makes bats functionally different compared to other predators, opening new perspectives on the interpretation of nesting‐birds anti‐predatory strategies. They represented 8% of all recorded potential predations in the bird community studied, being more important than reptiles, and were responsible for 33% of nest losses for at least one bird species. Our data suggest the potential for nest depredation by bats to be an important selective factor in shaping anti‐predatory strategies of nesting birds. Then, the use of devices capable to detect bats will be essential for reliable interpretations of birds nest defense mechanisms in future works.
Morphologie comparée des derniers segments du gastre et des genitalia mâles des Vespidae. 2. Sous-famille des Masarinae (Hymenoptera)

Le present article propose une description des derniers segments du gastre et des genitalia mâles de plusieurs especes de Ceramius et de Celonites, ainsi que de Jugurtia dispar et de Masaris vespiformis, faisant ressortir la grande diversite des structures (anneau basal, gonocoxites, volselles, aedeagus) au sein de la sous-famille des Masarinae. Les caracteristiques morphologiques detaillees de ces diverses structures, jointes a l'etude de la chetotaxie, doivent fournir des donnees precises utilisables en systematique.
KİNOA (CHENOPODIUM QUINOA WILLD.) ÜZERİNE BİR DERLEME

Amac: Bu derlemede, gecmisiyle baslayip kinoa hakkindaki guncel bilgileri, kinoanin botanik, kimyasal ve biyolojik ozelliklerini, beslenme profilini de kapsayacak sekilde ozetlemek amaclanmistir. Sonuc ve Tartisma: Kinoa (Chenopodium quinoa Willd.) geleneksel olarak Guney Amerika kulturleri tarafindan binlerce yildir tuketilen ve gunumuzde dunya genelinde islevsel bir gida olarak dikkat ceken tahil benzeri (pseudocereal) bir bitkidir. Yuksek miktarda icerdigi protein, lipid, lif, vitamin ve minerallerin yani sira mukemmel bir esansiyel amino asit dengesine sahiptir. Kinoanin saponinler, fitosteroller, fitoekdisteroitler, fenolikler, betalinler ve glisin betain gibi cok sayida fitokimyasal madde icerdigi bulunmustur. Bu bilesikler, metabolik, kardiyovaskuler ve gastrointestinal saglik uzerine faydali etkiler gosterebilir. Kinoanin biyolojik ozelliklerini tam olarak anlayabilmek icin klinik calismlari da kapsayacak sekilde fitokimyasal biyoyararlanimi, etki mekanizmalari ve etkilesimleri uzerinde daha cok arastirma yapilmasi gerekmektedir.
Sex differences in Variability of Brain Structure Across the Lifespan

Several brain disorders exhibit sex differences in onset, presentation, and prevalence. Increased understanding of the neurobiology of sex-based differences across the lifespan can provide insight into potential disease risk and protective mechanisms. We focused on sex-related differences in variability, which may be indicative of both disease vulnerability and resilience. In n=3,069 participants, from 8-95 years of age, we first analyzed the variance ratio in females vs. males of cortical surface area and global and subcortical volumes for discrete brain regions, and found widespread greater variability in males. In contrast, variance in cortical thickness was similar for males and females. Multivariate analysis that accounts for structural covariance supported variance ratio findings. Findings were present from early life and stable with age. We then examined variability among brain regions by sex. We found significant age-by-sex interactions across neuroimaging metrics, whereby in very early life males had reduced among-region variability compared to females, while in very late life this was reversed. Overall, our findings of greater regional variability but less among-region variability in males in early life may aid our understanding of sex-based risk for neurodevelopmental disorders. In contrast, our findings in late life may provide a potential sex-based risk mechanism for dementia.
Cavefish brain atlases reveal functional and anatomical convergence across independently evolved populations

Brain atlases reveal neuroanatomical and activity signatures associated with behavioral evolution in cavefish. Environmental perturbation can drive behavioral evolution and associated changes in brain structure and function. The Mexican fish species, Astyanax mexicanus, includes eyed river-dwelling surface populations and multiple independently evolved populations of blind cavefish. We used whole-brain imaging and neuronal mapping of 684 larval fish to generate neuroanatomical atlases of surface fish and three different cave populations. Analyses of brain region volume and neural circuits associated with cavefish behavior identified evolutionary convergence in hindbrain and hypothalamic expansion, and changes in neurotransmitter systems, including increased numbers of catecholamine and hypocretin/orexin neurons. To define evolutionary changes in brain function, we performed whole-brain activity mapping associated with behavior. Hunting behavior evoked activity in sensory processing centers, while sleep-associated activity differed in the rostral zone of the hypothalamus and tegmentum. These atlases represent a comparative brain-wide study of intraspecies variation in vertebrates and provide a resource for studying the neural basis of behavioral evolution.
Theoretical relation between axon initial segment geometry and excitability

In most vertebrate neurons, action potentials are triggered at the distal end of the axon initial segment (AIS). Both position and length of the AIS vary across and within neuron types, with activity, development and pathology. What is the impact of AIS geometry on excitability? Direct empirical assessment has proven difficult because of the many potential confounding factors. Here we carried a principled theoretical analysis to answer this question. We provide a simple formula relating AIS geometry and sodium conductance density to the somatic voltage threshold. A distal shift of the AIS normally produces a (modest) increase in excitability, but we explain how this pattern can reverse if a hyperpolarizing current is present at the AIS, due to resistive coupling with the soma. This work provides a theoretical tool to assess the significance of structural AIS plasticity for electrical function.
INDUCED SYSTEMIC RESISTANCE AND PROMOTION OF PLANT GROWTH IN OIL PALM SEEDLINGS BY ENDOPHYTIC Trichoderma virens

Trichoderma spp. have been widely used as a biological control agent for plant disease including basal stem rot (BSR) in oil palm. Trichoderma spp. control pathogens through mycoparasitism, antibiosis and triggering induced systemic resistance (ISR) in plants during the colonisation of plant roots, limiting the manifestation of the pathogenic fungi. In this study, we investigated the role of endophytic Trichoderma virens as a plant-growth promoter and its ability to prime the immune system of the host through ISR in oil palm. Mixed application of two endophytic isolates of T. virens 7b and 159c was found to significantly enhance the growth and development of oil palm seedlings, in terms of height, girth and chlorophyll content compared to individual treatment. However, results showed that individual treatment of 7b and 159c was better in lignin biosynthesis. Plant defence-related enzyme activities; peroxidase, polyphenol oxidase, superoxide dismutase and phenylalanine lyase were prominently elevated in the leaves of oil palm seedlings upon treatment of the respective T. virens isolates via plant roots. This study demonstrated the triggering of ISR in oil palm seedlings via T. virens treatment and proving that the inoculation of T. virens isolates 7b and 159c were able to promote the vegetative growth and development of oil palm seedlings.