Miracle-dz/UniFAR-FTUs huggingface dataset:
A contribution of FcγRIIIa cosignaling in TFH subset development in Systemic Lupus Erythematosus

Background Expansion of follicular helper T cells (TFH) population occurs in systemic lupus erythematosus (SLE) and their numbers correlate with autoantibody titers. In this study, we sought to examine the role of ICs (FcγRIIIa costimulation) play in TFH cells development. Methods We examined the presence of blood TFH cells using multicolor flow analysis in SLE patients in vivo. We then examined the development of these cells in vitro using plate-bound ICs. Performed differential expression analysis in cells activated via FcγRIIIa and compared to CD28 cosignaling. Results In SLE patients PBMCs, CD4+ gated T cells show IC binding and phosphorylated spleen tyrosine kinase (pSyk). These pSyk+ cells express PD1, ICOS, IL-21, and Bcl6, the TFH population markers. In vitro activation from plate-bound ICs of human naïve CD4+ T cells results in the differentiation of TFH like cells phenotype. We show that FcγRIIIa-pSyk cosignaling in Bcl6+IL-21+ cells drives the production of both IFN-γ (TFH1) and IL-17A (TFH17) production. TLR9 engagement by CpG ODN 2006 combined with FcγRIIIa costimulation of CD4+ T cells augments, IL-17A, IL-21 production in Bcl6+ T cells. FcγRIIIa cosignaling induced the overexpression of microRNAs that participate in TLR signaling and are associated with TFH cell differentiation. RNA-seq data reveal pathways that may contribute to the development of TFH cells and nucleic acid sensing. Conclusion Our results suggest a role for FcγRIIIa receptors in TFH development and a role for nucleic acid sensing in the expansion of TFH cells.
Towards a functional characterization of meiotic recombination in rapeseed : analysis of the meiotic transcriptome and hyper-recombinant mutants

Meiotic recombination driven by Crossing-Over (CO) is a limiting factor for the efficiency of plant breeding. One way to produce hyper-recombinant plants is to use the existing interspecific variability for recombination frequencies. Identification of the causal polymorphisms, either link to gene sequence or expression, represents a long-term endeavour. Another possibility is to mutate anti-meiotic CO genes. In rapeseed, a young allotetraploid species (AACC, 2n=38), both of these approaches are possible. First I wanted to check how much varies the meiotic transcriptome between 2 varieties that differ in term of recombination between homoeologous chromosomes (inherited from parental genomes). Unexpectedly, the meiotic transcriptome turned out to be very variable, the main source of this variation being notably the origin of the genome (A or C) and the variety. I also showed that homoeologous exchanges (HEs; the replacement of one chromosomal region with a duplicate of the homeologous region) contributed to this variation and led to large changes in expression both between and within varieties. Then I assessed whether FANCM, an anti-CO protein identified in Arabidopis thaliana had the same function in the Brassica genus. In Brassica rapa, a fancm mutant complements as expected a meiosis mutant defective in the main formation pathway for the formation of meiotic COs. In Brassica napus, I observed a slight increase in both homologous and homoeologous recombination frequencies. This work emphasizes the importance of characterizing HEs in allopolyploids species. Beyond their impact on gene content and expression, HEs most have likely phenotypic consequences. This study also presents an example of translational biology for an important trait in crop breeding.
QTL mapping to anthracnose leaf blight resistance in tropical maize

The objectives were to map genomic regions associated with quantitative trait loci (QTL) to anthracnose leaf blight (ALB) in tropical maize, and to determine the effects of the loci on resistance to the pathogenic fungus Colletotrichum graminicola (Ces.). QTL analysis to ALB was carried out in a population of F2:3 progenies resulting from the cross between the contrasting lines LR 04-2 and LS 95-1. Seventeen QTL were located by mapping analysis by composite interval on eight chromosomes. Four QTL mapped on chromosomes 9 (1 QTL) and 10 (3 QTL) were the most stable, detected in at least two experiments, and represented the most part of the phenotypic variation (27.7 to 54.3%) of resistance. The majority of QTL mapped were associated to specific severity evaluations/development stage of maize growth, and may explain the quantitative inheritance of resistance of tropical maize to ALB.
The role of macronutrients in the evolution of sex differences in reproduction and lifespan: lessons from novel holidic, medium-based diets

Life-history traits form an integral part of evolutionary biology as they closely relate to an individual’s fitness. There is a huge archive of empirical research that has shown diet influences the expression of nearly all life-history traits, ranging from immune response to sperm number. Exactly how diet actually influences the expression of important life-history traits, however, is often poorly understood, as traditionally diet has been viewed in a one-dimensional context, namely energy or calories. More recent research has begun to challenge this notion, by suggesting that it is actually the intake of specific nutrients that influences trait expression and fitness. Clearly, our understanding of the role of diet is shifting, yet more empirical studies are needed, which focus on how the intake of specific nutrients influence key life-history traits, whether these regulate lifehistory trade-offs and how this may impact an individual’s fitness. In this thesis, I use the Geometric Framework (GF) of nutrition to examine the role nutrition plays in the expression of key life-history traits (reproduction and lifespan) and any trade-offs that may exist between them. Historically, the type of diet used in some nutritional studies has been suboptimal, with some researchers proposing that CAFÉ assays, in particular, effect trait expression in Drosophila melanogaster. This is because they are a foreign substrate for the fly to feed from and thus it is difficult for flies to acquire the nutrients they need to function properly. Therefore, I formulated novel diets that represent the smallest deviation from natural feeding conditions, when compared to previous nutritional research, for D. melanogaster. I used these diets to focus on the effect two macronutrients, protein and carbohydrate, have on lifespan and reproduction in male and female D. melanogaster. I found that both protein and carbohydrates play a role in the expression of these traits, and not calories per se, and that there are divergent nutritional demands for reproduction between the sexes. I also found evidence that implies the type of diet (liquid versus medium-based) used to study nutritional effects on life-history traits could influence findings, with flies fed a medium-based diet living longer and having greater reproductive success. This could possibly be due to greater nutrient acquisition by flies fed medium-based diets. Overall, my thesis highlights that nutrition is multifaceted and complex, which is paramount to understanding life-history trait expression and the trade-offs that may exist between them. My work challenges the central dogma that calories are responsible for changes in trait expression and lifehistory trade-offs, and advances our understanding of diet composition and also the way that diet is delivered to organisms. In addition, it opens the door to new questions relating to how the type of
Fauna de mosquitos (Diptera, Culicidae) presentes en el humedal de La Grajera (Logroño) y sus implicaciones en salud pública

espanolLa vigilancia entomologica constituye una herramienta muy util para conocer el riesgo de las enfermedades transmitidas por artropodos vectores, ademas de ser un pilar basico en la vision “One Health”. El presente trabajo supone el primer estudio de vigilancia de mosquitos (Diptera, Culicidae) usando trampas cebadas con dioxido de carbono en un humedal en La Rioja. Los muestreos realizados con trampas BG-Sentinel y con la tecnica de cebo humano entre los meses de julio y septiembre de 2016 en el humedal de La Grajera han permitido la captura de 1.932 mosquitos correspondientes a 16 especies diferentes. Entre las especies identificadas, ocho constituyen nuevos registros para La Rioja: Anopheles algeriensis, Aedes vexans, Aedes detritus, Coquillettidia richiardii, Culex theileri, Culex perexiguus, Culiseta subochrea y Culiseta morsitans. Se han detectado varias especies de naturaleza antropofilica y con capacidad para transmitir diferentes patogenos. Ademas de discutir las posibles implicaciones sanitarias de las especies registradas, se analiza el patron temporal de la composicion de especies de culicidos durante el periodo de estudio. EnglishEntomological surveillance is a very useful tool to know the transmission risk of arthropod vector-borne diseases as well as being a basic pillar in the vision “One Health”. In this paper, the first mosquito (Diptera, Culicidae) surveillance study with carbon dioxide-baited traps in a wetland from La Rioja is reported. The sampling performed with BG-Sentinel traps and human bait technique between July and September 2016 in the wetland of La Grajera allowed the capture of 1,932 mosquitoes belonging to 16 different species. Among the identified species, eight represent new records for La Rioja: Anopheles algeriensis, Aedes vexans, Aedes detritus, Coquillettidia richiardii, Culex theileri, Culex perexiguus, Culiseta subochrea and Culiseta morsitans. Several species with anthropophilic nature and competent to transmit several pathogens have been detected. In addition to discussing the possible health implications of the recorded species, the temporal pattern of the mosquito species composition during the study period is discussed.
Cat Wars: The Devastating Consequences of a Cuddly Killer

Cat Wars: The Devastating Consequences of a Cuddly Killer by Peter P. Marra and Chris Santella. 2016. Princeton University Press, Princeton, NJ, USA. 216 pp., 16 color plates. $24.95 (hardcover). ISBN 978-0-691-16741-1. In 2013, Loss et al. reviewed the scientific literature and generated estimates of the numbers of birds, mammals, and herpetofauna killed by domestic cats annually. The paper caught the attention of a variety of media outlets and sparked a polarizing and sometimes rancorous public debate about the impacts of freeroaming cats on wildlife. In Cat Wars, Peter P. Marra, a coauthor of the Nature Communications paper, teams up with writer Chris Santella to explore the issue in more detail. Cat Wars is an aptly evocative title, referring to both the heated controversy over the impacts of free-ranging domestic cats and the wildlife casualties that are at the heart of the debate. Without reading the book, detractors might conclude that the authors are proposing a war on cats, which is unfortunate because those critics are precisely the audience that would most benefit from this highly readable missive. Although the book primarily emphasizes how freeroaming cats affect wildlife—either directly, via predation, or indirectly, by inducing behavioral changes or transmitting diseases (e.g., Cresswell 2008, Bonnington et al. 2013, Loss and Marra 2017)—a wide range of subjects and relevant history is discussed. One sobering chapter focuses on the burgeoning public health crisis posed by Toxoplasma gondii, a parasite linked to a range of human ills— including miscarriages, birth defects, and schizophrenia— for which felines, including domestic cats, are the definitive hosts. Because it persists in the environment and can wash downstream into ocean ecosystems, T. gondii has also been implicated in the deaths of a number of imperiled marine mammal species, a fact that may come as a surprise to many readers. While less common in the United States, the authors also discuss the role that cats play in the transmission of other zoonotic diseases such as plague and rabies. The book is interspersed with engaging narratives and profiles of both bird and cat lovers, and even delves into such topics as the rise of birding in North America and the prominent role of cats in Internet culture. Most chapters are written clearly enough for a nonscientific readership, but important subjects occasionally are not sufficiently explained for a reader who has never been exposed to certain ecological concepts. For example, in Chapter 2 the authors describe the domestic cat’s status as one of the world’s worst invasive species, outcompeting or edging native species from their established niches (e.g., Lowe et al. 2000), but they neither define an ecological niche nor expand upon the concept of niche overlap, which might have been useful to someone unfamiliar with these terms. Overall, however, the authors nicely summarize and distill the scientific literature, such as when they cogently explain the quantitative modeling
Relative growth and reproductive cycle of the hermaphroditic Cardites antiquatus (Mollusca: Bivalvia) collected from the Bizerte channel (northern Tunisia)

Abstract The relative growth and the reproductive cycle of Cardites antiquatus (L., 1758) from the Bizerte channel (northern Tunisia) were investigated from July 2008 to June 2009. Individuals presented a broad size range, with shell length ranging between 8 and 37 mm. The study of the species relative growth revealed that shell thickness, total wet weight, shell dry weight, soft tissues dry weight and visceral mass dry weight grow proportionally faster than shell length throughout ontogeny. The species reproductive cycle was described and followed through the calculation of the condition index, gonadosomatic index and histological analyses of the gonads. This hermaphroditic species has three spawning periods: gamete emission with low intensity from July to August, an important emission but shorter in time from October to November and an extended spawning period, comprehended from February until June. Being the first study focusing on C. antiquatus in Tunisian waters, it greatly improves the current knowledge on the relative growth and reproductive cycle of this species, thus providing valuable baseline information in a hypothetical scenario of commercial exploitation of this species for seafood.
Comparison of Sensitivity to Glyphosate of Euphorbia davidii Populations

Euphorbia davidii (Euphorbiaceae) is a summer annual weed present in the Province of Buenos Aires, Argentina. The aim of this study was to compare the sensitivity to glyphosate of different populations of Euphorbia davidii. Two techniques were used: a seed bioassay and shikimate determination in glyphosatetreated plants. Germination rates of seeds belonging to the populations from Espartillar, Barrow, Olavarria and Azul exposed to different concentrations of glyphosate were compared. Plants from the same locations treated with glyphosate were evaluated to determine shikimate levels. The most sensitive population was from Espartillar, with a CE50 (average effective concentration) of 4.00 g e.a. L-1. Based on this finding, the resistance index for each population was 1.76, 2.39 and 2.48 for Azul, Olavarria and Barrow respectively. Regarding glyphosate-treated plants in which shikimate levels were determined, a significant increase in the concentration of this metabolite was only observed in the population from Espartillar. Accumulation of shikimate was not detected in the other groups. These results show differential sensitivity to glyphosate of the evaluated populations.
Small RNA Extraction using Fractionation Approach and Library Preparation for NGS Platform

Spandan Chaudhary1*, Pooja S. Chaudhary2 and Toral A. Vaishnani3 1Department of Medical Genetics, Xcelris Labs Limited, Old Premchandnagar Road, Opp. Satyagrah Chhavani, Bodakdev, Ahmedabad-380015, Gujarat, India 2NGS department, Xcelris Labs Limited, Old Premchandnagar Road, Opp. Satyagrah Chhavani, Bodakdev, Ahmedabad-380015, Gujarat, India 3Bioinformatics department, Xcelris Labs Limited, Old Premchandnagar Road, Opp. Satyagrah Chhavani, Bodakdev, Ahmedabad-380015, Gujarat, India Journal of Advanced Research in Biotechnology Open Access Research Article
Anticipating fire‐mediated impacts of climate change using a demographic framework

Handling Editor: Charles Fox Abstract 1. Climate change indirectly affects forest ecosystems through changes in the frequency, size, and/or severity of wildfires. In addition to its direct effects prior to fire, climate also influences immediate postfire recruitment, with consequences for future vegetation structure and fire activity. A major uncertainty, therefore, is if, when and where vegetation shifts will occur. 2. With an emphasis on species traits, we use a demographic framework to examine how the interaction of changing climate and fire will affect postfire woody vegetation recruitment and the likelihood of vegetation shifts. Each demographic stage – adult mortality, propagule availability, seed germination, seedling establishment, and seedling survival – serves as a filter through which a species must pass for establishment and recovery to occur. 3. We apply this framework to case studies in western North American forests, including boreal and southwestern U.S. Pinus ponderosa forests, to help understand the mechanisms behind recent postfire vegetation changes. The case studies highlight how changes in climate and fire properties will make it increasingly difficult for some species to pass through each demographic filter in the future. 4. As climate warming continues, we expect increased dominance of species that resprout following fire, maintain canopy or soil seed banks, have long distance seed dispersal, produce drought-tolerant seedlings, and/or reach reproductive maturity quickly. The persistence of postfire vegetation shifts will depend the on ratio of recovery time to disturbance interval(s). 5. An advantage of the demographic-filter framework is that it places emphasis on mechanisms, thus improving our ability to anticipate future vegetation shifts. As such, it highlights the clear need for more mechanistic studies of postfire recruitment to disentangle the relative effects of multiple drivers in postfire environments.
Development, and genetic and metabolic characterization of new tomato mutants with enhanced and deficient carotenoid content

ABSTRACT Tomato (Solanum lycopersicum) is a valuable vegetable crop rich in health-protective carotenoids, but breeding improvements are limited by its narrow genetic diversity. New mutants with enhanced and deficient carotenoid content in a single genetic background of tomato cv. MicroTom were developed via chemical mutagenesis. Genetic and metabolic analyses showed that mutant DC260, which exhibited fruit color alteration from red to deep red interlaced with orange color, had significant (P < 0.05) increases of lycopene (up to 42.8%) and ß-carotene (up to 61.5%) compared with control plants. Pearson correlation analysis of M1 and M2 generations in DC260 revealed that fruit color alteration was significantly (P < 0.05) correlated with lycopene (coefficient = 0.55) and ß-carotene content (coefficient = 0.63). The fruit color alteration of DC260 was controlled by a single gene at a heterozygous locus. In contrast, mutant DC107 and DC624, which exhibited fruit color alteration from red to orange-yellow, was significantly (P < 0.05) carotenoid-deficient with up to 346.3-, 10.8-, and 185.2- fold reductions of lycopene, ß-carotene, and total carotenoids, respectively, compared with the control plants. Carotenoid deficiency in DC170 and DC624 was responsible for the fruit color alteration and was controlled by a dominant gene at a homozygous locus.
Sex‐linked inheritance of diapause induction in the butterfly Pieris napi

Many temperate insects survive harsh environmental conditions, such as winter, by entering a state of developmental arrest. This diapause state is predominantly induced by photoperiod. The photoperiod varies with latitude and has led to local adaptation in the photoperiodic induction of diapause in many insects. To understand the rapid evolution of the photoperiodic threshold, it is important to investigate and understand the underlying genetic mechanisms. In the present study, the genetic basis of photoperiodic diapause induction is investigated in the green‐veined white butterfly Pieris napi (Lepidoptera, Pieridae) by assaying diapause induction in a range of conditions for a Swedish and Spanish population. Furthermore, the inheritance of diapause induction is assessed in reciprocal F1 hybrids and backcrosses between the two populations. The southern population shows a clear photoperiodic threshold determining diapause or direct development, whereas the northern populations show a high incidence of diapause, regardless of photoperiod. The hybrid crosses reveal that the inheritance of diapause induction is strongly sex‐linked, and that diapause incidence in the genetic crosses is highly dependent on photoperiod. This emphasizes the importance of assaying a range of conditions in diapause inheritance studies. The results indicate a strongly heritable diapause induction with a major component on the Z‐chromosome, as well as a minor effect of the autosomal background.
Anticipated ITD statistics built-in human sound localization

The variability of natural scenes places perceptual processes in the realm of statistical inference, where sensory evidence must be weighted by its reliability. Absent prior information, estimating environmental variability requires real-time sampling and computations. However, a portion of environmental variability can be assumed invariant across conditions. Perceptual tasks relying on time-dependent information may be vastly enhanced if the invariant statistical structure of sensory cues is built into the underlying neural processing. We investigated this question in human sound localization, where the statistics of spatial cues can be estimated. Localizing low frequency sounds in the horizontal plane relies on interaural time differences (ITD). We estimated the ITD statistics across frequency and azimuth from human head-related transfer functions (HRTFs). The mean ITD varied with azimuth following a sigmoid relationship, whose slope is steepest at the center. In addition, ITD was more variable over time for sounds located in the periphery compared to the center, in a frequency-dependent manner. We investigated the role of these statistics -- ITD slope and ITD variability -- in low-frequency lateralization of human subjects, to test the hypothesis that high-order sensory statistics are represented in the human brain influencing spatial discriminability and novelty detection. Thresholds for discriminating ITD changes reported by classical studies (Mills, 1958) were predicted by a model that considered both ITD slope and ITD variability. To further test our hypothesis, EEG novelty responses were recorded in human subjects undergoing an oddball stimulation sequence, where repetitive ("standard") tones of a given ITD were combined with sporadic ("deviant") tones of a different ITD. By using insert earphones, ITD was shifted with zero variability across time and location. Mismatch negativity (MMN) brain signals were used as an index of discriminability between standard and deviant stimuli. We found that MMNs were weaker for standards in the periphery, where the ITD slope is lower and the ITD variability is higher. Overall, the amplitude of novelty EEG signals was predicted by the difference in ITD between the standard and deviant normalized by the anticipated discriminability of the standard location, indicating that change detection is weighted by expected statistics of the sensory input. In sum, our results show that spatial discriminability thresholds and deviant detection are consistent with a representation of anticipated ITD statistics in the human brain, supporting the hypothesis that high-order statistics are built into human perceptual processes biasing behavior.