Miracle-dz/UniFAR-FTUs huggingface dataset:
MADS-box factor AGL16 negatively regulates drought resistance via stomatal density and stomatal movement

Drought is one of the most severe environmental factors limiting plant growth and productivity. Plants respond to drought by closing stomata to reduce water loss. The molecular mechanisms underlying plant drought resistance are very complex and yet to be fully understood. While much research attention has been focused on the positive regulation of stomatal closure, less is known about its negative regulation, equally important in this reversible process. Here we show that the MADS-box transcriptional factor AGL16 acts as a negative regulator in drought resistance by regulating both stomatal density and movement. Loss-of-function mutant agl16 was more resistant to drought stress with higher relative water content, which was attributed to a reduced leaf stomatal density and more sensitive stomatal closure due to a higher leaf ABA level compared with wild type, while AGL16 overexpression lines displayed the opposite phenotypes. AGL16 is preferentially expressed in guard cells and down regulated in response to drought stress. The expression of CYP707A3 and AAO3 in ABA metabolism and SDD1 in stomatal development was altered by AGL16 as shown in agl16 and overexpression lines. Chromatin immunoprecipitation, transient transactivation, and yeast-one-hybrid assays demonstrated that AGL16 bound the CArG motif in the promoter of the CYP707A3, AAO3, and SDD1 to regulate their transcription, and therefore alter leaf stomatal density and ABA level. Taken together, AGL16 acts as a negative regulator of drought resistance by modulating leaf stomatal density and ABA accumulation.
Molecular comparison of Egyptian and Saudi local chickens using RAPD Markers. I

This study aimed at comparing the genetic variation levels of two Egyptian (Fayoumi and Dandrawi) and two Saudi chicken lines (Hajar1 and Hajar2), with commercial broiler and layer chicken breeds. RAPD-PCR analysis, using 15 random primers, was used. 10 primers only were subjected to data analysis due to their productivity. The total number of amplified bands was 3967 on 123 loci. The percentage of polymorphic loci was averaged 34.56% and was the highest in Fayoumi, Dandrawi and layer (37.4%) and the lowest in broilers (26%). The average number of detected alleles was 1.173. However, the effective number of alleles averaged 1.238. The average of within-breed genetic variability estimates ranged between 0.135 in broilers to 0.229 in Fayoumi chickens. The Analysis of Molecular Variance (AMOVA) indicated that the six breeds were significantly different from each other. The phylogenic analysis revealed that the two Saudi breeds were too close to each other, although they are not in the same cluster. Also, all local breeds were close to the meat-type than the egg-type commercial breed.
Field relevant variation in ambient temperature modifies the density-dependent establishment of Plasmodium falciparum in mosquitoes: implications for the infectious reservoir and beyond?

The relationship between Plasmodium falciparum gametocyte density and infections in mosquitoes is central to understanding the rates of transmission with important implications for control. Here, we determined whether field relevant variation in environmental temperature could also modulate this relationship. Anopheles stephensi were challenged with three densities of P. falciparum gametocytes spanning a ∼10-fold gradient, and housed under diurnal/daily temperature range (“DTR”) of 9°C around means of 20°C, 24°C and 28°C. At the peak stages of infection for each temperature, the proportion of mosquitoes infected with oocysts in the midguts or infectious with sporozoites in the salivary glands were measured (referred to collectively as vector competence hereon), in addition to oocyst intensities from infected midguts. While vector competence was similar at 20 DTR 9°C and 24 DTR 9°C, the proportion of mosquitoes infected and subsequently infectious were also comparable, with evidence, surprisingly, for higher vector competence in mosquitoes challenged with intermediate gametocyte densities. For the same gametocyte densities however, severe reduction in the proportion of infectious mosquitoes was accompanied by a significant decline in vector competence at 28 DTR 9°C, although density per se showed a positive and linear effect at this temperature. Unlike vector competence, oocyst intensities decreased with increasing temperatures with a predominantly positive and linear association with gametocyte density, especially at 28 DTR 9°C. Oocyst intensities across individual infected midguts suggested temperature-specific differences in mosquito susceptibility/resistance: at 20 DTR 9°C and 24 DTR 9°C, dispersion (aggregation) increased in a density-dependent manner but not at 28 DTR 9°C where the distributions were consistently random. Limitations notwithstanding, our results have manifold implications in, for instance, how variation in temperature could modify seasonal dynamics of infectious reservoirs and transmission and the contribution of high-/patent- and low-density/sub-patent carriers, to suggestions for design and deployment of transmission-blocking vaccines/drugs, but with a cautionary note suggesting how low efficacy could lead to transmission enhancement in certain environments.
Development of multi-locus barcodes for identification of bacterial strains and species in environmental samples using next generation sequencing technologies

Different microorganisms are of important use in medicine and biotechnology. Despite the diverse bioactivity of these microorganisms, they are almost indistinguishable by phenotype and by the 16S rRNA, which makes it challenging to trace and identify them in nature. In this chapter, a novel software online tool, BarcodeGenerator, was used for the creation of barcode sequences. This allows identification of most suitable marker sequences for DNAbased multi-local barcoding for identification and monitoring of medical and biotechnological strains.
Environmental Toxicology and Chemistry

We illustrate that the Organisation for Economic Co‐operation and Development guideline 305 (OECD‐305) for growth‐correcting bioconcentration factors (BCFs) and biomagnification factors (BMFs) violates the mass‐balance assumption underlying the definition of BCFs and BMFs and provides unrealistic estimates of BCFs and BMFs of chemicals in nongrowing fish. We present and test alternative methods for growth‐correcting BCFs and BMFs that maintain mass balance. We conclude that the OECD‐305‐recommended growth correction of BCFs and BMFs causes error, is unnecessary, and should be revisited. Environ Toxicol Chem 2019;38:2065–2072. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Heterogeneities in intrinsic excitability and frequency-dependent response properties of granule cells across the blades of the rat dentate gyrus

The dentate gyrus (DG), the input gate to the hippocampus proper, is anatomically segregated into three different sectors, namely the suprapyramidal blade, the crest region and the infrapyramidal blade. Although there are well-established differences between these sectors in terms of neuronal morphology, connectivity patterns and activity levels, differences in electrophysiological properties of granule cells within these sectors have remained unexplored. Here, employing somatic whole-cell patch-clamp recordings from the rat DG, we demonstrate that granule cells in these sectors manifest considerable heterogeneities in their intrinsic excitability, temporal summation, action potential characteristics and frequency-dependent response properties. Across sectors, these neurons showed positive temporal summation of their responses to inputs mimicking excitatory postsynaptic currents, and showed little to no sag in their voltage responses to pulse currents. Consistently, the impedance amplitude profile manifested low-pass characteristics and the impedance phase profile lacked positive phase values at all measured frequencies, voltages and for all sectors. Granule cells in all sectors exhibited class I excitability, with broadly linear firing rate profiles, and granule cells in the crest region fired significantly less action potentials compared to those in the infrapyramidal blade. Finally, we found weak pairwise correlations across the 18 different measurements obtained individually from each of the three sectors, providing evidence that these measurements are indeed reporting distinct aspects of neuronal physiology. Together, our analyses show that granule cells act as integrators of afferent information, and emphasize the need to account for the considerable physiological heterogeneities in assessing their roles in information encoding and processing.
Cellulose, stem strength and the Endo-(1,4)-β-Glucanase gene family in barley and maize.

xxi Abbreviations.xxiii Chapter 1 . 1 From Stalk Lodging to the Endo-(1,4)-β-glucanase Gene Family in Plants: An Overview 1.1. LODGING IN CEREAL CROPS . 3 1.2. CELLULOSE . 7 1.3. THE PLANT CELL WALL . 12 1.3. 1. Primary cell wall . 17 1.3. 2. Secondary cell walls . 17 1.4. THE MONOCOTYLEDON STEM . 19 1.5. CELLULOSE AND STEM STRENGTH . 23 1.6. ENDO-(1,4)-Β-GLUCANASES . 24 1.6. 1. Plant endo(1,4)-β-glucanases . 29 1.6. 2. Endo-(1,4)-β-glucanases and CBDs . 29 1.6. 3. In vitro substrates . 31 1.6. 4. Endo-(1,4)-β-glucanases in cell wall breakdown . 31 1.6. 5. Endo-(1,4)-β-glucanases in plant cell wall synthesis . 32 1.7. SUMMARY . 36 Chapter 2 . 41 The Endo-(1,4)-β-glucanase Gene Families in Barley, Maize and Other Cereals 2.
Pharmaco-Genetic Screen To Uncover Actin Regulators Targeted by Prostaglandins During Drosophila Oogenesis

Prostaglandins (PGs) are lipid signaling molecules with numerous physiologic functions, including pain/inflammation, fertility, and cancer. PGs are produced downstream of cyclooxygenase (COX) enzymes, the targets of non-steroidal anti-inflammatory drugs (NSAIDs). In numerous systems, PGs regulate actin cytoskeletal remodeling, however, their mechanisms of action remain largely unknown. To address this deficiency, we undertook a pharmaco-genetic interaction screen during late-stage Drosophila oogenesis. Drosophila oogenesis is as an established model for studying both actin dynamics and PGs. Indeed, during Stage 10B, cage-like arrays of actin bundles surround each nurse cell nucleus, and during Stage 11, the cortical actin contracts, squeezing the cytoplasmic contents into the oocyte. Both of these cytoskeletal properties are required for follicle development and fertility, and are regulated by PGs. Here we describe a pharmaco-genetic interaction screen that takes advantage of the fact that Stage 10B follicles will mature in culture and COX inhibitors, such as aspirin, block this in vitro follicle maturation. In the screen, aspirin was used at a concentration that blocks 50% of the wild-type follicles from maturing in culture. By combining this aspirin treatment with heterozygosity for mutations in actin regulators, we quantitatively identified enhancers and suppressors of COX inhibition. Here we present the screen results and initial follow-up studies on three strong enhancers – Enabled, Capping protein, and non-muscle Myosin II Regulatory Light Chain. Overall, these studies provide new insight into how PGs regulate both actin bundle formation and cellular contraction, properties that are not only essential for development, but are misregulated in disease.
Quality Control Techniques and Related Factors for Hydroponic Leafy Vegetables

Hydroponics has been an increasingly important field of vegetable production. However, a big issue with hydroponics is that certain crops can quickly accumulate high levels of nitrate-N (NO3 ± -N) from the hydroponic system. The objective of this research was to decrease NO3 accumulation and increase the nutritional value and yield of vegetable crops using lettuce and oilseed rape as a model under hydroponic production. In this study, two technologies were applied to leafy vegetable production: 1) using supplementary lighting (blue-violet diode) by manipulating illumination and 2) removing fertilization before harvest for a short term (3 or 5 days), thus providing a practical experiment for improving yield and edible qualities of hydroponic leaf vegetable production. Illumination was applied 4 hours a day (0500–0700 hr and 1700–1900 hr) during good weather, or 12 hours a day during bad weather with insufficient natural light (<2000 lux) during the autumn and winter seasons. Results showed that the lettuce cultivar Ou-Luo and the oilseed rape cultivar Ao-Guan Pakchoi had increased yield (50.0% and 88.3%, respectively), decreased NO3 content (26.3% and 30.8%, respectively), and increased total soluble solids (24.1% and 30.6%, respectively). The 5-day fertilizer-free treatment before harvest resulted in 19.2%, 6.4%, and 16.5% yield increases; and 26.0%, 24.3%, and 47.8% NO3 decreases in oilseed rape cultivar Ao-Guan Pakchoi and lettuce cultivars Da-Su-Sheng and Ou-Luo, respectively.
Dispersal of a carabid beetle in farmland is driven by habitat‐specific motility and preference at habitat interfaces

Carabid beetles are common predators of pest insects and weed seeds in agricultural systems. Understanding their dispersal across farmland is important for designing farms and landscapes that support pest and weed biological control. Little is known, however, about the effect of farmland habitat discontinuities on dispersal behaviour and the resulting redistribution of these beetles. We released 1,985 well‐fed and 1,680 food‐deprived individuals of the predatory carabid beetle Pterostichus melanarius (Illiger) (Coleoptera: Carabidae) on a farm in Wageningen, The Netherlands. We recaptured 23.6% of those beetles over a period of 23 days in 2010. The farmland comprised agricultural fields with various crop species and tillage, separated by strips of perennial vegetation. We developed discrete Fokker‐Planck diffusion models to describe dispersal based on motility (m2 day−1) and preferential behaviour at habitat interfaces. We used model selection and Akaike’s information criterion to determine whether movement patterns were driven by variation in motility between habitats, preferential behaviour at habitat interfaces, or both. Model selection revealed differences in motility among habitats and gave strong support for preferential behaviour at habitat interfaces. Behaviour at interfaces between crop and perennial vegetation was asymmetric, with beetles preferentially moving towards the crop. Furthermore, beetles had lower motility in perennial strips than in arable fields. Also between arable habitats movement was asymmetric, with beetles preferentially moving towards the habitat in which motility was lowest. Neither crop type nor tillage explained differences in motility between crop habitats. Recapture data representing dispersal patterns of beetles were best described by a model that accounted for differences in motility between farmland habitats and preferential behaviour at habitat interfaces. Motility in farmland and behaviour at interfaces can also be estimated for other organisms and farmland habitats to support design of farmland conducive to natural pest suppression. Landscape design for early recruitment of carabids into arable fields should take into account the quantity and quality of resource habitats in the landscape, their proximity to crop fields, movement rates, and the possibility of movement responses at interfaces between landscape elements.
Developmental Genome-Wide DNA Methylation Asymmetry Between Mouse Placenta and Embryo

In early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.
Human bone marrow mesenchymal stem/stromal cell behaviour is coordinated via mechanically activated osteocyte-derived extracellular vesicles

Osteocytes are mechanosensitive cells that are believed to play a fundamental role in coordinating bone mechanoadaptation via the secretion of paracrine factors. However, the exact mechanisms by which osteocytes relay mechanical signals to effector cells is poorly understood. In this study, we demonstrated that osteocytes subjected to a physiologic fluid shear secrete a distinct collection of factors that significantly enhance human MSC recruitment and osteogenesis. Utilising proteomics we generated an extensive map of proteins within the mechanically activated osteocyte secretome, identifying numerous paracrine factors that are modified by mechanical stimulation. Moreover, we identified the presence of extracellular vesicles (EVs) and further demonstrated that these mechanically activated osteocyte derived EVs (MAEVs) coordinate human MSCs recruitment and osteogenesis. This indicates that mechanical conditioning of parent cells can modify EVs and demonstrates the pro-osteogenic potential of MAEVs as a cell-free therapy to enhance bone regeneration and repair in diseases such as osteoporosis.
Gram-positive and Gram-negative Bacteria Share Common Principles to Coordinate Growth and the Cell Cycle at the Single-cell Level

Bacillus subtilis and Escherichia coli are evolutionarily divergent model organisms that have elucidated fundamental differences between Gram-positive and Gram-negative bacteria, respectively. Despite their differences in cell cycle control at the molecular level, both organisms follow the same phenomenological principle for cell size homeostasis known as the adder. We thus asked to what extent B. subtilis and E. coli share common physiological principles in coordinating growth and the cell cycle. To answer this question, we measured physiological parameters of B. subtilis under various steady-state growth conditions with and without translation inhibition at both population and single-cell level. These experiments revealed core shared physiological principles between B. subtilis and E. coli. Specifically, we show that both organisms maintain an invariant cell size per replication origin at initiation, with and without growth inhibition, and even during nutrient shifts at the single-cell level. Furthermore, both organisms also inherit the same “hierarchy” of physiological parameters ranked by their coefficient of variation. Based on these findings, we suggest that the basic coordination principles between growth and the cell cycle in bacteria may have been established in the very early stages of evolution.
Richness, abundance and microhabitat use by Ardeidae (Aves: Pelecaniformes) during one seasonal cycle in the floodplain lakesof the lower Amazon River

The role of morphodynamic features such as grain size, swash climate and wave action on the macrofauna of beaches are well-known. However, few studies have investigated natural disturbances as potential drivers of temporal community variations. In southeastern Brazil, we sampled the intertidal macrofauna of two sandy beaches to test whether seasonal disturbances as the frequency of storm wave events (SWE) and rainfall have significant influence on their composition and abundance. The macrofauna assemblage differed significantly between the rainy and the dry seasons, but rainfall was not the main driver of community changes, although both beaches are in the vicinity of extensive river plumes. Actually, SWE explained most macrofauna richness overtime, with positive effects. Our results point to the importance of learning more about the effects of poorly studied disturbances on macrofaunal communities, and based on them we strongly recommend including these seasonal phenomena when monitoring sandy beaches.
Downscaling livestock census data using multivariate predictive models: Sensitivity to modifiable areal unit problem

The analysis of census data aggregated by administrative units introduces a statistical bias known as the modifiable areal unit problem (MAUP). Previous researches have mostly assessed the effect of MAUP on upscaling models. The present study contributes to clarify the effects of MAUP on the downscaling methodologies, highlighting how a priori scales and shapes choices could influence the results. We aggregated chicken and duck fine-resolution census in Thailand, using three administrative census levels in regular and irregular shapes. We then disaggregated the data within the Gridded Livestock of the World analytical framework, sampling predictors in two different ways. A sensitivity analysis on Pearson’s r correlation statistics and RMSE were carried out to understand how size and shapes of the response variables affect the goodness-of-fit and downscaling performances. We showed that scale, rather than shapes and sampling methods, affected downscaling precision, suggesting that training the model using the finest administrative level available is preferable. Moreover, datasets showing non-homogeneus distribution but instead spatial clustering seemed less affected by MAUP, yielding higher Pearson’s r values and lower RMSE compared to a more spatially homogenous dataset. Implementing aggregation sensitivity analysis in spatial studies could help to interpret complex results and disseminate robust products.
Saccadic adaptation in the presence of artificial central scotomas

Age-related macular degeneration (AMD) is characterized by the degradation of the macula resulting in poor central vision and difficulty performing daily tasks. Helping AMD patients optimally utilize their residual visual function is the focus of current rehabilitative strategies. Here we test whether saccadic adaptation is possible in the presence of an artificial central scotoma and if so, to what extent. The ultimate goal is to use saccadic adaptation to train patients in performing saccade re-referencing to better utilize their intact peripheral vision; patients would learn to make saccades to direct their preferred peripheral locus to the object of interest rather than the inutile fovea. We measured saccadic adaptation in healthy young participants using a central gaze-contingent artificial scotoma in two experiments, using a conventional double-step paradigm for both experiments, testing twelve and thirteen subjects respectively. Experiment 1 tested backward adaptation using a visible as well as an invisible 3° diameter scotoma. Experiment 2 consisted of forward adaptation using a 2° and a 4° invisible scotoma. We thus explored both backward and forward adaptation (known to involve different mechanisms), different-sized central scotomas, and different visibilities of scotomas. We found that in all scotoma conditions, participants adapted to similar amounts compared to control conditions without scotomas. We conclude that saccadic adaptation can occur sufficiently with central scotomas. Our results support the idea that central vision of the target is unnecessary for adaptation and that saccadic adaptation is driven primarily by peripheral retinal error.