Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity and Clonal Structure of Spartina alterniflora in a Virginia Marsh

Abstract - We asked how genetic diversity of Spartina alterniflora (Smooth Cordgrass) partitions across multiple spatial scales in mid-Atlantic salt marshes. We analyzed samples from 5 Virginia marshes, spanning ∼ 35 km of coastline, using microsatellite markers to examine genetic diversity and genotype clustering. In a single marsh, nested spatial analysis of the genotypes allowed indirect evaluation of colonization dynamics. Samples collected ≥10 m apart had clonal and allelic diversity levels similar to those of other geographic locations; however, genotypic richness and evenness of samples collected 0.2 and 1.0 m apart were reduced. Sampling scale had little effect on allelic diversity. Expected heterozygosity exceeded observed heterozygosity values at all sites and spatial scales, suggesting Smooth Cordgrass inbreeding is common in these marshes. We hypothesize that the observed spatial patterns indicate there is genetic dominance of a few, well-adapted clones balanced by sexual reproduction and recruitment, especially after disturbance, thereby creating genetically diverse and potentially resilient marshes.
Effect of Nitrogen Rates on Growth and Quality of Water Spinach (Ipomea aquatica)

Aims: The study was conducted to investigate the impact of nitrogen fertilization on growth, leaf gas exchange and bio-metabolite accumulation in Ipomea aquatica. Treatment and Experimental Design: Ipomea aquatica plants were exposed to four different rates of nitrogen (0, 30, 60 and 90 N kg/ha) using Urea (46% N) as a nitrogen source. The experiment was laid out in Complete Randomize Design (CRD). Place and Duration of Study: Department of Biology, Faculty of Science, Universiti Putra Malaysia between September to November 2016. Methodology: Four nitrogen rates were applied (0, 30, 60 and 90 N Kg/ha) using Urea as a nitrogen source. The growth data collections were conducted once a week after the application of Original Research Article Ibrahim et al.; ARRB, 26(1): 1-12, 2018; Article no.ARRB. 40352 2 the treatments for the plant growth parameters. The total chlorophyll content in the leaves was measured using a Soil Plant Analytical Device (SPAD-502) chlorophyll meter. The leaf gas exchange was determined using a LI-6400XT portable photosynthesis system. Total phenolics and flavonoid were determined using Folin-Ciocalteu reagent. Results: It was found that the highest measurements of growth parameters namely plant height, leaf numbers, branches numbers, total biomass and chlorophyll content were observed at 90 kg N/ha and the lowest at 0 kg N/ha. As for the leaf gas exchange, the positive effect of nitrogen fertilization on kangkung was shown by the increased in photosynthesis rate (A) and stomatal conductance (gs) where the highest measurement recorded at 90 kg N/ha, and the lowest at 0 kg N/ha. However, the water use efficiency (WUE) decreased as the nitrogen rates increased. At lower rates of nitrogen fertilization (30 kg N/ha) produced the highest production of secondary metabolites, where the total phenolics and flavonoids production were enhanced compared to other nitrogen treatments. Conclusion: In conclusion, as the nitrogen rates increased, the growth and leaf gas exchange properties was enhanced however the production of secondary metabolites was decreased in I. aquatica.
Solidity effects on the performance of vertical-axis wind turbines

Graphical Abstract Abstract The variety of configurations for vertical-axis wind turbines (VAWTs) make the development of universal scaling relationships for even basic performance parameters difficult. Rotor geometry changes can be characterized using the concept of solidity, defined as the ratio of solid rotor area to the swept area. However, few studies have explored the effect of this parameter at full-scale conditions due to the challenge of matching both the non-dimensional rotational rate (or tip speed ratio) and scale (or Reynolds number) in conventional wind tunnels. In this study, experiments were conducted on a VAWT model using a specialized compressed-air wind tunnel where the density can be increased to over 200 times atmospheric air. The number of blades on the model was altered to explore how solidity affects performance while keeping other geometric parameters, such as the ratio of blade chord to rotor radius, the same. These data were collected at conditions relevant to the field-scale VAWT but in the controlled environment of the lab. For the three highest solidity rotors (using the most blades), performance was found to depend similarly on the Reynolds number, despite changes in rotational effects. This result has direct implications for the modelling and design of high-solidity field-scale VAWTs.
A versatile ceramic capillary membrane reactor system for continuous enzyme‐catalyzed hydrolysis

As an alternative to classical batch processes, enzyme‐catalyzed hydrolysis can also be carried out continuously. To facilitate this, a continuous ceramic capillary membrane reactor system (CCCMRS) was developed which can be operated with various proteolytic enzymes immobilized on the porous ceramic capillary membranes. This system has several advantages over common batch processes regarding stability, reproducibility and controllability and can easily be adapted to optimal reaction conditions and individual preferences. Two exemplary applications utilizing the CCCMRS were carried out and investigated in long‐term stability studies. In the first application the continuous enzymatic cleavage of human IgG into the antibody fragments Fab and Fc by immobilized papain was performed. A total volume of 22 mL of 1 mg mL‐1 IgG‐solution was enzymatically cleaved over a period of 33.3 h. The antibody cleavage products could be detected in an SEC‐HPLC over the whole process time thus indicating long‐term stability of the continuous hydrolysis process. The second application investigated the continuous digestion of pea and almond protein isolates by immobilized Alcalase resulting in the generation of a large variety of different peptides. This peptide fingerprint remains constant over a long period of time enabling fractionation and thus making the peptides accessible for further bioactivity studies in sufficient quantities. The constant peptide fingerprint could be shown in the RP‐HPLC analysis for all 30 samples with a total volume of 29.7 mL collected over a period of 45 h.
Recombination facilitates genetic assimilation of new traits in gene regulatory networks

A new phenotypic variant may appear first in organisms through plasticity, that is, as a response to an environmental signal or other nongenetic perturbation. If such trait is beneficial, selection may increase the frequency of alleles that enable and facilitate its development. Thus, genes may take control of such traits, decreasing dependence on nongenetic disturbances, in a process called genetic assimilation. Despite an increasing amount of empirical studies supporting genetic assimilation, its significance is still controversial. Whether genetic assimilation is widespread depends, to a great extent, on how easily mutation and recombination reduce the trait's dependence on nongenetic perturbations. Previous research suggests that this is the case for mutations. Here we use simulations of gene regulatory network dynamics to address this issue with respect to recombination. We find that recombinant offspring of parents that produce a new phenotype through plasticity are more likely to produce the same phenotype without requiring any perturbation. They are also prone to preserve the ability to produce that phenotype after genetic and nongenetic perturbations. Our work also suggests that ancestral plasticity can play an important role for setting the course that evolution takes. In sum, our results indicate that the manner in which phenotypic variation maps unto genetic variation facilitates evolution through genetic assimilation in gene regulatory networks. Thus, we contend that the importance of this evolutionary mechanism should not be easily neglected.
WDR60-mediated dynein-2 loading into cilia powers retrograde IFT and transition zone crossing

The dynein-2 motor complex drives retrograde intraflagellar transport (IFT), playing a pivotal role in the assembly and functions of cilia. However, the mechanisms that regulate dynein-2 motility remain poorly understood. Here, we identify the Caenorhabditis elegans WDR60 homolog (WDR-60) and dissect the roles of this intermediate chain using genome editing and live imaging of endogenous dynein-2/IFT components. We find that loss of WDR-60 impairs dynein-2 recruitment to cilia and its incorporation onto anterograde IFT trains, reducing the availability of the retrograde motor at the ciliary tip. Consistently, we show that less dynein-2 motors power WDR-60-deficient retrograde IFT trains, which move at reduced velocities and fail to exit cilia, accumulating on the distal side of the transition zone. Remarkably, disrupting the transition zone’s NPHP module almost fully restores ciliary exit of underpowered retrograde trains in wdr-60 mutants. This work establishes WDR-60 as a major contributor to IFT and the NPHP module as a roadblock to dynein-2 passage through the transition zone.
Evaluation of cell segmentation methods without reference segmentations

Cell segmentation is a cornerstone of many bioimage informatics studies and inaccurate segmentation introduces error in downstream analysis. Evaluating segmentation results is thus a necessary step for developing segmentation methods as well as for choosing the most appropriate method for a particular type of sample. The evaluation process has typically involved comparison of segmentations to those generated by humans, which can be expensive and subject to unknown bias. We present here an approach to evaluating cell segmentation methods without relying upon comparison to results from humans. For this, we defined a number of segmentation quality metrics that can be applied to multichannel fluorescence images. We calculated these metrics for 14 previously-described segmentation methods applied to datasets from 4 multiplexed microscope modalities covering 5 tissues. Using principal component analysis to combine the metrics we defined an overall cell segmentation quality score and ranked the segmentation methods. We found that two deep learning-based methods performed the best overall, but that results for all methods could be significantly improved by postprocessing to ensure proper matching of cell and nuclear masks. Our evaluation tool is available as open source and all code and data are available in a Reproducible Research Archive.
A specific eIF4A paralog facilitates LARP1-mediated translation repression during mTORC1 inhibition

Eukaryotic translation initiation factor (eIF) 4A — a DEAD-box RNA-binding protein — plays an essential role in translation initiation. Two mammalian eIF4A paralogs, eIF4A1 and eIF4A2, have been assumed to be redundant because of their high homology, and the difference in their functions has been poorly understood. Here, we show that eIF4A1, but not eIF4A2, enhances translational repression during the inhibition of mechanistic target of rapamycin complex 1 (mTORC1), an essential kinase complex controlling cell proliferation. RNA-immunoprecipitation sequencing (RIP-Seq) of the two eIF4A paralogs revealed that eIF4A1 preferentially binds to mRNAs containing terminal oligopyrimidine (TOP) motifs, whose translation is rapidly repressed upon mTOR inhibition. This biased interaction depends on a La-related RNA-binding protein, LARP1. Ribosome profiling revealed that the deletion of EIF4A1, but not EIF4A2, rendered the translation of TOP mRNAs resistant to mTOR inactivation. Moreover, eIF4A1 enhances the affinity between TOP mRNAs and LARP1 and thus ensures stronger translation repression upon mTORC1 inhibition. Our data show that the distinct protein interactions of these highly homologous translation factor paralogs shape protein synthesis during mTORC1 inhibition and provide a unique example of the repressive role of a universal translation activator.
Robust Effects of Working Memory Demand during Naturalistic Language Comprehension in Language-Selective Cortex

To understand language, we must infer structured meanings from real-time auditory or visual signals. Researchers have long focused on word-by-word structure building in working memory as a mechanism that might enable this feat. However, some have argued that language processing does not typically involve rich word-by-word structure building, and/or that apparent working memory effects are underlyingly driven by surprisal (how predictable a word is in context). Consistent with this alternative, some recent behavioral studies of naturalistic language processing that control for surprisal have not shown clear working memory effects. In this fMRI study, we investigate a range of theory-driven predictors of word-by-word working memory demand during naturalistic language comprehension in humans of both sexes under rigorous surprisal controls. In addition, we address a related debate about whether the working memory mechanisms involved in language comprehension are language specialized or domain general. To do so, in each participant, we functionally localize (1) the language-selective network and (2) the “multiple-demand” network, which supports working memory across domains. Results show robust surprisal-independent effects of memory demand in the language network and no effect of memory demand in the multiple-demand network. Our findings thus support the view that language comprehension involves computationally demanding word-by-word structure building operations in working memory, in addition to any prediction-related mechanisms. Further, these memory operations appear to be primarily conducted by the same neural resources that store linguistic knowledge, with no evidence of involvement of brain regions known to support working memory across domains. SIGNIFICANCE STATEMENT This study uses fMRI to investigate signatures of working memory (WM) demand during naturalistic story listening, using a broad range of theoretically motivated estimates of WM demand. Results support a strong effect of WM demand in the brain that is distinct from effects of word predictability. Further, these WM demands register primarily in language-selective regions, rather than in “multiple-demand” regions that have previously been associated with WM in nonlinguistic domains. Our findings support a core role for WM in incremental language processing, using WM resources that are specialized for language.
Progenitor cell integration into a barrier epithelium during adult organ turnover

Barrier epithelial organs face the constant challenge of sealing the interior body from the external environment while simultaneously replacing the cells that contact this environment. These replacement cells—the progeny of basal stem cells—are born without apical, barrier-forming structures such as a protective, lumen-facing membrane and occluding junctions. How stem cell progeny acquire these structures to become part of the barrier is unknown. Here we use Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM), Correlative Light-Electron Microscopy (CLEM), and volumetric imaging of live and fixed organs to investigate progenitor integration in the intestinal epithelium of adult Drosophila. We find that stem cell daughters gestate their future lumenal-apical membrane beneath a transient, basal niche formed by an umbrella-shaped occluding junction that shelters the growing cell and adheres it to mature neighbor cells. The umbrella junction both targets formation of a deep, microvilli-lined, apical invagination and closes it off from the contents of the gut lumen. When the growing cell is sufficiently mature, the umbrella junction retracts to expose this Pre-Assembled Apical Compartment (PAAC) to the gut lumen, thus incorporating the new cell into the intestinal barrier. When we block umbrella junctions, stem cell daughters grow and attempt to differentiate but fail to integrate; when we block cell growth, no umbrella junctions form and daughters arrest in early differentiation. Thus, stem cell progeny build new barrier structures in the shelter of a transient niche, where they are protected from lumenal insults until they are prepared to withstand them. By coordinating this dynamic junctional niche with progenitor cell differentiation, a physiologically active epithelial organ incorporates new cells while upholding integrity of its barrier.
A ppGpp-mediated brake on photosynthesis is required for acclimation to nitrogen limitation in Arabidopsis

Guanosine pentaphosphate and tetraphosphate (together referred to as ppGpp) are hyperphosphorylated nucleotides found in bacteria and the chloroplasts of plants and algae. In plants and algae artificial ppGpp accumulation can inhibit chloroplast gene expression, and influence photosynthesis, nutrient remobilisation, growth, and immunity. However, it is so far unknown whether ppGpp is required for abiotic stress acclimation in plants. Here, we demonstrate that ppGpp biosynthesis is necessary for acclimation to nitrogen starvation in Arabidopsis. We show that ppGpp is required for remodeling the photosynthetic electron transport chain to downregulate photosynthetic activity and for protection against oxidative stress. Furthermore, we demonstrate that ppGpp is required for coupling chloroplastic and nuclear gene expression during nitrogen starvation. Altogether, our work indicates that ppGpp is a pivotal regulator of chloroplast activity for stress acclimation in plants.
Extensive Chromatin Structure-Function Associations Revealed by Accurate 3D Compartmentalization Characterization

A/B compartments are observed in Hi-C data and coincide with eu/hetero-chromatin. However, many genomic regions are ambiguous under A/B compartment scheme. We develop MOSAIC (MOdularity and Singular vAlue decomposition-based Identification of Compartments), an accurate compartmental state detection scheme. MOSAIC reveals that those ambiguous regions segregate into two additional compartmental states, which typically correspond to short genomic regions flanked by long canonical A/B compartments with opposite activities. They are denoted as micro-compartments accordingly. In contrast to the canonical A/B compartments, micro-compartments cover ∼30% of the genome and are highly dynamic across cell types. More importantly, distinguishing the micro-compartments underpins accurate characterization of chromatin structure-function relationship. By applying MOSAIC to GM12878 and K562 cells, we identify CD86, ILDR1 and GATA2 which show concordance between gene expression and compartmental states beyond the scheme of A/B compartments. Taken together, MOSAIC uncovers fine-scale and dynamic compartmental states underlying transcriptional regulation and disease.
Phytochemical Composition and Antibacterial Activity of Moroccan Lavandula angustifolia Mill.

Abstract Bacterial resistance to antibiotics is a major public health problem. The emergence and spread of multi-resistant bacteria, associated with the limited number of antibiotics in development have led to a therapeutic deadlock. So, finding new bioactive natural products has become a necessity. The aim of our study is to screen the chemical composition and to study the antibacterial activity of essential oils of Moroccan Lavandula angustifolia Mill. The essential oils used in this study were extracted by hydrodistillation using a clevenger-type apparatus according to the European Pharmacopoeia. The chemical composition was investigated using Gas Chromatography-Mass Spectrometry (GC-MS). The antibacterial activity was evaluated by the disc diffusion method and by the determination of MIC and MBC. The major compounds of Lavandula angustifolia were : linalool (21.81%), 1,8-cineole (18.07%), camphor (11.89%), linalyl acetate (10.21%), borneol (8.47%) and α-terpineol (5.00%) and the essential oils yield was of 2.32%. L. angustifolia essential oils demonstrated a strong antibacterial activity against tested bacteria : E. coli, S. aureus and P. aeruginosa, best known to be largely responsible for skin wounds infections. The results of this study suggest that the essential oils of L. angustifolia have an interesting antimicrobial effect and may be a new potential source for a natural antimicrobial applied in pharmaceutical field and to develop a new wound healing product.
Spatio-temporal analysis of remote sensing images provides early warning signals of forest mortality

Ecosystems are under unprecedented pressures, reflected in rapid changes in the regime of disturbances that may cause negative impacts on them. This highlights the importance of characterizing the state of an ecosystem and its response to disturbances, which is known as a notoriously difficult task. The state-of-the-art knowledge has been tested rarely in real ecosystems for a number of reasons such as mismatches between the time scale of ecosystem processes and data accessibility as well as weaknesses in the performance of available methods. This study aims to use remotely sensed spatio-temporal data to identify early warning signals of forest mortality using satellite images. For this purpose, I propose a new approach that measures local spatial autocorrelation (using local Moran’s I and local Geary’s c method) at each time, which proved to produce robust results in multiple different study sites examined in this article. This new approach successfully generates early warning signals from time series of local spatial autocorrelation values in unhealthy study sites 2 years prior to forest mortality occurrence. Furthermore, I develop a new R package, called “stew”, that enables users to explore spatio-temporal analysis of ecosystem state changes. This work corroborates the suggestion that spatio-temporal indicators have the potential to diagnose early warning signals to identify upcoming climate-induced forest mortality, up to two years before its occurrence.
Activity-dependent modulation of NMDA receptors by endogenous zinc shapes dendritic function in cortical neurons

Activation of NMDA receptors (NMDARs) has been proposed to be a key component of single neuron computations in vivo. However is unknown if specific mechanisms control the function of such receptors and modulate input-output transformations performed by cortical neurons under in vivo-like conditions. Here we found that in layer 2/3 pyramidal neurons (L2/3 PNs), repeated synaptic stimulation results in an activity-dependent decrease in NMDARs activity by vesicular zinc. Such a mechanism shifted the threshold for dendritic non-linearities and strongly reduced LTP induction. Modulation of NMDARs was cell- and pathway-specific, being present selectively in L2/3-L2/3 connections but absent in ascending bottom-up inputs originating from L4 neurons. Numerical simulations highlighted that activity-dependent modulation of NMDARs has an important influence in dendritic computations endowing L2/3 PN dendrites with the ability to sustain dendritic non-linear integrations constant across different regimes of synaptic activity like those found in vivo. The present results therefore provide a new perspective on the action of vesicular zinc in cortical circuits by highlighting the role of this endogenous ion in normalizing dendritic integration of PNs during a constantly changing synaptic input pattern.