Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolizable energy values of corn and wheat middlings in broiler chickens

Abstract: Two experiments were conducted to evaluate adaptation length (AL) and composition of reference diets on nitrogen (N)-corrected apparent metabolizable energy (AMEn) in 22-d-old broilers. Birds were allocated to nine treatments (n = 6) consisting of wheat – soybean meal (SBM) (reference diet), corn–wheat–SBM, and wheat middlings (WM)–wheat–SBM (exp. 1), or oats–SBM (reference diet), corn–oats–SBM, and WM–oats–SBM (exp. 2) in conjunction with three AL (12, 8, and 4 d) in a factorial arrangement of treatments (3 × 3). Dry matter (DM), N, energy (En) utilization, and AMEn of corn and WM were determined using the difference method. In exp. 1, birds on the WM–wheat–SBM-based diet had the lowest (P < 0.05) DM, N, and En utilization, as well as AMEn compared with the other two diets. Additionally, AMEn for corn was higher (P < 0.05) compared with that of WM. In exp. 2, N utilization in birds on the corn–oats–SBM-based diet was lower (P < 0.05) compared with birds on the oats–SBM-based diet; however, AMEn of corn and WM was not different. In both experiments, AL was not significantly different. Based on these results, the composition of the reference diet could influence AMEn values of corn and WM in 22-d-old broilers.
Hydrogen Sulfide Inhibits High Glucose-Induced Neuronal Senescence by Improving Autophagic Flux via Up-regulation of SIRT1

Hyperglycemia, a key characteristic and risk factor for diabetes mellitus (DM), causes neuronal senescence. Hydrogen sulfide (H2S) is a novel neuroprotectant. The present work was to investigate the potential effect of H2S on hyperglycemia-induced neuronal senescence and the underlying mechanisms. We found that NaHS, a donor of H2S, inhibited high glucose (HG)-induced cellular senescence in HT22 cells (an immortalized mouse hippocampal cell line), as evidenced by a decrease in the number of senescence associated-β-galactosidase (SA-β-gal) positive cells, increase in the growth of cells, and down-regulations of senescence mark proteins, p16INK4a and p21CIP1. NaHS improved the autophagic flux, which is judged by a decrease in the amount of intracellular autophagosome as well as up-regulations of LC3II/I and P62 in HG-exposed HT22 cells. Furthermore, blocked autophagic flux by chloroquine (CQ) significantly abolished NaHS-exerted improvement in the autophagic flux and suppression in the cellular senescence of GH-exposed HT22 cells, which indicated that H2S antagonizes HG-induced neuronal senescence by promoting autophagic flux. We also found that NaHS up-regulated the expression of silent mating type information regulation 2 homolog 1 (SIRT1), an important anti-aging protein, in HG-exposed HT22 cells. Furthermore, inhibition of SIRT1 by sirtinol reversed the protection of H2S against HG-induced autophagic flux blockade and cellular senescence in HT22 cells. These data indicated that H2S protects HT22 cells against HG-induced neuronal senescence by improving autophagic flux via up-regulation of SIRT1, suggesting H2S as a potential treatment strategy for hyperglycemia-induced neuronal senescence and neurotoxicity.
Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs

Genetic variation developed in plant breeding programs is fundamental to creating new combinations that result in cultivars with enhanced characteristics. Over the years, tomato (Solanum lycopersicum) breeding programs associated with the Texas A&M University system have developed morphologically diverse lines of tomatoes selected for heat tolerance, fruit quality, and disease resistance to adapt them to Texas growing conditions. Here we explored the intraspecific genetic variations of 322 cultivated tomato genotypes, including 300 breeding lines developed by three Texas A&M breeding programs, as an initial step toward implementing molecular breeding approaches. Genotyping by sequencing using low coverage whole-genome sequencing (SkimGBS) identified 10,236 high-quality single-nucleotide polymorphisms (SNPs) that were used to assess genetic diversity, population structure, and phylogenetic relationship between genotypes and breeding programs. Model-based population structure analysis, phylogenetic tree construction, and principal component analysis indicated that the genotypes were grouped into two main clusters. Genetic distance analysis revealed greater genetic diversity among the products of the three breeding programs. The germplasm developed at Texas A&M programs at Weslaco, College Station, and by Dr. Paul Leeper exhibited genetic diversity ranges of 0.175 - 0.434, 0.099 - 0.392, and 0.183 - 0.347, respectively, suggesting that there is enough variation within and between the lines from the three programs to perform selection for cultivar development. The SNPs identified here could be used to develop molecular tools for selecting various traits of interest and to select parents for future tomato breeding.
Plant growth-promoting rhizobacteria able to improve NPK availability: selection, identification and effects on tomato growth

Nitrogen, P and K are essential macronutrients that are not readily available to plants. Rhizobacteria are able to convert these unavailable forms for subsequent uptake by the plant, diverse species have been characterized as N2 fixers, P solubilizers and capable to solubilize mineral K from unavailable forms. The objective of this study was to select rhizobacteria capable of improving NPK availability and promoting tomato (Solanum lycopersicum L.) growth. Fifteen strains were studied. Four strains were selected for their capacity to fix N2, three for their ability to solubilize P, and six for their capacity to solubilize biotite and K-feldspar, isolated from tomato, lentil, chili pepper, faba bean and lettuce crops in Andisol and Alfisol soils. Through 16SrRNA sequencing, selected strains were identified as Pseudomonas gessardi, P. koreensis, P. brassicacearum, P. marginalis, Acinetobacter calcoaceticus and Rahnella aquatica. Phosphorus solubilizing strains did not show a positive effect on plant growth or an increase in available soil P. The N2 fixing bacteria Tmt-16 strain increased root growth in 23.57%; maintained the highest N content in plant tissue, 2.60%, higher amount of N available in the soil, 2.95 mg kg-1, and a higher content of N-NH4 1.95 mg kg-1. The K solubilizing strains Ls-C21, Ltj-62 and LsC-58 reached 17.0 to 19.0 mg kg-1 available K and 0.04 to 0.05 mg kg-1 exchangeable K (p ≤ 0.05.). These four endemic rhizobacteria can be potentially used as biofertilizers, allowing a reduction in the use of chemical fertilizers and a more sustainable production of tomatoes.
Dopamine transporter trafficking and Rit2 GTPase: In vivo impact and mechanism of action

Following its evoked release, extracellular dopamine (DA) levels are stringently controlled by presynaptic reuptake, mediated by the cocaine-sensitive dopamine (DA) transporter (DAT). Multiple DAT coding variants have been identified in DA-related neuropsychiatric disorders, illustrating DAT’s integral role in maintaining DAergic homeostasis. DAT is dynamically regulated by endocytic trafficking. Protein kinase C (PKC) activation accelerates DAT internalization and acutely diminishes DAT surface expression. In cell lines, PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether PKC-stimulated DAT endocytosis in DAergic terminals requires Rit2, or whether there are region- or sex-dependent differences in Rit2-dependent DAT trafficking. Moreover, the intrinsic determinants that mediate the DAT-Rit2 interaction are undefined, as are the mechanisms through which Rit2 controls PKC-stimulated DAT endocytosis. Here, we leveraged an AAV-mediated approach to conditionally knockdown Rit2 in vivo in DAergic neurons, and found that Rit2 was required for steady state DAT surface expression and PKC-stimulated DAT internalization, with marked sex- and region-specific differences. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation, and the DAT N-terminus is required for both DAT-Rit2 dissociation and stimulated DAT internalization in response to PKC activation. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization, and reveal striking region- and sex-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals.
Hemibiotrophic fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition

Yield losses caused by fungal pathogens represent a major threat to global food production. One of the most devastating fungal wheat pathogens is Zymoseptoria tritici. Despite the importance of this fungus and wheat as main staple food crop the underlying mechanisms of plant-pathogen interactions are poorly understood. Here we present a conceptual framework based on coinfection assays, comparative metabolomics, and microbiome profiling to study the interaction of Z. tritici in susceptible and resistant wheat. We demonstrate that Z. tritici suppresses the production of immune-related metabolites in a susceptible cultivar. Remarkably, this fungus-induced immune suppression spreads within the leaf and even to other leaves, a previously undescribed phenomenon that we term “systemic induced susceptibility”. Using a comparative metabolomics approach, we identified defense-related biosynthetic pathways that are suppressed and induced in susceptible and resistant cultivars, respectively. We show that these fungus-induced changes also dramatically affect the wheat leaf microbiome. Our findings emphasize that immune suppression by this hemibiotrophic pathogen impacts specialized plant metabolism, alters its associated microbial communities, and renders wheat vulnerable to further infections.
The complete mitochondrial genome of the hybrid offspring Epinephelus fuscoguttatus ♀ × Epinephelus tukula ♂

Abstract The hybrid offspring Epinephelus fuscoguttatus ♀ × E. tukula ♂ showed heterosis in terms of growth and disease resistance. The mitochondrial genome is 16,629 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The difference of total length is mainly caused by the difference of length in non-coding region. The nucleotide base composition is A = 29.15%, G = 15.62%, T = 26.91%, C = 28.32%, A + T = 56.06%, and C + G = 43.94%. The phylogenetic analysis using neighbour-joining (NJ) method showed that the hybrid offspring has a closer relationship to E. fuscoguttatus × E. lanceolatus.
The complete mitogenome of the Eastern Pacific sponge Aplysina gerardogreeni (Demospongiae, Verongida, Aplysinidae)

Abstract We report the first mitochondrial genome of a Verongid sponge, Aplysina gerardogreeni from the Pacific Ocean. This has 19,620 bp and includes 14 protein-coding genes, 2 rRNAs genes, and 25 tRNAs genes. The gene arrangement was similar to the one found in two Caribbean Aplysina mitogenomes previously reported. Comparative analyses revealed a few substitutions among congeneric mitogenomes. The mitogenome of A. gerardogreeni could be useful to study the evolution of Verongimorpha group and also to identify adequate genes for its molecular systematics.
Humans are primarily model-based and not model-free learners in the two-stage task

Distinct model-free and model-based learning processes are thought to drive both typical and dysfunctional behaviors. Data from two-stage decision tasks have seemingly shown that human behavior is driven by both processes operating in parallel. However, in this study, we show that more detailed task instructions lead participants to make primarily model-based choices that show little, if any, model-free influence. We also demonstrate that behavior in the two-stage task may falsely appear to be driven by a combination of model-based/model-free learning if purely model-based agents form inaccurate models of the task because of misunderstandings. Furthermore, we found evidence that many participants do misunderstand the task in important ways. Overall, we argue that humans formulate a wide variety of learning models. Consequently, the simple dichotomy of model-free versus model-based learning is inadequate to explain behavior in the two-stage task and connections between reward learning, habit formation, and compulsivity.
Benthic community history in the Changjiang (Yangtze River) mega-delta: Damming, urbanization, and environmental control

Abstract The coastal environment of the Changjiang delta has been influenced by recent anthropogenic activities such as dam construction and increased sewage and fertilizer inputs. Previous work examined the compositional shift of marine plankton to assess ecological impacts of these activities on marine ecosystems in the Changjiang discharge area. Here we used benthic marine ostracodes collected in the Changjiang estuary and the adjacent East China Sea in the 1980s and the 2010s, respectively, to investigate temporal changes of the benthic community and controlling factors for the benthic fauna. Our results revealed more shoreward distribution of some well-known offshore ostracode species in the 2010s compared with the 1980s and a relatively more important role for environmental processes (e.g., bottom-water temperature, bottom-water salinity, and eutrophic conditions of surface water) than spatial processes (e.g., the flow of ocean currents) in structuring ostracode compositions. The temporal changes in the ostracode community are likely attributable to the combined effects of reduced fresh water and sediment discharge and eutrophic conditions of the Changjiang due to the many dams constructed along the Changjiang and population expansion in the Changjiang Basin. Results of redundancy analysis and variation partitioning suggest that ocean currents facilitated environmental filtering of ostracode species such that they could disperse to preferred environmental conditions. These findings highlight the potential uses of marine microfossils to better understand ecological impacts on benthic ecosystems in vulnerable Asian mega-deltas and provide insights into the integration of metacommunity concepts in disentangling dynamics of marine benthic communities.
The Mechanistic Basis for Successful Spinal Cord Stimulation to Generate Steady Motor Outputs

Electrical stimulation of the spinal cord is a promising rehabilitation intervention to restore/augment motor function after spinal cord injury (SCI). Combining sensory feedback with stimulation of remaining motor circuits has been shown to be a prerequisite for the functional improvement of SCI patients. However, little is known about the cellular mechanisms potentially underlying this functional benefit in the injured spinal cord. Here, we combine computer simulations with an isolated whole-tissue adult mouse spinal cord preparation to examine synaptic, cellular, and system potentials measured from single motoneurons and ventral roots. The stimulation protocol included separate and combined activation of the sensory inputs (evoked by dorsal root stimulation) and motor inputs (evoked by stimulation of spinal cord tissue) at different frequencies, intensities, and neuromodulatory states. Our data show that, while sensory inputs exhibit short-term depression in response to a train of stimulation, motor inputs exhibit short-term facilitation. However, the concurrent activation of both inputs elicits a stronger and steadier motor output. This effect is enhanced by the application of pharmacological neuromodulators. Furthermore, sensorimotor excitatory postsynaptic potentials (EPSPs) summate sublinearly (i.e., their combination produces an excitatory potential smaller than the sum of the excitatory potentials they would individually produce). However, ventral root compound action potentials (CoAPs) summate supralinearly generating much higher outputs. Computer simulations revealed that the contrasting summation and disproportionality in plasticity between the excitatory postsynaptic potentials (EPSPs) and CoAPs result from the motoneuronal firing threshold acting as an amplitude-selective filter. Together, these results provide the mechanistic basis for the cellular processes contributing to the generation of steady motor outputs using spinal stimulation. This data has great potential to guide the design of more effective stimulation protocols in SCI patients.
The complete chloroplast genome of Primula tsiangii W. W. Smith (Primulaceae): a karst endemic primrose in Southwest China

Abstract Primula tsiangii W. W. Smith is a karst endemic species in Southwest China. Here, we report the complete chloroplast genome of P. tsiangii. The chloroplast (cp) genome was determined to be 153,281 bp and the GC contents was 37.2%. The sequence includes a large single copy (LSC) region of 84,524 bp, a small single copy (SSC) region of 17,357 bp, and two separated inverted regions of 25,700 bp each. It contains 127 unique genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This is the first report of cp genomes for karst endemic primrose, and will be useful for the genetic diversity of karst plants.
Negative effects of full spectrum light exposure along with UV radiation on survival and reproduction of Cladocera Daphnia magna (Straus, 1820)

Cladocera Daphnia magna (Straus, 1820) is one of the most important cladocerans having immense ecological and commercial significance. It is an important food for many aquatic organisms. Light intensity may have negative effect on it biological activities. That is why the study investigated the direct effects of full spectrum light with different intensities along with UV radiation on life history traits of single clonal cultured D. magna. Six-well multi plates were employed for rearing single clonal cultured of D. magna which were subjected to five different light and UV intensities respectively, with six replications. The results showed that number of neonate production and survival rate were significantly (p<0.05) affected by the intensities of light. Mortality rate was found significantly higher (P<0.05) under the highest light intensity. The offspring production decreased with increasing light intensity. The study reconfirms the negative effect of UV radiation on parthenogenetic reproduction physiology, growth and survivability of single clonal cultured Daphnia magna.
Grazing halos on coral reefs: predation risk, herbivore density, and habitat size influence grazing patterns that are visible from space

In order to conduct a systematic analysis of patch reef and halo geometries, we manually digitized 757 patch reefs and their respective halos in the Florida Keys National Marine Sanctuary (FKNMS) and along a ~250 km reef tract of the South Water Caye Marine Reserve (SWCMR) in Belize. We divided the FKNMS into latitudinal segments running roughly perpendicular to the forereef. The frequency of the segments depended on patch reef density. For the middle and lower Florida Keys we digitized every patch reef encountered in every other 0.8 km band, while in the upper Florida Keys, we examined 0.4 km wide bands spaced 0.8 km apart. In Belize, we manually selected every patch reef visible in the high-resolution satellite scene, and randomly selected 100 patch reefs where we digitized the patch reef boundary and surrounding halo. Patch reefs are not uniform. In our landscape analysis we only digitized patch reefs that 1) were singular (i.e., not highly aggregate), 2) where the image was of high enough quality to assess the halo and patch reef boundaries (i.e. not obscured by clouds, turbidity, sun glint, or water depth) and 3) had halos that were distinct for more than ~ 70% of the patch perimeter. All patch reefs large enough to clearly see in the imagery (> 10 m), were surrounded by a halo, suggesting the ubiquity of halo formation in Florida and Belize. To determine halo width (i.e., the average distance from the patch reef edge to the halo boundary), one observer (BD) digitized the patch reef and the halo boundary. The halo boundary was estimated as the point of greatest transition in substrate reflectance surrounding the reef. For the 13 patch reefs where we conducted fieldwork, three untrained and one trained observer estimated the patch and halo boundaries to establish halo estimation error (see error bars in Fig. 3a in text). Using ArcGIS (version 10.4, ESRI 2017) and QGIS (version 2.18.13, QGIS Development Team 2017) software, we estimated halo extent as the average nearest neighbor distance between densified point clouds located along the halo boundary and patch edge.
Morphomolecular genetic study of selected groundnut genotypes with microsatellite marker

Morphomolecular genetic studies were undertaken to identify ten divergent genotypes of groundnut at molecular level using PM-36, PM50 and PM238 SSR primers. All the microsatellite loci amplified by Polymerase Chain Reaction (PCR) were found to be polymorphic in all groundnut genotypes except ICGV-99233. Differences were observed in the proportion of polymorphic loci, observed and expected heterozygosity values, average number of alleles in the cultivars. Only three genotypes showed significant deviations from Hardy Weinberg Equilibrium (HWE). The UPGMA dendrogram based on Nei's (1972) genetic distance, resulted in two major clusters with several sub clusters. Specific alleles of five varieties were identified (able to distinguish specific varieties), and these were PM-36/153 (Accession 12), PM-36/164 (BARI Badam 6), PM50/106 (Accession 12), PM50/102 (ICGV-93232), and PM238/100 (Accession 12). The three primers produced a total of 17 alleles with size ranging from 100bp to 164bp. The PIC (Polymorphism Information Content) value for the primer PM-36, PM50 and PM238 were found 0.75, 0.77 and 0.75, respectively. This approach will be useful for developing a set of number of SSR loci and for the protection of the varieties through Genetic Finger Printing (GFP).
IQGAP1 connects phosphoinositide signaling to cytoskeletal reorganization

IQGAP1 is a multi-domain protein that acts as a scaffold for multiple signaling pathways. IQGAP1 generates the lipid messenger PI(3,4,5)P3 by scaffolding the phosphoinositide kinases PIPKIs and PI3K. The dynamics of this scaffolding protein complex in intact, living cells are unknown. Here, we delineate the role of IQGAP1 in PI(3,4,5)P3-mediated signaling in live cells under basal and stimulated conditions using fluorescence lifetime imaging microscopy. We demonstrate that IQGAP1 interacts strongly with PIPKIγ at intracellular entities and on the plasma membrane, and scaffolds PI3K and PIPKIγ in response to physiological changes. Additionally, we show that IQGAP1 scaffolds phosphoinositides with PI3K, PIPKIγ and EGFR, and forms clusters upon cell stimulation with epidermal growth factor. Importantly, we show that IQGAP1 connects PI(3,4,5)P3-mediated signaling and cytoskeletal signaling pathways by binding PIPKIγ in proximity of the cytoskeletal proteins talin and Cdc42. Our results support a model in which IQGAP1 mediates crosstalk between phosphoinositide signaling and the cytoskeleton to promote directed cell movement.