Miracle-dz/UniFAR-FTUs huggingface dataset:
Sulfatases, in Particular Sulf1, Are Important for the Integrity of the Glomerular Filtration Barrier in Zebrafish

The 6-O-endosulfatases (sulfs) are important enzymatic components involved in the regulation of heparan sulfate by altering the sulfatation pattern. Specifically in the kidney, sulfs have been implicated in the glomerular podocyte-endothelial cell crosstalk and in the preservation of the glomerular filtration barrier (GFB) in different mouse models. Since it has been shown that in zebrafish larvae, Sulf1, Sulf2a, and Sulf2b are expressed in the pronephric kidney we set out to establish if a reduction in sulf expression leads to GFB dysfunction. Here, we show that a reduced sulf expression following morpholino (MO) induced knockdown in zebrafish larvae promotes damage to the GFB leading to renal plasma protein loss from the circulation. Moreover, a combined knockdown of Sulf1, Sulf2a, and Sulf2b is associated with severe morphologic changes including narrowing of the fenestration between glomerular endothelial cells as well as thickening of the glomerular basement membrane and podocyte foot process effacement, suggesting that glomerular damage is an underlying cause of the circulatory protein loss observed after MO injection. Additionally, we show that a decrease in sulf expression reduces the bioavailability of VegfA in the glomerulus of the pronephros, which may contribute to the structural changes observed in the glomeruli of morphant fish. Furthermore, consistent with previous results, knockdown of the sulfs is associated with arteriovenous malformations in particular in the tail region of the larvae. Overall, taken together our results suggest that 6-O-endosulfatases are important in the preservation of GFB integrity and a reduction in their expression levels induces phenotypic changes that are indicative of renal protein loss.
Rising insecticide potency outweighs falling application rate to make US farmland increasingly hazardous to insects

Each year, millions of kilograms of insecticides are applied to crops in the US. While insecticide use supports food, fuel, and fiber production, it can also threaten non-target organisms, a concern underscored by mounting evidence of widespread insect decline. Nevertheless, answers to basic questions about the spatiotemporal patterns of insecticide use remain elusive, due in part to the inherent complexity of insecticide use, and exacerbated by the dispersed nature of the relevant data, divided between several government repositories. Here, we integrate these public datasets to generate county-level annual estimates of total ‘insect toxic load’ (honey bee lethal doses) for insecticides applied in the US between 1997-2012, calculated separately for oral and contact toxicity. To explore the underlying drivers of the observed changes, we divide insect toxic load into the components of extent (area treated) and intensity (application rate x potency). We show that while contact-based insect toxic load remained relatively steady over the period of our analysis, oral-based insect toxic load increased roughly 9-fold, with reductions in application rate outweighed by disproportionate increases in potency (toxicity/kg) and increases in extent. This pattern varied markedly by region, with the greatest increases seen in Heartland and Northern Great Plains regions, likely driven by use of neonicotinoid seed treatments in corn and soybean. In this “potency paradox,” US farmland has become more hazardous to insects despite lower volumes of insecticides applied, raising serious concerns about insect conservation and highlighting the importance of integrative approaches to pesticide use monitoring. Significance statement Previous analyses disagree about whether US insecticide use is increasing or decreasing, a question of significant importance given the putative role of insecticides in recent insect declines. We integrated information from multiple national databases to estimate ‘insect toxic load’ (represented as honey bee lethal doses) of the agricultural insecticides applied in each US county from 1997 to 2012, and factors responsible for its change. Across the US, insect toxic load – calculated on the basis of oral toxicity – increased 9-fold. This increase was due to increases in the potency (toxicity/kg) of insecticides applied and in the area treated; the volume of insecticides applied declined. Toxic load increased most dramatically in regions where neonicotinoid seed treatments for field crops are commonly used.
First Report on Identification of Fusarium graminearum Species Complex Members from Turkey and Iran

Fusarium graminearum species complex is the major Fusarium head blight disease pathogen in worldwide. Fusarium head blight disease lead to damages on small grain cereals. The identification of the F. graminearum species complex is important for improving disease control and management. Traditional identification methods such as macroscopy and microscopy analysis need to be supported by biochemical and genetics assays. Thus, DNA sequencing-based methods is one of the most preferred, reliable, low priced in the identification methods. In the study, 54 F. graminearum isolates obtained from diseased wheat, barley and corn fields in Turkey and Iran were identified by morphological characteristics and then characterized by species-specific SCAR marker. β-tubulin, Tef1-α, 28s rDNA and Histone H3 genes amplified, purified and then sequenced. The merged multiloci length was obtained as last of all 2215 bp. These sequencing results was used to multiloci genotyping assays. Last of all, 20 isolates were determined as F. graminearum sensu stricto by multiloci genotyping analysis. Remaining isolates were identified as F. asiaticum or Fusarium sp. The findings are important in terms of revealing the first-time identification in Turkish and Iranian isolates as F. graminearum species complex members by amplification four (β-tubulin, Tef1-α, 28s rDNA and Histone H3) highly conserved DNA regions.
Adult crowding induces sexual dimorphism in chronic stress-response in Drosophila melanogaster

Stress-induced mood disorders such as depression and anxiety are sexually dimorphic in human beings. Studying behavioural stress-responses in non-human animal models can help better understand the behavioural manifestations of these disorders and the dimorphism in their prevalence. Here we explore how sexes show differential behavioural responses to different chronic stressors, both abiotic and biotic, by using outbred populations of Drosophila melanogaster. The behaviours studied – namely, anhedonia, motivation to explore a novel habitat, locomotor activity and sleep levels – have been well-investigated in human and rodent-based models of stress disorders. These behaviours were studied in the context of two different stressors – mechanical perturbation and adult crowding. Responses to stress were found to be sexually dimorphic, and stressed females showed more behavioural changes, such as a reduced motivation to explore a novel habitat. Furthermore, adult crowding caused a greater number of sexually dimorphic behavioural changes than mechanical perturbation. For instance, while mechanical perturbation caused anhedonia across sexes, only females were anhedonic after crowding. We thus make a case for Drosophila melanogaster as a model system for studying sexual dimorphism in stress-induced mood disorders in humans. SUMMARY STATEMENT Female fruit flies, like their human counterparts, are more prone to chronic stress-induced mood disorders like anhedonia or reduced activity. This sexual dimorphism was more evident in a biotic stress.
Mini-review of Phytochemistry for Polyalithia Longiflia

Abstract: The review was aimed to review the phytochemical of the Polyalithia longiflia. Phytochemical screening for all parts of Polyalithia longiflia have been done and shown most of the chemical group compounds such as glycosides, Sterol, Carbohydrates, terpenoids, flavonoids. 174compounds have been isolated from five parts (leaves, steam bark, seeds, fruits, root) of Polyalithia longiflia, these compounds have been drown their structure. Leaves of Polyalithia longiflia were extracted and isolated 99 compounds most of these compounds were terpenoids, 59 compounds were isolated from the stem bark belong to different chemical groups such as Terpenoids, Alkaloids, Phenol, Fatty acids, and Steroids, 16 compounds were isolated from the fruit from several chemicals groups, 11 compounds were isolated from the root,7 compounds were isolated from the seeds which belong to different chemical groups which are Terpenoids, Fatty Acids, and Carbohydrate. Many of these compound have been used in medical filed in many applications due to their activities which make this plant very important in medicine filed. Root of Polyalithia longiflia only three articles about it. Also seeds of Polyalithia longiflia have not been studied yet its phytochemical screening. The compounds have been drown with chemdrow application, and with PubChem.
Effect of feeding frequency on growth performance, reproduction efficiency and skin coloration of rusty cichlids (Iodotropheus sprengerae)

ABSTRACT In the present study, the effects of five different feeding frequencies including every other day (2F1), one (F1), two (F2), three (F3), and four (F4) times daily on growth, reproduction, the coloration of rusty cichlid (mean body weight 2.04 ± 0.01 g and mean total length 4.35 ± 0.01 cm) were investigated. The trial was carried out in 15 100-L fiberglass circular tanks conducted to 4000-L freshwater recirculating system with three replicates for 16 weeks. Fish were stocked in each tank at a density of 10 individual with sex ratio 1:4 (male:female) and they were fed with a commercial ornamental cichlid diet to near satiation. At the end of the trial, final mean weight (FMW) and specific growth rate (SGR) increased with increasing feeding frequency (P < .05). The highest final mean total length (FMTL) was found in F3 group with 9.07 cm (P < .05). Although the average seed production (ASP) of F3 (mean of 98 ± 8.89) and F4 (mean of 93 ± 4.04) were significantly similar, the highest fecundity was observed in F4 group. For the coloration parameters, the final redness (a*) of F4 group was the highest (P < .05). The cost-effective groups of the present experiment were F3 and F4 groups. In conclusion, three times daily feeding is recommended the best application for profitable commercial cultures of rusty cichlid due to decreasing labor.
Comparison of Cold Responses for Orthologs of Cabbage Vernalization-related Genes

Vernalization, a floral transition stimulated by the prolonged exposure to cold temperatures, is an undesirable feature in the breeding of leafy vegetables that impairs productivity by promoting bolting. Cabbage is categorized as a green plant vernalization type; only older plants possess vernalization competence. Despite being of agricultural importance in the breeding of bolting resistance, the molecular mechanism of agedependent acquisition of vernalization competence is poorly understood. In Arabidopsis, FLOWERING LOCUS C (FLC) is a key vernalization response gene that functions as a floral repressor. Its expression decreases upon cold exposure, leading to floral induction. In this study, we characterized three FLC orthologs in cabbage (BoFLC1, BoFLC2, and BoFLC3). Predicted amino acid sequences of the three BoFLC cDNAs were highly conserved with the MADS-box domain. The overexpression of the three BoFLCs in Arabidopsis displayed late flowering phenotypes, indicating the functional conservation of these paralogs as floral repressors in cabbage. The expression analyses before and after constant cold treatment given at different plant ages showed that the three BoFLCs displayed distinct responses to prolonged cold exposure. Regardless of plant age, BoFLC1 declined less markedly, whereas BoFLC2 and BoFLC3 were repressed by sufficient long cold treatment. In both younger and older plants, the expression of the ortholog of floral integrator gene, FLOWERING LOCUS T (FT), was induced by cold treatment, probably due to a reduction in the repressive effect of BoFLCs, suggesting that the fate of age-dependent vernalization is determined independently or downstream of BoFT induction. Our results provide new insights into the mechanism of green plant vernalization in Brassica vegetables.
Shrub expansion and alpine plant community change: 40-year record from Niwot Ridge, Colorado

ABSTRACT Background: Alpine and arctic tundra are particularly sensitive ecosystems to the impacts of global climate change. Yet, warming studies versus observational studies in these ecosystems yield different and sometimes conflicting results. Many short-term changes may be phenotypic responses to warming rather than shifts at the community level. Aims: We posit that long-term monitoring of permanently marked plots provides data for making predictions of the impact of climate change on alpine tundra communities. Methods: We surveyed plant community composition and cover at four sampling time points over a forty-year span (1971–2011). Results: We observed an expansion of shrub cover, both within the shrub tundra and encroaching into moist and dry meadow communities. This shrub cover expansion coincides with increased litter and decreased species richness at the plot level. Overall, despite some shifts in functional group cover and species richness, plant community composition remained mostly intact across forty years. Conclusions: Our results corroborate with other published studies demonstrating the rapid expansion and impacts of woody shrubs in tundra ecosystems. This study demonstrates a surprising resistance of alpine tundra plant communities under current global climate change over a 40﻿-year period. Additional studies are needed to disentangle the many potential drivers that explain plant community shifts and community stability.
An alternative way to look at diffuse large B-cell lymphoma : the impact of frequent engagement of ReIB NF-κB subunit on cell survival and patient outcome

Les facteurs de transcription de NF-κB jouent un role crucial dans la proliferation et la survie cellulaire, et la physiopathologie de nombreux cancers. La deregulation de la voie classique de NF-κB est connue pour etre impliquee au moins dans le sous-groupe ABC du lymphome diffus a grandes cellules B (DLBCL). Cependant, l'etat d'activation de la sous-unite RelB de la voie alternative de NF-κB et son role restent inconnus. Nous avons demontre un engagement frequent de RelB dans des lignees cellulaires humaines derivees de DLBCL. L'activation RelB protege les cellules des dommages a l'ADN et de l'apoptose induites par la doxorubicine, le principal medicament utilise dans le traitement du DLBCL. RelB a egalement controle l'expression de la proteine anti-apoptotique cIAP2. Dans une cohorte de 66 patients atteints de DLBCL de novo, nous avons evalue directement l'activite de liaison a l'ADN de toutes les sous-unites de NF-κB par EMSA couple a des supershifts. L'activation de RelB etait presente dans 66,6% des cas, quelle que soit la classification ABC ou GCB, et constituait un predicteur independant d’un mauvais pronostique. Le statut d’activation de RelB etabli par l’EMSA a permis de definir une signature d’expression genique liee a RelB capable de confirmer l’impact negatif de RelB sur l’evolution des patients, lorsque etendue a une cohorte plus grande. Finalement, notre etude indique que RelB est potentiellement un nouveau biomarqueur pour le DLBCL et met en evidence son role important dans la biologie cellulaire de DLBCL.
Pathotype Identification of Rice Blast Pathogen, Pyricularia oryzae Using Differential Varieties in Peninsular Malaysia

Seven pathotypes of Pyricularia oryzae were differentiated from blast disease samples collected from 2014–2016, using eight Malaysian differential rice varieties. Pathotype P7.0 is the dominant pathotype identified (33.9%) followed by P0.0, P1.0 and P9.0 which are currently become more abundant in the field with frequency of 20.0% for P0.0, and 15.4% for both P1.0 and P9. Pathotype P7.0 was mostly isolated from MR220CL2, MR263 and MR219 rice varieties which are popular variety planted by farmers in Peninsular Malaysia. Interestingly, new emergence of pathotype P0.2 has been identified, which was isolated from a new released variety, MR284 as well as blast isogenic line IRBL 20 carrying *Corresponding author: lfah@usm.my; latiffahz@yahoo.com Siti Norsuha Misman and Lattifah Zakaria 182 Pi5(t) blast resistance gene. Prolong planting of more than 20 planting seasons and large scale planting of MR219 and MR220 with current varietal coverage areas of more than 90% in Peninsular Malaysia are suspected as possible reason for P7.0 become dominant. Varietal coverage of MR220CL2 and MR263 has reached about 50% might be the cause of changes in blast pathogen pathotype dominancy to P0.0, P1.0 and P9.0.
High-resolution view of the type III secretion export apparatus in situ reveals membrane remodeling and a secretion pathway

Significance Many bacteria capable of causing disease utilize a nanomachine to inject bacterial proteins into mammalian cells. Those proteins have the capacity to modulate cellular functions for the pathogen’s benefit. In this study, we visualized components of this injection machine at very high resolution, which has allowed us to obtain very important structural and functional information critical for the understanding of its function. Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into a holostructure or injectisome. The core component of the injectisome is the needle complex, which houses the export apparatus that serves as a gate for the passage of the secreted proteins through the bacterial inner membrane. Here, we describe a high-resolution structure of the export apparatus of the Salmonella type III secretion system in association with the needle complex and the underlying bacterial membrane, both in isolation and in situ. We show the precise location of the core export apparatus components within the injectisome and bacterial envelope and demonstrate that their deployment results in major membrane remodeling and thinning, which may be central for the protein translocation process. We also show that InvA, a critical export apparatus component, forms a multiring cytoplasmic conduit that provides a pathway for the type III secretion substrates to reach the entrance of the export gate. Combined with structure-guided mutagenesis, our studies provide major insight into potential mechanisms of protein translocation and injectisome assembly.
An evolutionary and biochemical characterization of a self-splicing group II intron and its encoded LAGLIDADG homing endonuclease in Leptographium truncatum

Acknowledgements Table of contents List of tables List of figures List of abbreviations General introduction Chapter 1. Literature review 1.1. Leptographium: fungal associates of insects and agents of blue-stain 1.1.1. General features of members of the fungal genus Leptographium 1.1.2. Taxonomy of Leptographium 1.1.3. Phylogenetic studies of Leptographium species 1.1. 4. Association with insect vectors 1.1. 5. Plant pathology and blue-stain production of members of Leptographium 1.2. Internal transcribed spacers in the nuclear ribosomal RNA gene cluster 1.2. 1. Internal transcribed spacers and ribosome biogenesis 1.2. 2. Sequence and structural features of ITS1 and ITS2 1.2. 3. Applications of ITS sequences in phylogenetic and barcoding studies 1.3. Fungal mitochondrial genomes Page II IV
The influence of feeding on muscle tissues composition in cage reared bluefin tuna (Thunnus thynnus)

Capture-based tuna aquaculture rates as one of the most important aquaculture activities in Cro-atia, where juvenile tuna are reared in cages for over a year long period in order to increase substan-tially their weight. The aim of this study was to assess the effect of length and intensity of feeding on biochemical composition (total fat, moisture, dry matter, carbohydrates and protein content) of tuna (Thunnus thynnus) white muscle tissues in newly caught tuna prior to feeding (NCTPF) versus far-med tuna kept in rearing circular cages in the Vela Grska Bay, Adriatic Sea (LAT 43°17’40,6984”N, LONG 016°28’58,4315”E (WGS84)) between 2001 and 2004. Farmed tunas from all cages were fed with the feed consisting of domestic small pelagic fish, or with mixtures containing North Sea herring (Clupea harengus) and Sardina pilchardus, for five months (cage 3), eight months (cage 4) or 21 months (cages 1 and 2). A low content of moisture and high content of dry matter including fat was observed in farmed tuna muscles compared to wild-caught tuna. In farmed tuna muscles, measured moisture was 55.26% in cage 1, 39.95% in cage 2, 54.64% in cage 3 and 49.70% in cage 4. These results are significantly lower than moisture measured in NCTPF (80.36%). Content of dry matter found in farmed tuna muscles also differed greatly between wild tuna (19.64%) and far-med tuna, but also between the cages (44.74% in cage 1, 60.05% in cage 2, 45.36% in cage 3 and 50.30% in cage 4). In NCTPF, muscle tissues total fat encompassed less than 1% of the total body weight, while it reached over 20% of total body mass in farmed fed tuna (20.62% in cage 1, 42.50% in cage 2, 20.97% in cage 3 and 20.57% in cage 4). These results demonstrate that high fat content can be achieved already after five months of intensive feeding. Higher content of proteins was also found in aquacultured tuna (18.60% in cage 1, 16.00% in cage 2, 15.09% in cage 3 and 20.58% in cage 4) compared to wild-caught tuna (13.77%). There were no differences in carbohydrates con-tent between tuna farmed in different cages and NCTPF tuna, indicating glycogen as a less optimal indicator of muscle tissue quality in farmed tuna of the present study.
Neural systems for memory-based value judgment and decision-making

Real life choices often require that we draw inferences about the value of options based on structured, schematic knowledge about their utility for our current goals. Other times, value information may be retrieved directly from a specific prior experience with an option. In a functional magnetic resonance imaging experiment, we investigated the neural systems involved in retrieving and assessing information from different memory sources to support value-based choice. Participants completed a task in which items could be conferred positive or negative value based on schematic associations (i.e. schema value), or learned directly from experience via deterministic feedback (i.e. experienced value). We found that ventromedial prefrontal cortex (vmPFC) activity correlated with the influence of both experience- and schema-based values on participants’ decisions. Connectivity between vmPFC and middle temporal cortex also tracked the inferred value of items based on schematic associations on the first presentation of ingredients, prior to any feedback. In contrast, the striatum responded to participants’ willingness to bet on ingredients as a function of the unsigned strength of their memory for those options’ values. These results argue that striatum and vmPFC play distinct roles in memory-based value judgment and decision-making. Specifically, the vmPFC assesses the value of options based on information inferred from schematic knowledge and retrieved from prior direct experience, while the striatum controls a decision to act on options based on memory strength.