Miracle-dz/UniFAR-FTUs huggingface dataset:
Spring distribution of ring-necked pheasants (Phasianus colchicus) following cattail reduction with glyphosate herbicide

To reduce blackbird (Icteridae) damage to field crops in the north-central United States, dense stands of cattail (Typha spp.) are thinned with glyphosate herbicide. The stands become unusable as roosting and loafing sites, which helps to protect susceptible crops nearby, particularly sunflower (Helianthus annus). Landscape-level impacts of cattail management on non-target avian species have not been studied. We measured use of upland breeding territories by male ring-necked pheasants (Phasianus colchicus) following cattail reduction in wetlands used by pheasants for overwintering. In August 1992, glyphosate was applied to all wetlands with ≥ 70% cattail coverage in four 23-km2 study blocks in south-eastern North Dakota. Four other blocks were used for controls. Habitat use was inferred from territorial crowing counts. No treatment effect or treatment*year interaction (all P ≥ 0.05) was evident during 2 years of post-treatment observations. Although the herbicide eradicated large contiguous stands of cattail that pheasants had used for winter cover, surface water levels rose in 1993, which created additional cattail growth in untreated wetlands within the blocks. The additional cattail may have lessened the effect of the herbicide treatments. During drier periods, when cattail growth slows, cattail reduction could affect use of upland breeding sites. We recommend more research to assess the effects of glyphosate during drier periods.
Lysosomal Biology and Function: Modern View of Cellular Debris Bin

Lysosomes are the main proteolytic compartments of mammalian cells comprising of a battery of hydrolases. Lysosomes dispose and recycle extracellular or intracellular macromolecules by fusing with endosomes or autophagosomes through specific waste clearance processes such as chaperone-mediated autophagy or microautophagy. The proteolytic end product is transported out of lysosomes via transporters or vesicular membrane trafficking. Recent studies have demonstrated lysosomes as a signaling node which sense, adapt and respond to changes in substrate metabolism to maintain cellular function. Lysosomal dysfunction not only influence pathways mediating membrane trafficking that culminate in the lysosome but also govern metabolic and signaling processes regulating protein sorting and targeting. In this review, we describe the current knowledge of lysosome in influencing sorting and nutrient signaling. We further present a mechanistic overview of intra-lysosomal processes, along with extra-lysosomal processes, governing lysosomal fusion and fission, exocytosis, positioning and membrane contact site formation. This review compiles existing knowledge in the field of lysosomal biology by describing various lysosomal events necessary to maintain cellular homeostasis facilitating development of therapies maintaining lysosomal function.
Aberrant expression of two miRNAs promotes proliferation, hepatitis B virus amplification, migration and invasion of hepatocellular carcinoma cells: evidence from bioinformatic analysis and experimental validation

Background As key negative regulators of gene expression, microRNAs (miRNAs) play an important role in the onset and progression of hepatocellular carcinoma (HCC). This study aimed to identify the miRNAs involved in HCC carcinogenesis and their regulated genes. Methods The Gene Expression Omnibus (GEO) dataset (GSE108724) was chosen and explored to identify differentially expressed miRNAs using GEO2R. For the prediction of potential miRNA target genes, the miRTarBase was explored. Enrichment analysis of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed by the DAVID online tool. The hub genes were screened out using the CytoHubba plug-in ranked by degrees. The networks between miRNAs and hub genes were constructed by Cytoscape software. MiRNA mimics and negative control were transfected into HCC cell lines and their effects on proliferation, hepatitis B virus DNA (HBV-DNA) replication, TP53 expression, migration, and invasion were investigated. The following methods were employed: MTT assay, quantitative PCR (qPCR) assay, western blotting, wound healing assay, and transwell assay. Results A total of 50 differentially expressed miRNAs were identified, including 20 upregulated and 30 downregulated miRNAs, in HCC tumor tissues compared to matched adjacent tumor-free tissues. The top three upregulated (miR-221-3p, miR-222-3p, and miR-18-5p) and downregulated (miR-375, miR-214-3p and miR-378d) miRNAs, ranked by |log2 fold change (log2FC)|, were chosen and their potential target genes were predicted. Two gene sets, targeted by the upregulated and the downregulated miRNAs, were identified respectively. GO and KEGG pathway analysis showed that the predicted target genes of upregulated and downregulated miRNAs were mainly enriched in the cell cycle and cancer-related pathways. The top ten hub nodes of gene sets ranked by degrees were identified as hub genes. Analysis of miRNA-hub gene network showed that miR-221-3p and miR-375 modulated most of the hub genes, especially involving regulation of TP53. The q-PCR results showed that miR-221-3p and miR-375 were markedly upregulated and downregulated, respectively, in HCC cells and HCC clinical tissue samples compared to non-tumoral tissues. Furthermore, miR-221-3p overexpression significantly enhanced proliferation, HBV-DNA replication, as well as the migration and invasion of HCC cells, whereas miR-375 overexpression resulted in opposite effects. Western blotting analysis showed that the overexpression of miR-221-3p and miR-375 reduced and increased TP53 expression, respectively. Conclusion The present study revealed that miR-211-3p and miR-375 may exert vital effects on cell proliferation, HBV-DNA replication, cell migration, and invasion through the regulation of TP53 expression in HCC.
Discovery of a new species of the Hypoxylon rubiginosum complex from Iran and antagonistic activities of Hypoxylon spp. against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in dual culture

Abstract During a survey of xylarialean fungi in Northern Iran, several specimens that showed affinities to the Hypoxylon rubiginosum complex were collected and cultured. A comparison of their morphological characters, combined with a chemotaxonomic study based on high performance liquid chromatography, coupled with diode array detection and mass spectrometry (HPLC-DAD/MS) and a multi-locus phylogeny based on ITS, LSU, rbp2 and tub2 DNA sequences, revealed a new species here described as Hypoxylon guilanense. In addition, Hypoxylon rubiginosumsensu stricto was also encountered. Concurrently, an endophytic isolate of the latter species showed strong antagonistic activities against the Ash Dieback pathogen, Hymenoscyphus fraxineus, in a dual culture assay in our laboratory. Therefore, we decided to test the new Iranian fungi for antagonistic activities against the pathogen, along with several cultures of other Hypoxylon species that are related to H. rubiginosum. Our results suggest that the antagonistic effects of Hypoxylon spp. against Hym. fraxineus are widespread and that they are due to the production of antifungal phomopsidin derivatives in the presence of the pathogen.
Bacillus halodurans OapB forms a high-affinity complex with the P13 region of the noncoding RNA OLE

Noncoding RNAs (ncRNAs) longer than 200 nucleotides are rare in bacteria, likely because bacterial genomes are under strong evolutionary pressures to maintain a small genome size. Of the long ncRNAs unique to bacteria, the OLE (ornate, large, extremophilic) RNA class is among the largest and most structurally complex. OLE RNAs form a ribonucleoprotein (RNP) complex by partnering with at least two proteins, OapA and OapB, that directly bind OLE RNA. The biochemical functions of the OLE RNP complex remain unknown, but are required for proper adaptation to certain environmental stresses, such as cold temperatures, short chain alcohols, and high magnesium concentrations. In the current study, we used electrophoretic mobility shift assays to examine the binding of OLE RNA fragments by OapB and found that OapB recognizes a small subregion of OLE RNA, including stem P13, with a dissociation constant (KD) of ∼700 pm. Analyses with mutated RNA constructs, and the application of in vitro selection, revealed that strong binding of OLE RNA by OapB requires a stem containing a precisely located single-nucleotide bulge and a GNRA tetraloop. Although the vast majority of bacteria with the ole gene also have the oapB gene, there are many whose genomes contain oapB but lack ole, suggesting that OapB has other RNA partners in some species that might exhibit similar structural features.
Ageism and COVID-19: what does our society’s response say about us?

Abstract The goal of this commentary is to highlight the ageism that has emerged during the COVID-19 pandemic. Over 20 international researchers in the field of ageing have contributed to this document. This commentary discusses how older people are misrepresented and undervalued in the current public discourse surrounding the pandemic. It points to issues in documenting the deaths of older adults, the lack of preparation for such a crisis in long-term care homes, how some ‘protective’ policies can be considered patronising and how the initial perception of the public was that the virus was really an older adult problem. This commentary also calls attention to important intergenerational solidarity that has occurred during this crisis to ensure support and social-inclusion of older adults, even at a distance. Our hope is that with this commentary we can contribute to the discourse on older adults during this pandemic and diminish the ageist attitudes that have circulated.
Enhancement in Xerostomia Patient Salivary Lubrication Using a Mucoadhesive

Oral lubrication mediated by mucin and protein containing salivary conditioning films (SCFs) with strong water retainability can get impaired due to disease such as xerostomia, that is, a subjective dry mouth feel associated with the changed salivary composition and low salivary flow rate. Aberrant SCFs in xerostomia patient cause difficulties in speech, mastication, and dental erosion while the prescribed artificial saliva is inadequate to solve the complications on a lasting basis. With the growing aging population, it is urgently needed to propose a new strategy to restore oral lubrication. Existing saliva substitutes often overwhelm the aberrant SCFs, generating inadequate relief. Here we demonstrated that the function of aberrant SCFs in a patient with Sjögren syndrome can be boosted through mucin recruitment by a simple mucoadhesive, chitosan-catechol (Chi-C). Chi-C with different conjugation degrees (Chi-C7.6%, Chi-C14.5%, Chi-C22.4%) was obtained by carbodiimide chemistry, which induced a layered structure composed of a rigid bottom and a soft secondary SCF (S-SCF) after reflow of saliva. The higher conjugation degree of Chi-C generates a higher glycosylated S-SCF by mucin recruitment and a lower friction in vitro. The layered S-SCF extends the “relief period” for Sjögren patient saliva over 7-fold, measured on an ex vivo tongue-enamel friction system. Besides lubrication, Chi-C-treated S-SCF reduces dental erosion depths from 125 to 70 μm. Chi-C shows antimicrobial activity against Streptococcus mutans. This research provides a new key insight in restoring the functionality of conditioning film at articulating tissues in living systems.
WHICH FACTORS ARE ASSOCIATED WITH MALIGNANCY IN THYROID NODULES CLASSIFIED AS BETHESDA CATEGORY 3 (AUS/FLUS) AND HOW DO THEY INFLUENCE THE PATIENT'S MANAGEMENT?

Background Thyroid nodules are a common pathology worldwide. Fine needle aspiration biopsy (FNAB) is an important diagnostic method for the investigation of malignancy in thyroid nodules. However, according to the Bethesda System used to classify the results, patients with atypia of undetermined significance/follicular lesion of undetermined significance (AUS / FLUS) may not be classified as benign or malignant. Therefore, it may be necessary to determine some clinical risk factors to apply the best treatment in these patients. Aim To determine the factors that increase the risk of malignancy in this patient group. Methods A retrospective study including 138 patients with an FNAB categorized as AUS/FLUS and operated between June 2015-September 2018. Demographical, Laboratory (TSH) and Ultrasound variables (number, size and characteristics of nodules) of the patients were compared among postoperative histopathological results. Results Hypo-echoic structure, microcalcification and irregular margin of the nodules were detected to be associated with malignancy in patients with FNAB results of AUS/FLUS (p <0.001). Conclusion We suggest that surgical treatment should be considered if the patients have nodules with the hypo-echoic structure, microcalcification and irregular margin with an FNAB histopathological result of AUS / FLUS.
Bumblebees land remarkably well in red–blue greenhouse LED light conditions

ABSTRACT Red–blue emitting LEDs have recently been introduced in greenhouses to optimise plant growth. However, this spectrum may negatively affect the performance of bumblebees used for pollination, because the visual system of bumblebees is more sensitive to green light than to red–blue light. We used high-speed stereoscopic videography to three-dimensionally track and compare landing manoeuvres of Bombus terrestris bumblebees in red–blue light and in regular, broad-spectrum white light. In both conditions, the landing approaches were interspersed by one or several hover phases, followed by leg extension and touchdown. The time between leg extension and touchdown was 25% (0.05 s) longer in red–blue light than in white light, caused by a more tortuous flight path in red–blue light. However, the total landing duration, specified as the time between the first hover phase and touchdown, did not differ between the light conditions. This suggests that the negative effects of red–blue light on the landing manoeuvre are confined to the final phase of the landing. This article has an associated First Person interview with the first author of the paper. Summary: Red–blue LED lights are being used in greenhouses to improve plant growth. The changed light spectrum may affect pollinators. We studied how these lights affect landing performance of foraging bumblebees.
Symplasmic Isolation Contributes to Somatic Embryo Induction and Development in the Tree Fern Cyathea delgadii Sternb

Abstract In this report, we describe studies on symplasmic communication and cellular rearrangement during direct somatic embryogenesis (SE) in the tree fern Cyathea delgadii. We analyzed changes in the symplasmic transport of low-molecular-weight fluorochromes, such as 8-hydroxypyrene-1,3,6-trisulfonic acid, trisodium salt (HPTS) and fluorescein (delivered to cells as fluorescein diacetate, FDA), within stipe explants and somatic embryos originating from single epidermal cells and developing during 16-d long culture. Induction of SE is preceded by a restriction in fluorochrome distribution between certain explant cells. Microscopic analysis showed a series of cellular changes like a decrease in vacuole size, increase in vacuole numbers, and increased density of cytoplasm and deposition of electron-dense material in cell walls that may be related with embryogenic transition. In somatic embryos, the limited symplasmic communication between cells was observed first in linear tri-cellular embryos. Further development of the fern embryo was associated with the formation of symplasmic domains corresponding to the four segments of the plant body. Using symplasmic tracers, we provided evidence that the changes in plasmodesmata permeability are corelated with somatic-to-embryogenic transition and somatic embryo development.
N-Glycans on EGF domain-specific O-GlcNAc transferase (EOGT) facilitate EOGT maturation and peripheral endoplasmic reticulum localization

Epidermal growth factor (EGF) domain-specific O-GlcNAc transferase (EOGT) is an endoplasmic reticulum (ER)-resident protein that modifies EGF repeats of Notch receptors and thereby regulates Delta-like ligand-mediated Notch signaling. Several EOGT mutations that may affect putative N-glycosylation consensus sites are recorded in the cancer database, but the presence and function of N-glycans in EOGT have not yet been characterized. Here, we identified N-glycosylation sites in mouse EOGT and elucidated their molecular functions. Three predicted N-glycosylation consensus sequences on EOGT are highly conserved among mammalian species. Within these sites, we found that Asn-263 and Asn-354, but not Asn-493, are modified with N-glycans. Lectin blotting, endoglycosidase H digestion, and MS analysis revealed that both residues are modified with oligomannose N-glycans. Loss of an individual N-glycan on EOGT did not affect its endoplasmic reticulum (ER) localization, enzyme activity, and ability to O-GlcNAcylate Notch1 in HEK293T cells. However, simultaneous substitution of both N-glycosylation sites affected both EOGT maturation and expression levels without an apparent change in enzymatic activity, suggesting that N-glycosylation at a single site is sufficient for EOGT maturation and expression. Accordingly, a decrease in O-GlcNAc stoichiometry was observed in Notch1 co-expressed with an N263Q/N354Q variant compared with WT EOGT. Moreover, the N263Q/N354Q variant exhibited altered subcellular distribution within the ER in HEK293T cells, indicating that N-glycosylation of EOGT is required for its ER localization at the cell periphery. These results suggest critical roles of N-glycans in sustaining O-GlcNAc transferase function both by maintaining EOGT levels and by ensuring its proper subcellular localization in the ER.
Circadian Clock and OxInflammation: Functional Crosstalk in Cutaneous Homeostasis

Circadian rhythms are biological oscillations that occur with an approximately 24 h period and optimize cellular homeostasis and responses to environmental stimuli. A growing collection of data suggests that chronic circadian disruption caused by novel lifestyle risk factors such as shift work, travel across time zones, or irregular sleep-wake cycles has long-term consequences for human health. Among the multiplicity of physiological systems hypothesized to have a role in the onset of pathologies in case of circadian disruption, there are redox-sensitive defensive pathways and inflammatory machinery. Due to its location and barrier physiological role, the skin is a prototypical tissue to study the influence of environmental insults induced OxInflammation disturbance and circadian system alteration. To better investigate the link among outdoor stressors, OxInflammation, and circadian system, we tested the differential responses of keratinocytes clock synchronized or desynchronized, in an in vitro inflammatory model exposed to O3. Being both NRF2 and NF-κB two key redox-sensitive transcription factors involved in cellular redox homeostasis and inflammation, we analyzed their activation and expression in challenged keratinocytes by O3. Our results suggest that a synchronized circadian clock not only facilitates the protective role of NRF2 in terms of a faster and more efficient defensive response against environmental insults but also moderates the cellular damage resulting from a condition of chronic inflammation. Our results bring new insights on the role of circadian clock in regulating the redox-inflammatory crosstalk influenced by O3 and possibly can be extrapolated to other pollutants able to affect the oxinflammatory cellular processes.
Comparison of the genetic relationships and osteological aspects in six branchiostegid fish species (perciformes)

Abstract We analyzed partial sequences of cytochrome b (cyt‐b), a mitochondrial DNA (mtDNA) gene, to determine the genetic relationships between six horsehead fish species: Branchiostegus japonicus, Branchiostegus albus, Branchiostegus auratus, Branchiostegus argentatus, Branchiostegus wardi, and an unidentified Branchiostegus species. The specimens were collected in Korea, China, Japan, and Vietnam. We compared their molecular phylogenetic relationships inferred from mtDNA cyt‐b sequences with an osteological analysis. The unidentified species, B. sp. , was similar to B. albus in terms of the lack of triangular silver‐white dot at the posterior region of eyes (vs. large one present in B. japonicus), but was also similar to B. japonicus in terms of the presence of a straight‐shaped first hemal spine (vs. a curve‐shaped hemal spine in B. albus). Analysis of the mtDNA cyt‐b sequences indicated that the smallest estimated sequence divergence was between the B. japonicus and B. sp. (0.70–0.94%), whereas the largest difference was between B. auratus and B. argentatus (23.06–23.36%). Both the maximum parsimony and maximum likelihood trees showed that the B. sp. was closely clustered with B. japonicus, and that B. auratus was most distant from the other species. When comparing the osteological characters, UPGMA tree showed that the B. japonicus and B. sp. were the most closely clustered species, and B. auratus was the most distantly clustered fish relative to the other species. The shape of the nasal, otolith and first hemal spine was informative for distinguishing B. auratus from the other species. These osteological differences were consistent with the differences in mtDNA.
Mechanisms underlying of antiretroviral drugs in different cellular reservoirs with a focus on macrophages

ABSTRACT Ongoing with current combinations of antiretroviral drugs for the treatment of Human Immunodeficiency Virus (HIV) infection can successfully maintain long-term suppression of HIV-1 replication in plasma. Still, none of these therapies is capable of extinguishing the virus from the long-lived cellular reservoir, including monocyte-derived macrophages (MDM), that means the principal obstacle to HIV cure. MDM are widely distributed in all tissues and organs, including central system nervous (CNS) where they represent the most frequent HIV-infected cells that means the principal obstacle to HIV cure. Current FDA-approved antiretroviral drugs target viral reverse transcriptase, protease, integrase, and entry processes (coreceptor or fusion blockade). It is desirable to continue to develop new antiretrovirals directed against alternative targets in the virus lifecycle in order to further optimize therapeutic options, overcome resistance to existing medications, and potentially contribute to the elimination of viral reservoirs. This review provides a comprehensive overview of the activity of antiretroviral drugs (classical and upcoming) in monocytes-derived macrophages (MDM). Defining the antiviral activity of these drugs in this important cellular HIV-1 reservoir provides crucial hints about their efficacy in HIV-1 infected patients.