Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Sugar-Regulated Gene Expression and Signaling in Suspension-Cultured Rice Cells

To better understand the mechanism of sugar signaling in rice cell, the suspension-cultured rice cells were transferred from sucrose-containing (+S) to sucrose-free (-S) of MS culture medium, we found that ribosomal RNAs (rRNAs) were degraded progressively. This suggests that carbon, nitrogen, and phosphate were recycled in this process and the reduction in cellular rRNAs might lead to decreased translation to save energy in response to sugar starvation. Differential screening revealed that two groups of genes, sugar-starvation-repressed (SSR) and sugar-starvation-activated (SSA) genes, were regulated by sugar in an opposing manner. Northern-blot analysis showed that two major hybridization signals of 0.8 and 1.9 kb were induced strongly under sugar starvation. The two populations of genes corresponded with homologs of α-amylases (1.9 kb) and the glycine-rich proteins (GRPs) gene family (0.8 kb), and all were SSA genes. Expression of GRP genes was strongly induced in sugar-starved cells, which suggests that GRPs may help to protect cells against nutritional stress. Treatment of +S and -S cells with the protein kinase (PK) inhibitor staurosporine (St) and the serine/theronine phosphoprotein phosphatases 1 (PP1) and 2A (PP2A) inhibitor okadaic acid (OA) revealed that PP1 and PP2A (PPs) might be involved in increasing SSR gene expression in +S cells, and that activation of the majority of the SSA genes in -S cells might be due to PKs activity. These results suggested that PKs and PPs might be involved in the sugar regulation of SSR and SSA gene expression. An in-gel PK activity assay demonstrated that the activity of two classes of PKs (50 and 66 kDa) may be induced rapidly after transfer of +S cells to -S medium. Following transfer of -S cells to +S medium, a novel class of 38 kDa PK was induced rapidly and showed high activity. The 38 kDa PK might play a role in sugar sensing, and the 50 and 66 kDa PKs might play roles in signal sensing under sugar starvation in rice cells. These results provide valuable information on three classes of protein kinases that might play key roles in sugar sensing and signaling in rice.
Gerhardtia sinensis (Agaricales, Lyophyllaceae), a new species and a newly recorded genus for China

Gerhardtia sinensis , as a new species discovered from southern China, is described, illustrated and compared with morphologically similar and phylogenetically related species. Morphologically, it is characterized by its white to yellowish or partially pale yellow pileus with faint striae, subdistant to fairly distant lamellae with intervenose veins, and slightly verruculose basidiospores (4.7–)5.2–6.2(–6.6) × (2.5–)3.0–3.4(–3.8) μm in size. Molecular phylogenetic analyses of the new species and related taxa are performed based on the sequences of nuclear ribosomal large subunit (nrLSU) and nuclear ribosomal internal transcribed spacer (ITS).
Fucoidan prevents LPS-induced production of nitric oxide and prostaglandin E2 by inhibiting MAPK-mediated signal pathways in RAW 264.7 macrophage cells

Fucoidan is a sulfated polysaccharide that is primarily extracted from brown seaweeds which has been broadly studied in recent years due to its numerous biological properties, including anticoagulant, antithrombotic, antitumor, and antiviral activities. In this study, we investigated whether fucoidan has the ability to attenuate the expression of pro-inflammatory mediators such as NO, prostaglandin E2 (PGE2), TNF-α, and IL-1β in LPS-stimulated RAW 264.7 macrophage cells. Fucoidan inhibited the expression of LPS-induced pro-inflammatory mediators including NO, PGE2, TNF-α, and IL-1β. In addition, gene expression of iNOS, cyclooxygenase-2 (COX-2), TNF-α, and IL-1β was inhibited both at mRNA and protein levels by fucoidan treatment, without any cytotoxic effect. Moreover, fucoidan significantly inhibited LPS-induced NF-κB activity NF-κB translocation into the nucleus by preventing the degradation of iκB-α. Taken together, these results indicate that fucoidan downregulates the expression of pro-inflammatory genes involved in the synthesis of NO, PGE2, TNF-α, and IL-1β in LPS-stimulated RAW 264.7 macrophage cells by suppressing NF-κB activity.
Copy number variants in clinical WGS: deployment and interpretation for rare and undiagnosed disease

Purpose Current diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, whole genome sequencing (WGS) has the potential to detect all genomic mutation types on a single platform and workflow. Here we sought to evaluate copy number variant (CNV) calling as part of a clinically accredited WGS test. Methods Using a depth-based copy number caller we performed analytical validation of CNV calling on a reference panel of 17 samples, compared the sensitivity of WGS-based variants to those from a clinical microarray, and set a bound on precision using orthogonal technologies. We developed a protocol for family-based analysis, annotation, filtering, visualization of WGS based CNV calls, and deployed this across a clinical cohort of 79 rare and undiagnosed cases. Results We found that CNV calls from WGS are at least as sensitive as those from microarrays, while only creating a modest increase in the number of variants interpreted (~10 CNVs per case). We identified clinically significant CNVs in 15% of the first 79 cases analyzed. This pipeline also enabled identification of cases of uniparental disomy (UPD) and a 50% mosaic trisomy 14. Directed analysis of some CNVs enabled break-point level resolution of genomic rearrangements and phasing of de-novo CNVs. Conclusion Robust identification of CNVs by WGS is possible within a clinical testing environment, and further developments will bring improvements in resolution of smaller and more complex CNVs.
Antioxidant, Anti-proliferation and Cytotoxicity Activities of Gossypium hirsutum toward Standard HepG2, A549, MCF-7 and U87 Cancer Cell Lines Compared to Huvec, 3T3 Normal Cells

Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran. Herbal and Traditional Medicines Research Center, Department of Pharmacognosy, Kerman University of Medical Sciences, Kerman, Iran. Leishmaniasis Research Center, Kerman University of Medical Sciences, Kerman, Iran. Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran. School of Medicine, Bam University of Medical Sciences, Bam, Iran. Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
The MS4A gene cluster is a key modulator of soluble TREM2 and Alzheimer’s disease risk

Common variants in the microglia-specific MS4A gene cluster modify risk for late-onset Alzheimer’s disease and modulate extracellular soluble TREM2. TREM2 takes center stage Genetic variants in triggering receptor expressed on myeloid cells 2 (TREM2) are associated with Alzheimer’s disease (AD) risk. Soluble TREM2 (sTREM2) concentrations in cerebrospinal fluid (CSF) change with AD progression; however, genetic modifiers of CSF sTREM2 remain unknown. Deming and colleagues now report two independent genetic associations in the membrane-spanning 4-domains subfamily A (MS4A) gene region. An AD risk variant was associated with reduced CSF sTREM2 concentrations, whereas a different variant leading to reduced AD risk was associated with elevated CSF sTREM2 concentrations. Gene expression analyses and molecular studies of human macrophages validated a functional relationship between MS4A4A and sTREM2 concentrations. Soluble triggering receptor expressed on myeloid cells 2 (sTREM2) in cerebrospinal fluid (CSF) has been associated with Alzheimer’s disease (AD). TREM2 plays a critical role in microglial activation, survival, and phagocytosis; however, the pathophysiological role of sTREM2 in AD is not well understood. Understanding the role of sTREM2 in AD may reveal new pathological mechanisms and lead to the identification of therapeutic targets. We performed a genome-wide association study (GWAS) to identify genetic modifiers of CSF sTREM2 obtained from the Alzheimer’s Disease Neuroimaging Initiative. Common variants in the membrane-spanning 4-domains subfamily A (MS4A) gene region were associated with CSF sTREM2 concentrations (rs1582763; P = 1.15 × 10−15); this was replicated in independent datasets. The variants associated with increased CSF sTREM2 concentrations were associated with reduced AD risk and delayed age at onset of disease. The single-nucleotide polymorphism rs1582763 modified expression of the MS4A4A and MS4A6A genes in multiple tissues, suggesting that one or both of these genes are important for modulating sTREM2 production. Using human macrophages as a proxy for microglia, we found that MS4A4A and TREM2 colocalized on lipid rafts at the plasma membrane, that sTREM2 increased with MS4A4A overexpression, and that silencing of MS4A4A reduced sTREM2 production. These genetic, molecular, and cellular findings suggest that MS4A4A modulates sTREM2. These findings also provide a mechanistic explanation for the original GWAS signal in the MS4A locus for AD risk and indicate that TREM2 may be involved in AD pathogenesis not only in TREM2 risk-variant carriers but also in those with sporadic disease.
Edge Detection of Cryptic Lamellipodia Assisted by Deep Learning

Cell protrusion plays important roles in cell migration by pushing plasma membrane forward. Cryptic lamellipodia induce the protrusion of submarginal cells in collective cell migration where cells are attached and move together. Although computational image analysis of cell protrusion has been done extensively, the study on protrusion activities of cryptic lamellipodia is limited due to difficulties in image segmentation. This study seeks to aid in the computational analysis of submarginal cell protrusion in collective cell migration by using deep learning to detect the cryptic lamellipodial edges from fluorescence time-lapse movies. Due to the noisy features within overlapping cells, the conventional image analysis algorithms such as Canny edge detector and intensity thresholding are limited. In this paper we combined Canny edge detector, Deep Neural Networks (DNNs), and local intensity thresholding. We were able to detect cryptic lamellipodial edges of submarginal cells with high accuracy from the fluorescence time-lapse movies of PtK1 cells using both simple convolutional neural networks and VGG-16 based neural networks. We used relatively small effort to prepare the training set to train the DNNs to detect the cryptical lamellipodial edges in fluorescence time-lapse movies. This work demonstrates that deep learning can be combined with the conventional image analysis algorithms to facilitate the computational analysis of highly complex time-lapse movies of collective cell migration.
Protocol for Increasing Carotenoid Levels in the Roots of Citrus Plants

[Abstract] Carotenoids in plants play several key functions such as acting as light-harvesters, antioxidants (Lado et al., 2016) or being precursors of strigolactones, abscisic acid, volatiles and other signaling compounds (Arbona et al., 2013). Although those functions are well-known in light-exposed tissues, information in belowground organs is limited because of reduced abundance of these pigments. In order to better understand the role of carotenoids in roots, we developed a methodology to increase the abundance of these pigments in underground tissues. We took advantage of the fact that citrus roots exposed to light develop pigmentation in order to increase the carotenoid content. Therefore, here we describe a simple method to increase carotenoids in citrus roots.
New insights into the role of chitosan oligosaccharide in enhancing growth performance, antioxidant capacity, immunity and intestinal development of weaned pigs

Chitosan oligosaccharide (COS), an oligomer of D-glucosamine, is a vital growth stimulant in the pig industry. However, the mechanisms by which COS mediates pig growth are not fully understood. Therefore, we further investigated how COS supplementation affects pig growth. A total of 32 Landrace × Yorkshire weaned pigs were randomly divided into a control group (basal diet without COS supplementation) and a COS group (100 mg COS per kg basal diet). The pigs that ingested COS for 21 days were associated with a higher (P < 0.05) average daily body weight gain compared to those in the control group. Relative to the control group, the apparent digestibility of crude protein, ash, fat, dry matter and gross energy were markedly elevated (P < 0.05) upon COS supplementation. COS supplementation not only increased (P < 0.05) the activities of superoxide dismutase, catalase and total antioxidant capacity but also elevated (P < 0.05) interleukin-6, tumour necrosis factor-α and immunoglobulin G concentrations in the serum. Moreover, the serum malondialdehyde concentration was decreased (P < 0.05) 26.59% by COS ingestion. COS supplementation also significantly enhanced (P < 0.05) secretory immunoglobulin A content, villus height and digestive enzyme activities (maltase, lactase and sucrase) in the small intestine. Intriguingly, dietary COS supplementation up-regulated (P < 0.05) the tight junction protein claudin-1 (CLDN-1) and occludin (OCLN) mRNA abundance, as well as the Na+–glucose co-transporter 1 (SGLT1) mRNA abundance in the jejunum. Importantly, COS not only increased (P < 0.05) the Bifidobacterium populations in the ileum but also decreased (P < 0.05) the total bacteria and Escherichia coli populations in the caecum and colon. Together, these results suggest that COS supplementation can accelerate weaned pig growth through enhancing antioxidant and immune properties, as well as intestinal development.
Ancient diversification in glacial refugia leads to intraspecific diversity in a Holarctic mammal

Glacial‐interglacial cycles influenced the contemporary genetic structure of many North American species. While phylogeographical lineage divergence among Pleistocene refugia has been proposed as a significant driver of subspecific and ecotypic differentiation, emerging evidence highlights the role of diversification within refugia in producing post‐glacial variation. Caribou (Rangifer tarandus) exhibit significant morphological, ecological and behavioural phenotypic variation and occurred within Beringian and sub‐Laurentide refugia. More specifically, the boreal ecotype of woodland caribou ranges from the southern regions of Canada to the Northwest Territories (NWT). Woodland caribou are generally accepted to have evolved south of the glacial extent, but the boreal ecotype in the northern part of their range co‐occurs with caribou that have a Beringian origin. This proximity provides an opportunity to test whether woodland caribou colonized boreal habitats from a single southern refugial source or if independent evolution to a common ecotype resulted from diversification within refugia.
Invasive Species Distribution Models: An Analysis of Scale, Sample Selection Bias, Transferability and Prediction

Species distribution models must balance the need for model generality with that for precision and accuracy. This is critical when modelling range-expanding species such as invasive species. Given the increased use of species distribution models to study invasive species-landscape relationships, a better understanding of the effect of spatial scales, sampling biases, model transferability and discrepancies between different models’ future predictions is necessary. This dissertation addresses these knowledge gaps using mute swans (Cygnus olor) as a case study species. I specifically examine mute swan’s distributions in parts of their native range of Britain and their non-native range of Ontario, Canada. I first investigate which environmental variables at which spatial scales best explain mute swan’s distribution in its non-native range. Second, I perform a sample selection bias study to examine predictive accuracy when species distribution models are built using varying ranges of environmental variables and applied to broader spatial extents. Third, I examine the potential for, and limitations of model transferability between native and non-native regions. Finally, I use two different modelling approaches and three
Evaluating a Survey Landscape for Tiger Abundance in the Confluence of the Western and Eastern Ghats

Due to the current depleting trends in tiger population, range countries have committed to double tiger numbers by the year 2022. However, some areas, including source sites, across the range countries lack scientifically estimated tiger numbers both at the larger landscape and at the protected area level. Here we report a population of tigers, from Biligiri Rangaswamy Temple Tiger Reserve (BRTTR), using camera trap based capture-mark recapture in a spatially explicit likelihood and Bayesian analyses that yielded an estimate of ~55 tigers with a density of about 6.8 tigers/100 km 2 . BRTTR nestled in a larger tiger landscape, perhaps contributes dispersing individuals to the adjoining forests, calling for integrated monitoring and management efforts for the entire landscape. This data set could help in designing long-term, landscape level plans and outcomes.
Expression of the bovine DNA (cytosine 5) methyltransferase family during preimplantation development and aberrations induced by somatic cell nuclear transfer

Expression of the Bovine DNA (cytosine 5) Methyltransferase Family During Preimplantation Development and Aberrations Induced by Somatic Cell Nuclear Transfer. (December 2003) Michael Cameron Golding, H.B.Sc., University of Western Ontario Chair of Advisory Committee: Dr. Mark Westhusin Bovine preimplantation embryos derived from nuclear transfer experiments exhibit a global state of genomic hypermethylation that likely account for the large number of developmental abnormalities observed to date. The central hypotheses of this work is that the genomic hypermethylation and improper epigenetic reprogramming reported in studies of bovine nuclear transfer, are in large part due to abnormal expression and regulation of the DNA methyltransferase proteins. Bovine Dnmt mRNAs display strong sequence homology to those of human and mouse and similar to other species, exist as multiple isoforms. Two of these splice variants, which have been termed Dnmt2γ and Dnmt3a4 represent previously unreported sequence combinations. Investigation of bovine DNA methyltransferase expression in the bovine oocyte and early preimplantation development has revealed an intricate system divergent from observations previously reported in the mouse. Specifically, the somatic version of Dnmt1 along with Dnmt2, 3a and 3b are all expressed during these initial stages of bovine development. Further, real time analyses of the Dnmt transcripts
SCREENING OF ROSE GENOTYPES AGAINST THRIPS, Scirtothrips dorsalis HOOD (THYSANOPTERA: THRIPIDAE) AND ITS MANAGEMENT

An investigations on screening of rose genotypes against incidence of Scirtothrips dorsalis Hood under naturally ventilated polyhouse condition, identifying resistant sources and efficacy of new molecules of insecticides against thrips were undertaken during the year 2014-2015 at the Department of Entomology, College of Horticulture, Bagalkot, Karnataka. Eleven genotypes were screened against thrips under naturally ventilated polyhouse condition. Amongst them, Prettybride, Nobless, Shakira, Bugati and Tropical were found to be superior by recording significantly lesser level of thrips incidence. Whereas, Grandgala found to be inferior genotype by recording higher level of thrips incidence as compared to other genotypes screened. Further, categorization of rose genotypes based on their reaction to thrips incidence on rose plants indicated that the Prettybride was categorised as highly resistant genotype, Goldstrike, Shakira, Bugati, Avalench and Tineke as resistant genotypes, Samurai, Tropical, Nobless and Bourdeux as susceptible and Grandgala as highly susceptible genotype. Among different biophysical and biochemical traits identified as sources of resistance to thrips, the genotypes categorised as highly resistant and resistant had lesser leaf area, lesser leaf thickness, higher trichomes density, lighter coloured flowers, moderate sized flowers, more flower compactness, lesser amount of sugars and higher level of phenol contents as compared to the genotypes which were categorized as susceptible and highly susceptible. The traits such as lesser leaf thickness, lesser leaf area, lesser sugars and light coloured flowers are proved important traits for breeding thrips resistant genotypes in future. Among the different insecticides evaluated against thrips on rose in open field condition, Imidacloprid 30.50 SC (0.3 ml/L) and Diafenthiuron 50 WP (1 ml/L) were found to be superior over the other chemicals in reducing the population of thrips and obtaining maximum net returns as compared to other chemicals tested.
A novel method of generating Dendritic cells in vitro using the KG-1 cell line and its use as a model for testing effects of lactic acid bacteria

Dendritic cells (DCs) are prime mediators of innate and adaptive immunity. In humans the DC population comprise only 0.1% of all leukocytes, making their isolation and ex vivo manipulation difficult. Since study of DC activity in vitro requires large numbers of DCs to be readily available, a cell line model, KG-1, was selected. KG-1 cells are a cytokine-responsive human CD34+ myelomonocytic cell line and can be induced to differentiate to a DC phenotype. A range of differentiation agents and protocols were compared, and differentiation efficiency was determined using both morphological features and cell surface marker expression. Expression of CD83, CD11c, CD123, CD86, HLA-DR and DC-SIGN was assessed by immunofluorescence and flow cytometry. KG-1 cells stimulated with 10 ng/ml PMA and 100 ng/ml Ionomycin were found to be the ideal model for obtaining Dendritic Like Cells (DLCs) in vitro. The effect of lactic acid bacteria on KG-1 differentiation was also tested using two immunomodulatory strains, Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052. After 5 days of incubation with R0011 the KG-1 cells expressed DC-specific surface markers CD83, CD86, CD11c, CD123, DC-SIGN and HLA-DR. Lactobacillus rhamnosus R0011 induced a marked rise in CD83 expression with a mean fluorescence intensity of 115.3 after 5 days, suggesting this strain promoted KG-1 differentiation to DLC. Analysis of cytokine by KG-1 DLC indicated that constitutive production of pro-inflammatory cytokines TNF-α and IL-12 was minimal. However IL-10 and TGF-β were detected after TLR-agonist stimulation of R0011-differentiated KG-1s. This study aimed to develop and assess the KG-1 cell model for screening effects of mediators and microbes on DC.
PAC$^m$-Bayes: Narrowing the Empirical Risk Gap in the Misspecified Bayesian Regime

The Bayesian posterior minimizes the"inferential risk"which itself bounds the"predictive risk". This bound is tight when the likelihood and prior are well-specified. However since misspecification induces a gap, the Bayesian posterior predictive distribution may have poor generalization performance. This work develops a multi-sample loss (PAC$^m$) which can close the gap by spanning a trade-off between the two risks. The loss is computationally favorable and offers PAC generalization guarantees. Empirical study demonstrates improvement to the predictive distribution.