Effects of nickel toxicity on seed germination and expression of genes associated with nickel resistance in Populus tremuloides

Although Nickel is an essential nutrient for plant growth in low concentrations, its excessive amounts in soil above threshold values can result in toxicity. The main objectives of the present research were to determine the effects of different doses of nickel on a) trembling aspen (Populus tremuloides) seed germination and b) gene expression. This study revealed that nickel in agarose media even at a low dose inhibits seed germination. In soil however, only the highest dose of 1, 600 mg of Ni per 1 kg of soil has detrimental effects on germination of P. tremuloides seeds. P. tremuloides seedlings were resistant to 150 mg /kg, 400 mg /kg, and 800 mg /kg of Ni doses in growth chamber screening tests. At high Ni dose of 1, 600 mg /kg, differential responses were observed as Ni- resistant, moderately resistant, and susceptible genotypes were identified. Expression of the AT2G16800 gene was repressed with increasing nickel concentration and this effect was most significant at the 800 mg/kg Ni dose. Surprisingly, the study also revealed that the higher concentration of potassium nitrate without nickel (800 mg/kg and 1, 600 mg/kg) induced a significant upregulation of the NAS3 and NRAMP4 genes.Master of Science (MSc) in Biolog

p53 immunocytochemistry and TP53 gene mutations in patients with chronic hepatitis C virus (HCV) infection.

Chronic infection with hepatitis C virus (HCV) is regarded as a risk factor for hepatocellular carcinoma (HCC), mostly in patients with liver cirrhosis. Present study aimed at evaluation of cellular expression of p53 protein, genetic TP53 changes in liver samples and anti-p53 in serum of patients with chronic hepatitis C virus infection. The expression of p53 protein were analysed by immunocytochemistry in liver biopsies from adult patients with chronic, long-lasting hepatitis C. In order to detect TP53 mutations, PCR/SSCP and sequencing were performed. Antibodies against p53 in serum were determined using enzyme immunoassay (ELISA).In two out of 14 examined patients TP53 point mutations were detected in the liver samples. In the first patient, a substitution of C to T was demonstrated in position 1 of the codon 250, resulting in substitution of proline by serine. The other patient carried a substitution of C to G in position 13274 of the intron 6. The patient carrying mutation in the codon 250 demonstrated morphological traits of liver cirrhosis and had high number of p53-immunoreactive cell nuclei in tissue. None of the patients manifested elevated titres of serum anti-p53. In the liver, significant positive correlations were disclosed between expression of p53 on one hand and grading and staging on the other. A negative correlation was disclosed between cellular expression of p53 and duration time of infection. In conclusions, genetic changes in TP53 can be detected also in non-neoplastic lesions linked to chronic HCV infection

The recent timberline changes in the Tatra Mountains : a case study of the Mengusovská Valley (Slovakia) and the Rybi Potok Valley (Poland)

A comparison was done of the timberline course from the mid-20th and beginning of 21st century, in Mengusovská Valley (Slovakia) and Rybi Potok Valley (Poland). These are two valleys in the High Tatra Mts. Aerial photos and satellite images were used to assess the changes of the timberline in the two valleys. The course of the timberline ecotone in both valleys is similar. In both valleys, the stable timberline section is almost half of the total timberline length. In both valleys there has been an increase in the elevation of the timberline (on average by 10 m in the Mengusovská Valley and 15 m in the Rybi Potok Valley), and free spaces have been increasingly closing up. The progressive changes of the timberline are mainly due to the limit placed on human economic activity, and to climate warming. Inactive avalanche paths have led to an enlargement of the forest area in both valleys. The reduction of avalanche activity is the direct result of climate warming in the Tatra Mts. and from the decrease in the amount of snow in winters

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Przekład jako akt mediacji kulturowej na przykładzie tłumaczenia adnotowanego powieści Toni Morrison „The Bluest Eye”

Przedmiotem niniejszej pracy magisterskiej jest przekład adnotowany pierwszego rozdziału powieści „The Bluest Eye” autorstwa Toni Morrison – pierwszej w historii laureatki literackiej Nagrody Nobla pochodzenia Afro-Amerykańskiego. Poza przekładem, praca obejmuje obszerną część teoretyczną, poświęconą życiu pisarki i głównym czynnikom, które miały wpływ na wykształcone przez nią poglądy i cechy charakteryzujące jej twórczość. W części tej autorka również omawia kontekst historyczno-polityczno-społeczny, który towarzyszył powstawaniu powieści oraz przedstawia krótkie streszczenie fabuły i szczegółową analizę krytyczno-literacką „The Bluest Eye”. Część następująca po przekładzie autorki stanowi próbę osadzenia tłumaczenia w teoriach przekładoznawczych, które ujmują zjawisko przekładu w kontekście transferu kulturowego i związanej z tym konieczności mediacji między oryginałem a tekstem tłumaczonym. Na ich podstawie autorka uzasadnia podejmowane w trakcie pracy wybory oraz omawia główne problemy przekładoznawcze i sposoby ich rozwiązania w celu osiągnięcia możliwie wiernego przekładu uwzględniającego zarówno jego odbiorców, jak i normy językowe oraz kulturę.The Master thesis constitutes an annotated translation of the first chapter of The Bluest Eye by Toni Morrison – the first African-American laureate of the Nobel Prize in literature. The thesis also includes an elaborate theoretical part devoted to the novelist’s life and key factors which shaped her worldviews and determined characteristic features of her literary output. In this part, the author also discusses historical, political and social circumstances under which the novel was written, and provides a brief summary of its plot and a comprehensive critical and literary analysis of The Bluest Eye. In the part following the translation, the author tries to anchor it in translation studies theories which see translation as inter-cultural transfer that necessitates mediating between the original and translated text. On their basis, the author justifies the choices made in the course of translation and discusses its main problems and their solutions aiming at a possibly most faithful translation which would take into consideration both its readers, culture and norms governing their language

Whole Genome Expression Analysis of Trembling Aspen (\u3ci\u3ePopulus tremuloides\u3c/i\u3e) Genotypes Exposed to Increasing Concentrations of Nickel

Excess metals in the soil are a known type of abiotic stress and many plant species have evolved specific metal resistance mechanisms to cope and avoid or reduce toxicity symptoms. Studies on P. tremuloides genetic response to nickel are limited. This present study aims to 1) Assess gene expression dynamics in P. tremuloides seedlings treated with varying concentrations of nickel salts and, 2) Compare gene expression profiles among the different treatment groups. Trembling aspen (Populus tremuloides) seedlings were treated with varying concentrations of nickel nitrates (150mg Ni / 1 kg of dry soil, 800mg / kg, and 1, 600mg / kg). The whole genome expression was analyzed using Illumina sequencing. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. In general, there was an increase in number of differentially expressed genes as the nickel concentration increased when compared to water. The number of downregulated (439-600) and upregulated (123-560) genes increases with the nickel concentration increase. A detailed analysis suggested that the 800mg / kg nickel concentration is the threshold at which an early abiotic stress response may be triggered as seen by the highly upregulated LEA protein and two calcium binding proteins when compared to water. For the highest nickel concentration, 7-deoxyloganetin glucosyltransferase was highly upregulated while an auxin response factor, Flavonol 3-sulfotransferase, and a predicted ABC transporter family protein were downregulated. The heatmap showed that the genes were grouped into six clusters based on the changes in expression as nickel concentration increased. The cluster of genes that had increased gene expression with increasing nickel concentration also had multiple enriched Gene ontology (GO) terms related to heavy metal and abiotic stress including metal ion transport, antioxidant activity, photosynthesis, and ribosomal activity. GO terms that decreased in expression with increasing nickel concentrations include ATP and ADP binding, protein kinase activity, integral component of membrane, protein phosphorylation and transmembrane transport

Gene expression profiling of Jack Pine (Pinus banksiana) under copper stress: Identification of genes associated with copper resistance.

Understanding the genetic response of plants to copper stress is a necessary step to improving the utility of plants for environmental remediation and restoration. The objectives of this study were to: 1) characterize the transcriptome of Jack Pine (Pinus banksiana) under copper stress, 2) analyze the gene expression profile shifts of genotypes exposed to copper ion toxicity, and 3) identify genes associated with copper resistance. Pinus banksiana seedlings were treated with 10 mmoles of copper and screened in a growth chamber. There were 6,213 upregulated and 29,038 downregulated genes expressed in the copper resistant genotypes compared to the susceptible genotypes at a high stringency based on the false discovery rate (FDR). Overall, 25,552 transcripts were assigned gene ontology. Among the top upregulated genes, the response to stress, the biosynthetic process, and the response to chemical stimuli terms represented the highest proportion of gene expression for the biological processes. For the molecular function category, the majority of expressed genes were associated with nucleotide binding followed by transporter activity, and kinase activity. The majority of upregulated genes were located in the plasma membrane while half of the total downregulated genes were associated with the extracellular region. Two candidate genes associated with copper resistance were identified including genes encoding for heavy metal-associated isoprenylated plant proteins (AtHIP20 and AtHIP26) and a gene encoding the pleiotropic drug resistance protein 1 (NtPDR1). This study represents the first report of transcriptomic responses of a conifer species to copper ions

How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis

Abstract The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues

p53 immunocytochemistry and TP53 gene mutations in patients with chronic hepatitis C virus (HCV) infection.

Chronic infection with hepatitis C virus (HCV) is regarded as a risk factor for hepatocellular carcinoma (HCC), mostly in patients with liver cirrhosis. Present study aimed at evaluation of cellular expression of p53 protein, genetic TP53 changes in liver samples and anti-p53 in serum of patients with chronic hepatitis C virus infection. The expression of p53 protein were analysed by immunocytochemistry in liver biopsies from adult patients with chronic, long-lasting hepatitis C. In order to detect TP53 mutations, PCR/SSCP and sequencing were performed. Antibodies against p53 in serum were determined using enzyme immunoassay (ELISA).In two out of 14 examined patients TP53 point mutations were detected in the liver samples. In the first patient, a substitution of C to T was demonstrated in position 1 of the codon 250, resulting in substitution of proline by serine. The other patient carried a substitution of C to G in position 13274 of the intron 6. The patient carrying mutation in the codon 250 demonstrated morphological traits of liver cirrhosis and had high number of p53-immunoreactive cell nuclei in tissue. None of the patients manifested elevated titres of serum anti-p53. In the liver, significant positive correlations were disclosed between expression of p53 on one hand and grading and staging on the other. A negative correlation was disclosed between cellular expression of p53 and duration time of infection. In conclusions, genetic changes in TP53 can be detected also in non-neoplastic lesions linked to chronic HCV infection

Molecular Mechanisms Associated with Antifungal Resistance in Pathogenic <i>Candida</i> Species

Candidiasis is a highly pervasive infection posing major health risks, especially for immunocompromised populations. Pathogenic Candida species have evolved intrinsic and acquired resistance to a variety of antifungal medications. The primary goal of this literature review is to summarize the molecular mechanisms associated with antifungal resistance in Candida species. Resistance can be conferred via gain-of-function mutations in target pathway genes or their transcriptional regulators. Therefore, an overview of the known gene mutations is presented for the following antifungals: azoles (fluconazole, voriconazole, posaconazole and itraconazole), echinocandins (caspofungin, anidulafungin and micafungin), polyenes (amphotericin B and nystatin) and 5-fluorocytosine (5-FC). The following mutation hot spots were identified: (1) ergosterol biosynthesis pathway mutations (ERG11 and UPC2), resulting in azole resistance; (2) overexpression of the efflux pumps, promoting azole resistance (transcription factor genes: tac1 and mrr1; transporter genes: CDR1, CDR2, MDR1, PDR16 and SNQ2); (3) cell wall biosynthesis mutations (FKS1, FKS2 and PDR1), conferring resistance to echinocandins; (4) mutations of nucleic acid synthesis/repair genes (FCY1, FCY2 and FUR1), resulting in 5-FC resistance; and (5) biofilm production, promoting general antifungal resistance. This review also provides a summary of standardized inhibitory breakpoints obtained from international guidelines for prominent Candida species. Notably, N. glabrata, P. kudriavzevii and C. auris demonstrate fluconazole resistance