Multi-omics and functional analysis reveal novel consequences of monosomy

Every organism contains a characteristic number of chromosomes that have to be segregated equally into two daughter cells during mitosis. Any error during chromosome segregation results in daughter cells that lost or gained a chromosome, a condition known as aneuploidy. Several studies from our laboratory and across the world have previously shown that aneuploidy per se strongly affects cellular physiology. However, these studies were limited mainly to the chromosomal gains due to the availability of several model systems. Strikingly, no systemic study to evaluate the impact of chromosome loss in the human cells has been performed so far. This is mainly due to the lack of model systems, as chromosome loss is incompatible with survival and drastically reduces cellular fitness. During my PhD thesis, for the first time, I used diverse omics and biochemical approaches to investigate the consequences of chromosome losses in human somatic cells. Using isogenic monosomic cells derived from the human cell line RPE1 lacking functional p53, we showed that, similar to the cells with chromosome gains, monosomic cells proliferate slower than the parental cells and exhibit genomic instability. Transcriptome and proteome analysis revealed that the expression of genes encoded on the monosomic chromosomes was reduced, as expected, but the abundance was partially compensated towards diploid levels by both transcriptional and post transcriptional mechanisms. Furthermore, we showed that monosomy induces global gene expression changes that are distinct to changes in response to chromosome gains. The most consistently deregulated pathways among the monosomies were ribosomes and translation, which we validated using polysome profiling and analysis of translation with puromycin incorporation experiments. We showed that these defects could be attributed to the haploinsufficiency of ribosomal protein genes (RPGs) encoded on monosomic chromosomes. Reintroduction of p53 into the monosomic cells uncovered that monosomy is incompatible with p53 expression and that the monosomic cells expressing p53 are either eliminated or outgrown by the p53 negative population. Given the RPG haploinsufficiency and ribosome biogenesis defects caused by monosomy, we show an evidence that the p53 activation in monosomies could be caused by the defects in ribosomes. These findings were further supported by computational analysis of cancer genomes revealing those cancers with monosomic karyotype accumulated frequently p53 pathway mutations and show reduced ribosomal functions. Together, our findings provide a rationale as to why monosomy is embryonically lethal, but frequently occurs in p53 deficient cancers

L-carnitine attenuates cardiac impairment but not vascular dysfunction in DOCA-salt hypertensive rats

L-Carnitine is an important co-factor in fatty acid metabolism by mitochondria. This study has determined whether oral administration of L-carnitine prevents remodelling and the development of impaired cardiovascular function in deoxycorticosterone acetate (DOCA)-salt hypertensive rats (n = 6–12; #p < 0.05 versus DOCA-salt). Uninephrectomized rats administered DOCA (25 mg every 4th day s.c.) and 1% NaCl in drinking water for 28 days developed cardiovascular remodelling shown as systolic hypertension, left ventricular hypertrophy, increased thoracic aortic and left ventricular wall thickness, increased left ventricular inflammatory cell infiltration together with increased interstitial collagen and increased passive diastolic stiffness and vascular dysfunction with increased plasma malondialdehyde concentrations. Treatment with L-carnitine (1.2% in food; 0.9 mg⁄g⁄day in DOCA-salt rats) decreased blood pressure (DOCA-salt 169 € 2; + L-carnitine 148 € 6# mmHg), decreased left ventricular wet weights (DOCA-salt 3.02 € 0.07; + L-carnitine 2.72 € 0.06# mg⁄ g body-wt), decreased inflammatory cells in the replacement fibrotic areas, reduced left ventricular interstitial collagen content (DOCA-salt 14.4 € 0.2; + L-carnitine 8.7 € 0.5# % area), reduced diastolic stiffness constant (DOCA-salt 26.9 € 0.5; + L-carnitine 23.8 € 0.5# dimensionless) and decreased plasma malondialdehyde concentrations (DOCA-salt 26.9 € 0.8; + L-carnitine 21.2 € 0.4# lmol ⁄ l) without preventing endothelial dysfunction. L-carnitine attenuated the cardiac remodelling and improved cardiac function in DOCA-salt hypertension but produced minimal changes in aortic wall thickness and vascular function. This study suggests that the mitochondrial respiratory chain is a significant source of reactive oxygen species in the heart but less so in the vasculature in DOCA-salt rats, underlying the relatively selective cardiac responses to L-carnitine treatment

FTIR PHYTOCHEMICAL FINGERPRINTING AND ANTIOXIDANT ANLYSES OF SELECTED INDOOR NON-FLOWERING INDOOR PLANTS AND THEIR INDUSTRIAL IMPORTANCE

Objective: phytochemical screening and antioxidant activity analyses of selected indoor plants and to evaluate commercial applications.Methods: Qualitative and quantitative phytochemical analyses of alcoholic and aquatic crude extracts of leaves of selected non-flowering indoor plants were assessed using standard protocols and later compared with FTIR analyses. Antioxidant and antibacterial activities of the extracts were studiedResults: Phytochemical analysis of polar solvent extractions of the four selected plants Pedilanthus tithymaloides, Cordyline terminalis, Tradescantia zebrine and Rhoeo discolou. Indicated the presence of tannins in all four varieties terpenoids in 3, flavonols, phytosterols and phenols in two plants, followed by alkaloids. The phytochemical analyses were supported by FTIR reports. Quantitative studies indicated variations in flavonol, tannin and phenols concentrations among the four species. High concentrations of Total flavonols (P. tithymaloides) and Tannins (C. terminalis) were observed. C. terminalis extract showed comparatively highest reducing power followed by R. discolour and P. tithymaloides extracts. Antibiotic Sensitivity Testing indicated P. tithymaloides showed a maximum zone of inhibition compared to R. discolor. C. terminalis plant leaf extract showed a faint zone of inhibition against E. fecalis while others couldnot. Intense colors of C. terminalis and T. zebrine plants could be used as a natural dye as well as pH indicator. Conclusion: The rich concentrations of the tannins from non-flowering indoor plants could be the future option of dyes and dyeing industry as natural colorants as well as pH indicators. These plants were rich sources of phytochemicals (phenols, flavonols, tannins, and phytosterols), with antioxidant and antibacterial activity

Evaluation of in Vitro Antioxidant Activity and L Asparaginase Enzyme Production of Four Endophytic Fungi Isolated from Acanthus Ilicifolius

The need for novel and useful bioactive secondary metabolites to help and relieve people from all aspects of human conditions is constantly expanding. Every plant tissue has a variety of endophytic fungi, which are thought to be highly effective producers of natural products. In this work, the determination of total phenolics, antioxidants, and L-asparaginase enzyme activity in four fungal endophytes associated with the mangrove plant Acanthus ilicifolius was evaluated. The study indicated that total phenolic content (1633+8.7 μg equivalent to gallic acid) and reducing power (0.96) were the highest for methanolic extracts of the isolate Aspergillus terreus while scavenging activity was highest for the isolate Colletotrichum xishuangbannaense (78.2+4.5 %). The enzyme activity of L-asparaginase was expressed predominantly by all the isolates except Colletotrichum xishuangbannaense. Maximum enzyme activities of 50.1 U/mL, 48.1 U/mL, and 47.7 U/mL were observed in Aspergillus terreus, Colletotrichum cobbiƫense, and Fusarium multiceps respectively. The current research demonstrated that mangrove-associated fungi have a high potential for producing bioactive molecules and L-asparaginase, which can be used as a possible source for the creation of anticancer drugs

CHARACTERIZATION OF STROKE LESION USING FRACTAL ANALYSIS

Objective: The characterization of stroke lesions is a challenging research issue due to the wide variability in the structure of lesion patterns. The objective of this research work is to characterize the stroke lesion structures using fractal analysis.Methods: To characterize the complex nature of the lesion structures, fractal box counting analysis is presented in this work. Three parameters from fractal dimension (FD) are considered to characterize the nature of the normal and abnormal brain tissues.Results: The experimental results are presented for 15 different datasets. Three different parameters namely FD average, FD deviation, and FDlacunarity are extracted to quantify the properties of the stroke lesion. The observations indicate that there is a significant proportion of separationof feature values between the normal and abnormal brain tissues.Conclusion: This work presents an efficient scheme for characterizing the stroke lesions using fractal parameters. It could be further enhanced by incorporating features extracted from other non-linear techniques.Â

A Learning Analytics-informed Activity to Improve Student Performance in a First Year Physiology Course

Learning Analytics (LA) can be employed to identify course-specific factors that hinder student course (outcome) performance, which can be subsequently rectified using targeted interventions. Supplementing interventions with predictive modelling also permits the identification of students who are at-risk of failing the course and encourages their participation. LA findings suggested that a targeted intervention for our course should focus on improving student short answer question (SAQ) performance, which we attempted to achieve by improving their understanding of features pertaining to various SAQ answer standards and how to achieve them using examples of varying scores. Every student was invited to the intervention via a course-wide announcement through the course learning management system. At-risk students identified using predictive models were given an additional invitation in the form of a personalised email. Results suggest that intervention improved student understanding of SAQ performance criteria. The intervention also enhanced student end-of-semester SAQ performance by 12% and 11% for at-risk and no-risk students respectively. Course failure rate was also lower by 26% and 9% among at-risk and no-risk intervention participants. Student perception of the intervention was also positive where an overwhelming majority of participants (96%) found the interventional activity to be useful for their learning and exam preparations

Improving concept learning in green building by addressing students\u27 learning styles and prior knowledge

In green building there is a requirement for the collaboration of students from different disciplines in order to solve challenging problems. Successful collaboration depends on the establishment of a common understanding of the subject matter among those involved. To gain common understanding concept learning is critical. A concept learning process may be improved when factors affecting it are addressed. Prior knowledge and learning styles of the students may influence the way they learn concepts. This thesis is focused on studying the relationship between a concept learning process and prior knowledge and learning styles of students. An experiment was conducted by giving students concepts customized to their prior knowledge and learning styles. Tests were conducted at various stages and they were statistically analyzed with t-tests to determine if a difference existed between the two groups. The results indicated that the group which was given the customized material showed improvement in their concept learning over the group who were taught conventionally

Consequences of Chromosome Loss:Why Do Cells Need Each Chromosome Twice?

Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to maintain the correct chromosome content over generations. The rare errors often lead to cell death, cell cycle arrest, or impaired proliferation. At the same time, aneuploidy can provide a growth advantage under selective conditions in a stressful, frequently changing environment. This is likely why aneuploidy is commonly found in cancer cells, where it correlates with malignancy, drug resistance, and poor prognosis. To understand this "aneuploidy paradox", model systems have been established and analyzed to investigate the consequences of aneuploidy. Most of the evidence to date has been based on models with chromosomes gains, but chromosome losses and recurrent monosomies can also be found in cancer. We summarize the current models of chromosome loss and our understanding of its consequences, particularly in comparison to chromosome gains