Shaping tRNA

2013 ◽  
Vol 75 (9) ◽  
pp. 708-709
Author(s):  
Christine Priano

This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the importance of molecular shape, the consequences of genetic mutation, and similarities and differences between DNA and RNA.

1993 ◽  
Vol 16 (3) ◽  
pp. 429-441 ◽  
Author(s):  
A. Bame Nsamenang ◽  
Michael E. Lamb

Among the Nso of Northwest Cameroon, the primary purpose of socialisation is the development of social intelligence and a sense of social responsibility. This process is dependent on and shaped more by "tacit lessions" built into children's apprenticeship in routine tasks and interpersonal encounters with both peers and adults than on role instruction. Nso children are co-participants in their own "hands-on" socialisation. The traditional niche is now in total flux. In order to compare the ideas and values of different parental cohorts inherent in the tension of continuity and change, we interviewed 389 Nso men and women using the Lamnso Parent Interview Guide. The results revealed both similarities and differences in the values of various parental cohorts. Although traditional values were widely endorsed, mothers, parents, and urban respondents tended to manifest less indigenous viewpoints than fathers, grandparents, and rural subjects, perhaps because of their greater exposure to alien modifiers of cultural knowledge and values.


2015 ◽  
Vol 61 ◽  
pp. 5-22
Author(s):  
Sir Dai Rees

Struther Arnott worked tirelessly as a researcher, teacher, leader and maker and implementer of policy in universities in Britain and the USA, always carrying his colleagues along with him through his infectious energy and breadth of academic enthusiasms and values. His outlook was shaped by the stimulus of a broad Scottish education that launched wide interests inside and outside science, including the history and literature of classical civilizations. His early research, with John Monteath Robertson FRS, was into structure determination by X-ray diffraction methods for single crystals, at a time when the full power of computers was just becoming realized for solution of the phase problem. With tenacity and originality, he then extended these approaches to materials that were to a greater or lesser extent disordered and even more difficult to solve because their diffraction patterns were poorer in information content. He brought many problems to definitive and detailed conclusion in a field that had been notable for solutions that were partial or vague, especially with oriented fibres of DNA and RNA but also various polysaccharides and synthetic polymers. His first approach was to use molecular model building in combination with difference Fourier analysis. This was followed later, and to even greater effect, by a computer refinement method that he developed himself and called linkedatom least-squares refinement. This has now been adopted as the standard approach by most serious centres of fibre diffraction analysis throughout the world. After the 10 years in which he consolidated his initial reputation at the Medical Research Council Biophysics Unit at King's College, London, in association with Maurice Wilkins FRS, he moved to Purdue University in the USA, first as Professor of Biology then becoming successively Head of the Department of Biological Sciences and Vice-President for Research and Dean of the Graduate School. As well as continuing his research, he contributed to the transformation of biological sciences at that university and to the development of the university's general management. He finally returned to his roots in Scotland as Principal and Vice-Chancellor of the University of St Andrews, to draw on his now formidable experience of international scholarship and institutional management, to reshape the patterns of academic life and mission to sit more happily and successfully within an environment that had become beset with conflict and change. He achieved this without disturbance to the harmony and wisdom embodied in the venerable traditions of that ancient Scottish yet cosmopolitan university.


2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii343-iii343
Author(s):  
Aaron M Taylor ◽  
Jianhe Shen ◽  
Lingzhao Ren ◽  
Keita Terashima ◽  
Lei Huang ◽  
...  

Abstract Intracranial germ cell tumors (IGCTs) account for 3% of CNS tumors in children in the U.S. and 11% in Japan and East Asian countries. IGCTs are separated into two distinct subtypes based on histology: germinomas and non-germinomatous germ cell tumors (NGGCTs). The deep central location of IGCTs makes surgical resection and therefore molecular subtype classification difficult, and previous gene expression studies are limited. We performed mRNA expression profiling (Human Genome U133 Plus 2.0) and microRNA expression profiling (ABI TaqMan) with 36 and 49 IGCTs, respectively. Sample stratification using non-negative matrix factorization clustering of gene expression revealed two distinct subgroups that delineated germinomas from NGGCTs. Employing stepwise model building in each data set separately, we were able to separate these groups using only mRNA probes for the LIN28B and L1TD1 genes, and two microRNA, microRNA-26a and microRNA-373. MicroRNA26a suppresses the LIN28B gene and is down-regulated in germinoma. LIN28B directly binds and suppresses the let-7 microRNA family, which suppress the KRAS oncogene, previously found to be mutated in ~19% of IGCTs. L1TD1 is required for human stem cell renewal and directly interacts with LIN28B for its RNA binding function. LIN28B and L1TD1 are both known to be upregulated in other systemic germ cell tumors, but this has not yet been documented in IGCTs. In conclusion, these results show that intracranial germinomas have similar gene expression compared to systemic seminoma, and suggest a mechanism by which activation of LIN28B and L1TD1 downregulates the let-7 microRNA and subsequently upregulates KRAS.


2016 ◽  
Vol 15 (1) ◽  
pp. ar4 ◽  
Author(s):  
Adam Reinagel ◽  
Elena Bray Speth

In an introductory biology course, we implemented a learner-centered, model-based pedagogy that frequently engaged students in building conceptual models to explain how genes determine phenotypes. Model-building tasks were incorporated within case studies and aimed at eliciting students’ understanding of 1) the origin of variation in a population and 2) how genes/alleles determine phenotypes. Guided by theory on hierarchical development of systems-thinking skills, we scaffolded instruction and assessment so that students would first focus on articulating isolated relationships between pairs of molecular genetics structures and then integrate these relationships into an explanatory network. We analyzed models students generated on two exams to assess whether students’ learning of molecular genetics progressed along the theoretical hierarchical sequence of systems-thinking skills acquisition. With repeated practice, peer discussion, and instructor feedback over the course of the semester, students’ models became more accurate, better contextualized, and more meaningful. At the end of the semester, however, more than 25% of students still struggled to describe phenotype as an output of protein function. We therefore recommend that 1) practices like modeling, which require connecting genes to phenotypes; and 2) well-developed case studies highlighting proteins and their functions, take center stage in molecular genetics instruction.


2018 ◽  
Author(s):  
Mary Miyaji ◽  
Ryohei Furuta ◽  
Osamu Hosoya ◽  
Kuniaki Sano ◽  
Norikazu Hara ◽  
...  

AbstractBackgroundType II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T-segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be placed far from each other on the same chromosome. However, no direct evidence for this to occur has been described so far due to lack of proper methodology.ResultsThe beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. To elucidate the enzyme’s role in the process, here we devise a genome-wide mapping technique for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It became clear that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that the DSP sites are intertwined or knotted and topo IIβ is engaged in unknotting reaction that leads to chromatin decondensation and gene regulation.ConclusionsWhen combined with categorized gene expression analysis, the model-based prediction of DSP sites reveals that DSP is one of the key factors for topo IIβ-dependency of neuronal gene regulation.


1993 ◽  
Vol 73 (2) ◽  
pp. 175-180 ◽  
Author(s):  
B. Mollet ◽  
A. Constable ◽  
M. Delley ◽  
J. Knol ◽  
O. Marciset ◽  
...  

2009 ◽  
Vol 16 (1) ◽  
Author(s):  
Reidun Øvstebø ◽  
Peter Kierulf ◽  
Kari Bente Foss Haug

<p>This short review on a rapidly expanding domain in biomarkers focuses on the value of markers derived from either circulating intracellular DNA and RNA (leukocytes) or from free DNA and RNA in plasma or serum. In circulating intracellular DNA biomarkers, importance has been pointed to reside in the ever increasing number of SNPs directly related to disease such as hemochromatosis or associated with genetic make up that leads to different drug-susceptibility. Quantitative gene expression profiling, increasingly using global expression platforms, is gaining momentum in various disease states such as cancer, inflammation, cardiovascular disease and diabetes. Circulating free nucleic acids in plasma or serum gain in importance as biomarkers particularly in cancer and foeto-maternal understanding. The surprising recent findings of circulating free mRNA carries the potential of examining normal and diseased plasma for global gene expression profiling – opening avenues to new biomarkers. When appropriate, this review gives reference to methodological considerations and refers the readers to important literature in the fields</p><p>I denne korte oversiktsartikkelen redegjøres det for et biomarkørfelt som utvikler seg hurtig. Gjennom en blodprøve kan man få kjennskap til forandringer i sirkulerende leucocytter, intracellulære nukleinsyrer (DNA og RNA) og fritt DNA og RNA fra plasma eller serum. Single Nucleotide Polymorphisms (SNPs) i DNA har allerede bekreftet sine muligheter som biomarkører (f.eks. Hemokromatose, Faktor V Leiden, Cytochrom P450 (CYP’er)). Stadig flere SNP’er vinner innpass i klinisk sammenheng. Siden sirkulerende hvite blodlegemer kan sies kontinuerlig å overvåke kroppens organer og vev, og dette avspeiles i disse blodcellers genekspresjon (RNA), knyttes det i dag forventninger til sykdomsspesifikke genekspresjonsprofiler. Både ved visse kreftformer, betennelsestilstander og hjertekar-sykdom viser hvite blodlegemer mer eller mindre tydelig sykdomsspesifikke genekspresjonsprofiler. Denne type sykdomsspesifikke genekspresjonsmarkører vil bli økende viktig fremover. Ved slike markører vil man kunne ha nytte av kvantitativ måling av enkeltmarkører, og også globale genekspresjonsprofiler på mikroarray-plattformer. Sirkulerende fritt DNA og kanskje særlig RNA i plasma åpner for nye sykdomsmarkører i første rekke ved forskjellige kreftformer og ved foeto-maternelle problemstillinger. Oversikten gir også en henvisning til metodologiske referanser i disse feltene.</p>


2014 ◽  
Vol 21 (3) ◽  
pp. 495-504 ◽  
Author(s):  
Jenny Welander ◽  
Adam Andreasson ◽  
Michael Brauckhoff ◽  
Martin Bäckdahl ◽  
Catharina Larsson ◽  
...  

Pheochromocytomas are neuroendocrine tumors arising from the adrenal medulla. While heritable mutations are frequently described, less is known about the genetics of sporadic pheochromocytoma. Mutations in genes involved in the cellular hypoxia response have been identified in tumors, and recentlyEPAS1, encoding HIF2α, has been revealed to be a new gene involved in the pathogenesis of pheochromocytoma and abdominal paraganglioma. The aim of this study was to further characterizeEPAS1alterations in non-familial pheochromocytomas. Tumor DNA from 42 adrenal pheochromocytoma cases with apparently sporadic presentation, without known hereditary mutations in predisposing genes, were analyzed for mutations inEPAS1by sequencing of exons 9 and 12, which contain the two hydroxylation sites involved in HIF2α degradation, and also exon 2. In addition, the copy number at theEPAS1locus as well as transcriptome-wide gene expression were studied by DNA and RNA microarray analyses, respectively. We identified six missenseEPAS1mutations, three in exon 9 and three in exon 12, in five of 42 pheochromocytomas (12%). The mutations were both somatic and constitutional, and had no overlap in 11 cases (26%) with somatic mutations inNF1orRET. One sample had two differentEPAS1mutations, shown by cloning to occur incis, possibly indicating a novel mechanism of HIF2α stabilization through inactivation of both hydroxylation sites. One of the tumors with anEPAS1mutation also had a gain in DNA copy number at theEPAS1locus. AllEPAS1-mutated tumors displayed a pseudo-hypoxic gene expression pattern, indicating an oncogenic role of the identified mutations.


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