Telomeric nucleic acids: C-strand structure and a telomerase RNA mutant

Telomeres, the ends of linear chromosomes, are composed of simple tandem repeats which are usually G·C rich. Telomeres are essential for chromosome stability, organizing the nuclear architecture and ensuring complete replication of the chromosomal terminus. To understand how telomeres carry out these fundamental cellular roles, one must understand the structural and dynamic properties of telomeric repeat sequences. Structural and genetic approaches were taken to learn more about telomeric nucleic acids;The structural portion of my research concerned an unusual DNA structure formed by the C-rich strand of telomeric DNA. Telomeric C-strand sequences form non-Watson-Crick structures in supercoiled plasmids at low pH. Absorbance thermal denaturation, chemical modification and non-denaturing gel electrophoresis showed that telomeric C-strand oligonucleotides form stable structures at low pH. H1[superscript]\u27-H1[superscript]\u27 nuclear Overhauser effects indicated that these structures were four-stranded. In addition, these four-stranded C-structures were shown to mediate recognition and binding of identical nucleic acid sequences. Thus, a novel nucleic acid dimerization motif was discovered;The genetic portion of my research concerned analysis of a Tetrahymena mutant with short telomeres. This mutant was heterozygous for a telomerase RNA mutation. Telomerase is a ribonucleoprotein that uses its RNA component as a template for addition of telomeric repeats to chromosome termini. Therefore, telomerase is involved in telomere length regulation, a process that has been implicated in both aging and cancer. The mutant telomerase RNA gene caused telomere shortening when introduced into wildtype cells, and thus identifies a functionally important domain of the telomerase RNA. Although mutant telomerase activity was indistinguishable from wildtype activity in vitro, cells expressing high levels of the mutant telomerase RNA exhibited lethal phenotypes that were due to the presence of very short telomeres

Intermittent Bolus versus Continuous Infusion of Propofol for Deep Sedation during ABR/Nuclear Medicine Studies

Objective  A comparison of intermittent bolus (IB) versus continuous infusion of propofol for deep sedation. Material and Methods  A retrospective review of patients sedated for Auditory Brainstem Response (ABR)/nuclear medicine studies between September 2008 and February 2015. A ketamine bolus (0.5 mg/kg 20 kg) followed by propofol bolus of 1 mg/kg over 2 minutes. In the IB group, maintenance of deep sedation was with incremental bolus of 10 to 20 mg of propofol. In continuous infusion group (CG), maintenance was with a continuous infusion of 83 mcg/kg/min of propofol. Results  Of the 326 cases completed, 181 were in CG group and 145 were in IB group. There were no statistical differences in patient's age, weight, and American Society of Anesthesiologist (ASA) classification. The cardiovascular and respiratory parameters in the two groups were not different statistically. Mean total propofol dose was higher in CG group versus IB group (CG 7.6 mg ± 3.6 mg, IB 6.5 mg ± 3.6 mg; p  = 0.008). Procedure time in CG group was longer by 8 minutes compared with IB group (CG 49.8 min ± 25.4 min versus 42.3 min ± 19.2 min; p  = .003). CG group has both shorter recovery time (CG 8.1 min ± 4.7 min versus IB 10.0 min ± 8.5 min; p  = 0.01) and discharge time. Conclusion  Satisfactory sedation and completion of the procedure was accomplished with both sedation protocols

Checkpoints: Chromosome pairing takes an unexpected twist

When meiotic cells complete S phase, homologous chromosomes pair, synapse and undergo recombination. A checkpoint protein is somehow required for meiotic chromosome pairing in C. elegans, thus providing a direct link between S phase and the rest of the meiotic program

Formation of novel hairpin structures by telemeric C-strand oligonucleotides

Telomeres are specialized structures at the ends of chromosomes that are required for long term chromosome stability and replication of the chromosomal terminus. Telomeric DNA consists of simple repetitive sequences with one strand G-rich relative to the other, C-rich, strand. Evolutionary conservation of this feature of telomeric repeat sequences suggests that they have specific structural characteristics involved in telomere function. Absorbance thermal denaturation, chemical modification and non-denaturing gel electrophoretic analyses showed that telomeric C-strand oligonucIeotides form stable non-Watson-Crick hairpin structures containing C.C + base pairs.Formation of such hairpins may facilitate previously reported G-strand exclusive interactions

Propofol-Based Procedural Sedation with or without Low-Dose Ketamine in Children

Objective Examine comparative dosing, efficacy, and safety of propofol alone or with an initial, subdissociative dose of ketamine approach for deep sedation. Background Propofol is a sedative-hypnotic agent used increasingly in children for deep sedation. As a nonanalgesic agent, use in procedures (e.g., bone marrow biopsies/aspirations, renal biopsies) is debated. Our intensivist procedural sedation team sedates using one of two protocols: propofol-only (P-O) approach or age-adjusted dose of 0.25 or 0.5 mg/kg intravenous ketamine (K + P) prior to propofol. With either approach, an initial induction dose of 1 mg/kg propofol is recommended and then intermittent dosing throughout the procedure to achieve adequate sedation to safely and effectively perform the procedure. Approach: Retrospective evaluation of 754 patients receiving either the P-O or K + P approach to sedation. Results A total of 372 P-O group patients and 382 K + P group. Mean age (7.3 ± 5.5 years for P-O; 7.3 ± 5.4 years for K + P) and weight (30.09 ± 23.18 kg for P-O; 30.14 ± 24.45 kg for K + P) were similar in both groups (p = NS). All patients successfully completed procedures with a 16% combined incidence of hypoxia (SPO2 < 90%). Procedure time was 3 minutes longer for K + P group than P-O group (18.68 ± 15.13 minutes for K + P; 15.11 ± 12.77 minutes for P-O; p < 0.01), yet recovery times were 5 minutes shorter (17.04 ± 9.36 minutes for K + P; 22.17 ± 12.84 minutes for P-O; p < 0.01). Mean total dose of propofol was significantly greater in P-O than in K + P group (0.28 ± 0.20 mg/kg/min for K + P; 0.40 ± 0.26 mg/kg/min for P-O; p < 0.0001), and might explain the shorter recovery time. Conclusion Both sedation approaches proved to be well tolerated and equally effective. Addition of ketamine was associated with reduction in the recovery time, probably explained by the statistically significant decrease in the propofol dose

Uncoupling of pathways that promote postmitotic life span and apoptosis from replicative immortality of Caenorhabditis elegans germ cells

A dichotomy exists between germ and somatic cells in most organisms, such that somatic cell lineages proliferate for a single generation, whereas the germ cell lineage has the capacity to proliferate from one generation to the next, indefinitely. Several theories have been proposed to explain the unlimited replicative life span of germ cells, including the elimination of damaged germ cells by apoptosis or expression of high levels of gene products that prevent aging in somatic cells. These theories were tested in the nematode Caenorhabditis elegans by examining the consequences of eliminating either apoptosis or the daf-16, daf-18 or sir-2.1 genes that promote longevity of postmitotic somatic cells. However, germ cells of strains deficient for these activities displayed an unlimited proliferative capacity. Thus, C. elegans germ cells retain their youthful character via alternative pathways that prevent or eliminate damage that accumulates as a consequence of cell proliferation

Nematode chromosomes

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed

Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease

Chromosomal translocations are frequent features of cancer genomes that contribute to disease progression. These rearrangements result from formation and illegitimate repair of DNA double-strand breaks (DSBs), a process that requires spatial colocalization of chromosomal breakpoints. The “contact first” hypothesis suggests that translocation partners colocalize in the nuclei of normal cells, prior to rearrangement. It is unclear, however, the extent to which spatial interactions based on three-dimensional genome architecture contribute to chromosomal rearrangements in human disease. Here we intersect Hi-C maps of three-dimensional chromosome conformation with collections of 1,533 chromosomal translocations from cancer and germline genomes. We show that many translocation-prone pairs of regions genome-wide, including the cancer translocation partners BCR-ABL and MYC-IGH, display elevated Hi-C contact frequencies in normal human cells. Considering tissue specificity, we find that translocation breakpoints reported in human hematologic malignancies have higher Hi-C contact frequencies in lymphoid cells than those reported in sarcomas and epithelial tumors. However, translocations from multiple tissue types show significant correlation with Hi-C contact frequencies, suggesting that both tissue-specific and universal features of chromatin structure contribute to chromosomal alterations. Our results demonstrate that three-dimensional genome architecture shapes the landscape of rearrangements directly observed in human disease and establish Hi-C as a key method for dissecting these effects.National Human Genome Research Institute (U.S.) (grant T32 HG002295)United States. Dept. of Defense (National Defense Science and Engineering Graduate Fellowship Program)Fannie and John Hertz FoundationNational Institute of General Medical Sciences (U.S.) (grant 5T32 GM008313)National Institute of General Medical Sciences (U.S.) (Medical Scientist Training Program

Higher Order Nyquist Zone Sampling with RFSoC Data Converters for Astronomical and High Energy Physics Readout Systems

From generation to generation, the maximum RF frequency and sampling rate of the integrated data converters in RF system-on-chip (RFSoC) family devices from Xilinx increases significantly. With the integrated digital mixers and up and down conversion blocks in the datapaths of the data converters, those RFSoC devices offer the capability for implementing a full readout system of ground and space-based telescopes and detectors across the electromagnetic spectrum within the devices with minimum or no analog mixing circuit. In this paper, we present the characterization results for the the data converters sampling at higher orders of Nyquist zones to extend the frequency range covered for our targeted readout systems of microwave-frequency resonator-based cryogenic detector and multiplexer systems and other astronomical and high-energy physics instrumentation applications, such as, axion search and dark matter detection. The initial evaluation of the data converters operating higher order Nyquist zones covers two-tones and comb of tones tests to address the concerns in the RF inter-modulation distortion, which is the key performance index for our targeted applications. The characterization of the data converters is performed in the bandwidth of 4-6 GHz and results meet our requirements. The settings and operating strategies of the data converters for our targeted applications will be summarised