Single-Cell Gene Expression Variation as A Cell-Type Specific Trait: A Study of Mammalian Gene Expression Using Single-Cell RNA Sequencing

In this dissertation, we used single-cell RNA sequencing data from five mammalian tissues to characterize patterns of gene expression across single cells, transcriptome-wide and in a cell-type-specific manner (Part 1). Additionally, we characterized single-cell RNA sequencing methods as a resource for experimental design and data analysis (Part 2). Part 1: Differentiation of metazoan cells requires execution of different gene expression programs but recent single cell transcriptome profiling has revealed considerable variation within cells of seemingly identical phenotype. This brings into question the relationship between transcriptome states and cell phenotypes. We used high quality single cell RNA sequencing for 107 single cells from five mammalian tissues, along with 30 control samples, to characterize transcriptome heterogeneity across single cells. We developed methods to filter genes for reliable quantification and to calibrate biological variation. We found evidence that ubiquitous expression across cells may be indicative of critical gene function and that, for a subset of genes, biological variability within each cell type may be regulated in order to perform dynamic functions. We also found evidence that single-cell variability of mouse pyramidal neurons was correlated with that in rats consistent with the hypothesis that levels of variation may be conserved. Part 2: Many researchers are interested in single-cell RNA sequencing for use in identification and classification of cell types, finding rare cells, and studying single-cell expression variation; however, experimental and analytic methods for single-cell RNA sequencing are young and there is little guidance available for planning experiments and interpreting results. We characterized single-cell RNA sequencing measurements in terms of sensitivity, precision and accuracy through analysis of data generated in a collaborative control project, where known reference RNA was diluted to single-cell levels and amplified using one of three single-cell RNA sequencing protocols. All methods perform comparably overall, but individual methods demonstrate unique strengths and biases. Measurement reliability increased with expression level for all methods and we conservatively estimated measurements to be quantitative at an expression level of ~5-10 molecules

Sightings of Belugas and Other Marine Mammals in the North Water, Late March 1993

Surveys of belugas were flown during March 1993 in Lancaster Sound and the North Water of Baffin Bay. Most belugas were observed along the shore leads off southeastern Devon Island and in the polynya at the mouth of Jones Sound. Our results confirm other published winter observations that belugas regularly occupy the North Water's leads and polynyas in winter. Walruses, narwhals, and bowhead whales were also seen during these surveys; their presence confirms the use of the North Water wintering area by several other marine mammal species.  En mars 1993, on a effectué des relevés aériens dans le détroit de Lancaster et dans l'Eau du Nord située dans la baie de Baffin. La majorité des bélugas ont été observés dans les chenaux longeant la banquise fixe le long du sud-est de l'île Devon et dans la polynie à l'embouchure du détroit de Jones. Nos résultats confirment d'autres observations publiées sur l'utilisation régulière par les bélugas des chenaux et polynies de l'Eau du Nord en hiver. On a également observé des morses, des narvals et des baleines boréales durant ces relevés, ce qui confirme l'utilisation de l'Eau du Nord comme aire d'hivernage pour plusieurs autres espèces de mammifères marins

Strong Secrecy for Multiple Access Channels

We show strongly secret achievable rate regions for two different wiretap multiple-access channel coding problems. In the first problem, each encoder has a private message and both together have a common message to transmit. The encoders have entropy-limited access to common randomness. If no common randomness is available, then the achievable region derived here does not allow for the secret transmission of a common message. The second coding problem assumes that the encoders do not have a common message nor access to common randomness. However, they may have a conferencing link over which they may iteratively exchange rate-limited information. This can be used to form a common message and common randomness to reduce the second coding problem to the first one. We give the example of a channel where the achievable region equals zero without conferencing or common randomness and where conferencing establishes the possibility of secret message transmission. Both coding problems describe practically relevant networks which need to be secured against eavesdropping attacks.Comment: 55 page

The planetary data system educational CD-ROM

The Planetary Data System (PDS) is producing a special educational CD-ROM that contains samples of PDS datasets and is expected to be released in 1993. The CD-ROM will provide university-level instructors with PDS-compatible materials and information that can be used to construct student problem sets using real datasets. The main purposes of the CD-ROM are to facilitate wide use of planetary data and to introduce a large community to the PDS. To meet these objectives the Educational CD-ROM will also contain software to manipulate the data, background discussions about scientific questions that can be addressed with the data, and a suite of exercises that illustrate analysis techniques. Students will also be introduced to the SPICE concept, which is a new way of maintaining geometry and instrument information. The exercises will be presented at the freshman through graduate student levels. With simplification, some of the material should also be of use at the high school level

Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants

Background: Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages. Results: Using this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs. Conclusion: Our analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells

Neoadjuvant chemoradiation compared to neoadjuvant radiation alone and surgery alone for Stage II and III soft tissue sarcoma of the extremities

<p>Abstract</p> <p>Background</p> <p>Neoadjuvant chemoradiation (NCR) prior to resection of extremity soft tissue sarcoma (STS) has been studied, but data are limited. We present outcomes with NCR using a variety of chemotherapy regimens compared to neoadjuvant radiation without chemotherapy (NR) and surgery alone (SA).</p> <p>Methods</p> <p>We conducted a retrospective chart review of 112 cases.</p> <p>Results</p> <p>Treatments included SA (36 patients), NCR (39 patients), and NR (37 patients). NCR did not improve the rate of margin-negative resections over SA or NR. Loco-regional relapse-free survival, distant metastases-free survival, and overall survival (OS) were not different among the treatment groups. Patients with relapsed disease (OR 11.6; p = 0.01), and tumor size greater than 5 cm (OR 9.4; p = 0.01) were more likely to have a loco-regional recurrence on logistic regression analysis. Significantly increased OS was found among NCR-treated patients with tumors greater than 5 cm compared to SA (3 year OS 69 vs. 40%; p = 0.03). Wound complication rates were higher after NCR compared to SA (50 vs. 11%; p = 0.003) but not compared to NR (p = 0.36). Wet desquamation was the most common adverse event of NCR.</p> <p>Conclusions</p> <p>NCR and NR are acceptable strategies for patients with STS. NCR is well-tolerated, but not clearly superior to NR.</p

Transfer RNA-derived small RNAs in the cancer transcriptome

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis.These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity.RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of inter-est in a‘larger’small RNA, the transfer RNA (tRNA).Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation.Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing

Neutrinoless double-beta decay and seesaw mechanism

From the standard seesaw mechanism of neutrino mass generation, which is based on the assumption that the lepton number is violated at a large (~10exp(+15) GeV) scale, follows that the neutrinoless double-beta decay is ruled by the Majorana neutrino mass mechanism. Within this notion, for the inverted neutrino-mass hierarchy we derive allowed ranges of half-lives of the neutrinoless double-beta decay for nuclei of experimental interest with different sets of nuclear matrix elements. The present-day results of the calculation of the neutrinoless double-beta decay nuclear matrix elements are briefly discussed. We argue that if neutrinoless double-beta decay will be observed in future experiments sensitive to the effective Majorana mass in the inverted mass hierarchy region, a comparison of the derived ranges with measured half-lives will allow us to probe the standard seesaw mechanism assuming that future cosmological data will establish the sum of neutrino masses to be about 0.2 eV.Comment: Some changes in sections I, II, IV, and V; two new figures; additional reference