Use of a weighted matching algorithm to sequence clusters in spatial join processing

One of the most expensive operations in a spatial database is spatial join processing. This study focuses on how to improve the performance of such processing. The main objective is to reduce the Input/Output (I/O) cost of the spatial join process by using a technique called cluster-scheduling. Generally, the spatial join is processed in two steps, namely filtering and refinement. The cluster-scheduling technique is performed after the filtering step and before the refinement step and is part of the housekeeping phase. The key point of this technique is to realise order wherein two consecutive clusters in the sequence have maximal overlapping objects. However, finding the maximal overlapping order has been shown to be Nondeterministic Polynomial-time (NP)-complete. This study proposes an algorithm to provide approximate maximal overlapping (AMO) order in a Cluster Overlapping (CO) graph. The study proposes the use of an efficient maximum weighted matching algorithm to solve the problem of finding AMO order. As a result, the I/O cost in spatial join processing can be minimised

Early steps in mitochondrial protein import

The process of insertion of precursor proteins into mitochondrial membranes was investigated using a hybrid protein (pSc1-c) that contains dual targeting information and, at the same time, membrane insertion activity. pSc1-c is composed of the matrix-targeting domain of the cytochrome c1 presequence joined to the amino terminus of apocytochrome c. It can be selectively imported along either a cytochrome c1 route into the mitochondrial matrix or via the cytochrome c route into the intermembrane space. In contrast to cytochrome c1, pSc1-c does not require the receptor system/GIP for entry into the matrix. The apocytochrome c in the pSc1-c fusion protein appears to exert its membrane insertion activity in such a manner that the matrix-targeting sequence gains direct access to the membrane potential-dependent step. These results attribute an essential function to the receptor system in facilitating the initial insertion of precursors into the mitochondrial membranes

Joint profiling of DNA methylation and chromatin architecture in single cells.

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues

A unified mechanism for intron and exon definition and back-splicing.

The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes

Comparative systemic analysis of human immunoglobulin repertoires

The humoral immune system is majorly composed of B cells producing effector immunoglobulin molecules, the vast diversity of which allow for the neutralization of pathogenic threats never previously seen by the immune system. High-throughput sequencing technology has allowed this vast repertoire to be characterized and quantified, but understanding this complex system requires methods of comparison to identify and differentiate B cell populations. In this thesis, differences between groups of repertoires within individuals are analyzed at both the cellular and proteomic level. Novel experimental techniques and visualization methods will allow for the analyses of several such high-dimensional complex systems, leading to a fuller picture of the B cells’ contribution to the immune system.Microbiolog