Improving PacBio Long Read Accuracy by Short Read Alignment

The recent development of third generation sequencing (TGS) generates much longer reads than second generation sequencing (SGS) and thus provides a chance to solve problems that are difficult to study through SGS alone. However, higher raw read error rates are an intrinsic drawback in most TGS technologies. Here we present a computational method, LSC, to perform error correction of TGS long reads (LR) by SGS short reads (SR). Aiming to reduce the error rate in homopolymer runs in the main TGS platform, the PacBio® RS, LSC applies a homopolymer compression (HC) transformation strategy to increase the sensitivity of SR-LR alignment without scarifying alignment accuracy. We applied LSC to 100,000 PacBio long reads from human brain cerebellum RNA-seq data and 64 million single-end 75 bp reads from human brain RNA-seq data. The results show LSC can correct PacBio long reads to reduce the error rate by more than 3 folds. The improved accuracy greatly benefits many downstream analyses, such as directional gene isoform detection in RNA-seq study. Compared with another hybrid correction tool, LSC can achieve over double the sensitivity and similar specificity.     

Who pays for community care? The same old question.

Trends in mental health service funding over the past 40 years show that the programme of hospital closures has not resulted in a significant release of resources to fund community based services. Far from being excessive, the current provision of residential services (both NHS and non-NHS) for mentally ill people is now below levels recommended as sufficient by the government, the Royal College of Psychiatrists, and the National Schizophrenia Fellowship. What clinical research evidence there is suggests that more rather than fewer residential places are required. This situation is likely to be compounded by the recent transfer of responsibility for funding private and voluntary residential care from the Department of Social Security to local authority social services departments.     

Activation of a UBC4-dependent pathway of ubiquitin conjugation during postnatal development of the rat testis.

During spermatogenesis, germ cells undergo mitotic and meiotic divisions to form haploid round spermatids which mature to functional elongated spermatozoa. During this process there occurs remodeling of cell structure and loss of most of the cytoplasm and a large fraction of cellular proteins. To evaluate the role of the ubiquitin proteolytic system in this protein loss, we measured levels of ubiquitinated proteins and rates of ubiquitin conjugation in extracts of testes from rats of different ages. Endogenous ubiquitin-protein conjugates increased till day 30 and then reached a plateau. In parallel, there was a progressive increase in the rate of conjugation of ubiquitin to proteins in testis extracts from these animals. To test the importance of two major ubiquitin conjugating enzyme families in the conjugation, immunoprecipitation of UBC2 or UBC4 from 10- and 30-day-old testis extracts was carried out and the remaining conjugation activity in supernatants was assayed. Depletion of either enzyme family resulted in decreased conjugation. However, most of the conjugation activity and, more importantly, the increased conjugation during development were UBC4-dependent. Immunocytochemistry demonstrated a marked increase in expression of UBC4 in spermatids, consistent with the UBC4-dependent activation of conjugation seen in vitro. In situ hybridization studies evaluated the contribution of various UBC4 isoforms to this induction. UBC4-1 mRNA was expressed in most cells. UBC4-2 mRNA was restricted to germ cells with high levels of expression in round and elongated spermatids. UBC4-testis had previously been shown to be expressed only in spermatids. Our data suggest that induction of various UBC4 isoforms activates overall conjugation and plays an important role in the cellular remodeling and protein loss occurring during spermatogenesis.     

Self-Rotation of Cells in an Irrotational AC E-Field in an Opto-Electrokinetics Chip

The use of optical dielectrophoresis (ODEP) to manipulate microparticles and biological cells has become increasingly popular due to its tremendous flexibility in providing reconfigurable electrode patterns and flow channels. ODEP enables the parallel and free manipulation of small particles on a photoconductive surface on which light is projected, thus eliminating the need for complex electrode design and fabrication processes. In this paper, we demonstrate that mouse cells comprising melan-a cells, RAW 267.4 macrophage cells, peripheral white blood cells and lymphocytes, can be manipulated in an opto-electrokinetics (OEK) device with appropriate DEP parameters. Our OEK device generates a non-rotating electric field and exerts a localized DEP force on optical electrodes. Hitherto, we are the first group to report that among all the cells investigated, melan-a cells, lymphocytes and white blood cells were found to undergo self-rotation in the device in the presence of a DEP force. The rotational speed of the cells depended on the voltage and frequency applied and the cells'' distance from the optical center. We discuss a possible mechanism for explaining this new observation of induced self-rotation based on the physical properties of cells. We believe that this rotation phenomenon can be used to identify cell type and to elucidate the dielectric and physical properties of cells.     

Characterisation of suppressor cells generated following cryosurgery of an HSV-2-induced fibrosarcoma

Summary Cryosurgery of a primary HSV-2-induced hamster fibrosarcoma resulted in the generation of a population of suppressor cells. These cells were detectable in the spleen 1–10 days post-cryosurgery by their ability to suppress the proliferation of immunocompetent splenic T-lymphocytes following exposure to concanavalin A (Con A). The spleens of tumour-bearing (t.b.) animals which received cryosurgery 3 days previously displayed gross splenomegaly due to the generation of large numbers of highly proliferative erythroblasts. The erythroblast cells were unlikely to be the source of suppression since time course studies have demonstrated the presence of suppressor cells before and after their appearance in the spleen. The erythroblasts therefore probably reflected a response by the host to regenerate the erythrocytes lost during surgery and their presence was independent of the appearance of suppressor cells. Characterisation of the suppressor cell has revealed it to be non-adherent and esterase negative making it unlikely to be of macrophage (MØ) lineage. This was confirmed by the ability of splenic MØs from day 3 t.b. cryosurgery-treated animals to completely restore Con A-dependent T-lymphocyte proliferation following MØ depletion. As nylonwool column-eluted cells are able to suppress Con A-dependent T-lymphocyte proliferation, it seemed unlikely that B-lymphocytes play a role in cryosurgery-induced immunosuppression. These findings suggest that cryosurgery of a t.b. animal results in the generation of a population of T-lymphocytes capable of suppressing Con A-dependent T-lymphocyte proliferation, and infers that these cells contribute to the inferior prognosis following cryosurgery as compared to excision of a metastatic tumour.