Postoperative outcome of caesarean sections and other major emergency obstetric surgery by clinical officers and medical officers in Malawi

<p>Abstract</p> <p>Background</p> <p>Clinical officers perform much of major emergency surgery in Malawi, in the absence of medical officers. The aim of this study was to validate the advantages and disadvantages of delegation of major obstetric surgery to non-doctors.</p> <p>Methods</p> <p>During a three month period, data from 2131 consecutive obstetric surgeries in 38 district hospitals in Malawi were collected prospectively. The interventions included caesarean sections alone and those that were combined with other interventions such as subtotal and total hysterectomy repair of uterine rupture and tubal ligation. All these surgeries were conducted either by clinical officers or by medical officers.</p> <p>Results</p> <p>During the study period, clinical officers performed 90% of all straight caesarean sections, 70% of those combined with subtotal hysterectomy, 60% of those combined with total hysterectomy and 89% of those combined with repair of uterine rupture. A comparable profile of patients was operated on by clinical officers and medical officers, respectively. Postoperative outcomes were almost identical in the two groups in terms of maternal general condition – both immediately and 24 hours postoperatively – and regarding occurrence of pyrexia, wound infection, wound dehiscence, need for re-operation, neonatal outcome or maternal death.</p> <p>Conclusion</p> <p>Clinical officers perform the bulk of emergency obstetric operations at district hospitals in Malawi. The postoperative outcomes of their procedures are comparable to those of medical officers. Clinical officers constitute a crucial component of the health care team in Malawi for saving maternal and neonatal lives given the scarcity of physicians.</p

Genome Stability of Lyme Disease Spirochetes: Comparative Genomics of Borrelia burgdorferi Plasmids

Lyme disease is the most common tick-borne human illness in North America. In order to understand the molecular pathogenesis, natural diversity, population structure and epizootic spread of the North American Lyme agent, Borrelia burgdorferi sensu stricto, a much better understanding of the natural diversity of its genome will be required. Towards this end we present a comparative analysis of the nucleotide sequences of the numerous plasmids of B. burgdorferi isolates B31, N40, JD1 and 297. These strains were chosen because they include the three most commonly studied laboratory strains, and because they represent different major genetic lineages and so are informative regarding the genetic diversity and evolution of this organism. A unique feature of Borrelia genomes is that they carry a large number of linear and circular plasmids, and this work shows that strains N40, JD1, 297 and B31 carry related but non-identical sets of 16, 20, 19 and 21 plasmids, respectively, that comprise 33–40% of their genomes. We deduce that there are at least 28 plasmid compatibility types among the four strains. The B. burgdorferi ∼900 Kbp linear chromosomes are evolutionarily exceptionally stable, except for a short ≤20 Kbp plasmid-like section at the right end. A few of the plasmids, including the linear lp54 and circular cp26, are also very stable. We show here that the other plasmids, especially the linear ones, are considerably more variable. Nearly all of the linear plasmids have undergone one or more substantial inter-plasmid rearrangements since their last common ancestor. In spite of these rearrangements and differences in plasmid contents, the overall gene complement of the different isolates has remained relatively constant

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Outer Continental Shelf Issues: Central Gulf of Mexico

A report on the issues associated with Outer Continental Shelf (OCS) oil and gas activities in the Central Gulf of Mexico

Identification of the Genomic Insertion Site of Pmel-1 TCR α and β Transgenes by Next-Generation Sequencing

<div><p>The pmel-1 T cell receptor transgenic mouse has been extensively employed as an ideal model system to study the mechanisms of tumor immunology, CD8⁺ T cell differentiation, autoimmunity and adoptive immunotherapy. The ‘zygosity’ of the transgene affects the transgene expression levels and may compromise optimal breeding scheme design. However, the integration sites for the pmel-1 mouse have remained uncharacterized. This is also true for many other commonly used transgenic mice created before the modern era of rapid and inexpensive next-generation sequencing. Here, we show that whole genome sequencing can be used to determine the exact pmel-1 genomic integration site, even with relatively ‘shallow’ (8X) coverage. The results were used to develop a validated polymerase chain reaction-based genotyping assay. For the first time, we provide a quick and convenient polymerase chain reaction method to determine the dosage of pmel-1 transgene for this freely and publically available mouse resource. We also demonstrate that next-generation sequencing provides a feasible approach for mapping foreign DNA integration sites, even when information of the original vector sequences is only partially known.</p></div

Read alignments around the insertion site of pmel-1.

<p>An ideogram of chromosome 2 is shown at the top with the red bar indicating the area of insertion. Gray bars represent concordant read pairs. Red and blue colors represent read pairs where the insert size is larger than expected (deletion) or smaller than expected (insertion), respectively. Discordantly mapped reads are coded by the chromosome on which their mates can be found, so reads represented by magenta and aquamarine rectangles have mates that mapped to chromosomes 6 and 14, respectively. Other colors represent genomic “noise”. Multicolored blocks represent misaligned areas within reads. Soft-clipped reads were represented by grey bar with multicolored blocks at the ends. Misaligned bases in soft-clipped reads are shown in blue (C), green (A), red (T) and orange (G) color, respectively. (<b>A</b>) A snap shot of pmel-1 sequence reads aligned to the reference mouse genome near the integration area. Eight magenta-colored discordant reads are on the left side and five aquamarine-colored are on the right side. (<b>B</b>) An enlarged view of pmel-1 sequence reads, which shows five soft-clipped reads, one on right side, four on left sides of the insertion area. (<b>C</b>) A nucleotide level view of pmel-1 reads near the insertion area. This panel shows four soft-clipped reads that mapped partially to the β chain on chromosome 6 and partially to chromosome 2 of the reference genome.</p

PCR analysis distinguishes the homozygosity or heterozygosity of pmel-1 transgene.

<p>(<b>A</b>) Diagram of PCR primers designed from the predicted pmel-1 TCR β transgene insertion site on chromosome 2. (<b>B</b>) PCR results of pmel-1 homozygous or heterozygous animals. (<b>C</b>) Conceptual model of tandem integration of the pmel-1 α and β chains in the genome.</p

NGS data analysis workflow.

<p>This chart depicts the analysis of NGS data from Whole Genome Sequencing. In this analysis, standard tools for small structural variation detection were used to predict large insertions based on short paired-end (2*100 bp) sequence reads. Both SVDetect and DELLY extract data from a reference sequence file and a sequence alignment (BAM) file and generate filtered lists of predicted structural variations, their genomic coordinates, and confidence scores as a tab-separated text. Downstream steps, such as data visualization, cross-sectioning and ranking of SVs were done in the Integrative Genomics Viewer and Excel.</p