Characterization Of The G93a Hsod1 Transgene Complex In The Mouse Model Of Amyotrophic Lateral Sclerosis

Mutations in the human superoxide dismutase gene (hSOD1) cause Amyotrophic Lateral Sclerosis (ALS), a paralytic disorder that leads to degeneration of the motor neurons in the brain and spinal cord and generally causes death within five years of onset. This work focused on characterizing the site of insertion of the human SOD1 G93A mutant transgene in a mouse model for ALS. These transgenic mice exhibit a phenotype similar to that of human ALS patients, although the exact number of gene copies and the precise location of the transgene have not been determined. Since the number and location of the transgene may affect the expression of nearby loci, which in turn may alter the phenotype of these animals, it is important to map precisely the site of insertion with respect to possible deletions or additions in DNA sequences and to determine the exact number of copies present. Previous experiments have suggested that there are approximately 25 copies of the transgene and that they are present on mouse chromosome 12, band E. We confirmed the chromosomal location by fluorescence in situ hybridization, but our real-time PCR analyses showed the copy number to be 102 +/- 5 (mean +/- S.E.). Although the mouse flanking sequence has not been determined, our results indicate that all the concatamerized transgene monomers are present in the head-to-tail orientation, and that the individual hSOD1 gene monomers appear to be adjacent to each other with perhaps only a few bases added or deleted at the junctions. Our results also indicate the presence of (a) ~3.3 kb of the pBR322 plasmid, which was used to create the transgenic mouse, at the 5\u27 end of the transgene complex, (b) plasmid SVneo sequence at the 3\u27 end of the transgene complex, (c) at least two SVneo regions in tail-to-tail orientation at locations that remain to be determined, and (d) DNA sequences in the transgene complex from vector(s) that were supposedly not used in making these transgenic mice. The presence of plasmid sequences at the 5\u27 and the 3\u27 ends of the transgene complex was unexpected, and raises the possibility that such sequences may also exist in between at least some of the hSOD1 monomers. This observation as well as the presence of sequences from other vectors, significantly complicates the efforts to identify the flanking mouse sequences

Draft Genome Sequence of Staphylococcus aureus 118 (ST772), a Major Disease Clone from India

We report the draft genome sequence of an ST772 Staphylococcus aureus disease isolate carrying staphylococcal cassette chromosome mec (SCCmec) type V from a pyomyositis patient. Our de novo short read assembly is similar to 2.8 Mb and encodes a unique Panton-Valentine leukocidin (PVL) phage with structural genes similar to those of phi 7247PVL and novel lysogenic genes at the N termini

Draft Genome Sequence of Staphylococcus aureus ST672, an Emerging Disease Clone from India

We report the draft genome sequence of methicillin-resistant Staphylococcus aureus (MRSA) strain ST672, an emerging disease clone in India, from a septicemia patient. The genome size is about 2.82 Mb with 2,485 open reading frames (ORFs). The staphylococcal cassette chromosome mec (SCCmec) element (type V) and immune evasion cluster appear to be different from those of strain ST772 on preliminary examination

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways

Patient experience and perceived acceptability of whole-body magnetic resonance imaging for staging colorectal and lung cancer compared with current staging scans: a qualitative study

OBJECTIVE: To describe the experience and acceptability of whole-body magnetic resonance imaging (WB-MRI) staging compared with standard scans among patients with highly suspected or known colorectal or lung cancer. DESIGN: Qualitative study using one-to-one interviews with thematic analysis. SETTING: Patients recruited from 10 hospitals in London, East and South East England between March 2013 and July 2014. PARTICIPANTS: 51 patients (31 male, age range 40-89 years), with varying levels of social deprivation, were recruited consecutively from two parallel clinical trials comparing the diagnostic accuracy and cost-effectiveness of WB-MRI with standard scans for staging colorectal and lung cancer ('Streamline-C' and 'Streamline-L'). WB-MRI was offered as an additional scan as part of the trials. RESULTS: In general WB-MRI presented a greater challenge than standard scans, although all but four patients completed the WB-MRI. Key challenges were enclosed space, noise and scan duration; reduced patient tolerance was associated with claustrophobia, pulmonary symptoms and existing comorbidities. Coping strategies facilitated scan tolerance and were grouped into (1) those intended to help with physical and emotional challenges, and (2) those focused on motivation to complete the scan, for example focusing on health benefit. Our study suggests that good staff communication could reduce anxiety and boost coping strategies. CONCLUSIONS: Although WB-MRI was perceived as more challenging than standard scans, it was sufficiently acceptable and tolerated by most patients to potentially replace them if appropriate. TRIAL REGISTRATION NUMBER: ISRCTN43958015 and ISRCTN50436483

Additional file 12: Table S5. of Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

Repeat elements identified in Tulsi genome assembly and classified in different groups of repeats

Additional file 25: Table S11. of Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

Metabolites with unknown pathways with their disease implications. There are 15 medicinally relevant metabolites in Ocimum sp. with unknown pathways