Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding

Whole-genome sequencing and assembly have revolutionized plant genetics and molecular biology over the last two decades. However, significant shortcomings in first- and second-generation technology resulted in imperfect reference genomes: numerous and large gaps of low quality or undeterminable sequence in areas of highly repetitive DNA along with limited chromosomal phasing restricted the ability of researchers to characterize regulatory noncoding elements and genic regions that underwent recent duplication events. Recently, advances in long-read sequencing have resulted in the first gapless, telomere-to-telomere (T2T) assemblies of plant genomes. This leap forward has the potential to increase the speed and confidence of genomics and molecular experimentation while reducing costs for the research community

Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures

MicroRNAs (miRNAs) are key regulators of gene expression and contribute to a variety of biological processes. Abnormal miRNA expression has been reported in various diseases including pathophysiology of breast cancer, where they regulate protumorigenic processes including vascular invasiveness, estrogen receptor status, chemotherapy resistance, invasion and metastasis. The miRBase sequence database, a public repository for newly discovered miRNAs, has grown rapidly with approximately >10,000 entries to date. Despite this rapid growth, many miRNAs have not yet been validated, and several others are yet to be identified. A lack of a full complement of miRNAs has imposed limitations on recognizing their important roles in cancer, including breast cancer. Using deep sequencing technology, we have identified 189 candidate novel microRNAs in human breast cancer cell lines with diverse tumorigenic potential. We further show that analysis of 500-nucleotide pri-microRNA secondary structure constitutes a reliable method to predict bona fide miRNAs as judged by experimental validation. Candidate novel breast cancer miRNAs with stem lengths of greater than 30 bp resulted in the generation of precursor and mature sequences in vivo. On the other hand, candidates with stem length less than 30 bp were less efficient in producing mature miRNA. This approach may be used to predict which candidate novel miRNA would qualify as bona fide miRNAs from deep sequencing data with approximately 90% accuracy

Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on ∼1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses

Genetic and Physical Characterization of Tn904.

The possibility that a streptomycin resistance determinant was part of a transposon was confirmed. Genetic techniques were used to demonstrate definitively that the genetic element, designated Tn904, was capable of transposition in a recA('-) genetic background. Physical analysis of plasmids that had acquired Tn904 showed that in all cases acquisition of the transposon was accompanied by the acquisition of a discrete DNA segment. Transposition was not site-specific with respect to the recipient molecule. It was shown at the level of resistance to streptomycin conferred by Tn904 was directly related to the copy number of the transposon. As a result, recovery of cells in which transposition of Tn904 from a low copy number plasmid to a high copy number plasmid had occurred could be enriched for by growth of the cells on Sm containing media. The practical implications of this phenomenon were discussed. Restriction endonuclease digest analysis of Tn904 showed that the transposon had a size of 5.2 kb. Electron microscopic heteroduplex analysis showed that the transposon was flanked by inverted repeats of about 125 bp. A coordinate system based on this data was devised for Tn904. The approximate site of the Sm resistance determinant was localized on the transposon. The transposon was shown not to increase in size when exposed to high levels of streptomycin. The transposon was shown not to include markers for mercury or spectinomycin resistance. Transposition frequency in two different experimental situations was determined. Precise excision of Tn904 from plasmid molecules was not observed to occur.Ph.D.GeneticsUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/159047/1/8225007.pd

The beauties of modern sacred poetry, systematically arranged, with preface.

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Cost-effectiveness of obesity treatment

Limitations in epidemiological data means that most health economic analyses have provided incomplete estimates of the total financial burden of obesity on healthcare: more complete data are needed on multiple disease risks and costs attributable to overweight and obesity, stratified by age, sex and BMI, particularly for severe and complicated obesity. UK primary care data indicate that the annual healthcare costs of patients with BMI 20–21 kg/m2 (ideal body weight) are about half those at BMI 40 kg/m2, for both men and women. Cost-effectiveness of structured weight management is high over patients' lifetimes (potentially cost-saving). Drug treatments and bariatric surgery are also highly cost-effective, but have greater unit costs and so afford less net benefit at a population level. Before these interventions can reduce the spiralling healthcare costs associated with obesity, short-term spending is necessary to establish services that will become cost-effective over a longer period

Cost-effectiveness of obesity treatment

Limitation on the available epidemiological data means that most health economic analyses have provided incomplete estimates of the total financial burden of obesity on healthcare. Figures from UK Primary Care indicate that the total healthcare costs of BMI 20–21 (ideal body weight) are half those of BMI 40 kg/m2. Cost-effectiveness of a structured weight management programme (Counterweight) is high over patients’ lifetimes (even cost-saving). Drug treatments and bariatric surgery are also highly cost-effective according to the NICE criteria. Planners need to understand that short-term increase in spending is necessary before obesity treatments become cost-effective