ChloroMitoSSRDB 2.00: More genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

© The Author(s) 2015. Published by Oxford University Press. Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics

ChloroMitoSSRDB: open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics

This article has been accepted for publication in DNA Research Published by Oxford University Press.[EN] Microsatellites or simple sequence repeats (SSRs) are repetitive stretches of nucleotides (A, T, G, C) that are distributed either as single base pair stretches or as a combination of two- to six-nucleotides units that are non-randomly distributed within coding and in non-coding regions of the genome. ChloroMitoSSRDB is a complete curated web-oriented relational database of perfect and imperfect repeats in organelle genomes. The present version of the database contains perfect and imperfect SSRs of 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes). We detected a total of 5838 chloroplast perfect SSRs, 37 297 chloroplast imperfect SSRs, 5898 mitochondrial perfect SSRs and 50 355 mitochondria! imperfect SSRs across these genomes. The repeats have been further hyperlinked to the annotated gene regions (coding or non-coding) and a link to the corresponding gene record in National Center for Biotechnology Information(vvww.ncbi.nlm.nih.gov/) to identify and understand the positional relationship of the repetitive tracts. ChloroMitoSSRDB is connected to a user-friendly web interface that provides useful information associated with the location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, etc. ChloroMitoSSRDB will serve as a repository for developing functional markers for molecular phylogenetics, estimating molecular variation across speciesThis work was supported by BIOMASFOR (Z0912003I, Italy) and EC FP7 (BIOSUPPORT, Bulgaria). M.A.F. was supported by a grant from the Spanish Ministerio de Ciencia e Inovacio´n (BFU2009- 12022).Sablok, G.; Mudunuri, SB.; Patnana, S.; Popova, M.; Fares Riaño, MA.; La Porta, N. (2013). ChloroMitoSSRDB: open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics. DNA Research. 20(2):127-133. https://doi.org/10.1093/dnares/dss038S12713320

Abdominal and pelvic complications of nonoperative oncologic therapy.

Oncologic patients are treated with a combination of chemotherapy, radiation therapy, and surgery. Advances in therapeutic options have greatly improved the survival of patients with cancer. Examples of these advances are newer chemotherapeutic agents that target the cell receptors and advanced radiation therapy delivery systems. It is imperative that radiologists be aware of the variety of imaging findings seen after therapy in patients with cancer. Complications may occur with classic cytotoxic therapies (eg, 5-fluorouracil), usually at higher or prolonged doses or when administered to radiosensitive areas. Newer targeted systemic agents, such as bevacizumab and imatinib, have associated characteristic toxicities because their effects on cells do not depend on dose. Radiation may induce early and late effects in local normal tissues that may be seen at imaging. Imaging findings after chemotherapy include fatty liver, pseudocirrhosis, hepatic veno-occlusive disease, and splenic rupture. Complications of radiation therapy include large and small bowel strictures and radiation-induced hepatitis and tumors. Awareness of the various therapeutic options and knowledge of the spectrum of posttherapeutic complications allows radiologists to provide a comprehensive report that may impact patient management

Multimethod imaging, staging, and spectrum of manifestations of metastatic melanoma.

The incidence of melanoma has been steadily increasing. Imaging plays an important role in tumour assessment as metastatic melanoma can involve multiple organs. Computed tomography (CT) is currently the most widely used technique for tumour staging, surveillance and assessment of therapeutic response, but ultrasound, magnetic resonance imaging (MRI) and positron-emission tomography (PET)-CT also play important roles in the imaging of this tumour. In this article, we review the pathways of spread, staging according to the recently updated TNM classification, pathology, typical and atypical imaging features at common and uncommon sites, and treatment of metastatic melanoma

High Metabolic Dependence on Oxidative Phosphorylation Drives Sensitivity to Metformin Treatment in MLL/AF9 Acute Myeloid Leukemia

Acute myeloid leukemia is a group of metabolic heterogeneous cancers, of which the long-term overall survival is still poor, especially in elderly patients. Targeting metabolic reprogramming in leukemic cells is becoming a promising strategy. The aim of our research was to explore the relation of genetic mutations with the metabolic phenotype and potential therapeutics to target metabolic pathway dependence. We confirmed the metabolic heterogeneity in AML cell lines and found the high dependence on oxidative phosphorylation in MLL/AF9 AML cells. Metformin could significantly repress the proliferation of MLL/AF9 AML cells by inhibiting oxidative phosphorylation.Acute myeloid leukemia (AML) is a group of hematological cancers with metabolic heterogeneity. Oxidative phosphorylation (OXPHOS) has been reported to play an important role in the function of leukemic stem cells and chemotherapy-resistant cells and are associated with inferior prognosis in AML patients. However, the relationship between metabolic phenotype and genetic mutations are yet to be explored. In the present study, we demonstrate that AML cell lines have high metabolic heterogeneity, and AML cells with MLL/AF9 have upregulated mitochondrial activity and mainly depend on OXPHOS for energy production. Furthermore, we show that metformin repressed the proliferation of MLL/AF9 AML cells by inhibiting mitochondrial respiration. Together, this study demonstrates that AML cells with an MLL/AF9 genotype have a high dependency on OXPHOS and could be therapeutically targeted by metformin