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https://www.readbyqxmd.com/read/28340380/the-origin-and-evolution-of-the-term-clone
#1
David P Steensma
In biology, the term "clone" is most widely used to designate genetically identical cells or organisms that are asexually descended from a common progenitor. The concept of clonality in hematology-oncology has received much attention in recent years, as the advent of next-generation sequencing platforms has provided new tools for detection of clonal populations in patients, and experiments on primary cells have provided fascinating new insights into the clonal architecture of human malignancies. The term "clone" is used more loosely by the general public to mean any close or identical copy...
March 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28340323/a-key-to-the-backdoor-into-the-castle-the-clinical-ramifications-of-immunoediting-driven-by-antigenic-competition
#2
M G Hanna, Jason David Howard
Over the last decade the field of cancer biology has gained considerable data on genomic heterogeneity. This situation creates challenges and possibly opportunities for cancer treatment. The evolution of the tumor at all stages also requires the growing malignancy to confront and avoid the immune system. What we describe here is the interaction of two immune phenomena that work together to change the characteristics of the tumor, i.e., antigenic competition and immune editing. These two systems are mutually functional and their interaction is capable of altering the characteristics of the tumor for protection and survival in an immune competent host as well as restricting the diversity of the tumor clones...
March 24, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28335411/how-the-cobra-got-its-flesh-eating-venom-cytotoxicity-as-a-defensive-innovation-and-its-co-evolution-with-hooding-aposematic-marking-and-spitting
#3
Nadya Panagides, Timothy N W Jackson, Maria P Ikonomopoulou, Kevin Arbuckle, Rudolf Pretzler, Daryl C Yang, Syed A Ali, Ivan Koludarov, James Dobson, Brittany Sanker, Angelique Asselin, Renan C Santana, Iwan Hendrikx, Harold van der Ploeg, Jeremie Tai-A-Pin, Romilly van den Bergh, Harald M I Kerkkamp, Freek J Vonk, Arno Naude, Morné A Strydom, Louis Jacobsz, Nathan Dunstan, Marc Jaeger, Wayne C Hodgson, John Miles, Bryan G Fry
The cytotoxicity of the venom of 25 species of Old World elapid snake was tested and compared with the morphological and behavioural adaptations of hooding and spitting. We determined that, contrary to previous assumptions, the venoms of spitting species are not consistently more cytotoxic than those of closely related non-spitting species. While this correlation between spitting and non-spitting was found among African cobras, it was not present among Asian cobras. On the other hand, a consistent positive correlation was observed between cytotoxicity and utilisation of the defensive hooding display that cobras are famous for...
March 13, 2017: Toxins
https://www.readbyqxmd.com/read/28334892/inhibition-of-homologous-phosphorolytic-ribonucleases-by-citrate-may-represent-an-evolutionarily-conserved-communicative-link-between-rna-degradation-and-central-metabolism
#4
Carlanne M Stone, Louise E Butt, Joshua C Bufton, Daniel C Lourenco, Darren M Gowers, Andrew R Pickford, Paul A Cox, Helen A Vincent, Anastasia J Callaghan
Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli...
March 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334658/extraction-of-the-3d-local-orientation-of-myocytes-in-human-cardiac-tissue-using-x-ray-phase-contrast-micro-tomography-and-multi-scale-analysis
#5
François Varray, Iulia Mirea, Max Langer, Françoise Peyrin, Laurent Fanton, Isabelle E Magnin
This paper presents a methodology to access the 3D local myocyte arrangements in fresh human post-mortem heart samples. We investigated the cardiac micro-structure at a high and isotropic resolution of 3.5 µm in three dimensions using X-ray phase micro-tomography at the European Synchrotron Radiation Facility. We then processed the reconstructed volumes to extract the 3D local orientation of the myocytes using a multi-scale approach with no segmentation. We created a simplified 3D model of tissue sample made of simulated myocytes with known size and orientations, to evaluate our orientation extraction method...
February 20, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28333638/a-comparative-study-for-identifying-the-chromosome-wide-spatial-clusters-from-high-throughput-chromatin-conformation-capture-data
#6
Xiangtao Li, Ka-Chun Wong
In the past years, the high-throughput sequencing technologies have enabled massive insights into genomic annotations. In contrast, the full-scale three-dimensional arrangements of genomic regions are relatively unknown. Thanks to the recent breakthroughs in High-throughput Chromosome Conformation Capture (Hi-C) techniques, non-negative matrix factorization (NMF) has been adopted to identify local spatial clusters of genomic regions from Hi-C data. However, such non-negative matrix factorization entails a high-dimensional non-convex objective function to be optimized with non-negative constraints...
March 20, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28333345/detection-of-pathways-affected-by-positive-selection-in-primate-lineages-ancestral-to-humans
#7
J T Daub, S Moretti, I I Davydov, L Excoffier, M Robinson-Rechavi
Gene set enrichment approaches have been increasingly successful in finding signals of recent polygenic selection in the human genome. In this study, we aim at detecting biological pathways affected by positive selection in more ancient human evolutionary history. Focusing on four branches of the primate tree that lead to modern humans, we tested all available protein coding gene trees of the Primates clade for signals of adaptation in these branches, using the likelihood-based branch site test of positive selection...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333343/centromere-destiny-in-dicentric-chromosomes-new-insights-from-the-evolution-of-human-chromosome-2-ancestral-centromeric-region
#8
Giorgia Chiatante, Giuliana Giannuzzi, Francesco Maria Calabrese, Evan E Eichler, Mario Ventura
Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells...
March 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28332348/molecular-epidemiology-of-hiv
#9
REVIEW
Bum Sik Chin
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea...
March 22, 2017: Infection & Chemotherapy
https://www.readbyqxmd.com/read/28332253/sex-and-ancestry-determine-the-free-running-circadian-period
#10
Charmane I Eastman, Victoria A Tomaka, Stephanie J Crowley
The endogenous, free-running circadian period (τ) determines the phase relationship that an organism assumes when entrained to the 24-h day. We found a shorter circadian period in African Americans compared to non-Hispanic European Americans (24.07 versus 24.33 h). We speculate that a short circadian period, closer to 24 h, was advantageous to humans living around the equator, but when humans migrated North out of Africa, where the photoperiod changes with seasons, natural selection favoured people with longer circadian periods...
March 23, 2017: Journal of Sleep Research
https://www.readbyqxmd.com/read/28331993/molecular-characterization-and-phylogenetic-analysis-of-human-influenza-a-viruses-isolated-in-iran-during-the-2014-2015-season
#11
Elham Moasser, Farida Behzadian, Afagh Moattari, Fatemeh Fotouhi, Amir Rahimi, Hassan Zaraket, Seyed Younes Hosseini
Influenza A viruses are an important cause of severe infectious diseases in humans and are characterized by their fast evolution rate. Global monitoring of these viruses is critical to detect newly emerging variants during annual epidemics. Here, we sought to genetically characterize influenza A/H1N1pdm09 and A/H3N2 viruses collected in Iran during the 2014-2015 influenza season. A total of 200 nasopharyngeal swabs were collected from patients with influenza-like illnesses. Swabs were screened for influenza A and B using real-time PCR...
March 22, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28331548/discovering-feature-relevancy-and-dependency-by-kernel-guided-probabilistic-model-building-evolution
#12
Nestor Rodriguez, Sergio Rojas-Galeano
BACKGROUND: Discovering relevant features (biomarkers) that discriminate etiologies of a disease is useful to provide biomedical researchers with candidate targets for further laboratory experimentation while saving costs; dependencies among biomarkers may suggest additional valuable information, for example, to characterize complex epistatic relationships from genetic data. The use of classifiers to guide the search for biomarkers (the so-called wrapper approach) has been widely studied...
2017: BioData Mining
https://www.readbyqxmd.com/read/28331089/diversity-distribution-and-evolution-of-tomato-viruses-in-china-uncovered-by-small-rna-sequencing
#13
Chenxi Xu, Xuepeng Sun, Angela Taylor, Chen Jiao, Yimin Xu, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Guanghui Pan, Quanxi Wang, Zhangjun Fei, Quanhua Wang
Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with coldspots and hotspots. Most samples were co-infected by multiple viruses and the majority of identified viruses are positive-sense single-stranded RNA viruses...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28331087/feline-immunodeficiency-virus-evolutionarily-acquires-two-proteins-vif-and-protease-capable-of-antagonizing-feline-apobec3
#14
Rokusuke Yoshikawa, Junko S Takeuchi, Eri Yamada, Yusuke Nakano, Naoko Misawa, Yuichi Kimura, Fengrong Ren, Takayuki Miyazawa, Yoshio Koyanagi, Kei Sato
The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated anti-viral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28330987/architecture-and-mechanism-of-the-central-gear-in-an-ancient-molecular-timer
#15
REVIEW
Martin Egli
Molecular clocks are the product of natural selection in organisms from bacteria to human and their appearance early in evolution such as in the prokaryotic cyanobacterium Synechococcus elongatus suggests that these timers served a crucial role in genetic fitness. Thus, a clock allows cyanobacteria relying on photosynthesis and nitrogen fixation to temporally space the two processes and avoid exposure of nitrogenase carrying out fixation to high levels of oxygen produced during photosynthesis. Fascinating properties of molecular clocks are the long time constant, their precision and temperature compensation...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330888/defining-a-core-genome-multilocus-sequence-typing-scheme-for-the-global-epidemiology-of-vibrio-parahaemolyticus
#16
Narjol Gonzalez-Escalona, Keith A Jolley, Elizabeth Reed, Jaime Martinez-Urtaza
Vibrio parahaemolyticus is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 2008 and a large number of clones have been identified causing severe outbreaks worldwide (ST3), recurrent outbreaks in certain regions (e.g., ST36) or spreading to other regions where they are non-endemic (e.g...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330742/fellow-travellers-working-memory-and-mental-time-travel-in-rodents
#17
REVIEW
Ekrem Dere, Dorothea Dere, Maria Angelica de Souza Silva, Joseph P Huston, Armin Zlomuzica
The impairment of mental time travel is a severe cognitive symptom in patients with brain lesions and a number of neuropsychiatric disorders. Whether animals are also able to mentally travel in time both forward and backward is still a matter of debate. In this regard, we have proposed a continuum of mental time travel abilities across different animal species, with humans being the species with the ability to perform most sophisticated forms of mental time travel. In this review and perspective article, we delineate a novel approach to understand the evolution, characteristics and function of human and animal mental time travel...
March 18, 2017: Behavioural Brain Research
https://www.readbyqxmd.com/read/28327131/transcriptome-analysis-of-pancreatic-cells-across-distant-species-highlights-novel-important-regulator-genes
#18
Estefania Tarifeño-Saldivia, Arnaud Lavergne, Alice Bernard, Keerthana Padamata, David Bergemann, Marianne L Voz, Isabelle Manfroid, Bernard Peers
BACKGROUND: Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28326016/early-origin-and-evolution-of-the-angelman-syndrome-ubiquitin-ligase-gene-ube3a
#19
REVIEW
Masaaki Sato
The human Ube3a gene encodes an E3 ubiquitin ligase and exhibits brain-specific genomic imprinting. Genetic abnormalities that affect the maternal copy of this gene cause the neurodevelopmental disorder Angelman syndrome (AS), which is characterized by severe mental retardation, speech impairment, seizure, ataxia and some unique behavioral phenotypes. In this review article, I highlight the evolution of the Ube3a gene and its imprinting to provide evolutionary insights into AS. Recent comparative genomic studies have revealed that Ube3a is most phylogenetically similar to HECTD2 among the human HECT (homologous to the E6AP carboxyl terminus) family of E3 ubiquitin ligases, and its distant evolutionary origin can be traced to common ancestors of fungi and animals...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28325903/whole-genome-analysis-of-human-papillomavirus-types-16-18-and-58-isolated-from-cervical-precancer-and-cancer-samples-in-chinese-women
#20
Ying Liu, Yaqi Pan, Weijiao Gao, Yang Ke, Zheming Lu
Human papillomavirus (HPV) types 16, 18 and 58 are ranked the top three high-risk HPV types for cervical intraepithelial neoplasia (CIN) and invasive carcinoma. We aimed to evaluate the diversity of HPV16, HPV18, and HPV58 genetic variants by HPV capture technology combined with next generation sequencing. 295, 73, and 148 variations were observed in 51 HPV16, 7 HPV18, and 11 HPV58 genomes, respectively. HPV16 isolates were predominantly of the A variant lineage, and sublineage A4 (Asian) was the most common...
March 21, 2017: Scientific Reports
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