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Neutral evolution

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https://www.readbyqxmd.com/read/28732395/microalgae-bacteria-models-evolution-from-microalgae-steady-state-to-integrated-microalgae-bacteria-wastewater-treatment-models-a-comparative-review
#1
REVIEW
Alessandro Solimeno, Joan García
The search for environmentally neutral alternative fuels had revived the interest for microalgae-bacteria wastewater treatment systems. The potential achieving of bioproducts from microalgae biomass has also greatly contributed. The reactions that occur in these systems are complex, and the degree of scientific knowledge is still scarce compared to that of conventional bacteria wastewater treatments. Mathematical models offer a great opportunity to study the simultaneous effect of the multiple factors affecting microalgae and bacteria, thus allowing for the prediction of final biomass production, and contributing to the system design optimization in terms of operation and control...
July 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28731794/a-neutral-model-for-the-evolution-of-diet-breadth
#2
Matthew L Forister, Stephen H Jenkins
Variation in diet breadth among organisms is a pervasive feature of the natural world that has resisted general explanation. In particular, trade-offs in the ability to use one resource at the expense of another have been expected but rarely detected. We explore a spatial model for the evolution of specialization, motivated by studies of plant-feeding insects. The model is neutral with respect to the causes and consequences of diet breadth: the number of hosts utilized is not constrained by trade-offs, and specialization or generalization does not confer a direct advantage with respect to the persistence of populations or the probability of diversification...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28731790/the-biased-evolution-of-generation-time
#3
Mélissa Verin, Salomé Bourg, Frédéric Menu, Etienne Rajon
Many life-history traits are important determinants of the generation time. For instance, semelparous species whose adults reproduce only once have shorter generation times than iteroparous species that reproduce on several occasions, assuming equal development duration. A shorter generation time ensures a higher growth rate in stable environments where resources are in excess and is therefore a positively selected feature in this situation. In a stable and limiting environment, all combinations of traits that produce the same number of viable offspring are selectively equivalent...
August 2017: American Naturalist
https://www.readbyqxmd.com/read/28727700/therapeutic-role-of-placebo-evolution-of-a-new-paradigm-in-understanding-research-and-clinical-practice
#4
Laxmaiah Manchikanti, Mark V Boswell, Alan D Kaye, Standiford Helm Ii, Joshua A Hirsch
Research into interventional techniques in managing chronic spinal pain continues to be challenging, mystifying, confusing, and biased. Insight, or lack thereof, into placebo and nocebo phenomena contributes mightily to these difficulties. Unfortunately, placebo-nocebo responses are the subject of numerous controversies and challenges from not only a research perspective, but also clinical perspective. While interventionalists consider the biggest threat to interventional pain management research is inappropriate and outdated interpretation of the data, a greater problem is the misuse of the placebo response in research, with the declaration that all and everything as a placebo effect: with a misinterpretation of the nature of the placebo the, associated conclusions can be inaccurate...
July 2017: Pain Physician
https://www.readbyqxmd.com/read/28726562/gene-therapy-for-age-related-macular-degeneration
#5
Nicholas A Moore, Peter Bracha, Rehan M Hussain, Nuria Morral, Thomas A Ciulla
In neovascular age related macular degeneration (nAMD), gene therapy to chronically express anti-vascular endothelial growth factor (VEGF) proteins could ameliorate the treatment burden of chronic intravitreal therapy and improve limited visual outcomes associated with 'real world' undertreatment. Areas covered: In this review, the authors assess the evolution of gene therapy for AMD. Adeno-associated virus (AAV) vectors can transduce retinal pigment epithelium; one such early application was a phase I trial of AAV2-delivered pigment epithelium derived factor gene in advanced nAMD...
July 20, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/28722265/control-of-redox-events-by-dye-encapsulation-applied-to-light-driven-splitting-of-hydrogen-sulfide
#6
Xu Jing, Yang Yang, Cheng He, Zhiduo Chang, Joost N H Reek, Chunying Duan
Inspired by the pocket feature of enzymes, a synthetic platform to combine photocatalytic hydrogen evolution with sulfide oxidation in a one-pot process via control over the location of electron transfer steps is reported in this paper. The redox-active coordination vessel Ni-TFT, which exhibits an octahedral pocket, encapsulates an organic dye to pre-organize for photocatalytic proton reduction via an oxidative quenching pathway using the nickel corners as catalysts, generating molecular hydrogen and the oxidized dye...
July 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28720580/detecting-ancient-positive-selection-in-humans-using-extended-lineage-sorting
#7
Séphane Peyégne, Michael James Boyle, Michael Dannemann, Kay Prüfer
Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation...
July 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28710260/big-bang-tumor-growth-and-clonal-evolution
#8
Ruping Sun, Zheng Hu, Christina Curtis
The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution...
July 14, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28710259/phylogenetic-quantification-of-intratumor-heterogeneity
#9
Thomas B K Watkins, Roland F Schwarz
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased. Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions in ways impractical with single samples alone. In this article, we discuss and show the benefits of such multisample studies...
July 14, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28709374/nanoparticles-as-efflux-pump-and-biofilm-inhibitor-to-rejuvenate-bactericidal-effect-of-conventional-antibiotics
#10
REVIEW
Divya Gupta, Ajeet Singh, Asad U Khan
The universal problem of bacterial resistance to antibiotic reflects a serious threat for physicians to control infections. Evolution in bacteria results in the development of various complex resistance mechanisms to neutralize the bactericidal effect of antibiotics, like drug amelioration, target modification, membrane permeability reduction, and drug extrusion through efflux pumps. Efflux pumps acquire a wide range of substrate specificity and also the tremendous efficacy for drug molecule extrusion outside bacterial cells...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28709354/crossing-fitness-canyons-by-a-finite-population
#11
David B Saakian, Alexander S Bratus, Chin-Kun Hu
We consider the Wright-Fisher model of the finite population evolution on a fitness landscape defined in the sequence space by a path of nearly neutral mutations. We study a specific structure of the fitness landscape: One of the intermediate mutations on the mutation path results in either a large fitness value (climbing up a fitness hill) or a low fitness value (crossing a fitness canyon), the rest of the mutations besides the last one are neutral, and the last sequence has much higher fitness than any intermediate sequence...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28696188/evolution-of-cross-neutralizing-antibodies-and-mapping-epitope-specificity-in-plasma-of-chronic-hiv-1-infected-antiretroviral-therapy-na%C3%A3-ve-children-from-india
#12
Muzamil A Makhdoomi, Lubina Khan, Sanjeev Kumar, Heena Aggarwal, Ravinder Singh, Rakesh Lodha, Mohit Singla, Bimal K Das, Sushil K Kabra, Kalpana Luthra
Delineating the factors leading to the development of broadly neutralizing antibodies (bnAbs) during natural HIV-1 infection and dissecting their epitope specificities generates useful information for vaccine design. This is the first longitudinal study to assess the plasma-neutralizing antibody response and neutralizing determinants in HIV-1-infected children from India. We enrolled 26 and followed up 20 antiretroviral therapy (ART)-naïve, asymptomatic, chronic HIV-1-infected children. Five (19.2 %) baseline and 10 (50 %) follow-up plasma samples neutralized ≥50 % of subtypes A, B and C tier 2 viruses at an ID50 titre ≥150...
July 12, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28694798/dynamic-co-evolution-and-interaction-of-avian-leukosis-virus-genetic-variants-and-host-immune-responses
#13
Xuan Dong, Fanfeng Meng, Tao Hu, Sidi Ju, Yang Li, Peng Sun, Yixin Wang, Wenqing Chen, Fushou Zhang, Hongqin Su, Sifei Li, He Cui, Junxia Chen, Shuzhen Xu, Lichun Fang, Huaibiao Luan, Zhenjie Zhang, Shuang Chang, Jianliang Li, Lei Wang, Peng Zhao, Weifeng Shi, Zhizhong Cui
Subgroup J avian leukosis virus (ALV-J), a typical retrovirus, is characterized of existence of a cloud of diverse variants and considerable genetic diversity. Previous studies describing the evolutionary dynamics of ALV-J genetic variants mainly focused on the early infection period or few randomly selected clones. Here, we inoculated 30 specific-pathogen-free chickens with the same founder ALV-J stock of known genetic background. Six (three antibody positive and three antibody negative) chickens were selected among 15 chickens with viremia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28692195/homologous-catalysts-based-on-fe-doped-cop-nanoarray-toward-high-performance-full-water-splitting-under-benign-conditions
#14
Min Ma, Guilei Zhu, Fengli Qu, Zhiang Liu, Gu Du, Abdullah M Asiri, Yadong Yao, Xuping Sun
The design and development of earth-abundant electrocatalysts for efficient full water splitting under mild conditions are highly desired but still remain a challenging task. In this study, we describe the development of homologous Fe-doped Co-based nanoarray as complementary catalysts for high-performance and durable water splitting in near-neutral media. Fe-doped Co-phosphate-borate nanoarray on carbon cloth (Fe-Co-Pi-Bi/CC) derived from Fe-doped CoP nanoarray on CC (Fe-CoP/CC) via oxidative polarization behaves as a highly active bimetallic electrocatalyst for water oxidation with the demand of overpotential of 382 mV to afford a geometrical catalytic current density of 10 mA cm-2 in 0...
July 10, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28690799/sex-biased-oviposition-by-a-nursery-pollinator-on-a-gynodioecious-host-plant-implications-for-breeding-system-evolution-and-evolution-of-mutualism
#15
Laura A D Doubleday, Lynn S Adler
Dioecy, a breeding system where individual plants are exclusively male or female, has evolved repeatedly. Extensive theory describes when dioecy should arise from hermaphroditism, frequently through gynodioecy, where females and hermaphrodites coexist, and when gynodioecy should be stable. Both pollinators and herbivores often prefer the pollen-bearing sex, with sex-specific fitness effects that can affect breeding system evolution. Nursery pollination, where adult insects pollinate flowers but their larvae feed on plant reproductive tissues, is a model for understanding mutualism evolution but could also yield insights into plant breeding system evolution...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28690785/rates-and-relations-of-mitochondrial-genome-evolution-across-the-echinoidea-with-special-focus-on-the-superfamily-odontophora
#16
Áki Jarl Láruson
In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28690628/comparison-of-salt-tolerance-in-soja-based-on-metabolomics-of-seedling-roots
#17
Mingxia Li, Rui Guo, Yang Jiao, Xiaofei Jin, Haiyan Zhang, Lianxuan Shi
Soybean is an important economic crop that is continually threatened by abiotic stresses, especially salt stress. Wild soybean is an important germplasm resource for the breeding of cultivated soybean. The root system plays a very important role in plant salt tolerance. To explore the salt tolerance-related mechanisms among Soja, we have demonstrated the seedling roots' growth and metabolomics in wild soybean, semi-wild soybean, and cultivated soybean under two types of salt stress by using gas chromatography-mass spectrometry...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28688916/venom-proteome-of-the-yellow-lipped-sea-krait-laticauda-colubrina-from-bali-insights-into-subvenomic-diversity-venom-antigenicity-and-cross-neutralization-by-antivenom
#18
Choo Hock Tan, Kin Ying Wong, Kae Yi Tan, Nget Hong Tan
The venom proteome of Laticauda colubrina (Bali, Indonesia) was elucidated by nano-ESI-LCMS/MS of the venom reverse-phase HPLC fractions. Altogether 31 distinct forms of proteins were identified and clustered into three toxin families: three-finger toxin (3FTX, 66.12% of total venom proteins), phospholipase A2 (PLA2, 33.26%) and cysteine-rich secretory protein (CRiSP, 0.05%). The 3FTX were α-neurotoxins (five long neurotoxins, LNTX, 48.87%; two short neurotoxins, SNTX, 16.70%) and a trace amount of two cytotoxins (CTX, 0...
July 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28679760/co-operation-between-strain-specific-and-broadly-neutralizing-responses-limited-viral-escape-and-prolonged-exposure-of-the-broadly-neutralizing-epitope
#19
Colin Anthony, Talita York, Valerie Bekker, David Matten, Philippe Selhorst, Roux-Cil Ferreria, Nigel J Garrett, Salim S Abdool Karim, Lynn Morris, Natasha T Wood, Penny L Moore, Carolyn Williamson
V3-glycan targeting broadly neutralizing antibodies (bNAbs) are a focus of HIV-1 vaccine development. Understanding the viral dynamics that stimulate the development of these antibodies can provide insights for immunogen design. We used a deep sequencing approach, together with neutralization phenotyping, to investigate the rate and complexity of escape from V3-glycan directed bNAbs, compared to overlapping early strain-specific neutralizing antibody (ssNAb) responses to the V3/C3 region in donor CAP177. Escape from the ssNAb response occurred rapidly, via a N334 to N332 glycan switch, which took just 7...
July 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28676046/retention-of-functional-variation-despite-extreme-genomic-erosion-mhc-allelic-repertoires-in-the-lynx-genus
#20
Elena Marmesat, Krzysztof Schmidt, Alexander P Saveljev, Ivan V Seryodkin, José A Godoy
BACKGROUND: Demographic bottlenecks erode genetic diversity and may increase endangered species' extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species...
July 4, 2017: BMC Evolutionary Biology
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