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Evolutionary biology

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https://www.readbyqxmd.com/read/29222753/integration-of-comparative-genomics-with-genome-scale-metabolic-modeling-to-investigate-strain-specific-phenotypical-differences
#1
Jonathan Monk, Emanuele Bosi
Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222102/tracking-the-taxonomy-of-the-genus-bifidobacterium-based-on-a-phylogenomic-approach
#2
Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta, Francesca Turroni, Alice Viappiani, Douwe van Sinderen, Marco Ventura
For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species with reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy...
December 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29221677/epigenetic-regulation-of-biological-rhythms-an-evolutionary-ancient-molecular-timer
#3
REVIEW
Tyler J Stevenson
Biological rhythms are pervasive in nature, yet our understanding of the molecular mechanisms that govern timing is far from complete. The rapidly emerging research focus on epigenetic plasticity has revealed a system that is highly dynamic and reversible. In this Opinion, I propose an epigenetic clock model that outlines how molecular modifications, such as DNA methylation, are integral components for timing endogenous biological rhythms. The hypothesis proposed is that an epigenetic clock serves to maintain the period of molecular rhythms via control over the phase of gene transcription and this timing mechanism resides in all cells, from unicellular to complex organisms...
December 5, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29220506/a-molecular-portrait-of-de-novo-genes-in-yeasts
#4
Nikolaos N Vakirlis, Alex S Hebert, Dana A Opulente, Guillaume Achaz, Chris Todd Hittinger, Gilles Fischer, Joshua J Coon, Ingrid Lafontaine
New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29220109/population-transcriptomics-in-daphnia-the-role-of-thermal-selection
#5
Maike Herrmann, Suda Parimala Ravindran, Klaus Schwenk, Mathilde Cordellier
The complex interplay of forces influencing genetic divergence among populations complicates the discovery of the genetic basis underlying local adaptation. Here, we utilized for the first time a combined reverse ecology and population transcriptomic approach to assess the contribution of thermal selection to population differentiation, thereby considering transcriptome-wide variation in both gene expression profiles and DNA sequences. We compared transcriptomes among four Daphnia galeata populations and identified transcripts potentially responding to local thermal selection based on an extensive literature search for candidate genes possibly under thermal selection in arthropods...
December 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29219108/origin-history-and-meanings-of-the-word-transmission
#6
Joaquín Villalba, Fernando A Navarro, Francisco Cortés
The origin of the words transmit and transmission and their derivatives can be traced to the Latin transmittere, in turn formed by prefixing the preposition trans ("across or beyond") to the verb mittere ("to let go or to send"). From the times of Ancient Rome in the 3rd century b.c.e., the Latin word transmissio has been "transmitted" (through Romance languages such as French, Italian, Spanish, and Portuguese) to all the major languages of culture, English among them. And through English, the international language of biomedical science in the 21st century, the term transmission is increasingly present today in some of the most dynamic disciplines of modern natural science, including genomics, molecular microbiology, hospital epidemiology, molecular genetics, biotechnology, evolutionary biology, and systems biology...
December 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/29218763/single-cell-mass-spectrometry-approaches-to-explore-cellular-heterogeneity
#7
Linwen Zhang, Akos Vertes
Compositional diversity is a fundamental property in cell populations that is responsible for evolutionary adaptation and resilience. Single-cell analysis promises new insights into this cellular heterogeneity and the corresponding subpopulations on the genomic, transcriptomic, proteomic, and metabolomic levels. Mass spectrometry (MS) is a label-free technique that enables the multiplexed analysis of proteins, peptides, lipids, and metabolites in individual cells. The abundances of these molecular classes are correlated with the physiological states and environmental responses of the cells...
December 7, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29218634/walking-the-seven-lines-binuclear-copper-a-in-cytochrome-c-oxidase-and-nitrous-oxide-reductase
#8
REVIEW
Peter M H Kroneck
The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N2O to N2 in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O2 to H2O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu1...
December 7, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29218300/the-dual-role-of-cellular-senescence-in-developing-tumors-and-their-response-to-cancer-therapy
#9
REVIEW
Markus Schosserer, Johannes Grillari, Michael Breitenbach
Cellular senescence describes an irreversible growth arrest characterized by distinct morphology, gene expression pattern, and secretory phenotype. The final or intermediate stages of senescence can be reached by different genetic mechanisms and in answer to different external and internal stresses. It has been maintained in the literature but never proven by clearcut experiments that the induction of senescence serves the evolutionary purpose of protecting the individual from development and growth of cancers...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29218053/marker-development-for-phylogenomics-the-case-of-orobanchaceae-a-plant-family-with-contrasting-nutritional-modes
#10
Xi Li, Baohai Hao, Da Pan, Gerald M Schneeweiss
Phylogenomic approaches, employing next-generation sequencing (NGS) techniques, have revolutionized systematic and evolutionary biology. Target enrichment is an efficient and cost-effective method in phylogenomics and is becoming increasingly popular. Depending on availability and quality of reference data as well as on biological features of the study system, (semi-)automated identification of suitable markers will require specific bioinformatic pipelines. Here, we established a highly flexible bioinformatic pipeline, BaitsFinder, to identify putative orthologous single copy genes (SCGs) and to construct bait sequences in a single workflow...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29217838/an-evolutionary-perspective-on-field-cancerization
#11
REVIEW
Kit Curtius, Nicholas A Wright, Trevor A Graham
Tumorigenesis begins long before the growth of a clinically detectable lesion and, indeed, even before any of the usual morphological correlates of pre-malignancy are recognizable. Field cancerization, which is the replacement of the normal cell population by a cancer-primed cell population that may show no morphological change, is now recognized to underlie the development of many types of cancer, including the common carcinomas of the lung, colon, skin, prostate and bladder. Field cancerization is the consequence of the evolution of somatic cells in the body that results in cells that carry some but not all phenotypes required for malignancy...
December 8, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29217592/loss-of-lofsep-transcription-factor-function-converts-spikelet-to-leaf-like-structures-in-rice
#12
Di Wu, Wanqi Liang, Wanwan Zhu, Mingjiao Chen, Cristina Ferrandiz, Rachel A Burton, Ludovico Dreni, Dabing Zhang
SEPALLATA (SEP)-like genes, which encode a subfamily of MADS-box transcription factors, are essential for specifying floral organ and meristem identity in angiosperms. Rice (Oryza sativa L.) has five SEP-like genes with partial redundancy and overlapping expression domains, yet their functions and evolutionary conservation are only partially known. Here, we describe the biological role of one of the SEP genes of rice, OsMADS5, in redundantly controlling spikelet morphogenesis. OsMADS5 belongs to the conserved LOFSEP subgroup along with OsMADS1 and OsMADS34...
December 7, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29216829/the-role-of-isolation-on-contrasting-phylogeographic-patterns-in-two-cave-crustaceans
#13
Jorge L Pérez-Moreno, Gergely Balázs, Blake Wilkins, Gábor Herczeg, Heather D Bracken-Grissom
BACKGROUND: The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution...
December 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29216822/bayesian-estimation-of-scaled-mutation-rate-under-the-coalescent-a-sequential-monte-carlo-approach
#14
Oyetunji E Ogundijo, Xiaodong Wang
BACKGROUND: Samples of molecular sequence data of a locus obtained from random individuals in a population are often related by an unknown genealogy. More importantly, population genetics parameters, for instance, the scaled population mutation rate Θ=4N e μ for diploids or Θ=2N e μ for haploids (where N e is the effective population size and μ is the mutation rate per site per generation), which explains some of the evolutionary history and past qualities of the population that the samples are obtained from, is of significant interest...
December 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29216398/atted-ii-in-2018-a-plant-coexpression-database-based-on-investigation-of-statistical-property-of-the-mutual-rank-index
#15
Takeshi Obayashi, Yuichi Aoki, Shu Tadaka, Yuki Kagaya, Kengo Kinoshita
ATTED-II (http://atted.jp) is a coexpression database for plant species to aid in the discovery of unknown gene relationships within a species. As an advanced coexpression analysis method, multi-species comparisons have the potential to detect alterations in gene relationships within an evolutionary context. However, determining the validity of comparative coexpression studies is difficult without quantitative assessments of the quality of coexpression data. ATTED-II (version 9) provides 16 coexpression platforms for nine plant species, including seven species supported by both microarray- and RNA sequencing (RNAseq)-based coexpression data...
December 4, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29215911/weird-animals-sex-and-genome-evolution
#16
Jennifer A Marshall Graves
Making my career in Australia exposed me to the tyranny of distance, but it gave me opportunities to study our unique native fauna. Distantly related animal species present genetic variation that we can use to explore the most fundamental biological structures and processes. I have compared chromosomes and genomes of kangaroos and platypus, tiger snakes and emus, devils (Tasmanian) and dragons (lizards). I particularly love the challenges posed by sex chromosomes, which, apart from determining sex, provide stunning examples of epigenetic control and break all the evolutionary rules that we currently understand...
December 7, 2017: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29213489/in-search-of-the-moral-psychological-and-neuroevolutionary-basis-of-political-partisanship
#17
REVIEW
Vitor Geraldi Haase, Isabella Starling-Alves
In many countries, a radical political divide brings several socially relevant decisions to a standstill. Could cognitive, affective and social (CAS) neuroscience help better understand these questions? The present article reviews the moral-psychological and neuroevolutionary basis of the political partisanship divide. A non-systematic literature review and a conceptual analysis were conducted. Three main points are identified and discussed: 1) Political partisan behavior rests upon deep moral emotions. It is automatically processed and impervious to contradiction...
January 2017: Dementia & Neuropsychologia
https://www.readbyqxmd.com/read/29212893/comparative-physiology-of-nociception-and-pain
#18
REVIEW
Lynne U Sneddon
The study of diverse animal groups allows us to discern the evolution of the neurobiology of nociception. Nociception functions as an important alarm system alerting the individual to potential and actual tissue damage. All animals possess nociceptors, and, in some animal groups, it has been demonstrated that there are consistent physiological mechanisms underpinning the nociceptive system. This review considers the comparative biology of nociception and pain from an evolutionary perspective.
January 1, 2018: Physiology
https://www.readbyqxmd.com/read/29212725/the-functional-syndrome-linking-individual-trait-variability-to-ecosystem-functioning
#19
Allan Raffard, Antoine Lecerf, Julien Cote, Mathieu Buoro, Remy Lassus, Julien Cucherousset
Phenotypic variability is increasingly assessed through functional response and effect traits, which provide a mechanistic framework for investigating how an organism responds to varying ecological factors and how these responses affect ecosystem functioning. Covariation between response and effect traits has been poorly examined at the intraspecific level, thus hampering progress in understanding how phenotypic variability alters the role of organisms in ecosystems. Using a multi-trait approach and a nine-month longitudinal monitoring of individual red-swamp crayfish (Procambarus clarkii), we demonstrated that most of the measured response and effect traits were partially stable during the ontogeny of individuals...
December 6, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29212717/adaptation-in-response-to-environmental-unpredictability
#20
Lluis Franch-Gras, Eduardo M García-Roger, Manuel Serra, María José Carmona
Understanding how organisms adaptively respond to environmental fluctuations is a fundamental question in evolutionary biology. The Mediterranean region typically exhibits levels of environmental unpredictability that vary greatly in habitats over small geographical scales. In cyclically parthenogenetic rotifers, clonal proliferation occurs along with occasional bouts of sex. These bouts contribute to the production of diapausing eggs, which allows survival between growing seasons. Here, we studied two diapause-related traits in rotifers using clones from nine Brachionus plicatilis natural populations that vary in the degree of environmental unpredictability...
December 6, 2017: Proceedings. Biological Sciences
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