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Journal of Bacteriology Oct 2016Microbial adaptation is conspicuous in essentially every environment, but the mechanisms of adaptive evolution are poorly understood. Studying evolution in the... (Review)
Review
Microbial adaptation is conspicuous in essentially every environment, but the mechanisms of adaptive evolution are poorly understood. Studying evolution in the laboratory under controlled conditions can be a tractable approach, particularly when new, discernible phenotypes evolve rapidly. This is especially the case in the spatially structured environments of biofilms, which promote the occurrence and stability of new, heritable phenotypes. Further, diversity in biofilms can give rise to nascent social interactions among coexisting mutants and enable the study of the emerging field of sociomicrobiology. Here, we review findings from laboratory evolution experiments with either Pseudomonas fluorescens or Burkholderia cenocepacia in spatially structured environments that promote biofilm formation. In both systems, ecotypes with overlapping niches evolve and produce competitive or facilitative interactions that lead to novel community attributes, demonstrating the parallelism of adaptive processes captured in the lab.
Topics: Biofilms; Burkholderia cenocepacia; Directed Molecular Evolution; Pseudomonas fluorescens
PubMed: 27044625
DOI: 10.1128/JB.01018-15 -
Anais Brasileiros de Dermatologia 2022Little is known about the ultrastructure of pili annulati.
BACKGROUND
Little is known about the ultrastructure of pili annulati.
OBJECTIVES
To examine with transmission electron microscopy affected hairs of a family, whose diagnosis had been confirmed in five individuals with scanning electron microscopy, which showed surface undulations with "curtain-like" folding of the hair cuticula and to compare the findings with normal control.
METHODS
Hairs of two affected patients and one control were embedded in resin and cut lengthwise to produce ultra-thin sections.
RESULTS
The normal hair showed a parallel arrangement of dark lines associated with less electron-dense wide bands. Small cavities could be observed, mostly in the dark lines, affected hairs had a large number of cavities, associated or not with the insertion of melanosomes and loss of parallelism of the dark lines. Higher magnification showed a significant loss of this parallelism, resembling "wood grooves". Widened dark lines were observed in some areas.
STUDY LIMITATIONS
Only a few hairs were examined.
CONCLUSIONS
The present results suggest that the microcanaliculi of the hair surface, easily found with scanning electron microscopy, may be secondary not only to the cavities seen in the sections but also to the disorder of proteins that form this region, demonstrated by the changes of the cortex dark lines.
Topics: Hair; Hair Diseases; Hair Follicle; Humans; Microscopy, Electron, Scanning; Microscopy, Electron, Transmission
PubMed: 36100477
DOI: 10.1016/j.abd.2021.10.011 -
Journal of Evolutionary Biology Jan 2021Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide... (Comparative Study)
Comparative Study
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxF > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
Topics: Animals; Biological Evolution; Bivalvia; Gene Flow; Genetic Introgression; Introduced Species; RNA, Long Noncoding; Transcriptome
PubMed: 33251632
DOI: 10.1111/jeb.13746 -
Biology Letters Feb 2022Parallelism between evolutionary trajectories in a trait space is often seen as evidence for repeatability of phenotypic evolution, and angles between trajectories play... (Review)
Review
Parallelism between evolutionary trajectories in a trait space is often seen as evidence for repeatability of phenotypic evolution, and angles between trajectories play a pivotal role in the analysis of parallelism. However, properties of angles in multidimensional spaces have not been widely appreciated by biologists. To remedy this situation, this study provides a brief overview on geometric and statistical aspects of angles in multidimensional spaces. Under the null hypothesis that trajectory vectors have no preferred directions (i.e. uniform distribution on hypersphere), the angle between two independent vectors is concentrated around the right angle, with a more pronounced peak in a higher-dimensional space. This probability distribution is closely related to - and beta distributions, which can be used for testing the null hypothesis concerning a pair of trajectories. A recently proposed method with eigenanalysis of a vector correlation matrix can be connected to the test of no correlation or concentration of multiple vectors, for which simple test procedures are available in the statistical literature. Concentration of vectors can also be examined by tools of directional statistics such as the Rayleigh test. These frameworks provide biologists with baselines to make statistically justified inferences for (non)parallel evolution.
Topics: Biological Evolution; Phenotype
PubMed: 35168376
DOI: 10.1098/rsbl.2021.0638 -
GigaScience May 2020Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned,...
BACKGROUND
Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data.
RESULTS
To overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version.
CONCLUSIONS
parSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF.
Topics: Algorithms; Computational Biology; Databases, Genetic; Genetic Predisposition to Disease; Genetic Variation; Genome-Wide Association Study; Genomics; Humans; Machine Learning; Reproducibility of Results; Software
PubMed: 32444882
DOI: 10.1093/gigascience/giaa052 -
BMC Psychiatry Jun 202322q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal interstitial-deletion disorder, occurring in approximately 1 in 2000 to 6000 live births. Affected...
BACKGROUND
22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal interstitial-deletion disorder, occurring in approximately 1 in 2000 to 6000 live births. Affected individuals exhibit variable clinical phenotypes that can include velopharyngeal anomalies, heart defects, T-cell-related immune deficits, dysmorphic facial features, neurodevelopmental disorders, including autism, early cognitive decline, schizophrenia, and other psychiatric disorders. Developing comprehensive treatments for 22q11.2DS requires an understanding of both the psychophysiological and neural mechanisms driving clinical outcomes. Our project probes the core psychophysiological abnormalities of 22q11.2DS in parallel with molecular studies of stem cell-derived neurons to unravel the basic mechanisms and pathophysiology of 22q11.2-related psychiatric disorders, with a primary focus on psychotic disorders. Our study is guided by the central hypothesis that abnormal neural processing associates with psychophysiological processing and underlies clinical diagnosis and symptomatology. Here, we present the scientific background and justification for our study, sharing details of our study design and human data collection protocol.
METHODS
Our study is recruiting individuals with 22q11.2DS and healthy comparison subjects between the ages of 16 and 60 years. We are employing an extensive psychophysiological assessment battery (e.g., EEG, evoked potential measures, and acoustic startle) to assess fundamental sensory detection, attention, and reactivity. To complement these unbiased measures of cognitive processing, we will develop stem-cell derived neurons and examine neuronal phenotypes relevant to neurotransmission. Clinical characterization of our 22q11.2DS and control participants relies on diagnostic and research domain criteria assessments, including standard Axis-I diagnostic and neurocognitive measures, following from the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) and the North American Prodrome Longitudinal Study (NAPLS) batteries. We are also collecting measures of autism spectrum (ASD) and attention deficit/hyperactivity disorder (ADHD)-related symptoms.
DISCUSSION
Studying 22q11.2DS in adolescence and adulthood via deep phenotyping across multiple clinical and biological domains may significantly increase our knowledge of its core disease processes. Our manuscript describes our ongoing study's protocol in detail. These paradigms could be adapted by clinical researchers studying 22q11.2DS, other CNV/single gene disorders, or idiopathic psychiatric syndromes, as well as by basic researchers who plan to incorporate biobehavioral outcome measures into their studies of 22q11.2DS.
Topics: Adolescent; Adult; Humans; Child; Young Adult; Middle Aged; DiGeorge Syndrome; Longitudinal Studies; Psychotic Disorders; Autistic Disorder; Child Development Disorders, Pervasive; Chromosome Deletion
PubMed: 37312091
DOI: 10.1186/s12888-023-04888-5 -
Journal of Evolutionary Biology Nov 2022Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in... (Review)
Review
Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyse the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive - but not significant - trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary 'replicates' can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.
Topics: Animals; Poecilia; Biological Evolution; Predatory Behavior; Adaptation, Physiological; Selection, Genetic
PubMed: 36098479
DOI: 10.1111/jeb.14086 -
International Journal of Implant... Feb 2019The outcome of the evaluation of impression techniques accuracy may improve the selection criteria for an ideal technique. The aim was to evaluate the accuracy of the...
BACKGROUND
The outcome of the evaluation of impression techniques accuracy may improve the selection criteria for an ideal technique. The aim was to evaluate the accuracy of the open and closed tray techniques for implant impressions, in a partially edentulous maxilla, replaced with a three-unit fixed partial denture, as well as to assess the effect of implants parallelism on accuracy.
MATERIAL AND METHODS
This is an experimental in vitro study to evaluate impressions accuracy of a simulated area restored with an implant retained FPD, using the open and closed tray implant impression techniques. The effect of implant position angulation, parallelism, and implant systems (Straumann, SIC Invent, Osstem) was also evaluated. Three custom-made acrylic resin test models were prepared with two parallel and two non-parallel implants, on either side of a maxillary arch. One hundred and ninety-two impressions were made using monophase VPS impression material. Their master casts were obtained and evaluated for the horizontal and vertical discrepancy. The casts were scanned using a model scanner. The distances between the two reference points were measured.
RESULTS
The Straumann and SIC Invent implants showed no statistically significant differences (Mann-Whitney U test), regarding accuracy for both the open and closed tray impression techniques (P = 0.667 and P = 0.472). There were no significant differences for the parallel and non-parallel implants (P = 0.323 and P = 0.814), respectively, while the Osstem system showed statistically significant differences for both the open and closed tray impression techniques (P = 0.035) and between the parallel and non-parallel implants (P = 0.045). For the vertical discrepancies, significant differences were detected (chi-square test) between the open and closed tray impression techniques (P = 0.037).
CONCLUSIONS
Within the limitations of this study, there were generally no significant differences between open and closed, although better results were obtained for the open tray techniques. On the use of the non-parallel implants, the open tray technique provided a better result than the closed tray technique.
PubMed: 30778790
DOI: 10.1186/s40729-019-0159-5 -
Human Molecular Genetics Oct 2022Linkage disequilibrium and the incomplete regulatory annotation of the noncoding genome complicates the identification of functional noncoding genetic variants and their...
Linkage disequilibrium and the incomplete regulatory annotation of the noncoding genome complicates the identification of functional noncoding genetic variants and their causal association with disease. Current computational methods for variant prioritization have limited predictive value, necessitating the application of highly parallelized experimental assays to efficiently identify functional noncoding variation. Here, we summarize two distinct approaches, massively parallel reporter assays and CRISPR-based pooled screens and describe their flexible implementation to characterize human noncoding genetic variation at unprecedented scale. Each approach provides unique advantages and limitations, highlighting the importance of multimodal methodological integration. These multiplexed assays of variant effects are undoubtedly poised to play a key role in the experimental characterization of noncoding genetic risk, informing our understanding of the underlying mechanisms of disease-associated loci and the development of more robust predictive classification algorithms.
Topics: Humans; Genome; Genomics; Linkage Disequilibrium; Algorithms; Genome-Wide Association Study
PubMed: 36057282
DOI: 10.1093/hmg/ddac194 -
Molecular Systems Biology Sep 2022Current strategies to improve the throughput of continuous directed evolution technologies often involve complex mechanical fluid-controlling system or robotic...
Current strategies to improve the throughput of continuous directed evolution technologies often involve complex mechanical fluid-controlling system or robotic platforms, which limits their popularization and application in general laboratories. Inspired by our previous study on bacterial range expansion, in this study, we report a system termed SPACE for rapid and extensively parallelizable evolution of biomolecules by introducing spatial dimensions into the landmark phage-assisted continuous evolution system. Specifically, M13 phages and chemotactic Escherichia coli cells were closely inoculated onto a semisolid agar. The phages came into contact with the expanding front of the bacterial range, and then comigrated with the bacteria. This system leverages competition over space, wherein evolutionary progress is closely associated with the production of spatial patterns, allowing the emergence of improved or new protein functions. In a prototypical problem, SPACE remarkably simplified the process and evolved the promoter recognition of T7 RNA polymerase (RNAP) to a library of 96 random sequences in parallel. These results establish SPACE as a simple, easy to implement, and massively parallelizable platform for continuous directed evolution in general laboratories.
Topics: Agar; Bacteria; Bacteriophages; Escherichia coli; Promoter Regions, Genetic
PubMed: 36129229
DOI: 10.15252/msb.202210934