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Journal of Evolutionary Biology Jun 2021Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the...
Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the way increasingly large amounts of molecular data are generated (e.g. with high-throughput sequencing), but also in the way these data are analysed. This includes a growing appreciation and quantitative treatment of covariation among units within the same data type (e.g. genes) or across data types (e.g. genes and phenotypes). The development and adoption of more and more integrative tools have resulted in richer and more interesting empirical work. This special issue - comprising methodological, empirical, and review papers - aims to capture a 'snapshot' of this rapidly evolving field. We discuss in particular three important themes in the study of adaptation: the genetic architecture of adaptive variation, protein-coding and regulatory changes, and parallel evolution. We highlight how more traditional key themes in the study of genetic architecture (e.g. the number of loci underlying adaptive traits and the distribution of their effects) are now being complemented by other factors (e.g. how patterns of linkage and number of loci interact to affect the ability to adapt). Similarly, apart from addressing the relative importance of protein-coding and regulatory changes, we now have the tools to look in-depth at specific types of regulatory variation to gain a clearer picture of regulatory networks. Finally, parallel evolution has always been central to the study of adaptation, but now we are often able to address the question of whether - and to what extent - parallelism at the organismal or phenotypic level is matched by parallelism at the genetic level. Perhaps most importantly, we can now determine what mechanisms are driving parallelism (or lack thereof) across levels of biological organization. All these recent methodological developments open up new directions for future studies of adaptive changes across traits, levels of biological organization, demographic contexts and time scales.
Topics: Adaptation, Biological; Biological Evolution; Genetic Variation; Genomics
PubMed: 34145685
DOI: 10.1111/jeb.13871 -
Orthopaedics & Traumatology, Surgery &... Oct 2021Since its introduction in the early 1960s, the multiple cannulated screw fixation method has been developed for use in femoral neck fractures (FNFs); however, the... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Since its introduction in the early 1960s, the multiple cannulated screw fixation method has been developed for use in femoral neck fractures (FNFs); however, the parallelism of screws remains controversial.
MATERIALS AND METHODS
MEDLINE, Embase, and the Cochrane Library were systematically searched for studies published before June 2, 2020, that compared the use of parallel and non-parallel screw fixation for the treatment of FNF. The pooled analysis was designed to identify differences between the two groups and focused on postoperative complications, including fracture nonunion and osteonecrosis of the femoral head (ONFH).
RESULTS
Over four studies, we enrolled 445 patients, including 195 patients with fixed FNF with parallel trajectory screws and 250 patients with fixed FNF with non-parallel screws. The pooled analysis showed no difference in the nonunion rates (odds ratio (OR)=0.91; 95% confidence interval (CI), 0.24-3.44; p=0.89) and no significant difference in the incidence of ONFH between parallel and non-parallel screw fixation (OR=0.74; 95% CI: 0.21-2.63; p=0.64).
CONCLUSIONS
The results of this meta-analysis reveal that screw parallelism in multiple cannulated screw fixation of FNF has no relationship with either the fracture nonunion rate or the incidence of postoperative ONFH.
LEVEL OF EVIDENCE
III; meta-analysis.
Topics: Bone Screws; Femoral Neck Fractures; Fracture Fixation, Internal; Fractures, Ununited; Humans; Postoperative Complications
PubMed: 34217865
DOI: 10.1016/j.otsr.2021.103005 -
Developmental Biology Jan 2018Studying regeneration in animals where and when it occurs is inherently interesting and a challenging research topic within developmental biology. Historically,... (Review)
Review
Studying regeneration in animals where and when it occurs is inherently interesting and a challenging research topic within developmental biology. Historically, vertebrate regeneration has been investigated in animals that display enhanced regenerative abilities and we have learned much from studying organ regeneration in amphibians and fish. From an applied perspective, while regeneration biologists will undoubtedly continue to study poikilothermic animals (i.e., amphibians and fish), studies focused on homeotherms (i.e., mammals and birds) are also necessary to advance regeneration biology. Emerging mammalian models of epimorphic regeneration are poised to help link regenerative biology and regenerative medicine. The regenerating rodent digit tip, which parallels human fingertip regeneration, and the regeneration of large circular defects through the ear pinna in spiny mice and rabbits, provide tractable, experimental systems where complex tissue structures are regrown through blastema formation and morphogenesis. Using these models as examples, we detail similarities and differences between the mammalian blastema and its classical counterpart to arrive at a broad working definition of a vertebrate regeneration blastema. This comparison leads us to conclude that regenerative failure is not related to the availability of regeneration-competent progenitor cells, but is most likely a function of the cellular response to the microenvironment that forms following traumatic injury. Recent studies demonstrating that targeted modification of this microenvironment can restrict or enhance regenerative capabilities in mammals helps provide a roadmap for eventually pushing the limits of human regeneration.
Topics: Amputation, Surgical; Animals; Antlers; Deer; Ear Auricle; Finger Injuries; Fingers; Humans; Mammals; Mice; Morphogenesis; Murinae; Regeneration; Stem Cells; Toes; Wound Healing
PubMed: 29291973
DOI: 10.1016/j.ydbio.2017.08.007 -
Current Opinion in Lipidology Feb 2022In contrast to other saturated fatty acids, very long-chain saturated fatty acids (VLSFAs) have received limited attention The purpose of this review is to summarize the... (Review)
Review
PURPOSE OF REVIEW
In contrast to other saturated fatty acids, very long-chain saturated fatty acids (VLSFAs) have received limited attention The purpose of this review is to summarize the associations of VLSFAs, including arachidic acid, behenic acid, and lignoceric acid, with cardiovascular disease outcomes and type 2 diabetes; to discuss the findings implications; and to call for future studies of the VLSFAs.
RECENT FINDINGS
Increased levels of circulating VLSFAs have been found associated with lower risks of incident heart failure, atrial fibrillation, coronary heart disease, mortality, sudden cardiac arrest, type 2 diabetes, and with better aging. The VLSFA associations are paralleled by associations of plasma ceramide and sphingomyelin species carrying a VLSFA with lower risks of heart failure, atrial fibrillation, and mortality, suggesting VLSFAs affect the biological activity of ceramides and sphingomyelins thereby impacting health. For diabetes, there is no such parallel and the associations of VLSFAs with diabetes may be confounded or mediated by triglyceride and circulating palmitic acid, possible biomarkers of de novo lipogenesis.
SUMMARY
In many ways, the epidemiology has preceded our knowledge of VLSFAs biology. We hope this review will spur interest from the research community in further studying these potentially beneficial fatty acids.
Topics: Atrial Fibrillation; Cardiovascular Diseases; Ceramides; Diabetes Mellitus, Type 2; Fatty Acids; Heart Failure; Humans
PubMed: 34907969
DOI: 10.1097/MOL.0000000000000806 -
Science Advances Jul 2022pH controls a large repertoire of chemical and biochemical processes in water. Densely arrayed pH microenvironments would parallelize these processes, enabling their...
pH controls a large repertoire of chemical and biochemical processes in water. Densely arrayed pH microenvironments would parallelize these processes, enabling their high-throughput studies and applications. However, pH localization, let alone its arrayed realization, remains challenging because of fast diffusion of protons in water. Here, we demonstrate arrayed localizations of picoliter-scale aqueous acids, using a 256-electrochemical cell array defined on and operated by a complementary metal oxide semiconductor (CMOS)-integrated circuit. Each cell, comprising a concentric pair of cathode and anode with their current injections controlled with a sub-nanoampere resolution by the CMOS electronics, creates a local pH environment, or a pH "voxel," via confined electrochemistry. The system also monitors the spatiotemporal pH profile across the array in real time for precision pH control. We highlight the utility of this CMOS pH localizer-imager for high-throughput tasks by parallelizing pH-gated molecular state encoding and pH-regulated enzymatic DNA elongation at any selected set of cells.
PubMed: 35895813
DOI: 10.1126/sciadv.abm6815 -
Frontiers in Plant Science 2022The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or... (Review)
Review
The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.
PubMed: 36072310
DOI: 10.3389/fpls.2022.868565 -
Chemical Science Aug 2023We present an automated droplet reactor platform possessing parallel reactor channels and a scheduling algorithm that orchestrates all of the parallel hardware...
We present an automated droplet reactor platform possessing parallel reactor channels and a scheduling algorithm that orchestrates all of the parallel hardware operations and ensures droplet integrity as well as overall efficiency. We design and incorporate all of the necessary hardware and software to enable the platform to be used to study both thermal and photochemical reactions. We incorporate a Bayesian optimization algorithm into the control software to enable reaction optimization over both categorical and continuous variables. We demonstrate the capabilities of both the preliminary single-channel and parallelized versions of the platform using a series of model thermal and photochemical reactions. We conduct a series of reaction optimization campaigns and demonstrate rapid acquisition of the data necessary to determine reaction kinetics. The platform is flexible in terms of use case: it can be used either to investigate reaction kinetics or to perform reaction optimization over a wide range of chemical domains.
PubMed: 37621435
DOI: 10.1039/d3sc02082g -
Evolutionary Bioinformatics Online 2018Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal... (Review)
Review
Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task. In this article, we study how to develop efficient parallel implementations of this method for the fine-grained parallel architecture of graphics processing units (GPUs) using the compute unified device architecture (CUDA) platform. An exhaustive and methodical study of various parallel genetic algorithm schemes-master-slave, island, cellular, and hybrid models, and various individual selection methods (roulette, elitist)-is carried out for this problem. Several procedures that optimize the use of the GPU's resources are presented. We conclude that the implementation that produces better results (both from the performance and the genetic algorithm fitness perspectives) is simulating a few thousands of individuals grouped in a few islands using elitist selection. This model comprises 2 mighty factors for discovering the best solutions: finding good individuals in a short number of generations, and introducing genetic diversity via a relatively frequent and numerous migration. As a result, we have even found the optimal solution for the analyzed gene regulatory network (GRN). In addition, a comparative study of the performance obtained by the different parallel implementations on GPU versus a sequential application on CPU is carried out. In our tests, a multifold speedup was obtained for our optimized parallel implementation of the method on medium class GPU over an equivalent sequential single-core implementation running on a recent Intel i7 CPU. This work can provide useful guidance to researchers in biology, medicine, or bioinformatics in how to take advantage of the parallelization on massively parallel devices and GPUs to apply novel metaheuristic algorithms powered by nature for real-world applications (like the method to solve the temporal dynamics of GRNs).
PubMed: 29662297
DOI: 10.1177/1176934318767889 -
Frontiers in Neuroscience 2015Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a... (Review)
Review
Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues.
PubMed: 26029043
DOI: 10.3389/fnins.2015.00171 -
International Journal of Molecular... Jan 2022As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate... (Review)
Review
As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate new avenues for disease treatment and lead to new hypotheses that would advance gene regulatory research. Recent studies using the model fission yeast () and powerful parallel sequencing technologies have provided many insights in this area. This review will give an overview of key findings in that relate long RNAs to multiple levels of chromatin regulation: histone modifications, gene neighborhood regulation in and higher-order chromosomal ordering. Moreover, we discuss parallels recently found in mammals to help bridge the knowledge gap between the study systems.
Topics: Chromatin; Histone Code; Protein Processing, Post-Translational; RNA, Fungal; RNA, Long Noncoding; Schizosaccharomyces; Schizosaccharomyces pombe Proteins
PubMed: 35055152
DOI: 10.3390/ijms23020968