scholarly journals Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts

mBio ◽  
2013 ◽  
Vol 4 (3) ◽  
Author(s):  
Manuel Kleiner ◽  
Jacque C. Young ◽  
Manesh Shah ◽  
Nathan C. VerBerkmoes ◽  
Nicole Dubilier
Keyword(s):  
Transposable Elements ◽  
Recent Work ◽  
Current Model ◽  
Evolutionary Mechanisms ◽  
Host Environment ◽  
Underlying Causes ◽  
Mutagenic Effects ◽  
Current Paradigm ◽  
Rapid Emergence ◽  
Transposase Expression

ABSTRACTTransposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that the expression of transposase genes is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine wormOlavius algarvensiswith metaproteomics. At least 26 different transposases from 12 different families were detected, and genomic and proteomic analyses suggest that many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or no longer exist.IMPORTANCEThe expansion of transposable elements (TE) within the genomes of host-restricted symbionts and pathogens plays an important role in their emergence and evolution and might be a key mechanism for adaptation to the host environment. However, little is known so far about the underlying causes and evolutionary mechanisms of this TE expansion. The current model of genome evolution in host-restricted bacteria explains TE expansion within the confines of the paradigm that transposase expression is always low. However, recent work failed to verify this model. Based on our data, we hypothesize that increased transposase expression, which has not previously been described, may play a role in TE expansion, and could be one explanation for the sometimes very rapid emergence and evolution of new obligate symbionts and pathogens from facultative ones.

Emotion

2020 ◽  
pp. 966-982
Author(s):  
Michael Spitzer ◽  
Derek Matravers
Keyword(s):  
Recent Work ◽  
Conceptual Analysis ◽  
Future Of Work ◽  
American Philosophy ◽  
Expression Of Emotion ◽  
Dual Perspective ◽  
Underlying Causes ◽  
Psychology Of Music ◽  
Anglo American ◽  
Jerrold Levinson

This chapter considers the expression of emotion by music, the most interesting of the relations between music and the emotions. It is written from the dual perspective of Anglo-American philosophy and of musicology. The former focuses on the conceptual analysis of emotion, the latter on the underlying causes of the listeners’ experience. The theories of Stephen Davies and Jerrold Levinson are considered and criticized, and recent work in the psychology of music is examined in the light of the pioneering account of expression from Leonard Meyer. Finally, there is some speculation as to the future of work in this area.

scholarly journals Organization and Chromosomal Distribution of Histone Genes and Transposable Rex Elements in the Genome of Astyanax bockmanni (Teleostei, Characiformes)

2015 ◽  
Vol 146 (4) ◽  
pp. 311-318 ◽  
Author(s):  
Sandro N. Daniel ◽  
Manolo Penitente ◽  
Duílio M.Z.A. Silva ◽  
Diogo T. Hashimoto ◽  
Daniela C. Ferreira ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
B Chromosome ◽  
Gene Probe ◽  
Histone Genes ◽  
Chromosomal Distribution ◽  
Evolutionary Mechanisms ◽  
Small Sites ◽  
Eukaryotic Organisms

An important feature of eukaryotic organisms is the number of different repetitive DNA sequences in their genome, a feature not observed in prokaryotes. These sequences are considered to be important components for understanding evolutionary mechanisms and the karyotypic differentiation processes. Thus, we aimed to physically map the histone genes and transposable elements of the Rex family in 6 fish populations of Astyanax bockmanni. FISH results using a histone H1 gene probe showed fluorescent clusters in 2 chromosome pairs in all 6 samples analyzed. In contrast, FISH with a histone H3 probe showed conspicuous blocks in 4 chromosomes in 5 of the 6 populations analyzed. The sixth population revealed 7 chromosomes marked with this probe. Probes for the transposable elements Rex1 and Rex6 showed small sites dispersed on most chromosomes of the 6 populations, and the Rex3 element is located in a big block concentrated in only 1 acrocentric chromosome of 2 populations. As for the other populations, a Rex3 probe showed large blocks in more than 1 chromosome. Fish from Alambari and Campo Novo Stream have Rex3 elements dispersed along most of the chromosomes. Additionally, the conspicuous signals of Rex1, Rex3, and Rex6 were identified in the acrocentric B microchromosome of A. bockmanni found only in individuals of the Alambari River. Thus, we believe that different mechanisms drive the spread of repetitive sequences among the populations analyzed, which appear to be organized differently in the genome of A. bockmanni. The presence of transposable elements in the B chromosome also suggests that these sequences could play a role in the origin and maintenance of the supernumerary element in the genome of this species.

scholarly journals Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sarah Farhat ◽  
Phuong Le ◽  
Ehsan Kayal ◽  
Benjamin Noel ◽  
Estelle Bigeard ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Protein Evolution ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Gene Families ◽  
Gene Organization ◽  
Host Specialization ◽  
Evolutionary Mechanisms ◽  
Symbiotic Relationships ◽  
Intergenic Regions

Abstract Background Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. Results We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. Conclusion These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.

scholarly journals POSE-AWARE EMBEDDING NETWORKS AND MULTI-MODAL IMAGE-LANGUAGE RETRIEVAL

2021 ◽  
Author(s):  
Domenico Curro
Keyword(s):  
Recent Work ◽  
Metric Spaces ◽  
Current Model ◽  
Metric Learning ◽  
Image Similarity ◽  
Similarity Retrieval ◽  
Human Pose ◽  
Human Joint

Inspired by recent work in human pose metric learning this thesis explores a family of pose-aware embedding networks designed for the purpose of image similarity retrieval. Circumventing the need for direct human joint localization, a series of CNN embedding networks are trained to respect a variety of Euclidean and language-primitive metric spaces. Querying with imagery alone presents certain limitations and thus this thesis proposes a multi-modal image-language embedding space, extending the current model to allow for language-primitive queries. This additional language mode provides the benefit of improving retrieval quality by 3% to 14% under the hit@k metric. Finally, two approaches are constructed to address the issues of conducting partial language-primitive queries, with the former generating maximally likely descriptors and the latter exploiting the network’s tendency to factorize the embedding space into (mostly) linearly separable sub-spaces. These two approaches improve upon recall by 13% and 17% over the provided baselines.

scholarly journals Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Daniel R Fuentes ◽  
Tomek Swigut ◽  
Joanna Wysocka
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Recent Work ◽  
Human Gene ◽  
Sequence Divergence ◽  
Specific Class ◽  
Human Genes ◽  
Recent Method ◽  
Systematic Perturbation ◽  
Crispr Activation

Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our recent method for CRISPR gRNA multiplexing, to facilitate targeting of LTR5HS, an ape-specific class of HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout the human genome. We combine CARGO with CRISPR activation or interference to, respectively, induce or silence LTR5HS en masse, and demonstrate that this system robustly targets the vast majority of LTR5HS insertions. Remarkably, activation/silencing of LTR5HS is associated with reciprocal up- and down-regulation of hundreds of human genes. These effects require the presence of retroviral sequences, but occur over long genomic distances, consistent with a pervasive function of LTR5HS elements as early embryonic enhancers in apes.

scholarly journals Feeding the world with soil science: embracing sustainability, complexity and uncertainty

2016 ◽  
Author(s):  
P. Tittonell
Keyword(s):  
Ecosystem Services ◽  
21St Century ◽  
Agricultural Production ◽  
Current Model ◽  
Three Dimensions ◽  
Soil Science ◽  
Future Challenges ◽  
Environmental Goals ◽  
New Research ◽  
Current Paradigm

Abstract. Feeding a growing and wealthier population while providing other ecosystem services and meeting social and environmental goals poses serious challenges to soil scientists of the 21st Century. In particular, three dimensions inherent to agricultural systems shape the current paradigm under which science has to contribute knowledge and innovations: sustainability, complexity and uncertainty. The current model of agricultural production, which is also often the source of inspiration to propose solutions for future challenges, fails at internalizing these dimensions. It simply does not provide the necessary means to address sustainability, complexity or uncertainties. Part of the problem is that these are soft concepts, as opposed to hard goals, and so their definition and their translation into concrete actions is always subjective. They have to be sufficiently defined for soil science to embrace them in order to propose viable solutions to (i) produce food where it is most needed, (ii) decouple agricultural production from its dependence on non-renewable resources, (iii) recycle and make efficient use of available resources, (iv) reduce the risks associated with global change, and (v) restore the capacity of degraded soils to provide ecosystem services. This paper examines what the concepts of sustainability, complexity and uncertainty mean and imply for soil science, focusing on the five priorities enunciated above. It also summarizes and proposes new research challenges for soil scientists of the 21st Century.

scholarly journals Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen

2019 ◽  
Vol 37 (3) ◽  
pp. 839-848 ◽  
Author(s):  
Manuel Poretti ◽  
Coraline Rosalie Praz ◽  
Lukas Meile ◽  
Carol Kälin ◽  
Luisa Katharina Schaefer ◽  
...  
Keyword(s):  
Immune Response ◽  
Transposable Elements ◽  
Small Rna ◽  
Wheat Genome ◽  
Wide Spread ◽  
Evolutionary Mechanisms ◽  
Plant Genomes ◽  
Evolutionary Force ◽  
Obligate Pathogen ◽  
Powdery Mildew Pathogen

Abstract Plant genomes have evolved several evolutionary mechanisms to tolerate and make use of transposable elements (TEs). Of these, transposon domestication into cis-regulatory and microRNA (miRNA) sequences is proposed to contribute to abiotic/biotic stress adaptation in plants. The wheat genome is derived at 85% from TEs, and contains thousands of miniature inverted-repeat transposable elements (MITEs), whose sequences are particularly prone for domestication into miRNA precursors. In this study, we investigate the contribution of TEs to the wheat small RNA immune response to the lineage-specific, obligate powdery mildew pathogen. We show that MITEs of the Mariner superfamily contribute the largest diversity of miRNAs to the wheat immune response. In particular, MITE precursors of miRNAs are wide-spread over the wheat genome, and highly conserved copies are found in the Lr34 and QPm.tut-4A mildew resistance loci. Our work suggests that transposon domestication is an important evolutionary force driving miRNA functional innovation in wheat immunity.

scholarly journals POSE-AWARE EMBEDDING NETWORKS AND MULTI-MODAL IMAGE-LANGUAGE RETRIEVAL

2021 ◽  
Author(s):  
Domenico Curro
Keyword(s):  
Recent Work ◽  
Metric Spaces ◽  
Current Model ◽  
Metric Learning ◽  
Image Similarity ◽  
Similarity Retrieval ◽  
Human Pose ◽  
Human Joint

Inspired by recent work in human pose metric learning this thesis explores a family of pose-aware embedding networks designed for the purpose of image similarity retrieval. Circumventing the need for direct human joint localization, a series of CNN embedding networks are trained to respect a variety of Euclidean and language-primitive metric spaces. Querying with imagery alone presents certain limitations and thus this thesis proposes a multi-modal image-language embedding space, extending the current model to allow for language-primitive queries. This additional language mode provides the benefit of improving retrieval quality by 3% to 14% under the hit@k metric. Finally, two approaches are constructed to address the issues of conducting partial language-primitive queries, with the former generating maximally likely descriptors and the latter exploiting the network’s tendency to factorize the embedding space into (mostly) linearly separable sub-spaces. These two approaches improve upon recall by 13% and 17% over the provided baselines.

scholarly journals Problems with Estimating Anthesis Phenology Parameters in Zea mays: Consequences for Combining Ecophysiological Models with Genetics

2016 ◽  
Author(s):  
Abhishes Lamsal ◽  
Stephen M. Welch ◽  
Jeffrey W. White ◽  
Kelly R. Thorp ◽  
Nora Bello
Keyword(s):  
Zea Mays ◽  
Genetic Mapping ◽  
Recent Work ◽  
Accurate Estimation ◽  
Parameter Estimates ◽  
Crop Models ◽  
Predictive Quality ◽  
Original Goal ◽  
Current Paradigm ◽  
Process Based Models

AbstractEcophysiological crop models encode intra-species behaviors using constant parameters that are presumed to summarize genotypic properties. Accurate estimation of these parameters is crucial because much recent work has sought to link them to genotypes. The original goal of this study was to fit the anthesis date component of the CERES-Maize model to 5266 genetic lines grown at 11 site-years and genetically map the resulting parameter estimates. Although the resulting estimates had high predictive quality, numerous artifacts emerged during estimation. The first arose in situations where the model was unable to express the observed data for many lines, which ended up sharing the same parameter value. In the second (2254 lines), the model reproduced the data but there were often many parameter sets that did so equally well (equifinality). These artifacts made genetic mapping impossible, thus, revealing cautionary insights regarding a major current paradigm for linking process based models to genetics.

scholarly journals Massive intron gain in the most intron-rich eukaryotes is driven by introner-like transposable elements of unprecedented diversity and flexibility

2020 ◽  
Author(s):  
Scott William Roy ◽  
Landen Gozashti ◽  
Bradley A. Bowser ◽  
Brooke N. Weinstein ◽  
Graham E. Larue
Keyword(s):  
Transposable Elements ◽  
Insertion Site ◽  
Intron Loss ◽  
Intron Gain ◽  
Nuclear Genes ◽  
Spliceosomal Intron ◽  
Intron Evolution ◽  
Evolutionary Mechanisms ◽  
Spliceosomal Introns ◽  
History Of

SummarySpliceosomal introns, which interrupt nuclear genes and are removed from RNA transcripts by machinery termed spliceosomes, are ubiquitous features of eukaryotic nuclear genes [1]. Patterns of spliceosomal intron evolution are complex, with some lineages exhibiting virtually no intron creation while others experience thousands of intron gains [2–5]. One possibility is that this punctate phylogenetic distribution is explained by intron creation by Introner-Like Elements (ILEs), transposable elements capable of creating introns, with only those lineages harboring ILEs undergoing massive intron gain [6–10]. However, ILEs have been reported in only four lineages. Here we study intron evolution in dinoflagellates. The remarkable fragmentation of nuclear genes by spliceosomal introns reaches its apex in dinoflagellates, which have some twenty introns per gene [11,12]. Despite this, almost nothing is known about the molecular and evolutionary mechanisms governing dinoflagellate intron evolution. We reconstructed intron evolution in five dinoflagellate genomes, revealing a dynamic history of intron loss and gain. ILEs are found in 4/5 studied species. In one species, Polarella glacialis, we find an unprecedented diversity of ILEs, with ILE insertion leading to creation of some 12,253 introns, and with 15 separate families of ILEs accounting for at least 100 introns each. These ILE families range in mobilization mechanism, mechanism of intron creation, and flexibility of mechanism of intron creation. Comparison within and between ILE families provides evidence that biases in so-called intron phase, the distribution of introns relative to codon periodicity, are driven by ILE insertion site requirements [9,13,14]. Finally, we find evidence for multiple additional transformations of the spliceosomal system in dinoflagellates, including widespread loss of ancestral introns, and alterations in required, tolerated and favored splice motifs. These results reveal unappreciated intron creating elements diversity and spliceosomal evolutionary capacity, and suggest complex evolutionary dependencies shaping genome structures.

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