scholarly journals Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

2021 ◽  
Vol 22 (9) ◽  
pp. 4707
Author(s):  
Mariana Lopes ◽  
Sandra Louzada ◽  
Margarida Gama-Carvalho ◽  
Raquel Chaves
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Nucleotide Composition ◽  
Genomic Component ◽  
Genomic Studies ◽  
Human Genomic ◽  
Definition Of ◽  
High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

Cloning and characterization of a transposable-like repeat in the heterochromatin of the darkling beetle Misolampus goudoti

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 769-774 ◽  
Author(s):  
Joan Pons
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Satellite Dna ◽  
Molecular Mechanisms ◽  
Repeat Unit ◽  
Nucleotide Composition ◽  
Crossing Over ◽  
Unequal Crossing Over ◽  
Darkling Beetle

A long repeat unit of the PstI family in Misolampus goudoti (Coleoptera, Tenebrionodae) is characterized in this work. The 30 sequenced units have small differences in length (consensus 1169 bp), but very similar nucleotide composition (mean 61.1% A+T). PstI repeats contain a 36-bp-long inverted repeat at both the 5′ and 3′ ends, with a fully conserved 16-bp-long motif similar to those found in class II transposable elements. However, the transposable-like PstI repeats seems to be defective, since they do not encode for any protein related with transposition. Interestingly, energetically stable hairpins resembled the structure of a miniature interspersed transposable element, suggesting that the PstI satellite DNA family in M. goudoti may have originated from an ancestral active transposable element as also described in Drosophila guanche. The presence of transposable-like structure along with the non-detection of gene conversion or unequal crossing-over events suggest that transposition could be one of the putative molecular mechanisms involved in the strong amplification and (or) homogenization of these repeats. A putative transposition of PstI repeats allowing their genomic mobility also could explain why this satellite is widely distributed to all heterochromatic regions, telomeres, pericentromeric regions, and on the Y chromosome, whereas satellites of other tenebrionids lacking transposable-like structures are restricted only to pericentromeric regions.Key words: transposable elements, MITE, satellite DNA, heterochromatin, telomere, beetle, Tenebrionidae.

scholarly journals Descriptive and Functional Genomics in Acute Myeloid Leukemia (AML): Paving the Road for a Cure

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 748
Author(s):  
Hélène Pasquer ◽  
Maëlys Tostain ◽  
Nina Kaci ◽  
Blandine Roux ◽  
Lina Benajiba
Keyword(s):  
Functional Genomics ◽  
Myeloid Leukemia ◽  
Residual Disease ◽  
Genetic Sequencing ◽  
The Road ◽  
Genomic Studies ◽  
Molecular Prognosis ◽  
Molecular Landscape ◽  
Definition Of

Over the past decades, genetic advances have allowed a more precise molecular characterization of AML with the identification of novel oncogenes and tumor suppressors as part of a comprehensive AML molecular landscape. Recent advances in genetic sequencing tools also enabled a better understanding of AML leukemogenesis from the preleukemic state to posttherapy relapse. These advances resulted in direct clinical implications with the definition of molecular prognosis classifications, the development of treatment recommendations based on minimal residual disease (MRD) measurement and the discovery of novel targeted therapies, ultimately improving AML patients’ overall survival. The more recent development of functional genomic studies, pushed by novel molecular biology technologies (short hairpin RNA (shRNA) and CRISPR-Cas9) and bioinformatics tools design on one hand, along with the engineering of humanized physiologically relevant animal models on the other hand, have opened a new genomics era resulting in a greater knowledge of AML physiopathology. Combining descriptive and functional genomics will undoubtedly open the road for an AML cure within the next decades.

Characterization of RF Sputtered ZnO Piezoelectric Films Using Transmission Electron Microscope

1975 ◽  
Vol 33 ◽  
pp. 86-87
Author(s):  
Kemining W. Yeh ◽  
Richard S. Muller ◽  
Wei-Kuo Wu ◽  
Jack Washburn
Keyword(s):  
Integrated Circuit ◽  
Acoustic Waves ◽  
New Technology ◽  
Surface Acoustic Waves ◽  
Electromechanical Properties ◽  
Leading Role ◽  
Saw Devices ◽  
Transmission Electron ◽  
High Degree

Considerable and continuing interest has been shown in the thin film transducer fabrication for surface acoustic waves (SAW) in the past few years. Due to the high degree of miniaturization, compatibility with silicon integrated circuit technology, simplicity and ease of design, this new technology has played an important role in the design of new devices for communications and signal processing. Among the commonly used piezoelectric thin films, ZnO generally yields superior electromechanical properties and is expected to play a leading role in the development of SAW devices.

scholarly journals Identification of effective spreaders in contact networks using dynamical influence

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Ruaridh A. Clark ◽  
Malcolm Macdonald
Keyword(s):  
Disease Transmission ◽  
Average Rate ◽  
Laplacian Matrix ◽  
Disease Spread ◽  
Eigenvector Centrality ◽  
Contact Networks ◽  
Human Contact ◽  
Spread Dynamics ◽  
Definition Of ◽  
High Degree

AbstractContact networks provide insights on disease spread due to the duration of close proximity interactions. For systems governed by consensus dynamics, network structure is key to optimising the spread of information. For disease spread over contact networks, the structure would be expected to be similarly influential. However, metrics that are essentially agnostic to the network’s structure, such as weighted degree (strength) centrality and its variants, perform near-optimally in selecting effective spreaders. These degree-based metrics outperform eigenvector centrality, despite disease spread over a network being a random walk process. This paper improves eigenvector-based spreader selection by introducing the non-linear relationship between contact time and the probability of disease transmission into the assessment of network dynamics. This approximation of disease spread dynamics is achieved by altering the Laplacian matrix, which in turn highlights why nodes with a high degree are such influential disease spreaders. From this approach, a trichotomy emerges on the definition of an effective spreader where, for susceptible-infected simulations, eigenvector-based selections can either optimise the initial rate of infection, the average rate of infection, or produce the fastest time to full infection of the network. Simulated and real-world human contact networks are examined, with insights also drawn on the effective adaptation of ant colony contact networks to reduce pathogen spread and protect the queen ant.

scholarly journals Experimental Evaluation of Shear Behavior of Stone Masonry Wall

Materials ◽  
2021 ◽  
Vol 14 (9) ◽  
pp. 2313
Author(s):  
Maria Luisa Beconcini ◽  
Pietro Croce ◽  
Paolo Formichi ◽  
Filippo Landi ◽  
Benedetta Puccini
Keyword(s):  
Shear Behavior ◽  
Stone Masonry ◽  
Masonry Walls ◽  
Mechanical Parameters ◽  
In Situ Tests ◽  
Capacity Curves ◽  
Historical Structures ◽  
Definition Of

The evaluation of the shear behavior of masonry walls is a first fundamental step for the assessment of existing masonry structures in seismic zones. However, due to the complexity of modelling experimental behavior and the wide variety of masonry types characterizing historical structures, the definition of masonry’s mechanical behavior is still a critical issue. Since the possibility to perform in situ tests is very limited and often conflicting with the needs of preservation, the characterization of shear masonry behavior is generally based on reference values of mechanical properties provided in modern structural codes for recurrent masonry categories. In the paper, a combined test procedure for the experimental characterization of masonry mechanical parameters and the assessment of the shear behavior of masonry walls is presented together with the experimental results obtained on three stone masonry walls. The procedure consists of a combination of three different in situ tests to be performed on the investigated wall. First, a single flat jack test is executed to derive the normal compressive stress acting on the wall. Then a double flat jack test is carried out to estimate the elastic modulus. Finally, the proposed shear test is performed to derive the capacity curve and to estimate the shear modulus and the shear strength. The first results obtained in the experimental campaign carried out by the authors confirm the capability of the proposed methodology to assess the masonry mechanical parameters, reducing the uncertainty affecting the definition of capacity curves of walls and consequently the evaluation of seismic vulnerability of the investigated buildings.

Fundamental relations and identities of fuzzy hyperalgebras

2021 ◽  
pp. 1-10
Author(s):  
Narjes Firouzkouhi ◽  
Abbas Amini ◽  
Chun Cheng ◽  
Mehdi Soleymani ◽  
Bijan Davvaz
Keyword(s):  
Universal Algebra ◽  
Equivalence Relation ◽  
Polynomial Function ◽  
Equivalence Relations ◽  
Fundamental Relation ◽  
Term Function ◽  
Biological Phenomena ◽  
Definition Of

Inspired by fuzzy hyperalgebras and fuzzy polynomial function (term function), some homomorphism properties of fundamental relation on fuzzy hyperalgebras are conveyed. The obtained relations of fuzzy hyperalgebra are utilized for certain applications, i.e., biological phenomena and genetics along with some elucidatory examples presenting various aspects of fuzzy hyperalgebras. Then, by considering the definition of identities (weak and strong) as a class of fuzzy polynomial function, the smallest equivalence relation (fundamental relation) is obtained which is an important tool for fuzzy hyperalgebraic systems. Through the characterization of these equivalence relations of a fuzzy hyperalgebra, we assign the smallest equivalence relation α i 1 i 2 ∗ on a fuzzy hyperalgebra via identities where the factor hyperalgebra is a universal algebra. We extend and improve the identities on fuzzy hyperalgebras and characterize the smallest equivalence relation α J ∗ on the set of strong identities.

scholarly journals Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1661-1672 ◽  
Author(s):  
Andrea Pedrosa ◽  
Niels Sandal ◽  
Jens Stougaard ◽  
Dieter Schweizer ◽  
Andreas Bachmair
Keyword(s):  
Repetitive Sequences ◽  
Lotus Japonicus ◽  
Chromosome Complement ◽  
Linkage Groups ◽  
Closely Related Species ◽  
F1 Hybrid ◽  
Bac Clones ◽  
Genomic Regions ◽  
Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal  et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals A lattice-theoretic characterization of pure subgroups of Abelian groups

2021 ◽  
Author(s):  
M. Ferrara ◽  
M. Trombetti
Keyword(s):  
Abelian Group ◽  
Abelian Groups ◽  
Subgroup Lattice ◽  
General Definition ◽  
Short Paper ◽  
Theoretic Characterization ◽  
Definition Of

AbstractLet G be an abelian group. The aim of this short paper is to describe a way to identify pure subgroups H of G by looking only at how the subgroup lattice $$\mathcal {L}(H)$$ L ( H ) embeds in $$\mathcal {L}(G)$$ L ( G ) . It is worth noticing that all results are carried out in a local nilpotent context for a general definition of purity.

scholarly journals Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy

2018 ◽  
Vol 115 (17) ◽  
pp. E3969-E3977 ◽  
Author(s):  
Sasikumar Rajoo ◽  
Pascal Vallotton ◽  
Evgeny Onischenko ◽  
Karsten Weis
Keyword(s):  
Nuclear Pore Complex ◽  
Yeast Cells ◽  
Nuclear Pore ◽  
Altered Expression ◽  
Copy Numbers ◽  
Quantitative Image ◽  
Multiple Copies ◽  
Almost All ◽  
High Degree

The nuclear pore complex (NPC) is an eightfold symmetrical channel providing selective transport of biomolecules across the nuclear envelope. Each NPC consists of ∼30 different nuclear pore proteins (Nups) all present in multiple copies per NPC. Significant progress has recently been made in the characterization of the vertebrate NPC structure. However, because of the estimated size differences between the vertebrate and yeast NPC, it has been unclear whether the NPC architecture is conserved between species. Here, we have developed a quantitative image analysis pipeline, termed nuclear rim intensity measurement (NuRIM), to precisely determine copy numbers for almost all Nups within native NPCs of budding yeast cells. Our analysis demonstrates that the majority of yeast Nups are present at most in 16 copies per NPC. This reveals a dramatic difference to the stoichiometry determined for the human NPC, suggesting that despite a high degree of individual Nup conservation, the yeast and human NPC architecture is significantly different. Furthermore, using NuRIM, we examined the effects of mutations on NPC stoichiometry. We demonstrate for two paralog pairs of key scaffold Nups, Nup170/Nup157 and Nup192/Nup188, that their altered expression leads to significant changes in the NPC stoichiometry inducing either voids in the NPC structure or substitution of one paralog by the other. Thus, our results not only provide accurate stoichiometry information for the intact yeast NPC but also reveal an intriguing compositional plasticity of the NPC architecture, which may explain how differences in NPC composition could arise in the course of evolution.

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