scholarly journals Point mutation impairs centromeric CENH3 loading and induces haploid plants

2015 ◽  
Vol 112 (36) ◽  
pp. 11211-11216 ◽  
Author(s):  
Raheleh Karimi-Ashtiyani ◽  
Takayoshi Ishii ◽  
Markus Niessen ◽  
Nils Stein ◽  
Stefan Heckmann ◽  
...  
Keyword(s):  
Single Point ◽  
Chromosome Elimination ◽  
Wild Type ◽  
Mutation Site ◽  
Crop Species ◽  
Wide Range ◽  
Histone H3 Variant ◽  
Centromere Inactivation ◽  
High Degree ◽  
Acid Exchange

The chromosomal position of the centromere-specific histone H3 variant CENH3 (also called “CENP-A”) is the assembly site for the kinetochore complex of active centromeres. Any error in transcription, translation, modification, or incorporation can affect the ability to assemble intact CENH3 chromatin and can cause centromere inactivation [Allshire RC, Karpen GH (2008) Nat Rev Genet 9 (12):923–937]. Here we show that a single-point amino acid exchange in the centromere-targeting domain of CENH3 leads to reduced centromere loading of CENH3 in barley, sugar beet, and Arabidopsis thaliana. Haploids were obtained after cenh3 L130F-complemented cenh3-null mutant plants were crossed with wild-type A. thaliana. In contrast, in a noncompeting situation (i.e., centromeres possessing only mutated or only wild-type CENH3), no uniparental chromosome elimination occurs during early embryogenesis. The high degree of evolutionary conservation of the identified mutation site offers promising opportunities for application in a wide range of crop species in which haploid technology is of interest.

scholarly journals Novel Polymorphisms in mec Genes and a New mec Complex Type in Methicillin-Resistant Staphylococcus aureus Isolates Obtained in Rural Wisconsin

2004 ◽  
Vol 48 (8) ◽  
pp. 3080-3085 ◽  
Author(s):  
Sanjay K. Shukla ◽  
Srinivas V. Ramaswamy ◽  
Jennifer Conradt ◽  
Mary E. Stemper ◽  
Robert Reich ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistance ◽  
Wild Type ◽  
Promoter Mutation ◽  
Complex Type ◽  
Methicillin Resistant ◽  
Type Iv ◽  
Wide Range ◽  
Complete Sequencing ◽  
High Degree

ABSTRACT We determined allelic polymorphisms in the mec complexes of 524 methicillin-resistant Staphylococcus aureus isolates by partial or complete sequencing of three mec genes, mecA, mecI, and mecR1. The isolates had been collected over a 10-year period from patients living in rural Wisconsin, where the use of antibiotics was expected to be lower than in the bigger cities. Of the 18 mutation types identified, 16 had not been described previously. The five most common mutations were a mutation 7 nucleotides (nt) upstream from the start site (G→T) in the mecA promoter (34.7%), an E246G change encoded by mecA (2.2%), a cytosine insertion at codon 257 in mecA (13.2%), an N121K change encoded by mecI (7.8%), and a major mecI-mecR1 deletion designated as a class B1 mec complex deletion type (25.4%). There was a high degree of conservation of the amino acid sequence of MecR1. Strains with the same mutations had variable resistance to oxacillin, and the median MIC for isolates that harbored the 7-nt-upstream mutation was lower than that for strains harboring other mutations. Our data suggest that the mecA promoter mutation plays a more important role in determining methicillin resistance than mutations in mecI and mecA do. Eighty-five percent of the tested isolates (n = 148) with the mecA promoter mutation and the class B1 mec complex deletion belonged to the same major clonal group, identified as MCG-2, and harbored the type IV staphylococcal cassette chromosome mec DNA. There was also a wide range of oxacillin MICs for strains with wild-type mecA, mecI, and mecR1 sequences, suggesting that the genetic backgrounds of clinical strains are significant in determining susceptibility to methicillin.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

Cerebellotrigeminal Dermal Dysplasia (Gómez-López-Hernández Syndrome)

2018 ◽  
Vol 16 (05) ◽  
pp. 362-368 ◽  
Author(s):  
Federica Sullo ◽  
Agata Polizzi ◽  
Stefano Catanzaro ◽  
Selene Mantegna ◽  
Francesco Lacarrubba ◽  
...  
Keyword(s):  
De Novo ◽  
Chromosomal Rearrangements ◽  
Number Of Patients ◽  
Wide Range ◽  
Visual Problems ◽  
Neurodevelopmental Abnormalities ◽  
Clinical Triad ◽  
High Degree ◽  
Motor Handicap

Cerebellotrigeminal dermal (CTD) dysplasia is a rare neurocutaneous disorder characterized by a triad of symptoms: bilateral parieto-occipital alopecia, facial anesthesia in the trigeminal area, and rhombencephalosynapsis (RES), confirmed by cranial magnetic resonance imaging. CTD dysplasia is also known as Gómez-López-Hernández syndrome. So far, only 35 cases have been described with varying symptomatology. The etiology remains unknown. Either spontaneous dominant mutations or de novo chromosomal rearrangements have been proposed as possible explanations. In addition to its clinical triad of RES, parietal alopecia, and trigeminal anesthesia, CTD dysplasia is associated with a wide range of phenotypic and neurodevelopmental abnormalities.Treatment is symptomatic and includes physical rehabilitation, special education, dental care, and ocular protection against self-induced corneal trauma that causes ulcers and, later, corneal opacification. The prognosis is correlated to the mental development, motor handicap, corneal–facial anesthesia, and visual problems. Follow-up on a large number of patients with CTD dysplasia has never been reported and experience is limited to few cases to date. High degree of suspicion in a child presenting with characteristic alopecia and RES has a great importance in diagnosis of this syndrome.

scholarly journals Silicon Effects on the Root System of Diverse Crop Species Using Root Phenotyping Technology

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 885
Author(s):  
Pooja Tripathi ◽  
Sangita Subedi ◽  
Abdul Latif Khan ◽  
Yong-Suk Chung ◽  
Yoonha Kim
Keyword(s):  
Root System ◽  
Root Morphology ◽  
Morphological Traits ◽  
Crop Production ◽  
Spatial Configuration ◽  
Global Climate ◽  
Learning Technologies ◽  
Climate Change Scenarios ◽  
Crop Species ◽  
Wide Range

Roots play an essential function in the plant life cycle, as they utilize water and essential nutrients to promote growth and plant productivity. In particular, root morphology characteristics (such as length, diameter, hairs, and lateral growth) and the architecture of the root system (spatial configuration in soil, shape, and structure) are the key elements that ensure growth and a fine-tuned response to stressful conditions. Silicon (Si) is a ubiquitous element in soil, and it can affect a wide range of physiological processes occurring in the rhizosphere of various crop species. Studies have shown that Si significantly and positively enhances root morphological traits, including root length in rice, soybean, barley, sorghum, mustard, alfalfa, ginseng, and wheat. The analysis of these morphological traits using conventional methods is particularly challenging. Currently, image analysis methods based on advanced machine learning technologies allowed researchers to screen numerous samples at the same time considering multiple features, and to investigate root functions after the application of Si. These methods include root scanning, endoscopy, two-dimensional, and three-dimensional imaging, which can measure Si uptake, translocation and root morphological traits. Small variations in root morphology and architecture can reveal different positive impacts of Si on the root system of crops, with or without exposure to stressful environmental conditions. This review comprehensively illustrates the influences of Si on root morphology and root architecture in various crop species. Furthermore, it includes recommendations in regard to advanced methods and strategies to be employed to maintain sustainable plant growth rates and crop production in the currently predicted global climate change scenarios.

scholarly journals Controlling Teleportation-Based Locomotion in Virtual Reality with Hand Gestures: A Comparative Evaluation of Two-Handed and One-Handed Techniques

Electronics ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 715
Author(s):  
Alexander Schäfer ◽  
Gerd Reis ◽  
Didier Stricker
Keyword(s):  
Virtual Reality ◽  
Virtual Worlds ◽  
User Preferences ◽  
Interaction Techniques ◽  
Hand Gestures ◽  
Wide Range ◽  
Effectiveness And Efficiency ◽  
High Degree ◽  
Additional Hardware ◽  
Comprehensive Study

Virtual Reality (VR) technology offers users the possibility to immerse and freely navigate through virtual worlds. An important component for achieving a high degree of immersion in VR is locomotion. Often discussed in the literature, a natural and effective way of controlling locomotion is still a general problem which needs to be solved. Recently, VR headset manufacturers have been integrating more sensors, allowing hand or eye tracking without any additional required equipment. This enables a wide range of application scenarios with natural freehand interaction techniques where no additional hardware is required. This paper focuses on techniques to control teleportation-based locomotion with hand gestures, where users are able to move around in VR using their hands only. With the help of a comprehensive study involving 21 participants, four different techniques are evaluated. The effectiveness and efficiency as well as user preferences of the presented techniques are determined. Two two-handed and two one-handed techniques are evaluated, revealing that it is possible to move comfortable and effectively through virtual worlds with a single hand only.

scholarly journals Biochemical and molecular characterization of Alternaria alternata isolates highly resistant to procymidone from broccoli and cabbage

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Bingran Wang ◽  
Tiancheng Lou ◽  
Lingling Wei ◽  
Wenchan Chen ◽  
Longbing Huang ◽  
...  
Keyword(s):  
Alternaria Alternata ◽  
Single Point ◽  
Sodium Dodecyl ◽  
Cross Resistance ◽  
Molecular Characteristics ◽  
Single Point Mutation ◽  
Wide Range ◽  
Significant Difference ◽  
Leaf Blights ◽  
High Level

AbstractAlternaria alternata, a causal agent of leaf blights and spots on a wide range of hosts, has a high risk of developing resistance to fungicides. Procymidone, a dicarboximide fungicide (DCF), has been widely used in controlling Alternaria leaf blights in China for decades. However, the resistance of A. alternata against DCFs has rarely been reported from crucifer plants. A total of 198 A. alternata isolates were collected from commercial fields of broccoli and cabbage during 2018–2019, and their sensitivities to procymidone were determined. Biochemical and molecular characteristics were subsequently compared between the high-level procymidone-resistant (ProHR) and procymidone-sensitive (ProS) isolates, and also between ProHR isolates from broccoli and cabbage. Compared with ProS isolates, the mycelial growth rate, sporulation capacity and virulence of most ProHR isolates were reduced; ProHR isolates displayed an increased sensitivity to osmotic stresses and a reduced sensitivity to sodium dodecyl sulfate (SDS); all ProHR isolates showed a reduced sensitivity to hydrogen peroxide (H2O2) except for the isolate B102. Correlation analysis revealed a positive cross-resistance between procymidone and iprodione, or fludioxonil. When treated with 10 μg/mL of procymidone, both mycelial intracellular glycerol accumulations (MIGAs) and relative expression of AaHK1 in ProS isolates were higher than those in ProHR isolates. Sequence alignment of AaHK1 from ten ProHR isolates demonstrated that five of them possessed a single-point mutation (P94A, V612L, E708K or Q924STOP), and four isolates had an insertion or a deletion in their coding regions. No significant difference in biochemical characteristics was observed among ProHR isolates from two different hosts, though mutations in AaHK1 of the cabbage-originated ProHR isolates were distinct from those of the broccoli-originated ProHR isolates.

Krypton 85 myocardial blood flow: precordial scintillation versus coronary sinus sampling

1965 ◽  
Vol 209 (4) ◽  
pp. 705-710 ◽  
Author(s):  
Michael D. Klein ◽  
Lawrence S. Cohen ◽  
Richard Gorlin
Keyword(s):  
Blood Flow ◽  
Myocardial Blood Flow ◽  
Coronary Sinus ◽  
Human Subjects ◽  
Radioactive Decay ◽  
Empirical Correction ◽  
Wide Range ◽  
Actual Flow ◽  
Flow Through ◽  
High Degree

Myocardial blood flow in human subjects was assessed by comparative simultaneous measurement of krypton 85 radioactive decay from coronary sinus and precordial scintillation. Empirical correction of postclearance background from precordial curves yielded a high degree of correlation between flows derived from the two sampling sites (r = .889, P < .001). Comparison of left and right coronary flows in nine subjects revealed similarity in flow through the two vessels over a wide range of actual flow values (r = .945, P < .001).

scholarly journals Genotype-Specific Signal Generation Based on Digestion of 3-Way DNA Junctions: Application to KRAS Variation Detection

2006 ◽  
Vol 52 (10) ◽  
pp. 1855-1863 ◽  
Author(s):  
Giulia Amicarelli ◽  
Daniel Adlerstein ◽  
Erlet Shehi ◽  
Fengfei Wang ◽  
G Mike Makrigiorgos
Keyword(s):  
Nucleic Acid ◽  
Concordance Rate ◽  
Signal Generation ◽  
Sequence Variants ◽  
Wild Type ◽  
Specific Signal ◽  
Novel Technology ◽  
Dna Junctions ◽  
Wide Range ◽  
Kras Codon

Abstract Background: Genotyping methods that reveal single-nucleotide differences are useful for a wide range of applications. We used digestion of 3-way DNA junctions in a novel technology, OneCutEventAmplificatioN (OCEAN) that allows sequence-specific signal generation and amplification. We combined OCEAN with peptide-nucleic-acid (PNA)-based variant enrichment to detect and simultaneously genotype v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) codon 12 sequence variants in human tissue specimens. Materials and Methods: We analyzed KRAS codon 12 sequence variants in 106 lung cancer surgical specimens. We conducted a PNA-PCR reaction that suppresses wild-type KRAS amplification and genotyped the product with a set of OCEAN reactions carried out in fluorescence microplate format. The isothermal OCEAN assay enabled a 3-way DNA junction to form between the specific target nucleic acid, a fluorescently labeled “amplifier”, and an “anchor”. The amplifier-anchor contact contains the recognition site for a restriction enzyme. Digestion produces a cleaved amplifier and generation of a fluorescent signal. The cleaved amplifier dissociates from the 3-way DNA junction, allowing a new amplifier to bind and propagate the reaction. Results: The system detected and genotyped KRAS sequence variants down to ∼0.3% variant-to-wild-type alleles. PNA-PCR/OCEAN had a concordance rate with PNA-PCR/sequencing of 93% to 98%, depending on the exact implementation. Concordance rate with restriction endonuclease-mediated selective-PCR/sequencing was 89%. Conclusion: OCEAN is a practical and low-cost novel technology for sequence-specific signal generation. Reliable analysis of KRAS sequence alterations in human specimens circumvents the requirement for sequencing. Application is expected in genotyping KRAS codon 12 sequence variants in surgical specimens or in bodily fluids, as well as single-base variations and sequence alterations in other genes.

scholarly journals CSE4 Genetically Interacts With the Saccharomyces cerevisiae Centromere DNA Elements CDE I and CDE II but Not CDE III: Implications for the Path of the Centromere DNA Around a Cse4p Variant Nucleosome

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 973-981
Author(s):  
Kevin C Keith ◽  
Molly Fitzgerald-Hayes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Loss ◽  
Structural Studies ◽  
Wild Type ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
Histone H3 Variant ◽  
Dna Elements ◽  
Mutant Cells ◽  
Loss Rates

Abstract Each Saccharomyces cerevisiae chromosome contains a single centromere composed of three conserved DNA elements, CDE I, II, and III. The histone H3 variant, Cse4p, is an essential component of the S. cerevisiae centromere and is thought to replace H3 in specialized nucleosomes at the yeast centromere. To investigate the genetic interactions between Cse4p and centromere DNA, we measured the chromosome loss rates exhibited by cse4 cen3 double-mutant cells that express mutant Cse4 proteins and carry chromosomes containing mutant centromere DNA (cen3). When compared to loss rates for cells carrying the same cen3 DNA mutants but expressing wild-type Cse4p, we found that mutations throughout the Cse4p histone-fold domain caused surprisingly large increases in the loss of chromosomes carrying CDE I or CDE II mutant centromeres, but had no effect on chromosomes with CDE III mutant centromeres. Our genetic evidence is consistent with direct interactions between Cse4p and the CDE I-CDE II region of the centromere DNA. On the basis of these and other results from genetic, biochemical, and structural studies, we propose a model that best describes the path of the centromere DNA around a specialized Cse4p-nucleosome.

Historical Dynamics

2018 ◽  
Author(s):  
Peter Turchin
Keyword(s):  
Religious Conversion ◽  
Synthetic Approach ◽  
Dynamical Processes ◽  
Factors Affecting ◽  
Historical Processes ◽  
Wide Range ◽  
Historical Dynamics ◽  
State Breakdown ◽  
Political Economic ◽  
High Degree

Many historical processes are dynamic. Populations grow and decline. Empires expand and collapse. Religions spread and wither. Natural scientists have made great strides in understanding dynamical processes in the physical and biological worlds using a synthetic approach that combines mathematical modeling with statistical analyses. Taking up the problem of territorial dynamics—why some polities at certain times expand and at other times contract—this book shows that a similar research program can advance our understanding of dynamical processes in history. The book develops hypotheses from a wide range of social, political, economic, and demographic factors: geopolitics, factors affecting collective solidarity, dynamics of ethnic assimilation/religious conversion, and the interaction between population dynamics and sociopolitical stability. It then translates these into a spectrum of mathematical models, investigates the dynamics predicted by the models, and contrasts model predictions with empirical patterns. The book's highly instructive empirical tests demonstrate that certain models predict empirical patterns with a very high degree of accuracy. For instance, one model accounts for the recurrent waves of state breakdown in medieval and early modern Europe. And historical data confirm that ethno-nationalist solidarity produces an aggressively expansive state under certain conditions (such as in locations where imperial frontiers coincide with religious divides). The strength of the book's results suggests that the synthetic approach advocated can significantly improve our understanding of historical dynamics.

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