scholarly journals Distribution, Function, and Evolution of a Gene Essential for Trichothecene Toxin Biosynthesis in Trichoderma

2021 ◽  
Vol 12 ◽  
Author(s):  
Santiago Gutiérrez ◽  
Susan P. McCormick ◽  
Rosa E. Cardoza ◽  
Hye-Seon Kim ◽  
Laura Lindo Yugueros ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Deletion Mutant ◽  
Phylogenetic Analyses ◽  
Parent Compound ◽  
Genomic Region ◽  
The Other ◽  
Terpene Synthase ◽  
Biosynthetic Gene ◽  
Study Analysis ◽  
Wide Range

Trichothecenes are terpenoid toxins produced by species in 10 fungal genera, including species of Trichoderma. The trichothecene biosynthetic gene (tri) cluster typically includes the tri5 gene, which encodes a terpene synthase that catalyzes formation of trichodiene, the parent compound of all trichothecenes. The two Trichoderma species, Trichoderma arundinaceum and T. brevicompactum, that have been examined are unique in that tri5 is located outside the tri cluster in a genomic region that does not include other known tri genes. In the current study, analysis of 35 species representing a wide range of the phylogenetic diversity of Trichoderma revealed that 22 species had tri5, but only 13 species had both tri5 and the tri cluster. tri5 was not located in the cluster in any species. Using complementation analysis of a T. arundinaceum tri5 deletion mutant, we demonstrated that some tri5 homologs from species that lack a tri cluster are functional, but others are not. Phylogenetic analyses suggest that Trichoderma tri5 was under positive selection following its divergence from homologs in other fungi but before Trichoderma species began diverging from one another. We propose two models to explain these diverse observations. One model proposes that the location of tri5 outside the tri cluster resulted from loss of tri5 from the cluster in an ancestral species followed by reacquisition via horizontal transfer. The other model proposes that in species that have a functional tri5 but lack the tri cluster, trichodiene production provides a competitive advantage.

scholarly journals Pratylenchus penetrans Parasitizing Potato Crops: Morphometric and Genetic Variability of Portuguese Isolates

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 603
Author(s):  
Diogo Gil ◽  
Joana M.S. Cardoso ◽  
Isabel Abrantes ◽  
Ivânia Esteves
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Phylogenetic Analyses ◽  
Intraspecific Variability ◽  
Its Region ◽  
Genomic Region ◽  
Internal Transcribed Spacers ◽  
Coi Gene ◽  
Pratylenchus Penetrans ◽  
Wide Range

The root lesion Pratylenchus penetrans is an economically important pest affecting a wide range of plants. The morphometry of five P. penetrans isolates, parasitizing potato roots in Portugal, was compared and variability within and between isolates was observed. Of the 15 characters assessed, vulva position (V%) in females and the stylet length in both females/males showed the lowest coefficient of intra and inter-isolate variability. Moreover, DNA sequencing of the internal transcribed spacers (ITS) genomic region and cytochrome c oxidase subunit 1 (COI) gene was performed, in order to evaluate the intraspecific genetic variability of this species. ITS revealed higher isolate genetic diversity than the COI gene, with 15 and 7 different haplotypes from the 15 ITS and 14 COI sequences, respectively. Intra- and inter-isolate genetic diversity was found considering both genomic regions. The differentiation of these isolates was not related with their geographical origin. In spite of the high intraspecific variability, phylogenetic analyses revealed that both ITS region and COI gene separate P. penetrans from other related species. Our findings contribute to increasing the understanding of P. penetrans variability.

2D Color-Intensity Representation of Ultrasonic Thickness Gauge Measurements

2020 ◽  
pp. 1192-1198
Author(s):  
M.S. Mohammad ◽  
Tibebe Tesfaye ◽  
Kim Ki-Seong
Keyword(s):  
Cost Effective ◽  
The Other ◽  
Thickness Gauge ◽  
Color Intensity ◽  
Digital Readout ◽  
Flat Surfaces ◽  
Video Cameras ◽  
Wide Range ◽  
Cost Effective Alternative ◽  
Ultrasonic Thickness

Ultrasonic thickness gauges are easy to operate and reliable, and can be used to measure a wide range of thicknesses and inspect all engineering materials. Supplementing the simple ultrasonic thickness gauges that present results in either a digital readout or as an A-scan with systems that enable correlating the measured values to their positions on the inspected surface to produce a two-dimensional (2D) thickness representation can extend their benefits and provide a cost-effective alternative to expensive advanced C-scan machines. In previous work, the authors introduced a system for the positioning and mapping of the values measured by the ultrasonic thickness gauges and flaw detectors (Tesfaye et al. 2019). The system is an alternative to the systems that use mechanical scanners, encoders, and sophisticated UT machines. It used a camera to record the probe’s movement and a projected laser grid obtained by a laser pattern generator to locate the probe on the inspected surface. In this paper, a novel system is proposed to be applied to flat surfaces, in addition to overcoming the other limitations posed due to the use of the laser projection. The proposed system uses two video cameras, one to monitor the probe’s movement on the inspected surface and the other to capture the corresponding digital readout of the thickness gauge. The acquired images of the probe’s position and thickness gauge readout are processed to plot the measured data in a 2D color-coded map. The system is meant to be simpler and more effective than the previous development.

p-Sulfonic acid calix[n]arene catalyzed synthesis of bioactive heterocycles: A review

2020 ◽  
Vol 24 ◽  
Author(s):  
Bubun Banerjee ◽  
Gurpreet Kaur ◽  
Navdeep Kaur
Keyword(s):  
Supramolecular Chemistry ◽  
Sulfonic Acid ◽  
Catalytic Efficiency ◽  
The Other ◽  
Reaction Conditions ◽  
Metal Free ◽  
Bioactive Scaffolds ◽  
Wide Range ◽  
Efficient Alternative ◽  
Bioactive Heterocycles

: Metal-free organocatalysts are becoming an important tool for the sustainable developments of various bioactive heterocycles. On the other hand, during last two decades, calix[n]arenes have been gaining considerable attention due to their wide range of applicability in the field of supramolecular chemistry. Recently, sulfonic acid functionalized calix[n] arenes are being employed as an efficient alternative catalyst for the synthesis of various bioactive scaffolds. In this review we have summarized the catalytic efficiency of p-sulfonic acid calix[n]arenes for the synthesis of diverse biologically promising scaffolds under various reaction conditions. There is no such review available in the literature showing the catalytic applicability of p-sulfonic acid calix[n]arenes. Therefore, we strongly believe that this review will surely attract those researchers who are interested about this fascinating organocatalyst.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

scholarly journals Density Guarantee on Finding Multiple Subgraphs and Subtensors

2021 ◽  
Vol 15 (5) ◽  
pp. 1-32
Author(s):  
Quang-huy Duong ◽  
Heri Ramampiaro ◽  
Kjetil Nørvåg ◽  
Thu-lan Dam
Keyword(s):  
Lower Bound ◽  
State Of The Art ◽  
The State ◽  
The Other ◽  
Exact Methods ◽  
Practical Solution ◽  
Novel Approach ◽  
Wide Range ◽  
Real World Datasets ◽  
Tensor Data

Dense subregion (subgraph & subtensor) detection is a well-studied area, with a wide range of applications, and numerous efficient approaches and algorithms have been proposed. Approximation approaches are commonly used for detecting dense subregions due to the complexity of the exact methods. Existing algorithms are generally efficient for dense subtensor and subgraph detection, and can perform well in many applications. However, most of the existing works utilize the state-or-the-art greedy 2-approximation algorithm to capably provide solutions with a loose theoretical density guarantee. The main drawback of most of these algorithms is that they can estimate only one subtensor, or subgraph, at a time, with a low guarantee on its density. While some methods can, on the other hand, estimate multiple subtensors, they can give a guarantee on the density with respect to the input tensor for the first estimated subsensor only. We address these drawbacks by providing both theoretical and practical solution for estimating multiple dense subtensors in tensor data and giving a higher lower bound of the density. In particular, we guarantee and prove a higher bound of the lower-bound density of the estimated subgraph and subtensors. We also propose a novel approach to show that there are multiple dense subtensors with a guarantee on its density that is greater than the lower bound used in the state-of-the-art algorithms. We evaluate our approach with extensive experiments on several real-world datasets, which demonstrates its efficiency and feasibility.

scholarly journals Grasp to See—Object Classification Using Flexion Glove with Support Vector Machine

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1461
Author(s):  
Shun-Hsin Yu ◽  
Jen-Shuo Chang ◽  
Chia-Hung Dylan Tsai
Keyword(s):  
Support Vector Machine ◽  
Daily Life ◽  
Object Classification ◽  
Target Object ◽  
The Other ◽  
Support Vector ◽  
Wide Range ◽  
Dark Space ◽  
Flex Sensors ◽  
Shape And Size

This paper proposes an object classification method using a flexion glove and machine learning. The classification is performed based on the information obtained from a single grasp on a target object. The flexion glove is developed with five flex sensors mounted on five finger sleeves, and is used for measuring the flexion of individual fingers while grasping an object. Flexion signals are divided into three phases, and they are the phases of picking, holding and releasing, respectively. Grasping features are extracted from the phase of holding for training the support vector machine. Two sets of objects are prepared for the classification test. One is printed-object set and the other is daily-life object set. The printed-object set is for investigating the patterns of grasping with specified shape and size, while the daily-life object set includes nine objects randomly chosen from daily life for demonstrating that the proposed method can be used to identify a wide range of objects. According to the results, the accuracy of the classifications are achieved 95.56% and 88.89% for the sets of printed objects and daily-life objects, respectively. A flexion glove which can perform object classification is successfully developed in this work and is aimed at potential grasp-to-see applications, such as visual impairment aid and recognition in dark space.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

scholarly journals Natural Science and Supernatural Thought Experiments

Religions ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 389
Author(s):  
James Robert Brown
Keyword(s):  
Natural Science ◽  
Thought Experiment ◽  
Thought Experiments ◽  
The Other ◽  
Space And Time ◽  
Wide Range ◽  
The Difference ◽  
Theological Thought

Religious notions have long played a role in epistemology. Theological thought experiments, in particular, have been effective in a wide range of situations in the sciences. Some of these are merely picturesque, others have been heuristically important, and still others, as I will argue, have played a role that could be called essential. I will illustrate the difference between heuristic and essential with two examples. One of these stems from the Newton–Leibniz debate over the nature of space and time; the other is a thought experiment of my own constructed with the aim of making a case for a more liberal view of evidence in mathematics.

Diversity, morphology, and phylogeny of coleoid cephalopods from the Upper Cretaceous Plattenkalks of Lebanon-Part I: Prototeuthidina

2011 ◽  
Vol 85 (2) ◽  
pp. 234-249 ◽  
Author(s):  
Dirk Fuchs ◽  
Neal Larson
Keyword(s):  
Digestive Tract ◽  
Upper Cretaceous ◽  
Soft Part ◽  
Phylogenetic Analyses ◽  
Early Jurassic ◽  
The Other ◽  
Large Collection ◽  
Shaped Body ◽  
Cretaceous Deposits

Morphologic analyses of a large collection of coleoid cephalopods from the Lebanese Upper Cretaceous yielded a much higher diversity than previously assumed and revealed numerous extraordinarily well-preserved, soft-part characters. An analysis of the Prototeuthidina, a gladius-bearing group with a slender torpedo-shaped body, revealed two species:Dorateuthis syriacaandBoreopeltis smithin. sp. Previously unknown soft-part characters, such as the digestive tract, the gills, and the cephalic cartilage considerably improved our knowledge ofD. syriaca.Since none of the investigated specimens show more than eight arms, similarities with modern squids are regarded as superficial.Boreopeltis smithin. sp. is erected on the basis of its comparatively wideParaplesioteuthis-like gladius. The latter species represents the first unambiguous record of this genus in Upper Cretaceous deposits. Phylogenetic analyses indicate that the prototeuthidid clade consists of two lineages. The plesioteuthidid lineage originates from early JurassicParaplesioteuthisand leads toPlesioteuthisandDorateuthis.The other lineage is morphologically more conservative and leads toBoreopeltis.

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