scholarly journals A Potential Method for Rapid Screening of Amphioxus Founder Harboring Germline Mutation and Transgene

2021 ◽  
Vol 9 ◽  
Author(s):  
Jiaqi Zou ◽  
Xiaotong Wu ◽  
Chenggang Shi ◽  
Yanhong Zhong ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Adult Stage ◽  
Model Organism ◽  
Potential Method ◽  
Rapid Screening ◽  
Phylogenetic Position ◽  
Origin And Evolution ◽  
Normal Number ◽  
Cas9 Protein ◽  
Speed Up ◽  
Mutation Type

Amphioxus is a promising model organism for understanding the origin and evolution of vertebrates due to its basal phylogenetic position among chordates. We here compared the mutation efficacy and mutation type of tail tips and gametes of amphioxus founders injected with Cas9 protein and six different sgRNAs targeting five distinct genes, and revealed a strong correlation for mutation efficacy and a mild correlation for mutation type among the two tissues. In addition, we also observed a positive relationship between gene insertions observed in tail tips and gametes of amphioxus founders injected with Tol2 transposase and two different transgenic constructs. Finally, we showed that amphioxus larvae which had their tail tips cut at the 3–4 gill-slit stage were able to recover within 6 days and developed a normal number of gonads at the adult stage, and that F0 larvae carry similar mutation efficacy and type in the posterior end to that in the tail tips after their metamorphosis. Together, these findings suggest a great potential for obtaining valid amphioxus founders with desired mutations and transgenes at as early as the early larval stage, which will certainly speed up the generation of amphioxus mutants and transgenes and make it more cost- and labor-effective.

Phylogeny, systematics and rarity assessment of New Zealand endemic Saphydrus beetles and related enigmatic larvae (Coleoptera : Hydrophilidae : Cylominae)

2020 ◽  
Author(s):  
Matthias Seidel ◽  
Yûsuke N. Minoshima ◽  
Richard A. B. Leschen ◽  
Martin Fikácek
Keyword(s):  
New Zealand ◽  
Adult Stage ◽  
Single Species ◽  
Species Level ◽  
Phylogenetic Position ◽  
Primary Reason ◽  
Altitudinal Distribution ◽  
Population Number ◽  
Threatened Status ◽  
Over Time

The New Zealand endemic beetle genus Saphydrus Sharp, 1884 (Coleoptera:Hydrophilidae:Cylominae) is studied in order to understand its phylogenetic position, species-level systematics, biology and distribution, and to reveal reasons for its rarity. The first complete genus-level phylogeny of Cylominae based on two mitochondrial (cox1, 16S) and two nuclear genes (18S, 28S) covering 18 of 19 genera of the subfamily reveals Saphydrus as an isolated lineage situated in a clade with Cylorygmus (South America), Relictorygmus (South Africa) and Eurygmus (Australia). DNA is used to associate two larval morphotypes with Saphydrus: one of them represents the larvae of S. suffusus Sharp, 1884; the other, characterised by unique characters of the head and prothorax morphology, is revealed as sister but not closely related to Saphydrus. It is described here as Enigmahydrus, gen. nov. with a single species, E. larvalis, sp. nov., whose adult stage remains unknown. Saphydrus includes five species, two of which (S. moeldnerae, sp. nov. and S. tanemahuta, sp. nov.) are described as new. Larvae of Enigmahydrus larvalis and Saphydrus suffusus are described and illustrated in detail based on DNA-identified specimens. Candidate larvae for Saphydrus obesus Sharp, 1884 and S. tanemahuta are illustrated and diagnosed. Specimen data are used to evaluate the range, altitudinal distribution, seasonality and population dynamics over time for all species. Strongly seasonal occurrence of adults combined with other factors (winter occurrence in S. obesus, occurrence at high altitudes in S. tanemahuta) is hypothesised as the primary reason of the rarity for Saphydrus species. By contrast, Enigmahydrus larvalis underwent a strong decline in population number and size since the 1970s and is currently known from a single, locally limited population; we propose the ‘nationally threatened’ status for this species. http://zoobank.org/urn:lsid:zoobank.org:pub:28D87163-29E8-418C-9380-262D3038023A

scholarly journals Application of CRISPR/Cas9 Nuclease in Amphioxus Genome Editing

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1311
Author(s):  
Liuru Su ◽  
Chenggang Shi ◽  
Xin Huang ◽  
Yiquan Wang ◽  
Guang Li
Keyword(s):  
Animal Model ◽  
Thermal Treatment ◽  
Genome Editing ◽  
Phylogenetic Position ◽  
Transcription Activator ◽  
Cell Stage ◽  
System A ◽  
Cas9 Nuclease ◽  
Cas9 Protein ◽  
Amphioxus Genome

The cephalochordate amphioxus is a promising animal model for studying the origin of vertebrates due to its key phylogenetic position among chordates. Although transcription activator-like effector nucleases (TALENs) have been adopted in amphioxus genome editing, its labor-intensive construction of TALEN proteins limits its usage in many laboratories. Here we reported an application of the CRISPR/Cas9 system, a more amenable genome editing method, in this group of animals. Our data showed that while co-injection of Cas9 mRNAs and sgRNAs into amphioxus unfertilized eggs caused no detectable mutations at targeted loci, injections of Cas9 mRNAs and sgRNAs at the two-cell stage, or of Cas9 protein and sgRNAs before fertilization, can execute efficient disruptions of targeted genes. Among the nine tested sgRNAs (targeting five genes) co-injected with Cas9 protein, seven introduced mutations with efficiency ranging from 18.4% to 90% and four caused specific phenotypes in the injected embryos. We also demonstrated that monomerization of sgRNAs via thermal treatment or modifying the sgRNA structure could increase mutation efficacies. Our study will not only promote application of genome editing method in amphioxus research, but also provide valuable experiences for other organisms in which the CRISPR/Cas9 system has not been successfully applied.

scholarly journals Phylogenetic relationships among extinct and extant turtles: the position of Pleurodira and the effects of the fossils on rooting crown-group turtles

2010 ◽  
Vol 79 (3) ◽  
pp. 93-106 ◽  
Author(s):  
Juliana Sterli
Keyword(s):  
Phylogenetic Relationships ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Separate Analysis ◽  
Crown Group ◽  
Rapid Radiation ◽  
Present Contribution ◽  
Origin And Evolution

The origin and evolution of the crown-group of turtles (Cryptodira + Pleurodira) is one of the most interesting topics in turtle evolution, second perhaps only to the phylogenetic position of turtles among amniotes. The present contribution focuses on the former problem, exploring the phylogenetic relationships of extant and extinct turtles based on the most comprehensive phylogenetic dataset of morphological and molecular data analyzed to date. Parsimony analyses were conducted for different partitions of data (molecular and morphological) and for the combined dataset. In the present analysis, separate analyses of the molecular data always retrieve Pleurodira allied to Trionychia. Separate analysis of the morphological dataset, by contrast, depicts a more traditional arrangement of taxa, with Pleurodira as the sister group of Cryptodira, being Chelonioidea the most basal cryptodiran clade. The simultaneous analysis of all available data retrieves all major extant clades as monophyletic, except for Cryptodira given that Pleurodira is retrieved as the sister group of Trionychia. The paraphyly of Cryptodira is an unorthodox result, and is mainly caused by the combination of two factors. First, the molecular signal allies Pleurodira and Trionychia. Second, the morphological data with extinct taxa locates the position of the root of crown-group Testudines in the branch leading to Chelonioidea. This study highlights major but poorly explored topics of turtle evolution: the alternate position of Pleurodira and the root of crown turtles. The diversification of crown turtles is characterized by the presence of long external branches and short internal branches (with low support for the internal nodes separating the major clades of crown turtles), suggesting a rapid radiation of this clade. This rapid radiation is also supported by the fossil record, because soon after the appearance of the oldest crown-group turtles (Middle-Late Jurassic of Asia) the number and diversity of turtles increases remarkably. This evolutionary scenario of a rapid diversification of modern turtles into the major modern lineages is likely the reason for the difficulty in determining the interrelationships and the position of the root of crown-group turtles.

scholarly journals A Novel Biological Role of Tachykinins as an Up-Regulator of Oocyte Growth: Identification of an Evolutionary Origin of Tachykininergic Functions in the Ovary of the Ascidian, Ciona intestinalis

Endocrinology ◽  
2008 ◽  
Vol 149 (9) ◽  
pp. 4346-4356 ◽  
Author(s):  
Masato Aoyama ◽  
Tsuyoshi Kawada ◽  
Manabu Fujie ◽  
Kohji Hotta ◽  
Tsubasa Sakai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Model Organism ◽  
Ciona Intestinalis ◽  
Enzymatic Activities ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Specific Expression ◽  
Oocyte Growth ◽  
Vitellogenic Stage

Tachykinins (TKs) and their receptors have been shown to be expressed in the mammalian ovary. However, the biological roles of ovarian TKs have yet to be verified. Ci-TK-I and Ci-TK-R, characterized from the protochordate (ascidian), Ciona intestinalis, are prototypes of vertebrate TKs and their receptors. In the present study, we show a novel biological function of TKs as an inducible factor for oocyte growth using C. intestinalis as a model organism. Immunostaining demonstrated the specific expression of Ci-TK-R in test cells residing in oocytes at the vitellogenic stage. DNA microarray and real-time PCR revealed that Ci-TK-I induced gene expression of several proteases, including cathepsin D, chymotrypsin, and carboxy-peptidase B1, in the ovary. The enzymatic activities of these proteases in the ovary were also shown to be enhanced by Ci-TK-I. Of particular significance is that the treatment of Ciona oocytes with Ci-TK-I resulted in progression of growth from the vitellogenic stage to the post-vitellogenic stage. The Ci-TK-I-induced oocyte growth was blocked by a TK antagonist or by protease inhibitors. These results led to the conclusion that Ci-TK-I enhances growth of the vitellogenic oocytes via up-regulation of gene expression and enzymatic activities of the proteases. This is the first clarification of the biological roles of TKs in the ovary and the underlying essential molecular mechanism. Furthermore, considering the phylogenetic position of ascidians as basal chordates, we suggest that the novel TK-regulated oocyte growth is an “evolutionary origin” of the tachykininergic functions in the ovary.

scholarly journals Origin and evolution of the Haustoriidae (Amphipoda): A eulogy for the Haustoriidira

2020 ◽  
Author(s):  
Zachary B. Hancock ◽  
Hiroshi Ogawa ◽  
Jessica E. Light ◽  
Mary K. Wicksten
Keyword(s):  
New Genus ◽  
Impact Crater ◽  
Strong Support ◽  
Phylogenetic Position ◽  
Origin And Evolution ◽  
The Pacific ◽  
The Family ◽  
Limited Dispersal ◽  
Dispersal Abilities ◽  
Recent Attention

ABSTRACTHaustoriid amphipods, despite their ubiquity in coastal sand or mud, have received little recent attention and their systematics and phylogenetics are largely unresolved. Some efforts have been made at classifying the family within the broader Amphipoda, but there is persistent incongruence in its placement among different authors and techniques. Furthermore, there exists no phylogenetic hypothesis of intrafamilial relationships despite the potential for rich biogeographic information to be gained given the specific habitat requirements of haustoriids and their limited dispersal abilities. In this work, we evaluate the competing hypotheses on the phylogenetic position of the Haustoriidae within Amphipoda by examining new and previously published sequences of nearly 100 species across 38 families. We find strong support for the Haustoriidae as basal gammarids, and that other families placed within the parvorder “Haustoriidira” are spread across Amphipoda. The radiation began during the Eocene and may have been driven in North America by the rapid filling of a coastal niche opened by the Chesapeake Bay impact crater. Unlike previous work, we find that the Pacific-endemic genus Eohaustorius is the most basal haustoriid, and that it separated from the rest of the family ~31 Mya. Finally, based on ancestral reconstructions, we provide taxonomic recommendations for relationships within Haustoriidae, including the elevation of a new genus, Cryptohaustorius. We conclude by recommending that the “Haustoriidira” be abandoned.

Levipalatum texanum n. gen., n. sp. (Nematoda: Diplogastridae), an androdioecious species from the south-eastern USA

Nematology ◽  
2014 ◽  
Vol 16 (6) ◽  
pp. 695-709 ◽  
Author(s):  
Erik J. Ragsdale ◽  
Erik J. Ragsdale ◽  
Natsumi Kanzaki ◽  
Erik J. Ragsdale ◽  
Natsumi Kanzaki ◽  
...  
Keyword(s):  
New Species ◽  
Model Organism ◽  
Sister Group ◽  
Small Subunit ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Protein Coding ◽  
Eastern Usa ◽  
A New Species

A new species of diplogastrid nematode, Levipalatum texanum n. gen., n. sp., was isolated from scarab beetles (Coleoptera: Scarabaeidae) in Texas and baited from soil in Virginia, USA. Levipalatum n. gen. is circumscribed by stomatal and pharyngeal morphology, namely a long, hooked dorsal tooth connected to a ‘palate’ projecting anteriad and mediad, subventral telostegostomatal ridges of denticles, and the dorsal radius of the pharynx bulging anteriad. The males of the new species are distinguished from most other Diplogastridae by the frequent presence of ten pairs of genital papillae. Phylogenetic relationships inferred from 11 ribosomal protein-coding genes and a fragment of the small subunit rRNA gene strongly support L. texanum n. gen., n. sp. to be a sister group to Rhabditolaimus, which lacks all the stegostomatal and pharyngeal characters diagnosing the new genus. The new species expands comparative studies of the radiation of feeding morphology that are anchored on the model organism Pristionchus pacificus. The phylogenetic position of L. texanum n. gen., n. sp. indicates a new case of convergent evolution of hermaphroditism in Diplogastridae.

Assessment of phloem mobility of xenobiotics in Triticum aestivum and Brachypodium distachyon

2014 ◽  
Vol 41 (6) ◽  
pp. 598 ◽  
Author(s):  
Olena Zhivotovsky Castello ◽  
Andrew J. Bowling ◽  
Gerrit Deboer ◽  
Yelena Adelfinskaya
Keyword(s):  
Triticum Aestivum ◽  
Early Stage ◽  
Brachypodium Distachyon ◽  
Model Organism ◽  
Triticum Aestivum L ◽  
Rapid Screening ◽  
Developing Seed ◽  
Significant Difference ◽  
Microscopic Studies ◽  
Phloem Mobility

Due to evolved resistance and environmental regulations, there is a particular need in the agricultural market for a new graminicide. An essential requirement of a novel, foliar applied graminicide is sufficient phloem mobility in the plant to reach meristematic tissues for the expression of activity leading to the desired control of unwanted vegetative growth. A robust and reliable phloem bioassay utilising a monocot species is highly desirable for early stage experimental compounds. Vascular tissues and translocation patterns of organic compounds in purple false brome (Brachypodium distachyon L. P. Beauv.), a model organism for temperate grasses, were studied and compared with those of wheat (Triticum aestivum L.). Microscopic studies with tracer dyes were used to determine if B. distachyon has a xylem discontinuity between the developing seed and the rachilla xylem, the same as found in T. aestivum. Based on 14C-radiolabelled and non-radiolabelled studies using known xylem and phloem mobile pesticidal compounds, there was a significant difference in the amount of the xylem mobile compounds in the chaff and stem as compared with the phloem mobile compounds found in the grain. The findings described in this report show a clear evidence of xylem discontinuity in B. distachyon, and provide a novel system for a rapid screening of phloem mobility of herbicides in monocot species.

THE GAS-LIQUID CHROMATOGRAPHY OF STEROID FORMATES; AN APPLICATION IN CONGENITAL ADRENAL HYPERPLASIA

1970 ◽  
Vol 47 (1) ◽  
pp. 55-64 ◽  
Author(s):  
H. L. J. MAKIN
Keyword(s):  
Liquid Chromatography ◽  
Periodate Oxidation ◽  
Oxygenation Index ◽  
Rapid Screening ◽  
Gas Liquid Chromatography ◽  
Adrenal Hyperplasia ◽  
Trimethylsilyl Ethers ◽  
Rapid Screening Test ◽  
Speed Up ◽  
Urinary Steroid

SUMMARY The gas-liquid chromatography (GLC) of some C19 steroid formates has been investigated in an attempt to speed up the final stages of the estimation of the 11-oxygenation index. SE-30 was found to give the best separation of the urinary C19 steroids formed after borohydride reduction and periodate oxidation of urine. Formates, acetates, propionates, n-butyrates, valerates and trimethylsilyl ethers were examined; formate esters gave the best separation of androsterone and aetiocholanolone. Estimation of the 11-oxygenation index by GLC increases the specificity and speed of single estimations and it is suggested that this method may find use as a rapid screening test for abnormal urinary steroid patterns.

scholarly journals Explainable DCNN based chest X-ray image analysis and classification for COVID-19 pneumonia detection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jie Hou ◽  
Terry Gao
Keyword(s):  
Large Scale ◽  
Rapid Screening ◽  
X Rays ◽  
X Ray ◽  
Disease Mechanisms ◽  
Average Accuracy ◽  
Speed Up ◽  
Chest X Ray ◽  
Detection And Diagnosis ◽  
New Diagnosis

AbstractTo speed up the discovery of COVID-19 disease mechanisms by X-ray images, this research developed a new diagnosis platform using a deep convolutional neural network (DCNN) that is able to assist radiologists with diagnosis by distinguishing COVID-19 pneumonia from non-COVID-19 pneumonia in patients based on chest X-ray classification and analysis. Such a tool can save time in interpreting chest X-rays and increase the accuracy and thereby enhance our medical capacity for the detection and diagnosis of COVID-19. The explainable method is also used in the DCNN to select instances of the X-ray dataset images to explain the behavior of training-learning models to achieve higher prediction accuracy. The average accuracy of our method is above 96%, which can replace manual reading and has the potential to be applied to large-scale rapid screening of COVID-9 for widely use cases.

scholarly journals Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Tomoyuki Fukuda ◽  
Yuki Ebi ◽  
Tetsu Saigusa ◽  
Kentaro Furukawa ◽  
Shun-ichi Yamashita ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Mitochondrial Function ◽  
Outer Membrane Protein ◽  
Model Organism ◽  
Mitochondrial Outer Membrane ◽  
Independent Function ◽  
Mitochondrial Import ◽  
Origin And Evolution ◽  
Selective Degradation ◽  
Growth Ability

Degradation of mitochondria through mitophagy contributes to the maintenance of mitochondrial function. In this study, we identified that Atg43, a mitochondrial outer membrane protein, serves as a mitophagy receptor in the model organism Schizosaccharomyces pombe to promote the selective degradation of mitochondria. Atg43 contains an Atg8-family-interacting motif essential for mitophagy. Forced recruitment of Atg8 to mitochondria restores mitophagy in Atg43-deficient cells, suggesting that Atg43 tethers expanding isolation membranes to mitochondria. We found that the mitochondrial import factors, including the Mim1–Mim2 complex and Tom70, are crucial for mitophagy. Artificial mitochondrial loading of Atg43 bypasses the requirement of the import factors, suggesting that they contribute to mitophagy through Atg43. Atg43 not only maintains growth ability during starvation but also facilitates vegetative growth through its mitophagy-independent function. Thus, Atg43 is a useful model to study the mechanism and physiological roles, as well as the origin and evolution, of mitophagy in eukaryotes.

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