scholarly journals An atlas of seven zebrafish hox cluster mutants provides insights into sub/neofunctionalization of vertebrate Hox clusters

Development ◽  
2021 ◽  
Vol 148 (11) ◽  
Author(s):  
Kazuya Yamada ◽  
Akiteru Maeno ◽  
Soh Araki ◽  
Morimichi Kikuchi ◽  
Masato Suzuki ◽  
...  
Keyword(s):  
Hox Genes ◽  
Main Body ◽  
Loss Of Function ◽  
Micro Computed Tomography ◽  
Genetic Studies ◽  
Hox Cluster ◽  
Species Specific ◽  
First Time ◽  
Hox Clusters ◽  
Tomography Scan

ABSTRACT Vertebrate Hox clusters are comprised of multiple Hox genes that control morphology and developmental timing along multiple body axes. Although results of genetic analyses using Hox-knockout mice have been accumulating, genetic studies in other vertebrates have not been sufficient for functional comparisons of vertebrate Hox genes. In this study, we isolated all of the seven hox cluster loss-of-function alleles in zebrafish using the CRISPR-Cas9 system. Comprehensive analysis of the embryonic phenotype and X-ray micro-computed tomography scan analysis of adult fish revealed several species-specific functional contributions of homologous Hox clusters along the appendicular axis, whereas important shared general principles were also confirmed, as exemplified by serial anterior vertebral transformations along the main body axis, observed in fish for the first time. Our results provide insights into discrete sub/neofunctionalization of vertebrate Hox clusters after quadruplication of the ancient Hox cluster. This set of seven complete hox cluster loss-of-function alleles provide a formidable resource for future developmental genetic analysis of the Hox patterning system in zebrafish.

Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk

Development ◽  
1998 ◽  
Vol 125 (3) ◽  
pp. 407-420 ◽  
Author(s):  
V.E. Prince ◽  
L. Joly ◽  
M. Ekker ◽  
R.K. Ho
Keyword(s):  
Hox Genes ◽  
Genomic Organization ◽  
Expression Patterns ◽  
Regional Identity ◽  
Hoxa Cluster ◽  
Hox Cluster ◽  
Sequence Homologies ◽  
Race Pcr ◽  
Linkage Relationships ◽  
Hox Clusters

The Hox genes are implicated in conferring regional identity to the anteroposterior axis of the developing embryo. We have characterized the organization and expression of hox genes in the teleost zebrafish (Danio rerio), and compared our findings with those made for the tetrapod vertebrates. We have isolated 32 zebrafish hox genes, primarily via 3′RACE-PCR, and analyzed their linkage relationships using somatic cell hybrids. We find that in comparison to the tetrapods, zebrafish has several additional hox genes, both within and beyond the expected 4 hox clusters (A-D). For example, we have isolated a member of hox paralogue group 8 lying on the hoxa cluster, and a member of hox paralogue group 10 lying on the b cluster, no equivalent genes have been reported for mouse or human. Beyond the 4 clusters (A-D) we have isolated a further 3 hox genes (the hoxx and y genes), which according to their sequence homologies lie in paralogue groups 4, 6, and 9. The hoxx4 and hoxx9 genes occur on the same set of hybrid chromosomes, hinting at the possibility of an additional hox cluster for the zebrafish. Similar to their tetrapod counterparts, zebrafish hox genes (including those with no direct tetrapod equivalent) demonstrate colinear expression along the anteroposterior (AP) axis of the embryo. However, in comparison to the tetrapods, anterior hox expression limits are compacted over a short AP region; some members of adjacent paralogue groups have equivalent limits. It has been proposed that during vertebrate evolution, the anterior limits of Hox gene expression have become dispersed along the AP axis allowing the genes to take on novel patterning roles and thus leading to increased axial complexity. In the teleost zebrafish, axial organization is relatively simple in comparison to that of the tetrapod vertebrates; this may be reflected by the less dispersed expression domains of the zebrafish hox genes.

scholarly journals Annelids win again: the first evidence of Hox antisense transcription in Spiralia

2021 ◽  
Author(s):  
Elena L. Novikova ◽  
Nadezhda I. Bakalenko ◽  
Milana A. Kulakova
Keyword(s):  
Hox Genes ◽  
Expression Patterns ◽  
Antisense Transcription ◽  
Antisense Transcripts ◽  
Platynereis Dumerilii ◽  
Non Coding Rnas ◽  
And Control ◽  
First Time ◽  
Hox Clusters

AbstractTo date it is becoming more and more obvious that multiple non-coding RNAs, once considered to be transcriptional noise, play a huge role in gene regulation during animal ontogenesis. Hox genes are key regulators of embryonic development, growth and regeneration of all bilaterian animals. It was shown that mammalian Hox loci are transcribed in both directions and noncoding RNAs maintain and control the normal functioning of Hox clusters. We revealed antisense transcripts of most of Hox genes in two lophotrochozoans, errant annelids Alitta virens and Platynereis dumerilii. It is for the first time when non-coding RNAs associated with Hox genes are found in spiralian animals. All these asRNAs can be referred to as natural antisense transcripts (NATs). We analyzed the expression of all detected NATs using sense probes to their Hox mRNAs during larval and postlarval development and regeneration by whole mount in situ hybridization (WMISH). We managed to clone several asRNAs (Avi-antiHox4-1, Avi-antiHox4-2 and Avi-antiHox5) of these annelids and analyzed their expression patterns as well. Our data indicate variable and complicated interplay between sense and antisense Hox transcripts during development and growth of two annelids. The presence of Hox antisense transcription in the representatives of different bilaterian clades (mammals, myriapods and annelids) and similar expression relationships in sense-antisense pairs suggest that this can be the ancestral feature of Hox cluster regulation.

scholarly journals Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features

2021 ◽  
Author(s):  
Teresa Shippy ◽  
Prashant S Hosmani ◽  
Mirella Flores-Gonzalez ◽  
Lukas A Mueller ◽  
Wayne B Hunter ◽  
...  
Keyword(s):  
Hox Genes ◽  
Regional Identity ◽  
Asian Citrus Psyllid ◽  
Expression Data ◽  
Diaphorina Citri ◽  
Sex Combs Reduced ◽  
Hox Cluster ◽  
Sex Combs ◽  
First Time ◽  
Anterior Posterior

Hox genes and their cofactors are essential developmental genes that specify regional identity in animals, including insects. A particularly interesting feature of Hox genes is their conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. Among insects, breaks in the cluster have been reported in a few species, but these seem to be the exception rather than the rule. We have annotated the ten Hox genes of the Asian citrus psyllid, Diaphorina citri, and determined that there is a split in its Hox cluster between the Deformed and Sex combs reduced genes. This is the first time a break at this position has been observed in an insect Hox cluster. We have also annotated the D. citri orthologs of the Hox cofactor genes homothorax, PKNOX and extradenticle. Interestingly, we found an additional copy of extradenticle in D. citri that appears to be a retrogene. Expression data and sequence conservation suggest that the extradenticle retrogene may have retained the original extradenticle function and allowed the parental extradenticle gene to diverge.

scholarly journals Codon harmonization reduces amino acid misincorporation in bacterially expressed P. falciparum proteins and improves their immunogenicity

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Neeraja Punde ◽  
Jennifer Kooken ◽  
Dagmar Leary ◽  
Patricia M. Legler ◽  
Evelina Angov
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Codon Usage ◽  
Dna Sequences ◽  
Structural Integrity ◽  
Host Cells ◽  
Loss Of Function ◽  
Species Specific ◽  
And Function ◽  
The Impact

Abstract Codon usage frequency influences protein structure and function. The frequency with which codons are used potentially impacts primary, secondary and tertiary protein structure. Poor expression, loss of function, insolubility, or truncation can result from species-specific differences in codon usage. “Codon harmonization” more closely aligns native codon usage frequencies with those of the expression host particularly within putative inter-domain segments where slower rates of translation may play a role in protein folding. Heterologous expression of Plasmodium falciparum genes in Escherichia coli has been a challenge due to their AT-rich codon bias and the highly repetitive DNA sequences. Here, codon harmonization was applied to the malarial antigen, CelTOS (Cell-traversal protein for ookinetes and sporozoites). CelTOS is a highly conserved P. falciparum protein involved in cellular traversal through mosquito and vertebrate host cells. It reversibly refolds after thermal denaturation making it a desirable malarial vaccine candidate. Protein expressed in E. coli from a codon harmonized sequence of P. falciparum CelTOS (CH-PfCelTOS) was compared with protein expressed from the native codon sequence (N-PfCelTOS) to assess the impact of codon usage on protein expression levels, solubility, yield, stability, structural integrity, recognition with CelTOS-specific mAbs and immunogenicity in mice. While the translated proteins were expected to be identical, the translated products produced from the codon-harmonized sequence differed in helical content and showed a smaller distribution of polypeptides in mass spectra indicating lower heterogeneity of the codon harmonized version and fewer amino acid misincorporations. Substitutions of hydrophobic-to-hydrophobic amino acid were observed more commonly than any other. CH-PfCelTOS induced significantly higher antibody levels compared with N-PfCelTOS; however, no significant differences in either IFN-γ or IL-4 cellular responses were detected between the two antigens.

scholarly journals Bark traits, decomposition and flammability of Australian forest trees

2017 ◽  
Vol 65 (4) ◽  
pp. 327 ◽  
Author(s):  
Saskia Grootemaat ◽  
Ian J. Wright ◽  
Peter M. van Bodegom ◽  
Johannes H. C. Cornelissen ◽  
Veronica Shaw
Keyword(s):  
Forest Tree ◽  
Remarkable Feature ◽  
Interspecific Differences ◽  
Eucalypt Plantations ◽  
Physical Traits ◽  
Key Driver ◽  
Multiple Species ◽  
Species Specific ◽  
First Time ◽  
Different Tissues

Bark shedding is a remarkable feature of Australian trees, yet relatively little is known about interspecific differences in bark decomposability and flammability, or what chemical or physical traits drive variation in these properties. We measured the decomposition rate and flammability (ignitibility, sustainability and combustibility) of bark from 10 common forest tree species, and quantified correlations with potentially important traits. We compared our findings to those for leaf litter, asking whether the same traits drive flammability and decomposition in different tissues, and whether process rates are correlated across tissue types. Considerable variation in bark decomposability and flammability was found both within and across species. Bark decomposed more slowly than leaves, but in both tissues lignin concentration was a key driver. Bark took longer to ignite than leaves, and had longer mass-specific flame durations. Variation in flammability parameters was driven by different traits in the different tissues. Decomposability and flammability were each unrelated, when comparing between the different tissue types. For example, species with fast-decomposing leaves did not necessarily have fast-decomposing bark. For the first time, we show how patterns of variation in decomposability and flammability of bark diverge across multiple species. By taking species-specific bark traits into consideration there is potential to make better estimates of wildfire risks and carbon loss dynamics. This can lead to better informed management decisions for Australian forests, and eucalypt plantations, worldwide.

scholarly journals Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 481 ◽  
Author(s):  
Chen ◽  
Lin ◽  
Xie ◽  
Zhong ◽  
Zhang ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Single Molecule ◽  
Functional Categories ◽  
Genetic Studies ◽  
Sequencing Technologies ◽  
Clusters Of Orthologous Groups ◽  
Long Read ◽  
Main Gene ◽  
First Time ◽  
Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

scholarly journals The Morphological and Anatomical Traits of the Leaf in Representative Vinca Species Observed on Indoor- and Outdoor-Grown Plants

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 622
Author(s):  
Alexandra Ciorîță ◽  
Septimiu Cassian Tripon ◽  
Ioan Gabriel Mircea ◽  
Dorina Podar ◽  
Lucian Barbu-Tudoran ◽  
...  
Keyword(s):  
Spongy Parenchyma ◽  
Palisade And Spongy Parenchyma ◽  
Chemical Composition Of Plants ◽  
Ultrastructural Characteristics ◽  
Species Specific ◽  
Microscopy Techniques ◽  
First Time ◽  
Thick Layers ◽  
Space Ratio ◽  
Indoor And Outdoor

Morphological and anatomical traits of the Vinca leaf were examined using microscopy techniques. Outdoor Vinca minor and V. herbacea plants and greenhouse cultivated V. major and V. major var. variegata plants had interspecific variations. All Vinca species leaves are hypostomatic. However, except for V. minor leaf, few stomata were also present on the upper epidermis. V. minor leaf had the highest stomatal index and V. major had the lowest, while the distribution of trichomes on the upper epidermis was species-specific. Differentiated palisade and spongy parenchyma tissues were present in all Vinca species’ leaves. However, V. minor and V. herbacea leaves had a more organized anatomical aspect, compared to V. major and V. major var. variegata leaves. Additionally, as a novelty, the cellular to intercellular space ratio of the Vinca leaf’s mesophyll was revealed herein with the help of computational analysis. Lipid droplets of different sizes and aspects were localized in the spongy parenchyma cells. Ultrastructural characteristics of the cuticle and its epicuticular waxes were described for the first time. Moreover, thick layers of cutin seemed to be characteristic of the outdoor plants only. This could be an adaptation to the unpredictable environmental conditions, but nevertheless, it might influence the chemical composition of plants.

History of Headache Research in Denmark

Cephalalgia ◽  
2001 ◽  
Vol 21 (7) ◽  
pp. 748-752 ◽  
Author(s):  
P Tfelt-Hansen
Keyword(s):  
Migraine With Aura ◽  
Tension Type Headache ◽  
Regional Cerebral Blood ◽  
Danish Population ◽  
Genetic Studies ◽  
History Of ◽  
Headache Clinic ◽  
Type Headache ◽  
Acute Headache ◽  
First Time

Headache research in Denmark started with the description in 1949 by Dalsgaard-Nielsen of the percutaneous nitroglycerin test. In 1976 Jes Olesen started The Copenhagen Acute Headache Clinic and from that time modern headache research began in Denmark. Specific changes in regional cerebral blood flow during attacks of migraine with aura, spreading oligaemia, were described for the first time in 1980. The first headache classification with operational diagnostic criteria was published in 1988 and used in a Danish population study from 1989. The lifetime prevalence of migraine was 8% in men and 25% in women. An intravenous nitroglycerin test was introduced in 1989 and has been developed as an experimental headache model. In 1993 it was suggested by Jes Olesen et al. that NO supersensitivity could be a possible molecular mechanism of migraine pain. Recent genetic studies have supported the distinction between migraine with aura and migraine without aura. From the middle of the 1980s the pathophysiology of tension-type headache has been investigated and recent results indicate central sensitization in patients with chronic tension-type headache.

scholarly journals Somatic clones heterozygous for recessive disease alleles of BMPR1A exhibit unexpected phenotypes in Drosophila

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Takuya Akiyama ◽  
Sırma D User ◽  
Matthew C Gibson
Keyword(s):  
Somatic Mutation ◽  
Cancer Genetics ◽  
Spontaneous Mutation ◽  
Tissue Level ◽  
Loss Of Function ◽  
Genetic Studies ◽  
Cell Clones ◽  
Heterozygous Carriers ◽  
Disease Initiation ◽  
Central Paradigm

The majority of mutations studied in animal models are designated as recessive based on the absence of visible phenotypes in germline heterozygotes. Accordingly, genetic studies primarily rely on homozygous loss-of-function to determine gene requirements, and a conceptually-related ‘two-hit model’ remains the central paradigm in cancer genetics. Here we investigate pathogenesis due to somatic mutation in epithelial tissues, a process that predominantly generates heterozygous cell clones. To study somatic mutation in Drosophila, we generated inducible alleles that mimic human Juvenile polyposis-associated BMPR1A mutations. Unexpectedly, four of these mutations had no phenotype in heterozygous carriers but exhibited clear tissue-level effects when present in somatic clones of heterozygous cells. We conclude that these alleles are indeed recessive when present in the germline, but nevertheless deleterious when present in heterozygous clones. This unforeseen effect, deleterious heteromosaicism, suggests a ‘one-hit’ mechanism for disease initiation that may explain some instances of pathogenesis associated with spontaneous mutation.

Analysis of Hox-4.5 and Hox-3.6 expression during newt limb regeneration: differential regulation of paralogous Hox genes suggest different roles for members of different Hox clusters

Development ◽  
1993 ◽  
Vol 117 (4) ◽  
pp. 1397-1407 ◽  
Author(s):  
H.G. Simon ◽  
C.J. Tabin
Keyword(s):  
Hox Genes ◽  
Limb Regeneration ◽  
Differential Regulation ◽  
Epithelial Tissue ◽  
Cdna Clones ◽  
Rnase Protection ◽  
Adult Kidney ◽  
Early Expression ◽  
Hox Clusters ◽  
Newt Limb

Adult urodele amphibians can regenerate their limbs and tail. Based on their roles in other developing systems, Hox genes are strong candidates for genes that play a role in regulating pattern formation during regeneration. There are four homologous clusters of Hox genes in vertebrate genomes. We isolated cDNA clones of two newt homeobox genes from homologous positions within two Hox clusters; Hox-4.5 and Hox-3.6. We used RNase protection on nonamputated (normal) and regenerating newt appendages and tissue to compare their transcriptional patterns. Both genes show increased expression upon amputation with similar kinetics. Hox-4.5 and Hox-3.6 transcription is limited to the mesenchymal cells in the regenerates and is not found in the epithelial tissue. In addition to regenerating appendages, both genes are transcriptionally active in adult kidney of the newt. Striking differences were found in the regulation of Hox-4.5 and Hox-3.6 when they were compared in unamputated limbs and in regenerating forelimbs versus regenerating hindlimbs. Hox-4.5 is expressed in the blastema of regenerating fore- and hindlimbs, but Hox-4.5 transcripts are not detectable in normal limbs. In contrast, Hox-3.6 transcripts are found exclusively in posterior appendages, but are present in normal as well as regenerating hindlimbs and tails. Hox-4.5 is also expressed at a higher level in proximal (mid-humerus) regenerates than in distal ones (mid-radius). When we proximalized the positional memory of a distal blastema with retinoic acid, we find that the early expression level of Hox-4.5 is also proximalized. When the expression of these genes is compared to the expression of two previously reported newt Hox genes, a consistent pattern emerges, which can be interpreted in terms of differential roles for the different Hox clusters in determining regenerative limb morphology.

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