scholarly journals Molecular characterization of inversion breakpoints in the Drosophila nasuta species group

2021 ◽  
Author(s):  
Dat Mai ◽  
Doris Bachtrog
Keyword(s):  
Species Group ◽  
Functional Studies ◽  
Chromosomal Inversions ◽  
Reference Quality ◽  
Inversion Breakpoints ◽  
Drosophila Nasuta ◽  
Future Population ◽  
Chromosome Level ◽  
Rate Of Accumulation

Chromosomal inversions are fundamental drivers of genome evolution. In the Drosophila genus, inversions have been widely characterized cytologically, and play an important role in local adaptation. Here, we characterize chromosomal inversions in the Drosophila nasuta species group using chromosome-level, reference-quality assemblies of seven species and subspecies in this clade. Reconstruction of ancestral karyotypes allowed us to infer the order in which the 22 identified inversions occurred along the phylogeny. We found a higher rate of inversions on the X chromosome, and heterogeneity in the rate of accumulation across the phylogeny. We molecularly characterize the breakpoints of six autosomal inversions, and found that repeated sequences are associated with inversion breakpoints in four of these inversions, suggesting that ectopic recombination is an important mechanism in generating inversion. Characterization of inversions in this species group provides a foundation for future population genetic and functional studies in this recently diverged species group.

scholarly journals The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nathalie Raharimalala ◽  
Stephane Rombauts ◽  
Andrew McCarthy ◽  
Andréa Garavito ◽  
Simon Orozco-Arias ◽  
...  
Keyword(s):  
Wild Species ◽  
Illegitimate Recombination ◽  
Recombination Mechanism ◽  
Comparative Analyses ◽  
Robusta Coffee ◽  
Caffeine Synthase ◽  
The World ◽  
Decaffeinated Coffee ◽  
Chromosome Level

AbstractCaffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

scholarly journals Molecular Characterization of hobo-Mediated Inversions in Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 647-656
Author(s):  
William B Eggleston ◽  
Nac R Rim ◽  
Johng K Lim
Keyword(s):  
X Chromosome ◽  
Polymerase Chain Reaction Amplification ◽  
Polytene Chromosomes ◽  
Chromosomal Inversions ◽  
Hobo Element ◽  
Reaction Amplification ◽  
Notch Locus ◽  
Polymerase Chain

Abstract The structure of chromosomal inversions mediated by hobo transposable elements in the Uc-1 X chromosome was investigated using cytogenetic and molecular methods. Uc-1 contains a phenotypically silent hobo element inserted in an intron of the Notch locus. Cytological screening identified six independent Notch mutations resulting from chromosomal inversions with one breakpoint at cytological position 3C7, the location of Notch. In situ hybridization to salivary gland polytene chromosomes determined that both ends of each inversion contained hobo and Notch sequences. Southern blot analyses showed that both breakpoints in each inversion had hobo-Notch junction fragments indistinguishable in structure from those present in the Uc-1 X chromosome prior to the rearrangements. Polymerase chain reaction amplification of the 12 hobo-Notch junction fragments in the six inversions, followed by DNA sequence analysis, determined that each was identical to one of the two hobo-Notch junctions present in Uc-1. These results are consistent with a model in which hobo-mediated inversions result from homologous pairing and recombination between a pair of hobo elements in reverse orientation.

scholarly journals Characterization of adenylyl cyclase isoforms in rat peripheral pulmonary arteries

2001 ◽  
Vol 280 (6) ◽  
pp. L1359-L1369 ◽  
Author(s):  
Karen B. Jourdan ◽  
Nicola A. Mason ◽  
Lu Long ◽  
Peter G. Philips ◽  
Martin R. Wilkins ◽  
...  
Keyword(s):  
Smooth Muscle ◽  
Adenylyl Cyclase ◽  
Pulmonary Arteries ◽  
Bronchial Epithelium ◽  
Rt Pcr ◽  
Bronchial Smooth Muscle ◽  
Functional Studies ◽  
Kinase C ◽  
Rat Lungs

Activation of adenylyl cyclase (AC), of which there are 10 diversely regulated isoforms, is important in regulating pulmonary vascular tone and remodeling. Immunohistochemistry in rat lungs demonstrated that AC2, AC3, and AC5/6 predominated in vascular and bronchial smooth muscle. Isoforms 1, 4, 7, and 8 localized to the bronchial epithelium. Exposure of animals to hypoxia did not change the pattern of isoform expression. RT-PCR confirmed mRNA expression of AC2, AC3, AC5, and AC6 and demonstrated AC7 and AC8 transcripts in smooth muscle. Western blotting confirmed the presence of AC2, AC3, and AC5/6 proteins. Functional studies provided evidence of cAMP regulation by Ca2+ and protein kinase C-activated but not Gi-inhibited pathways, supporting a role for AC2 and a Ca2+-stimulated isoform, AC8. However, NKH-477, an AC5-selective activator, was more potent than forskolin in elevating cAMP and inhibiting serum-stimulated [3H]thymidine incorporation, supporting the presence of AC5. These studies demonstrate differential expression of AC isoforms in rat lungs and provide evidence that AC2, AC5, and AC8 are functionally important in cAMP regulation and growth pathways in pulmonary artery myocytes.

scholarly journals Simple and Efficient Protocol for Subcellular Fractionation of Normal and Apoptotic Cells

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 852
Author(s):  
Viacheslav V. Senichkin ◽  
Evgeniia A. Prokhorova ◽  
Boris Zhivotovsky ◽  
Gelina S. Kopeina
Keyword(s):  
Subcellular Fractionation ◽  
Nuclear Fraction ◽  
Apoptotic Cells ◽  
Apoptotic Bodies ◽  
Functional Studies ◽  
Ionic Detergents ◽  
Protein Functions ◽  
Indispensable Tool ◽  
Cell Fragments

Subcellular fractionation approaches remain an indispensable tool among a large number of biochemical methods to facilitate the study of specific intracellular events and characterization of protein functions. During apoptosis, the best-known form of programmed cell death, numerous proteins are translocated into and from the nucleus. Therefore, suitable biochemical techniques for the subcellular fractionation of apoptotic cells are required. However, apoptotic bodies and cell fragments might contaminate the fractions upon using the standard protocols. Here, we compared different nucleus/cytoplasm fractionation methods and selected the best-suited approach for the separation of nuclear and cytoplasmic contents. The described methodology is based on stepwise lysis of cells and washing of the resulting nuclei using non-ionic detergents, such as NP-40. Next, we validated this approach for fractionation of cells treated with various apoptotic stimuli. Finally, we demonstrated that nuclear fraction could be further subdivided into nucleosolic and insoluble subfractions, which is crucial for the isolation and functional studies of various proteins. Altogether, we developed a method for simple and efficient nucleus/cytoplasm fractionation of both normal and apoptotic cells.

Revision of the Metallactus kollari species-group with a new diagnosis of the genus (Coleoptera: Chrysomelidae: Cryptocephalinae)

Zootaxa ◽  
2018 ◽  
Vol 4413 (1) ◽  
pp. 57
Author(s):  
DAVIDE SASSI
Keyword(s):  
Type Species ◽  
Species Group ◽  
Identification Key ◽  
Original Diagnosis ◽  
Taxonomic Treatment ◽  
Species Groups ◽  
New Diagnosis ◽  
Good Resource

The genus Metallactus has been controversial since its introduction due to the ambiguous nature of the original diagnosis. This has caused some confusion in the taxonomy of Neotropical Pachybrachina. In this work the morphology of endophallus, which is useful for the characterization of species groups in several groups of Coleoptera, including Cryptocephalinae, has been analyzed. This has proven to be a good resource also in the taxonomic treatment of the species belonging to the genus Metallactus. After a careful survey on most of the species described so far, the endophallus shape in Metallactus turned out to be remarkably distinctive and very promising in the delimitation of species groups. The present work includes: a) a new diagnosis of the genus Metallactus on the basis of the aedeagal anatomy; b) the designation of the type species of the nominal genus; c) the revision of a first species-group of the genus, including the type species, hereinafter called Metallactus kollari species-group. Before this revision, catalogues had been reporting 13 species attributable to this group, in the present work three species have been synonymized and seven have been described as new to science. Therefore, the group includes 17 species. The species described as new are: Metallactus rileyi n. sp., M. bellatrix n. sp., M. longicornis n. sp.; M. londonpridei n. sp., M. regalini n. sp., M. bezoar n. sp., M. guarani n. sp. The new synonymies are as follows: Metallactus albipes Suffrian, 1866 (= M. nigrofasciatus Suffrian, 1866 n. syn.), M. albifrons Suffrian, 1866 (= M. flavofrontalis Jacoby, 1907 n. syn.), M. dodecastictus Suffrian, 1866 (= Griburius nigritarsis Jacoby, 1907 n. syn.). The lectotypes of all previously described species have been designated. The new synonymies, the name-bearing type fixations and designations and the nomenclatural acts have been critically discussed. An identification key for the species-group is also provided. 

scholarly journals Deletion of small ankyrin 1 (sAnk1) isoforms results in structural and functional alterations in aging skeletal muscle fibers

2015 ◽  
Vol 308 (2) ◽  
pp. C123-C138 ◽  
Author(s):  
E. Giacomello ◽  
M. Quarta ◽  
C. Paolini ◽  
R. Squecco ◽  
P. Fusco ◽  
...  
Keyword(s):  
Structural Damage ◽  
Skeletal Muscles ◽  
Functional Characterization ◽  
Sr Proteins ◽  
Endurance Test ◽  
Tubular Aggregates ◽  
Functional Studies ◽  
Old Mice ◽  
Contractile Performance

Muscle-specific ankyrins 1 (sAnk1) are a group of small ankyrin 1 isoforms, of which sAnk1.5 is the most abundant. sAnk1 are localized in the sarcoplasmic reticulum (SR) membrane from where they interact with obscurin, a myofibrillar protein. This interaction appears to contribute to stabilize the SR close to the myofibrils. Here we report the structural and functional characterization of skeletal muscles from sAnk1 knockout mice (KO). Deletion of sAnk1 did not change the expression and localization of SR proteins in 4- to 6-mo-old sAnk1 KO mice. Structurally, the main modification observed in skeletal muscles of adult sAnk1 KO mice (4–6 mo of age) was the reduction of SR volume at the sarcomere A band level. With increasing age (at 12–15 mo of age) extensor digitorum longus (EDL) skeletal muscles of sAnk1 KO mice develop prematurely large tubular aggregates, whereas diaphragm undergoes significant structural damage. Parallel functional studies revealed specific changes in the contractile performance of muscles from sAnk1 KO mice and a reduced exercise tolerance in an endurance test on treadmill compared with control mice. Moreover, reduced Qγcharge and L-type Ca2+current, which are indexes of affected excitation-contraction coupling, were observed in diaphragm fibers from 12- to 15-mo-old mice, but not in other skeletal muscles from sAnk1 KO mice. Altogether, these findings show that the ablation of sAnk1, by altering the organization of the SR, renders skeletal muscles susceptible to undergo structural and functional alterations more evident with age, and point to an important contribution of sAnk1 to the maintenance of the longitudinal SR architecture.

scholarly journals Non3 is an essential Drosophila gene required for proper nucleolus assembly

2019 ◽  
Vol 23 (2) ◽  
pp. 190-198
Author(s):  
E. N. Andreyeva ◽  
A. A. Ogienko ◽  
A. A. Yushkova ◽  
J. V. Popova ◽  
G. A. Pavlova ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Large Deletion ◽  
Protein Product ◽  
P Element ◽  
Post Translational Modification ◽  
Allelic Series ◽  
Larval Brain ◽  
Functional Studies ◽  
Mild Reduction

The nucleolus is a dynamic non-membrane-bound nuclear organelle, which plays key roles not only in ribosome biogenesis but also in many other cellular processes. Consistent with its multiple functions, the nucleolus has been implicated in many human diseases, including cancer and degenerative pathologies of the nervous system and heart. Here, we report the characterization of the Drosophila Non3 (Novel nucleolar protein 3) gene, which encodes a protein homologous to the human Brix domain-containing Rpf2 that has been shown to control ribosomal RNA (rRNA) processing. We used imprecise P-element excision to generate four new mutant alleles in the Non3 gene. Complementation and phenotypic analyses showed that these Non3 mutations can be arranged in an allelic series that includes both viable and lethal alleles. The strongest lethal allele (Non3∆600) is a genetically null allele that carries a large deletion of the gene and exhibits early lethality when homozygous. Flies heterozygous for Non3∆600 occasionally exhibit a mild reduction in the bristle size, but develop normally and are fertile. However, heteroallelic combinations of viable Non3 mutations (Non3197, Non3310 and Non3259) display a Minute-like phenotype, consisting in delayed development and short and thin bristles, suggesting that they are defective in ribosome biogenesis. We also demonstrate that the Non3 protein localizes to the nucleolus of larval brain cells and it is required for proper nucleolar localization of Fibrillarin, a protein important for post-translational modification and processing of rRNAs. In summary, we generated a number of genetic and biochemical tools that were exploited for an initial characterization of Non3, and will be instrumental for future functional studies on this gene and its protein product.

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

scholarly journals Characterization of MGC2, a Mycoplasma gallisepticum Cytadhesin with Homology to the Mycoplasma pneumoniae 30-Kilodalton Protein P30 and Mycoplasma genitalium P32

1998 ◽  
Vol 66 (7) ◽  
pp. 3436-3442 ◽  
Author(s):  
Linda L. Hnatow ◽  
Calvin L. Keeler ◽  
Laura L. Tessmer ◽  
Kirk Czymmek ◽  
John E. Dohms
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Reverse Transcription ◽  
Mycoplasma Genitalium ◽  
Mycoplasma Gallisepticum ◽  
Immunogold Labeling ◽  
Respiratory Pathogen ◽  
Functional Studies ◽  
Reverse Transcription Pcr ◽  
Attachment Inhibition

ABSTRACT A second cytadhesin-like protein, MGC2, was identified in the avian respiratory pathogen Mycoplasma gallisepticum. The 912-nucleotide mgc2 gene encodes a 32.6-kDa protein with 40.9 and 31.4% identity with the M. pneumoniae P30 andM. genitalium P32 cytadhesins, respectively. Functional studies with reverse transcription-PCR, immunoblotting, double-sided immunogold labeling, and attachment inhibition assays demonstrated homology to the human mycoplasmal P30 and P32 cytadhesins. These findings suggest that there is a family of cytadhesin genes conserved among pathogenic mycoplasmas infecting widely divergent hosts.

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