scholarly journals Gene identification and genome annotation in Caenorhabditis briggsae by high throughput 5' RNA end determination

2021 ◽  
Author(s):  
Nikita Jhaveri ◽  
Wouter van den Berg ◽  
Byung Joon Hwang ◽  
Hans-Michael Muller ◽  
Paul W Sternberg ◽  
...  
Keyword(s):  
Caenorhabditis Briggsae ◽  
Spliced Leader ◽  
C Elegans ◽  
Functional Studies ◽  
Biological Studies ◽  
Trans Splicing ◽  
Substantial Progress ◽  
End Sequences ◽  
First Time ◽  
Made In

The nematode Caenorhabditis briggsae is routinely used in comparative and evolutionary studies involving its well-known cousin C. elegans. The C. briggsae genome sequence has accelerated research by facilitating the generation of new resources, tools, and functional studies of genes. While substantial progress has been made in predicting genes and start sites, experimental evidence is still lacking in many cases. Here, we report an improved annotation of the C. briggsae genome using the Trans-spliced Exon Coupled RNA End Determination (TEC-RED) technique. In addition to identifying 5' ends of expressed genes, the technique has enabled the discovery of operons and paralogs. Application of TEC-RED yielded 10,243 unique 5' end sequences with matches in the C. briggsae genome. Of these, 6,395 were found to represent 4,252 unique genes along with 362 paralogs and 52 previously unknown exons. The method also identified 493 operons, including 334 that are fully supported by tags. Additionally, two SL1-type operons were discovered. Comparisons with C. elegans revealed that 40% of operons are conserved. Further, we identified 73 novel operons, including 12 that entirely lack orthologs in C. elegans. Among other results, we found that 14 genes are trans-spliced exclusively in C. briggsae compared with C. elegans. Altogether, the data presented here serves as a rich resource to aid biological studies involving C. briggsae. Additionally, this work demonstrates the use of TEC-RED for the first time in a non-elegans nematode and suggests that it could apply to other organisms with a trans-splicing reaction from spliced leader RNA.

trans-spliced Caenorhabditis elegans mRNAs retain trimethylguanosine caps

1990 ◽  
Vol 10 (4) ◽  
pp. 1764-1768
Author(s):  
R F Liou ◽  
T Blumenthal
Keyword(s):  
Caenorhabditis Elegans ◽  
Antibody Binding ◽  
Small Nuclear Rna ◽  
Nematode Caenorhabditis Elegans ◽  
Spliced Leader ◽  
C Elegans ◽  
Distinct Subset ◽  
Trans Splicing ◽  
Nuclear Rna ◽  
Spliced Leader Rna

The nematode Caenorhabditis elegans has an unusual small nuclear RNA, containing a 100-nucleotide RNA molecule, spliced leader RNA, which donates its 5' 22 nucleotides to a variety of recipient RNAs by a trans-splicing reaction. The spliced leader RNA has a 5' trimethylguanosine (TMG) cap, which becomes the 5' end of trans-spliced mRNAs. We found that mature trans-spliced mRNAs were immunoprecipitable with anti-TMG cap antibodies and that TMG-containing dinucleotides specifically competed with the trans-spliced mRNAs for antibody binding. We also found that these mRNAs retained their TMG caps throughout development and that the TMG-capped mRNAs were polysome associated. Since the large majority of C. elegans mRNAs are not trans-spliced, the addition of the spliced leader and its TMG cap to a limited group of recipient RNAs may create a functionally distinct subset of mRNAs.

Synthesis and Functionalization of Coumarin-Pyrazole Scaffold: Recent Development, Challenges and Opportunities

2021 ◽  
Vol 18 ◽  
Author(s):  
Nitin K. Jadhav ◽  
Balkrishna R. Kale ◽  
Mohammad S. Alam ◽  
Vishwas B. Gaikwad ◽  
Virendra Prasad ◽  
...  
Keyword(s):  
Heterocyclic Compounds ◽  
Structural Motif ◽  
Pharmacological Properties ◽  
Lead Compounds ◽  
Drug Molecules ◽  
Dna And Rna ◽  
Biological Studies ◽  
Challenges And Opportunities ◽  
First Time ◽  
Made In

: Heterocycles are the main structural motif of DNA and RNA and play crucial role in various chemical reactions of metabolisms. Therefore, heterocyclic compounds show good physiological and pharmacological properties. Coumarin and pyrazole scaffold present in many commercial drug molecules and natural products. This review gives first time gives an overview of the progress made in the synthesis and functionalization of coumarin-pyrazole hybrid heterocycle. It also includes discussion on the possible reactive sites of heterocycles, functionalization and mechanistic pathways to incorporate pyrazole pharmacophore unit in synthesis. Several synthesis and biological studies revealed that combination of coumarin-pyrazole moiety is a prominent structural motif to find lead compounds in drug discovery.

scholarly journals trans-spliced Caenorhabditis elegans mRNAs retain trimethylguanosine caps.

1990 ◽  
Vol 10 (4) ◽  
pp. 1764-1768 ◽  
Author(s):  
R F Liou ◽  
T Blumenthal
Keyword(s):  
Caenorhabditis Elegans ◽  
Antibody Binding ◽  
Small Nuclear Rna ◽  
Nematode Caenorhabditis Elegans ◽  
Spliced Leader ◽  
C Elegans ◽  
Distinct Subset ◽  
Trans Splicing ◽  
Nuclear Rna ◽  
Spliced Leader Rna

The nematode Caenorhabditis elegans has an unusual small nuclear RNA, containing a 100-nucleotide RNA molecule, spliced leader RNA, which donates its 5' 22 nucleotides to a variety of recipient RNAs by a trans-splicing reaction. The spliced leader RNA has a 5' trimethylguanosine (TMG) cap, which becomes the 5' end of trans-spliced mRNAs. We found that mature trans-spliced mRNAs were immunoprecipitable with anti-TMG cap antibodies and that TMG-containing dinucleotides specifically competed with the trans-spliced mRNAs for antibody binding. We also found that these mRNAs retained their TMG caps throughout development and that the TMG-capped mRNAs were polysome associated. Since the large majority of C. elegans mRNAs are not trans-spliced, the addition of the spliced leader and its TMG cap to a limited group of recipient RNAs may create a functionally distinct subset of mRNAs.

scholarly journals lir-2, lir-1 and lin-26 Encode a New Class of Zinc-Finger Proteins and Are Organized in Two Overlapping Operons Both in Caenorhabditis elegans and in Caenorhabditis briggsae

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 221-235 ◽  
Author(s):  
Pascale Dufourcq ◽  
Philippe Chanal ◽  
Serge Vicaire ◽  
Elise Camut ◽  
Sophie Quintin ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Genomic Organization ◽  
Null Mutation ◽  
Caenorhabditis Briggsae ◽  
Exon 2 ◽  
C Elegans ◽  
New Class ◽  
Finger Protein ◽  
Splicing Pattern ◽  
Trans Splicing

Abstract lin-26, which encodes a unique Zn-finger protein, is required for differentiation of nonneuronal ectodermal cells in Caenorhabditis elegans. Here, we show that the two genes located immediately upstream of lin-26 encode LIN-26-like Zn-finger proteins; hence their names are lir-1 and lir-2 (lin-26 related). lir-2, lir-1, and lin-26 generate several isoforms by alternative splicing and/or trans-splicing at different positions. On the basis of their trans-splicing pattern, their intergenic distances, and their expression, we suggest that lir-2, lir-1, and lin-26 form two overlapping transcriptional operons. The first operon, which is expressed in virtually all cells, includes lir-2 and long lir-1 isoforms. The second operon, which is expressed in the nonneuronal ectoderm, includes short lir-1 isoforms, starting at exon 2 and lin-26. This unusual genomic organization has been conserved in C. briggsae, as shown by cloning the C. briggsae lir-2, lir-1, and lin-26 homologs. Particularly striking is the sequence conservation throughout the first lir-1 intron, which is very long in both species. Structural conservation is functionally meaningful as C. briggsae lin-26 is also expressed in the nonneuronal ectoderm and can complement a C. elegans lin-26 null mutation.

Mosses and lichens of Shokalsky Island (Kara Sea, Yamal-Nenets Autonomous Area)

2020 ◽  
Vol 54 (2) ◽  
pp. 497-513 ◽  
Author(s):  
L. N. Beldiman ◽  
I. N. Urbanavichene ◽  
V. E. Fedosov ◽  
E. Yu. Kuzmina
Keyword(s):  
Plant Communities ◽  
Species Distribution ◽  
Arctic Tundra ◽  
Kara Sea ◽  
Lichenicolous Fungi ◽  
South West ◽  
West Part ◽  
First Time ◽  
Nenets Autonomous ◽  
Made In

We studied in detail a moss-lichen component of Shokalsky Island vegetation for the first time and identified 79 species of mosses and 54 species and 2 subspecies of lichens and lichenicolous fungi. All species of mosses and 23 species and 2 subspecies of lichens and lichenicolous fungi are recorded for the first time for the island. The study is based on collections made in South West part of the island, in arctic tundra. We also explored the participation of the mosses and lichens in the main types of plant communities and the species distribution in 10 ecotopes. The paper describes the noteworthy findings (Abrothallus parmeliarum, Aongstroemia longipes, Arthonia peltigerea, Caloplaca caesiorufella, Catillaria stereocaulorum, Ceratodon heterophyllus, Lecanora leptacinella, Sphagnum concinnum, S. olafii) and features of bryo- and lichenoflora of Shokalsky Island.

scholarly journals Evolution of Sex Determination in Caenorhabditis: Unusually High Divergence of tra-1 and Its Functional Consequences

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 587-595 ◽  
Author(s):  
Mario de Bono ◽  
Jonathan Hodgkin
Keyword(s):  
Sex Determination ◽  
Germ Line ◽  
Amino Acid Identity ◽  
Evolution Of Sex ◽  
Phenotypic Differences ◽  
C Elegans ◽  
Functional Studies ◽  
Somatic Gonad ◽  
Functional Consequences ◽  
Significant Divergence

Abstract The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra-1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(nul1) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defines several conserved regions likely to be important for tra-1 function. The phenotypic differences between Ce-tra-1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex.

Comparison of a New Wild-Type Caenorhabditis Briggsae With Laboratory Strains of C. Briggsae and C. Elegans

Nematologica ◽  
1983 ◽  
Vol 29 (2) ◽  
pp. 203-216 ◽  
Author(s):  
James W. Golden ◽  
F. Kenneth Nelson ◽  
Donald L. Riddle ◽  
Andras Fodor
Keyword(s):  
Caenorhabditis Briggsae ◽  
Wild Type ◽  
C Elegans

THE STATUS OF TWO-NEUTRINO AND NEUTRINOLESS DOUBLE BETA DECAY SEARCHES

1993 ◽  
Vol 02 (03) ◽  
pp. 507-546 ◽  
Author(s):  
M.K. MOE
Keyword(s):  
Beta Decay ◽  
Neutrinoless Double Beta Decay ◽  
Double Beta Decay ◽  
Experimental Activity ◽  
The Past ◽  
The Status ◽  
Substantial Progress ◽  
Direct Counting ◽  
Made In

Substantial progress has been made in double beta decay experiments in the past few years, including the beginning of sensitive new searches for neutrinoless double beta decay, and several additional positive detections of the two-neutrino mode by geochemical, radiochemical, and direct-counting techniques. This review discusses the recent experimental activity.

scholarly journals Stroke Prevention in Atrial Fibrillation: Where are We Now?

2012 ◽  
Vol 6 ◽  
pp. CMC.S8976 ◽  
Author(s):  
Yousif Ahmad ◽  
Gregory Y.H. Lip
Keyword(s):  
Atrial Fibrillation ◽  
Stroke Prevention ◽  
Management Strategies ◽  
Bleeding Risk ◽  
Long Term Study ◽  
Risk Patients ◽  
First Time ◽  
Major Progress ◽  
Made In

Atrial fibrillation is the commonest arrhythmia worldwide and is a growing problem. AF is responsible for 25% of all strokes, and these patients suffer greater mortality and disability. Warfarin has traditionally been the only successful therapy for stroke prevention, but its limitations have resulted in underutilisation. Major progress has been made in AF research, leading to improved management strategies. Better risk stratification permits identification of truly low-risk patients who do not require anticoagulation and we are able to simplify ourevaluation of a patient's bleeding risk. The advent of novel anticoagulants means warfarin is no longer the only choice for stroke prophylaxis. These drugs circumvent many of warfarin's inconveniences, but only long-term study and use will conclusively demonstrate how they compare to warfarin. The landscape of stroke prevention in AF has changed with effective alternatives to warfarin available for the first time in 60 years—but each new option brings new considerations.

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