scholarly journals Close relationship between coral-associated Chromera strains despite major differences within the Symbiodiniaceae

2019 ◽  
Author(s):  
Amin R. Mohamed ◽  
Cheong Xin Chan ◽  
Mark A. Ragan ◽  
Jia Zhang ◽  
Ira Cooke ◽  
...  
Keyword(s):  
Reference Strain ◽  
De Novo ◽  
Sequence Similarity ◽  
Temperature Tolerance ◽  
Coral Host ◽  
Reef Corals ◽  
Close Relationship ◽  
Mutualistic Relationship ◽  
Low Levels ◽  
High Level

SummaryReef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leading to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral (“GBR Chromera”) and compared to those of the reference strain of Chromera (“Sydney Chromera”), and to those of Symbiodiniaceae (Fugacium, Cladocopium and Breviolum), as well as the apicomplexan parasite, Plasmodium falciparum. By contrast with the Symbiodiniaceae, the two Chromera strains had a high level of sequence similarity evident by very low levels of divergence in orthologous genes. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization for the ubiquitous association of Cladocopium strains with Indo-Pacific reef corals. The presence of HSP20 genes may underlie the higher thermal tolerance of Chromera.

scholarly journals Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 979 ◽  
Author(s):  
Ping Liu ◽  
Wu Chen ◽  
Jin-Ping Chen
Keyword(s):  
De Novo ◽  
Sendai Virus ◽  
Sequence Similarity ◽  
Viral Metagenomics ◽  
Manis Javanica ◽  
Pathogenic Viruses ◽  
Viral Communities ◽  
High Level ◽  
Viral Sequences ◽  
Insight Into

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

Developmental regulation of the gibberellin pathway in pea shoots

2003 ◽  
Vol 30 (1) ◽  
pp. 83 ◽  
Author(s):  
John J. Ross ◽  
Sandra E. Davidson ◽  
Carla M. Wolbang ◽  
Emma Bayly-Stark ◽  
Jennifer J. Smith ◽  
...  
Keyword(s):  
De Novo ◽  
Developmental Regulation ◽  
Wild Type ◽  
Meristematic Tissue ◽  
Oxidase Gene ◽  
Pisum Sativum L ◽  
Intact Plants ◽  
Low Levels ◽  
High Level ◽  
Ga Biosynthesis

To investigate gibberellin (GA) biosynthesis in mature tissue of pea (Pisum sativum L.) in the absence of potentially GA-producing meristematic tissue we grafted wild-type scions to rootstocks of the GA-deficient ls-1 mutant and later decapitated the shoot. After 2 d, decapitated shoots contained as much GA19 (a precursor of the bioactive GA1) as comparable tissue from intact plants, even though applied [14C]GA19 was metabolised rapidly during this time. These results show that the pool size of endogenous GA19 was maintained, probably by de novo GA19 synthesis. We also found that the LS gene, which catalyses an early step in GA biosynthesis, is expressed in mature tissue, as are the shoot-expressed GA 20-oxidase and GA 3-oxidase genes. Nevertheless, mature tissue contained very low levels of GA1 and GA20 compared with immature tissue. Levels of GA19, GA29 and GA8 were less affected by tissue age. Metabolism studies using 14C-labelled GAs indicated that mature tissue rapidly converted GA19 to GA20 and GA20 to GA1; the latter step was promoted by IAA. However, the 2-oxidation steps GA1 to GA8, GA20 to GA29 and GA29 to GA29-catabolite appear to proceed very rapidly in mature tissue (regardless of IAA content), and we suggest this is the reason why GA1 and GA20 do not accumulate. This is supported by the high level of expression of a key GA 2-oxidase gene in mature tissue.

High world sugar prices: is Asia’s production cycle to blame?

2010 ◽  
pp. 169-173
Author(s):  
Martin Todd
Keyword(s):  
Supply Chain ◽  
Supply And Demand ◽  
Production Cycle ◽  
Low Levels ◽  
High Level ◽  
High World

The current high world sugar prices reflect a major imbalance between global supply and demand, which has reduced stocks to very low levels. Although it remains to be seen whether prices will rise much above current values, it is clear that the supply chain will remain stretched throughout 2010 and this will help to maintain prices at a high level.

scholarly journals Epigenetic Regulation of MicroRNA Clusters and Families during Tumor Development

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1333
Author(s):  
Jana Gregorova ◽  
Petra Vychytilova-Faltejskova ◽  
Sabina Sevcikova
Keyword(s):  
Histone Modifications ◽  
Sequence Similarity ◽  
Tumor Development ◽  
Hematologic Malignancies ◽  
Seed Region ◽  
Cancer Therapies ◽  
Rna Molecules ◽  
Physiological Processes ◽  
Close Relationship ◽  
Aberrant Dna Methylation

MicroRNAs are small non-coding single-stranded RNA molecules regulating gene expression on a posttranscriptional level based on the seed sequence similarity. They are frequently clustered; thus, they are either simultaneously transcribed into a single polycistronic transcript or they may be transcribed independently. Importantly, microRNA families that contain the same seed region and thus target related signaling proteins, may be localized in one or more clusters, which are in a close relationship. MicroRNAs are involved in basic physiological processes, and their deregulation is associated with the origin of various pathologies, including solid tumors or hematologic malignancies. Recently, the interplay between the expression of microRNA clusters and families and epigenetic machinery was described, indicating aberrant DNA methylation or histone modifications as major mechanisms responsible for microRNA deregulation during cancerogenesis. In this review, the most studied microRNA clusters and families affected by hyper- or hypomethylation as well as by histone modifications are presented with the focus on particular mechanisms. Finally, the diagnostic and prognostic potential of microRNA clusters and families is discussed together with technologies currently used for epigenetic-based cancer therapies.

scholarly journals Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species

2021 ◽  
Vol 9 (6) ◽  
pp. 1290
Author(s):  
Natalia Alvarez-Santullano ◽  
Pamela Villegas ◽  
Mario Sepúlveda Mardones ◽  
Roberto E. Durán ◽  
Raúl Donoso ◽  
...  
Keyword(s):  
Fatty Acids ◽  
De Novo ◽  
Reducing Power ◽  
Pentose Phosphate ◽  
Fine Tuning ◽  
Metabolic Reconstruction ◽  
Phylogenetic Groups ◽  
Outlier Group ◽  
Pha Genes ◽  
High Level

Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner–Doudoroff (ED), pentose-phosphate (PP), and lower Embden–Meyerhoff–Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.

scholarly journals AB0050 A NOVEL METHOD FOR ISOLATION OF EXOSOMES FROM SYNOVIAL FLUID

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1057.2-1057
Author(s):  
Y. Liu ◽  
Y. Huang ◽  
Q. Huang ◽  
S. Sun ◽  
Z. Ji ◽  
...  
Keyword(s):  
Synovial Fluid ◽  
Western Blot ◽  
Biological Fluid ◽  
High Sensitivity ◽  
Protein Distribution ◽  
Sds Page ◽  
Close Relationship ◽  
Novel Method ◽  
Low Levels

Background:Exosomes in synovial fluid (SF) has a close relationship with the pathogenesis of rheumatiod arthritis. As a complex biological fluid, SF presents challenges for exosomes isolation using standard methods, such as ExoquickTM kit and ultracentrifugation.Objectives:The study aims to compared the quality of exosomes separated by ExoquickTM kit (TM), ExoquickTM kit+ExoquickTC kit (TM-TC), ultracentrifugation (UC) and TM-TC+UC(TM-TC-UC) from SF.Methods:Exosomes was separated by TM, TM-TC, UC and TM-TC-UC respectively. The size and concentrations of exosomes were detected by high sensitivity flow cytometry for nanoparticle analysis. Total protein and RNA were extracted from exosomes. SDS-PAGE was used to detect the protein distribution of exosomes. Western blot was used to examine the level of albumin and exosomes marker (TSG101 and CD81).Results:There was no statistic difference in the diameters of exosomes separated by the four methods. The concentrations of exosomes in TM, TM-TC, TM-TC-UC and UC were (5.65±0.93), (3.02±1.19), (1.67±0.25) and (4.61±0.73) *109Particles/mL. The protein concentrations of exosomes separated by the four methods were consistent with the concentrations of exosomes. SDS-PAGE showed that the protein distribution of exosomes separated by the four methods were different. Low levels of albumin were detected in TM-TC and TM-TC-UC, while high levels of albumin in TM and UC. Total RNA concentrations from exosomes in TM-TC was higher than other groups.Conclusion:TM-TC can be used to obtain higher quality exosomes from SF for the study of exosome-enriched components.References:[1]Helwa I, et al, A Comparative Study of Serum Exosome Isolation Using Differential Ultracentrifugation and Three Commercial Reagents. PloS one, 2017. 12(1): p. e0170628-e0170628.Figure 1.A: SDS-PAGE showed the protein distribution of exosomes; B: the detection of albumin, TSG101 and CD81 by western blot.Disclosure of Interests:None declared

scholarly journals Testing Todd: family types and development

2021 ◽  
pp. 1-18
Author(s):  
Jerg Gutmann ◽  
Stefan Voigt
Keyword(s):  
Rule Of Law ◽  
Civil Society Organizations ◽  
The Rule Of Law ◽  
State Fragility ◽  
Family Types ◽  
Low Levels ◽  
Parsimonious Model ◽  
The One ◽  
High Level

Abstract Many years ago, Emmanuel Todd came up with a classification of family types and argued that the historically prevalent family types in a society have important consequences for its economic, political, and social development. Here, we evaluate Todd's most important predictions empirically. Relying on a parsimonious model with exogenous covariates, we find mixed results. On the one hand, authoritarian family types are, in stark contrast to Todd's predictions, associated with increased levels of the rule of law and innovation. On the other hand, and in line with Todd's expectations, communitarian family types are linked to racism, low levels of the rule of law, and late industrialization. Countries in which endogamy is frequently practiced also display an expectedly high level of state fragility and weak civil society organizations.

scholarly journals Transcriptomic and Proteomic Analyses Reveal the Diversity of Venom Components from the Vaejovid Scorpion Serradigitus gertschi

Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 359 ◽  
Author(s):  
Maria Romero-Gutiérrez ◽  
Carlos Santibáñez-López ◽  
Juana Jiménez-Vargas ◽  
Cesar Batista ◽  
Ernesto Ortiz ◽  
...  
Keyword(s):  
Serine Proteases ◽  
De Novo ◽  
Sequence Similarity ◽  
Scorpion Venom ◽  
Secretory Proteins ◽  
Host Defense Peptides ◽  
The Family ◽  
Pathogenesis Related ◽  
Molecular Masses

To understand the diversity of scorpion venom, RNA from venomous glands from a sawfinger scorpion, Serradigitus gertschi, of the family Vaejovidae, was extracted and used for transcriptomic analysis. A total of 84,835 transcripts were assembled after Illumina sequencing. From those, 119 transcripts were annotated and found to putatively code for peptides or proteins that share sequence similarities with the previously reported venom components of other species. In accordance with sequence similarity, the transcripts were classified as potentially coding for 37 ion channel toxins; 17 host defense peptides; 28 enzymes, including phospholipases, hyaluronidases, metalloproteases, and serine proteases; nine protease inhibitor-like peptides; 10 peptides of the cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein superfamily; seven La1-like peptides; and 11 sequences classified as “other venom components”. A mass fingerprint performed by mass spectrometry identified 204 components with molecular masses varying from 444.26 Da to 12,432.80 Da, plus several higher molecular weight proteins whose precise masses were not determined. The LC-MS/MS analysis of a tryptic digestion of the soluble venom resulted in the de novo determination of 16,840 peptide sequences, 24 of which matched sequences predicted from the translated transcriptome. The database presented here increases our general knowledge of the biodiversity of venom components from neglected non-buthid scorpions.

Flavonoids and UV Photoprotection in Arabidopsis Mutants

2001 ◽  
Vol 56 (9-10) ◽  
pp. 745-754 ◽  
Author(s):  
Ken G Ryan ◽  
Ewald E Swinny ◽  
Chris Winefield ◽  
Kenneth R Markham
Keyword(s):  
Crucial Role ◽  
Hydroxycinnamic Acid ◽  
Ultraviolet B ◽  
Uvb Radiation ◽  
Wild Type ◽  
Hydroxycinnamic Acid Derivatives ◽  
Quercetin Glycosides ◽  
Kaempferol Glycosides ◽  
Low Levels ◽  
High Level

AbstractWild-type Arabidopsis L. leaves exposed to low ultraviolet-B (U V B ) conditions contained predominantly kaempferol glycosides, with low levels of quercetin glycosides. The flavonoid level doubled on treatment with UVB and an increase in the ratio of quercetin: kaempferol was observed. These results suggest that flavonols protect Arabidopsis plants from UVB damage, and indicate that the flavonoid 3’-hydroxylase (F3’H) enzyme, which converts dihydrokaempferol to dihydroquercetin, may play a crucial role. The tt7 mutant lacks this gene and, after treatment with sub-ambient UVB, contained kaempferol glycosides exclusively, to a level of total flavonols similar to that in wild-type Arabidopsis. Total flavonols after enhanced UVB treatment were higher in tt7 than in similarly treated wild-type plants, and only kaempferol glycosides were detected. Despite this high level, tt7 plants were less tolerant of UVB radiation than wild-type plants. These observations suggests that kaempferol is a less effective photoprotectant than quercetin. The chalcone isomerase (CHI) mutant (tt5) surprisingly did not accumulate naringenin chalcone, and this suggests that the mutation may not be restricted to the CHI gene alone. The concentration of hydroxycinnamic acid derivatives did not change with UVB treatment in most varieties indicating that their role in UV photoprotection may be subordinate to that of the flavonoids.

DNA methylation in 5-aza-2'-deoxycytidine-resistant variants of C3H 10T1/2 C18 cells

1984 ◽  
Vol 4 (10) ◽  
pp. 2098-2102
Author(s):  
E Flatau ◽  
F A Gonzales ◽  
L A Michalowsky ◽  
P A Jones
Keyword(s):  
Cell Line ◽  
Cytosine Methylation ◽  
De Novo ◽  
Lethal Dose ◽  
Cytotoxic Effects ◽  
Drug Treatments ◽  
A Cell ◽  
Mouse Cells ◽  
Low Levels ◽  
Dna Cytosine Methylation

A cell line (T17) was derived from C3H 10T1/2 C18 cells after 17 treatments with increasing concentrations of 5-aza-2'-deoxycytidine. The T17 cell line was very resistant to the cytotoxic effects of 5-aza-2'-deoxycytidine, and the 50% lethal dose for 5-aza-2'-deoxycytidine was ca. 3 microM, which was 30-fold greater than that of the parental C3H 10T1/2 C18 cells. Increased drug resistance was not due to a failure of the T17 cell line to incorporate 5-aza-2'-deoxycytidine into DNA. The cells were also slightly cross-resistant to 5-azacytidine. The percentage of cytosines modified to 5-methylcytosine in T17 cells was 0.7%, a 78% decrease from the level of 3.22% in C3H 10T1/2 C18 cells. The DNA cytosine methylation levels in several clones isolated from the treated lines were on the order of 0.7%, and clones with methylation levels lower than 0.45% were not obtained even after further drug treatments. These highly decreased methylation levels appeared to be unstable, and DNA modification increased as the cells divided in the absence of further drug treatment. The results suggest that it may not be possible to derive mouse cells with vanishingly low levels of 5-methylcytosine and that considerable de novo methylation can occur in cultured lines.

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