scholarly journals Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Szymon Juszkiewicz ◽  
Greg Slodkowicz ◽  
Zhewang Lin ◽  
Paula Freire-Pritchett ◽  
Sew-Yeu Peak-Chew ◽  
...  
Keyword(s):  
Quality Control ◽  
Translation Initiation ◽  
Quantitative Proteomics ◽  
Feedback Inhibition ◽  
The Other ◽  
Cis Acting ◽  
Ribosome Density ◽  
In Cis

Translation of aberrant mRNAs can cause ribosomes to stall, leading to collisions with trailing ribosomes. Collided ribosomes are specifically recognised by ZNF598 to initiate protein and mRNA quality control pathways. Here we found using quantitative proteomics of collided ribosomes that EDF1 is a ZNF598-independent sensor of ribosome collisions. EDF1 stabilises GIGYF2 at collisions to inhibit translation initiation in cis via 4EHP. The GIGYF2 axis acts independently of the ZNF598 axis, but each pathway’s output is more pronounced without the other. We propose that the widely conserved and highly abundant EDF1 monitors the transcriptome for excessive ribosome density, then triggers a GIGYF2-mediated response to locally and temporarily reduce ribosome loading. Only when collisions persist is translation abandoned to initiate ZNF598-dependent quality control. This tiered response to ribosome collisions would allow cells to dynamically tune translation rates while ensuring fidelity of the resulting protein products.

scholarly journals Author response: Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

2020 ◽  
Author(s):  
Szymon Juszkiewicz ◽  
Greg Slodkowicz ◽  
Zhewang Lin ◽  
Paula Freire-Pritchett ◽  
Sew-Yeu Peak-Chew ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Feedback Inhibition ◽  
Author Response ◽  
Cis Acting

scholarly journals Matching the supply of bacterial nutrients to the nutritional demand of the animal host

2014 ◽  
Vol 281 (1791) ◽  
pp. 20141163 ◽  
Author(s):  
Calum W. Russell ◽  
Anton Poliakov ◽  
Meena Haribal ◽  
Georg Jander ◽  
Klaas J. van Wijk ◽  
...  
Keyword(s):  
Quantitative Proteomics ◽  
Acyrthosiphon Pisum ◽  
Feedback Inhibition ◽  
Essential Amino Acids ◽  
Host Cells ◽  
Host Proteins ◽  
Buchnera Aphidicola ◽  
Symbiotic Microorganisms ◽  
Precursor Supply ◽  
Host Regulation

Various animals derive nutrients from symbiotic microorganisms with much-reduced genomes, but it is unknown whether, and how, the supply of these nutrients is regulated. Here, we demonstrate that the production of essential amino acids (EAAs) by the bacterium Buchnera aphidicola in the pea aphid Acyrthosiphon pisum is elevated when aphids are reared on diets from which that EAA are omitted, demonstrating that Buchnera scale EAA production to host demand. Quantitative proteomics of bacteriocytes (host cells bearing Buchnera ) revealed that these metabolic changes are not accompanied by significant change in Buchnera or host proteins, suggesting that EAA production is regulated post-translationally. Bacteriocytes in aphids reared on diet lacking the EAA methionine had elevated concentrations of both methionine and the precursor cystathionine, indicating that methionine production is promoted by precursor supply and is not subject to feedback inhibition by methionine. Furthermore, methionine production by isolated Buchnera increased with increasing cystathionine concentration. We propose that Buchnera metabolism is poised for EAA production at certain maximal rates, and the realized release rate is determined by precursor supply from the host. The incidence of host regulation of symbiont nutritional function via supply of key nutritional inputs in other symbioses remains to be investigated.

The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers

1989 ◽  
Vol 9 (11) ◽  
pp. 4621-4630
Author(s):  
D J Mahoney ◽  
J R Broach
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Binding Sites ◽  
The Other ◽  
Functional Domains ◽  
Gene Products ◽  
Cis Acting ◽  
Full Expression ◽  
Mating Type Genes ◽  
Chromosome Iii

Mating-type genes resident in the silent cassette HML at the left arm of chromosome III are repressed by the action of four SIR gene products, most likely mediated through two cis-acting sites located on opposite sides of the locus. We showed that deletion of either of these two cis-acting sites from the chromosome did not yield any detectable derepression of HML, while deletion of both sites yielded full expression of the locus. In addition, each of these sites was capable of exerting repression of heterologous genes inserted in their vicinity. Thus, HML expression is regulated by two independent silencers, each fully competent for maintaining repression. This situation was distinct from the organization of the other silent locus, HMR, at which a single silencer served as the predominant repressor of expression. Examination of identifiable domains and binding sites within the HML silencers suggested that silencing activity can be achieved by a variety of combinations of various functional domains.

scholarly journals Gene Variations in Cis-Acting Elements between the Taiwan and Prototype Strains of Porcine Epidemic Diarrhea Virus Alter Viral Gene Expression

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 591
Author(s):  
Tsung-Lin Tsai ◽  
Chen-Chang Su ◽  
Ching-Chi Hsieh ◽  
Chao-Nan Lin ◽  
Hui-Wen Chang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Porcine Epidemic Diarrhea Virus ◽  
The Body ◽  
Economic Losses ◽  
Viral Gene ◽  
Sequence Motif ◽  
Cis Acting ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea ◽  
In Cis

In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis-acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 alter gene expression. For this aim, we analyzed the variations of the cis-acting elements in the 5’ and 3’ untranslated regions (UTRs) between the PEDV TW, CV777, and other reference strains. We also determined the previously unidentified transcription regulatory sequence (TRS), a sequence motif required for coronavirus transcription, and found that a nucleotide deletion in the TW strain, in comparison with CV777 strain, immediately downstream of the leader core sequence alters the identity between the leader TRS and the body TRS. Functional analyses using coronavirus defective interfering (DI) RNA revealed that such variations in cis-acting elements for the TW strain compared with the CV777 strain have an influence on the efficiency of gene expression. The current data show for the first time the evolution of PEDV in terms of cis-acting elements and their effects on gene expression, and thus may contribute to our understanding of recent PED outbreaks worldwide.

scholarly journals External Quality Assessment in the Evaluation of Laboratory Performance of Faecal Culture

2017 ◽  
Vol 10 ◽  
pp. 117863611769125
Author(s):  
Salla J Kiiskinen ◽  
Tarja Ojanen ◽  
Yvonne Björkman ◽  
Harri Laitinen ◽  
Anja Siitonen
Keyword(s):  
Public Health ◽  
Quality Control ◽  
External Quality Assessment ◽  
False Negative ◽  
The Other ◽  
Epidemiological Surveillance ◽  
External Quality Control ◽  
External Quality ◽  
Faecal Culture

In Finland, all laboratories carrying out diagnostics of infectious diseases in humans are approved by the Regional State Administrative Agencies and are obligated to participate in External Quality Assurance rounds. Performance in these rounds is thought to reflect the quality of laboratory work. In the 6-year study period, 17 Finnish laboratories received 48 simulated faecal specimens for the culturing of diarrhoeal pathogens, yielding altogether 586 faecal culture External Quality Control specimens and 581 reports. The results were correct in 92% of all reports and in 67% of all specimens. False-negative Salmonella results were given for 2 of the 18 specimens, one with biochemically atypical Salmonella strain and the other with a low count of Salmonella cells. False-negative Shigella report was given for 6 of the 7 specimens in some participating laboratory. Detection of all common faecal pathogens is especially relevant to patient safety, public health, and epidemiological surveillance.

scholarly journals DIFERENCIAÇÃO CATIÔNICA DE BENTONITAS POR INFRAVERMELHO: UM ESTUDO DOS EFEITOS DA HIDRATAÇÃO DOS CÁTIONS TROCÁVEIS

Química Nova ◽  
2021 ◽  
Author(s):  
Andréia Rodrigues ◽  
Rômulo Angélica ◽  
Simone Paz
Keyword(s):  
Quality Control ◽  
Near Infrared ◽  
Exchangeable Cations ◽  
The Other ◽  
Activation Process ◽  
Effective Technique ◽  
Common Procedure ◽  
Mir Spectroscopy ◽  
Sodium Activation ◽  
Hydrated Sample

CATIONIC DIFFERENTIATION OF BENTONITES BY INFRARED: A STUDY OF THE HYDRATION EFFECTS OF EXCHANGEABLE CATIONS. In the bentonite industry, the most common procedure for quality control of the ore and the sodium activation process is the swelling method. However, this tool is restricted only to the differentiation of the sodium and non-sodium types, not considering the other cationic varieties. The objective of this study was to establish parameters for cationic differentiation of bentonites based on Near Infrared (NIR) and Medium (MIR) spectroscopy, which proved to be an effective technique in the cationic differentiation of bentonites using the characteristic bands “7072 cm-1” and “3620 and 3430 cm-1” under the condition of the dry-hydrated sample and not under the anhydrous condition. NIRS can be considered a measure of great scientific and technological contribution, as it allows the cationic differentiation of bentonites in a practical way and with low analytical cost.

scholarly journals DNA-Based Herbal Teas’ Authentication: An ITS2 and psbA-trnH Multi-Marker DNA Metabarcoding Approach

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2120
Author(s):  
Jessica Frigerio ◽  
Giulia Agostinetto ◽  
Valerio Mezzasalma ◽  
Fabrizio De De Mattia ◽  
Massimo Labra ◽  
...  
Keyword(s):  
Quality Control ◽  
Quantitative Analysis ◽  
Medicinal Plants ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
The Other ◽  
Plant Component ◽  
Identification Rate ◽  
Dna Metabarcoding ◽  
Therapeutic Properties

Medicinal plants have been widely used in traditional medicine due to their therapeutic properties. Although they are mostly used as herbal infusion and tincture, employment as ingredients of food supplements is increasing. However, fraud and adulteration are widespread issues. In our study, we aimed at evaluating DNA metabarcoding as a tool to identify product composition. In order to accomplish this, we analyzed fifteen commercial products with DNA metabarcoding, using two barcode regions: psbA-trnH and ITS2. Results showed that on average, 70% (44–100) of the declared ingredients have been identified. The ITS2 marker appears to identify more species (n = 60) than psbA-trnH (n = 35), with an ingredients’ identification rate of 52% versus 45%, respectively. Some species are identified only by one marker rather than the other. Additionally, in order to evaluate the quantitative ability of high-throughput sequencing (HTS) to compare the plant component to the corresponding assigned sequences, in the laboratory, we created six mock mixtures of plants starting both from biomass and gDNA. Our analysis also supports the application of DNA metabarcoding for a relative quantitative analysis. These results move towards the application of HTS analysis for studying the composition of herbal teas for medicinal plants’ traceability and quality control.

scholarly journals PEMBERIAN STIMULAN PADA BIDANG SADAP DALAM MEMPENGARUHI PRODUKSI DAN KUALITAS LATEKS TANAMAN KARET (Hevea brasiliensis (Muell. Arg.)

2019 ◽  
Vol 4 (1) ◽  
pp. 38
Author(s):  
Hayata Hayata ◽  
Yulistiati Nengsih ◽  
Rahmanto Wibowo
Keyword(s):  
Quality Control ◽  
Ash Content ◽  
The Other ◽  
Rubber Content ◽  
Randomized Design ◽  
Treatment Factor ◽  
Completely Randomized Design ◽  
Four Levels ◽  
Latex Production

Production increasing of latex on rubber plants can be increased by using a stimulants. One of it  is Vicar 10 SL. The purpose of this study was to find out the effect of Vicar 10 SL on the production and quality of latex. This research was carried out in the Kasang Parit Village, Sekernan District, Muaro Jambi Regency, and the Goods Quality Control and Certification Center on Industry and trade department   in Jambi Province. The study was conducted in July to August 2017. The design used was a completely randomized design with one treatment factor as the Vicar 10 SL application with four levels of treatment, namely; Without treatment (V0/control), 1 ml/Tree (V1), 2 ml/tree (V2), 3 ml/tree (V3). There were 4 times  repeatation on each treatment. Using  fingers, a Vicar 10 SL solution was applied to the tapping groove which was adjusted to the treatment, and allowed to keep it 24 hours. Tapping is done in the next morning, by following the grooves and be stored in a cup and left until the latex stoped dripping. Vicar was given once a week during 30 days. Tapping was done 3 times a week. The variables observed were latex production (gram/tree/day), dry rubber content (%), latex ash content (%), and latex dirt content (%). Vicar giving 10 SL in the tapping site with a dose of 2 ml / tree gave the highest yield of latex production (93.38 grams / tree / day) and dry rubber content (75.50%) and was significantly different compared to the other treatments. Vicar giving 10 SL in tapping site had no significant effect on latex dirt content and latex ash contentKeywords: Latex, stimulant, product and quality Abstrak Peningkatan produksi lateks pada tanaman karet dapat ditingkatkan dengan menggunakan stimulan. Salah satu pemakaian yang digunakan adalah Vikar 10 SL. Tujuan penelitian ini adalah untuk megetahui penggunaan stimulan pada bidang sadap dalam mempengaruhi produksi dan kualitas lateks. Penelitian ini dilakukan di Desa kasang Parit Kecamatan Sekernan Kabupaten Muaro Jambi, dan Balai Pengujian dan Sertifikasi Mutu Barang (BPSMB) Disperindag Propinsi Jambi. Penelitian dilakukan pada bulan Juli sampai dengan Agustus 2017. Rancangan yang digunakan adalah Rancangan Acak Lengkap dengan satu faktor perlakuan pemberian stimulan (Vikar 10 SL) dengan empat taraf perlakuan  yaitu; Tanpa perlakuan (V0/kontrol),  1 ml/ Pohon (V1),  2 ml/pohon (V2), 3 ml/pohon  (V3). Setiap perlakuan diulang sebanyak 4 kali. Dengan menggunakan jari dioleskan larutan Vikar 10 SL pada alur sadap  yang disesuaikan dengan perlakuan, dan didiamkan selama 24 jam. Penyadapan dilakukan pada pagi hari esoknya, dengan mengikuti alur torehan dan ditampung dalam cawan dan dibiarkan sampai lateks berhenti menetes. Pemberian Vikar dilakukan sekali 7 hari selama 30 hari. Penyadapan dilakukan  3 kali dalam seminggu. Peubah yang diamati adalah produksi lateks (gram/pohon/hari)), kadar karet kering (%), kadar abu lateks (%), kadar kotoran lateks (%). Pemberian stimulan (Vikar 10 SL) pada bidang sadap dengan dosis 2 ml/pohon memberikan hasil yang tertinggi terhadap produksi lateks 93,38 gram/pohon/hari dan kadar karet kering 75,50 % dan berbeda nyata bila dibandingkan dengan perlakuan lainnya. Pemberian stimulan (Vikar 10 SL) pada bidang sadap berpengaruh tidak nyata terhadap kotoran lateks dan kadar abu lateksKata kunci :Lateks, stimulan, produksi dan kualitas

scholarly journals Adequacy of the Electrical Conductivity Test Methodology for Millet Seeds

2017 ◽  
Vol 9 (11) ◽  
pp. 130 ◽  
Author(s):  
Luanna Karoline Rinaldi ◽  
Diandra Javorski ◽  
Maicon Javorski ◽  
Ana Paula Mourão Simonetti ◽  
Tatiane Priscila Chiapetti ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Quality Control ◽  
The Other ◽  
Water Volume ◽  
Accelerated Ageing ◽  
Seed Imbibition ◽  
Test Methodology

Companies have sought to improve, more and more, the quality control of the seeds produced, improving tests that evaluate the vigor of the seeds with greater speed and precision. The objective of the present work was to study the effects of imbibition time on the results of the electrical conductivity test to evaluate the vigor of millet seeds and to correlate with the other tests carried out. Six seeds lots of the ADR300 cultivar with different vigor levels were used. Germination, first germination count, accelerated ageing, emergence and emergence speed of seedlings in sand and electrical conductivity with variations in water volume were performed (50 And 75 cm3), during the imbibition time of 2, 4, 6 and 8 hours, at 25 ºC. The time of 2 hours of the seed imbibition in 75 cm3 in water proved to be efficient to evaluate the vigor of millet seeds in all lots tested.

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