scholarly journals Revisiting the Non-Coding Nature of Pospiviroids

Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 265
Author(s):  
Konstantina Katsarou ◽  
Charith Raj Adkar-Purushothama ◽  
Emilios Tassios ◽  
Martina Samiotaki ◽  
Christos Andronis ◽  
...  
Keyword(s):  
Unknown Function ◽  
Bioinformatic Analysis ◽  
Economic Losses ◽  
In Vitro Experiments ◽  
Experimental Conditions ◽  
Circular Form ◽  
Size And Structure

Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study.

152 TRANSMISSION OF BOVINE VIRAL DIARRHEA VIRUS BY IN VITRO-FERTILIZED EMBRYOS UNDER EXPERIMENTAL CONDITIONS

2008 ◽  
Vol 20 (1) ◽  
pp. 156 ◽  
Author(s):  
A. Bielanski ◽  
J. Algire ◽  
A. Lalonde
Keyword(s):  
Bovine Viral Diarrhea Virus ◽  
Economic Losses ◽  
Bovine Viral Diarrhea ◽  
Experimental Conditions ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Diarrhea Virus

Bovine viral diarrhea virus (BVDV) infection affects cattle throughout the world. It causes significant economic losses in the cattle industry. The potential for transmission of a cytopathic biotype of BVDV by in vivo-derived embryos has been thought to be negligible. However, there is no study to prove non-transmission of the most common field isolate of noncytopathic biotype (NCPB) of BVDV by IVF embryos. Here we report on the preliminary outcome of embryo transfer (ET) of IVF embryos exposed in vitro to type-1 (NY-1) and type-2 (P-131) genotypes of NCPB of BVDV. For this experiment, IVF embryos were generated using standard methods which briefly involve: maturation of cumulus–oocyte complexes in TCM medium, fertilization of oocytes with BVDV-free semen, and culture of zygotes to the blastocyst stage in SOF medium without somatic cells. Day 7 blastocysts were exposed for 1 h to NY-1 or P-131 (103–107 TCID50 mL–1) BVDV strains before being washed (without trypsin) as recommended by IETS. Two embryos were transferred on each occasion. Embryo recipients were virus-free and anti-BVDV antibody-free prior to ET. The recipients remained individually in isolation premises after ET. In total, 126 ET procedures were performed resulting in 57 pregnancies and 34 calves born free of the infectious virus and BVDV antibodies (5 pregnancies are still pending). In total, 23 pregnancies were lost after 30 days. Exposure of embryos to type-2 BVDV resulted in a loss of 46% (17/37) of pregnancies after 30 days post-ET and 20 recipients seroconverted to BVDV. Within seroconverted and pregnant animals (n = 14), only 2 recipients maintained pregnancy and delivered uninfected calves at term. In contrast, exposure of embryos to type-1 caused 30% (6/20) of the pregnancy losses after 30 days and did not cause any seroconversion in ET recipients. After washing, 33% (3/9) and 38% (17/44) single embryos from the infected pool of IVF embryos tested positive for the BVDV. In conclusion, under these experimental conditions, a proportion of recipients was apparently infected after receipt of BVDV-exposed embryos. However, all of the calves that survived to term were BVDV-free and anti-BVDV antibody free.

An Analysis of the Postgastrula Differentiation of the Hypomere

Development ◽  
1961 ◽  
Vol 9 (2) ◽  
pp. 294-309
Author(s):  
Cyril V. Finnegan
Keyword(s):  
Early Age ◽  
In Vitro Experiments ◽  
Experimental Conditions ◽  
Tissue Mass ◽  
Intimate Association ◽  
Insight Into

Since the publication of earlier papers (Finnegan, 1953, 1955) the investigation of the capacity of the salamander hypomeric mesoderm for histogenesis under a variety of experimental conditions has continued. It is perhaps prudent at this time to initiate a series of reports with results obtained from in vitro experiments which were designed to gain some insight into the roles of competence, tissue mass, and endodermal influence relative to hypomeric differentiation in Ambystoma. This portion of the mesoderm is destined to undergo its differentiation far removed from the dorsal axial influences of the chorda-mesoderm but with its inner (splanchnic) material in rather intimate association with the endoderm, a tissue known to be determined at an early age and metabolically active, two conditions which lead one to suspect it of inductor potentialities (Nieuwkoop, 1947; Copenhaver, 1955).

In Vitro Models for Studying Renal Stone Formation: A Clear Alternative

1998 ◽  
Vol 26 (4) ◽  
pp. 481-503
Author(s):  
Felix Grases ◽  
Rafael M. Prieto ◽  
Antonia Costa-Bauzá
Keyword(s):  
Renal Stone ◽  
Stone Formation ◽  
Renal Stones ◽  
Renal Calculi ◽  
In Vitro Models ◽  
Laboratory Animals ◽  
In Vitro Experiments ◽  
Experimental Conditions

This paper discusses the limitations of using laboratory animals for direct in vivo observation of the development of renal stones. In fact, the majority of hypotheses related to mechanisms of stone formation have been based on the results of in vitro experiments. The relevance of in vitro experiments that allow the study of urolithiasis depends upon the degree of correspondence between the experimental conditions and those prevailing in the stone-forming kidney in vivo. For this reason, several in vitro experimental systems that attempt to reproduce the conditions found in vivo have been developed in order to study renal stone formation, which have been classified into two main groups: a) models to study papillary stone formation; and b) models to study “sedimentary” stone formation. These models are briefly described in this paper, and the information obtained was compared with that resulting from a study of the fine structure of real human renal calculi, in order to prove the validity of the models. It was concluded that the experimental in vitro models can closely reproduce the renal conditions under which human calculi are developed. This allows important data to be obtained about the aetiology of renal lithiasis, which is of great relevance to the development of effective treatments for this disease. Therefore, experimental in vitro models constitute a clear alternative to the use of laboratory animals.

scholarly journals Towards Biological Control of Aspergillus carbonarius and Botrytis cinerea in Grapevine Berries and Transcriptomic Changes of Genes Encoding Pathogenesis-Related (PR) Proteins

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 970
Author(s):  
Danai Gkizi ◽  
Eirini G. Poulaki ◽  
Sotirios E. Tjamos
Keyword(s):  
Biological Control ◽  
Botrytis Cinerea ◽  
Defense Responses ◽  
Economic Losses ◽  
Aspergillus Carbonarius ◽  
In Vitro Experiments ◽  
In Planta ◽  
Pathogenesis Related ◽  
Genes Encoding

Grapevine bunch rot, caused by Botrytis cinerea and Aspergillus carbonarius, causes important economic losses every year in grape production. In the present study, we examined the plant protective activity of the biological control agents, Paenibacillus alvei K165, Blastobotrys sp. FP12 and Arthrobacter sp. FP15 against B. cinerea and A. carbonarius on grapes. The in vitro experiments showed that strain K165 significantly reduced the growth of both fungi, while FP15 restricted the growth of A. carbonarius and FP12 was ineffective. Following the in vitro experiments, we conducted in planta experiments on grape berries. It was shown that K165, FP12 and FP15 reduced A. carbonarius rot severity by 81%, 57% and 37%, respectively, compared to the control, whereas, in the case of B. cinerea, the only protective treatment was that with K165, which reduced rot by 75%. The transcriptomic analysis of the genes encoding the pathogenesis-related proteins PR2, PR3, PR4 and PR5 indicates the activation of multiple defense responses involved in the biocontrol activity of the examined biocontrol agents.

scholarly journals Development, Biological Characterization, and Immunological Evaluation of Virosome Vaccine against Newcastle Disease in Pakistan

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Muhammad Hidayat Rasool ◽  
Asif Mehmood ◽  
Muhammad Saqalein ◽  
Muhammad Atif Nisar ◽  
Ahmad Almatroudi ◽  
...  
Keyword(s):  
Newcastle Disease ◽  
Fluorescent Protein ◽  
Virulent Strain ◽  
Negative Control ◽  
Economic Losses ◽  
Experimental Conditions ◽  
In Vivo Evaluation ◽  
Inactivated Vaccines

Newcastle disease (ND) is a highly fatal, infectious, viral disease, and despite immunization with live and inactivated vaccines, the disease is still endemic, causing heavy morbidity and mortality leading to huge economic losses to the poultry industry in Pakistan. Therefore, the present study was aimed for the first time in the country at using novel virosomal technology to develop the ND vaccine using an indigenous highly virulent strain of the virus. ND virosome was prepared using Triton X-100, and SM2 Bio-Beads were used to remove the detergent and reconstitute the viral membrane into virosome. Confirmation was done by transmission electron microscopy and protein analysis by SDS-PAGE. In vitro cell adhesion property was observed by incorporating green fluorescent protein (GFP), producing plasmid into virosome and in vitro cell culture assay. Sterility, safety, and stability of the vaccine were tested before in vivo evaluation of immunogenicity and challenge protection study in commercial broiler. The virosome vaccine was administered (30 μg/bird) at days 7 and 14 through the intranasal route in comparison with commercially available live and inactivated ND vaccines. Results revealed significantly high ( p < 0.05 ) and clinically protective hemagglutination inhibition (HI) antibody titers at 7, 14, 21, and 28 days postimmunization with the virosome vaccine in comparison to the negative control. The GMTs were comparable to live and inactivated vaccines with nonsignificant ( p > 0.05 ) differences throughout the experiment. Antibody levels increased in all vaccinated groups gradually from the 7th day and were maximum at 28th-day postvaccination. In the virosome-administered group, GMT was 83.18 and 77.62 at 21st and 28th-days postvaccination, respectively. Challenge revealed 100%, 90%, and 80% protection in virosome, live, and inactivated vaccinated groups, respectively. Under given experimental conditions, we can conclude that ND virosome vaccine prepared from the indigenous virus was found to be safe and immunogenic.

scholarly journals Improving Phage-Biofilm In Vitro Experimentation

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1175
Author(s):  
Stephen T. Abedon ◽  
Katarzyna M. Danis-Wlodarczyk ◽  
Daniel J. Wozniak ◽  
Matthew B. Sullivan
Keyword(s):  
Viable Count ◽  
Bacterial Biofilms ◽  
In Vitro Experiments ◽  
Experimental Conditions ◽  
Biofilm Growth ◽  
Bacterial Ecology ◽  
End Point ◽  
Biofilm Disruption ◽  
Free Phage

Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a critical look at the study of bacteriophage interactions with bacterial biofilms as carried out in vitro, since these studies serve as bases of our ecological and therapeutic understanding of phage impacts on biofilms. We suggest that phage-biofilm in vitro experiments often may be improved in terms of both design and interpretation. Specific issues discussed include (a) not distinguishing control of new biofilm growth from removal of existing biofilm, (b) inadequate descriptions of phage titers, (c) artificially small overlying fluid volumes, (d) limited explorations of treatment dosing and duration, (e) only end-point rather than kinetic analyses, (f) importance of distinguishing phage enzymatic from phage bacteriolytic anti-biofilm activities, (g) limitations of biofilm biomass determinations, (h) free-phage interference with viable-count determinations, and (i) importance of experimental conditions. Toward bettering understanding of the ecology of bacteriophage-biofilm interactions, and of phage-mediated biofilm disruption, we discuss here these various issues as well as provide tips toward improving experiments and their reporting.

scholarly journals In Silico Experiments in Scientific Papers on Molecular Biology

2011 ◽  
Vol 24 (2) ◽  
pp. 23-42
Author(s):  
Sabrina Moretti
Keyword(s):  
Molecular Biology ◽  
In Silico ◽  
In Vitro Experiments ◽  
Technical Object ◽  
Experimental Conditions ◽  
Biological Phenomena ◽  
Scientific Papers

This article explores the role of the so-called in silico experiments used in molecular biology. It is based on the analysis of some papers that present scientific applications which rely on in silico experiments. By means of this study I found two basic ways of viewing them. According to the first view, the in silico experiment is a computer program that realizes some specific operations: it constitutes some particular experimental conditions, which allow us to investigate biological phenomena, and which complement those present in in vivo and in vitro experiments. According to the second view, in silico experimentation has a different meaning, which corresponds more closely to the meaning of “simulation”: its identity is linked to that of the “model” used to construct such simulation. The authors of the analysed papers never express an intention to standardize a model, so its meaning remains contingent, and cannot be turned into a technical object.

Humoral induction of pyloric rhythmic output in lobster stomatogastric ganglion: in vivo and in vitro studies

1992 ◽  
Vol 163 (1) ◽  
pp. 209-230
Author(s):  
E. Rezer ◽  
M. Moulins
Keyword(s):  
Blood Serum ◽  
Stomatogastric Ganglion ◽  
In Vitro Studies ◽  
In Vitro Experiments ◽  
Experimental Conditions ◽  
Pyloric Network ◽  
Pyloric Rhythm

In the lobster Jasus lalandii, 14 neurones of the stomatogastric ganglion (STG) are organized in a network that produces rhythmic pyloric outputs. In vitro experiments have shown that the STG neurones receive, via the stomatogastric nerve (stn), neuromodulatory inputs that influence the expression of the bursting properties of the neurones and the ability of the network to produce its rhythmic output. In contrast to these in vitro observations, in vivo transection of the stn does not abolish the pyloric rhythm. Rhythmic output can be recorded by electromyography immediately after stn transection and for up to 2 years afterwards. We have shown that, under these experimental conditions, the STG appears to be isolated from any neuronal input that might account for the maintenance of the rhythmic output. Experiments carried out in the 2 days after stn transection showed that an in vitro preparation of the isolated STG was unable to produce any rhythmic output, but blood serum added to the system could restore the pyloric output. These results suggest strongly that the pyloric network receives neural and humoral modulatory influences in parallel and that each type of influence alone is able to maintain the bursting capability of the pyloric neurones.

scholarly journals Urinary Exosomal miRNAs as biomarkers of bladder Cancer and experimental verification of mechanism of miR-93-5p in bladder Cancer

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hao Lin ◽  
Xiaojun Shi ◽  
Haoran Li ◽  
Jialiang Hui ◽  
Ruiyu Liu ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Roc Curve ◽  
Validation Cohort ◽  
Bioinformatic Analysis ◽  
The Cancer Genome Atlas ◽  
In Vitro Experiments ◽  
Exosomal Mirnas ◽  
Healthy Control ◽  
Muscle Invasive

Abstract Background Bladder cancer (BC) is one of the most common malignancies globally. Early diagnosis of it can significantly improve patients’ survival and quality of life. Urinary exosomes (UEs)-derived miRNAs might be a promising biomarker for BC detection. Method A total of 12 patients with BC and 4 non-cancerous participants (as healthy control) were recruited from a single center between March 2018 and December 2019 as the discovery set. Midstream urine samples from each participants were collected and high-throughput sequencing and differentially expression analysis were conducted. Combined with miRNA expression profile of BC tissue from The Cancer Genome Atlas (TCGA), miRNAs biomarkers for BC were determined. Candidate miRNAs as biomarkers were selected followed by verification with a quantitative reverse-transcription polymerase chain reaction assay in an independent validation cohort consisting of 53 BC patients and 51 healthy controls. The receiver-operating characteristic (ROC) curve was established to evaluate the diagnostic performance of UE-derived miRNAs. The possible mechanism of miRNAs were revealed by bioinformatic analysis and explored in vitro experiments. Results We identified that miR-93-5p, miR-516a-5p were simultaneously significantly increased both in UEs from BC compared with healthy control and BC tissue compared with normal tissue, which were verified by RT-qPCR in the validation cohort. Subsequently, the performance to discover BC of the miR-93-5p, miR-516a-5p was further verified with an area under ROC curve (AUC) of 0.838 and 0.790, respectively, which was significantly higher than that of urine cytology (AUC = 0.630). Moreover, miR-93-5p was significantly increased in muscle-invasive BC compared with non-muscle-invasive BC with an AUC of 0.769. Bioinformatic analysis revealed that B-cell translocation gene 2(BTG2) gene may be the hub target gene of miR-93-5p. In vitro experiments verified that miR-93-5p suppressed BTG2 expression and promoted BC cells proliferation, invasion and migration. Conclusion Urine derived exosomes have a distinct miRNA profile in BC patients, and urinary exosomal miRNAs could be used as a promising non-invasive tool to detect BC. In vitro experiments suggested that miR-93-5p overexpression may contribute to BC progression via suppressing BTG2 expression.

Neurofilaments and Paired Helical Filaments

1985 ◽  
Vol 43 ◽  
pp. 740-743
Author(s):  
J. Metuzals
Keyword(s):  
Animal Model ◽  
Posttranslational Modifications ◽  
Posttranslational Modification ◽  
Giant Axon ◽  
Paired Helical Filaments ◽  
Squid Giant Axon ◽  
In Vitro Experiments ◽  
Thin Sections ◽  
Structural Relationships

It has been demonstrated that the neurofibrillary tangles in biopsies of Alzheimer patients, composed of typical paired helical filaments (PHF), consist also of typical neurofilaments (NF) and 15nm wide filaments. Close structural relationships, and even continuity between NF and PHF, have been observed. In this paper, such relationships are investigated from the standpoint that the PHF are formed through posttranslational modifications of NF. To investigate the validity of the posttranslational modification hypothesis of PHF formation, we have identified in thin sections from frontal lobe biopsies of Alzheimer patients all existing conformations of NF and PHF and ordered these conformations in a hypothetical sequence. However, only experiments with animal model preparations will prove or disprove the validity of the interpretations of static structural observations made on patients. For this purpose, the results of in vitro experiments with the squid giant axon preparations are compared with those obtained from human patients. This approach is essential in discovering etiological factors of Alzheimer's disease and its early diagnosis.

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