scholarly journals Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames in reference to cell signaling and neurological development

2019 ◽  
Author(s):  
Stefania Pacini ◽  
Marco Ruggiero
Keyword(s):  
Dna Sequences ◽  
Bovine Milk ◽  
Fermented Milk ◽  
Open Reading Frames ◽  
Neurological Development ◽  
Putative Role ◽  
Biological Entities ◽  
Reading Frames

AbstractBacteriophages (phages), Earth’s most numerous biological entities, are natural constituents of alimentary matrices; in this study we describe the characterization of phage populations in a product obtained by fermentation of bovine milk and colostrum. Such characterizations were achieved using a microarray consisting of a chip covered in short DNA sequences that are specific to certain target organisms for a total of approximately 12,000 species. The only viruses evidenced by the array belonged to Siphoviridae, the largest phage family that targets bacteria and archea. The array yielded 27 iterations corresponding to a unique target. We discuss the putative role of some open reading frames of these phages in conferring health-supporting properties with particular reference to cells signaling and neurological development. We also describe the in vitro interaction of this fermented product with alpha-N-acetylgalactosaminidase, an enzyme whose activity in serum is elevated in neurodevelopmental disorders.

scholarly journals Phage composition of a fermented milk and colostrum product assessed by microbiome array; putative role of open reading frames in reference to cell signaling and neurological development

2020 ◽  
Vol 10 (2) ◽  
Author(s):  
Stefania Pacini ◽  
Marco Ruggiero S
Keyword(s):  
Dna Sequences ◽  
Bovine Milk ◽  
Fermented Milk ◽  
Open Reading Frames ◽  
Neurological Development ◽  
Putative Role ◽  
Biological Entities ◽  
Reading Frames

Bacteriophages (phages), Earth's most numerous biological entities, are natural constituents of alimentary matrices; in this study we describe the characterization of phage populations in a product obtained by fermentation of bovine milk and colostrum. Such characterizations were achieved using a microarray consisting of a chip covered in short DNA sequences that are specific to certain target organisms for a total of approximately 12,000 species. The only viruses evidenced by the array belonged to Siphoviridae, the largest phage family that targets bacteria and archea. The array yielded 27 iterations corresponding to a unique target. We discuss the putative role of some open reading frames of these phages in conferring health-supporting properties with particular reference to cells signaling and neurological development. We also describe the in vitro interaction of this fermented product with alpha-N-acetylgalactosaminidase, an enzyme whose activity in serum is elevated in neurodevelopmental disorders.

scholarly journals Tuning microscale, retractable, membrane-breaking protein needles

2015 ◽  
Author(s):  
Jessica K Polka ◽  
Pamela A Silver
Keyword(s):  
Lipid Bilayers ◽  
Protein Structures ◽  
Open Reading Frames ◽  
Paramecium Tetraurelia ◽  
E Coli ◽  
Body State ◽  
High Throughput Assay ◽  
Reading Frames

The refractile (R) bodies found in Caedibacter taeniospiralis, a bacterial endosymbiont of Paramecium tetraurelia, are large, polymeric protein structures that can switch between two conformations. At cytoplasmic pH, they resemble coiled ribbons of protein 500nm in diameter. At low pH, they extend to form hollow needles up to 20 microns long. They can be expressed heterologously from an operon containing four short open reading frames and can function in vitro in diverse buffer conditions. In this study, R bodies purified from Escherichia coli were found to be capable of undergoing many consecutive extension-contraction cycles. Furthermore, the solubility of R bodies, which can easily be interpreted by eye, was found to correlate with their extension state. This macroscopic phenotype was used to develop a quantitative, high-throughput assay for R body state, enabling a visual screen of R body mutants defective in extension. The role of specific amino acids in extension was determined, and this information was used to construct rationally-designed mutants tailored to extend at higher pH. Furthermore, R bodies were able to rupture E. coli spheroplasts to release soluble proteins across lipid bilayers. Taken together, these results show that R bodies act as tunable, pH-actuated pistons suitable for a variety of membrane-breaking applications.

scholarly journals Comparison of the Complete DNA Sequences of Human Herpesvirus 6 Variants A and B

1999 ◽  
Vol 73 (10) ◽  
pp. 8053-8063 ◽  
Author(s):  
Yuji Isegawa ◽  
Tetsu Mukai ◽  
Kazushi Nakano ◽  
Miwa Kagawa ◽  
Jiguo Chen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Human Herpesvirus ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Human Herpesvirus 6 ◽  
Exanthem Subitum ◽  
Herpesvirus 6 ◽  
Different Strains ◽  
Reading Frames

ABSTRACT Human herpesvirus 6 (HHV-6), which belongs to the betaherpesvirus subfamily and infects mainly T cells in vitro, causes acute and latent infections. Two variants of HHV-6 have been distinguished on the basis of differences in several properties. We have determined the complete DNA sequence of HHV-6 variant B (HHV-6B) strain HST, the causative agent of exanthem subitum, and compared the sequence with that of variant A strain U1102. A total of 115 potential open reading frames (ORFs) were identified within the 161,573-bp contiguous sequence of the entire HHV-6 genome, including some genes with remarkable differences in amino acid identity. All genes with <70% identity between the two variants were found to contain deleted regions when ORFs that could not be expressed were excluded from the comparison. Except in the case of U47, these differences were found in immediate-early/regulatory genes, DR2, DR7, U86/90, U89/90, and U95, which may represent characteristic differences of variants A and B. Also, we have successfully typed 14 different strains belonging to variant A or B by PCR using variant-specific primers; the results suggest that the remarkable differences observed were conserved evolutionarily as variant-specific divergence.

In vitro yeast reconstituted translation system reveals function of eIF5A for synthesis of long polypeptide

2020 ◽  
Vol 167 (5) ◽  
pp. 451-462
Author(s):  
Taisho Abe ◽  
Riku Nagai ◽  
Shunta Shimazaki ◽  
Shunta Kondo ◽  
Satoshi Nishimura ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Translation System ◽  
Ribosome Stalling ◽  
Internal Position ◽  
Polyproline Motif ◽  
Reading Frames

Abstract We have recently developed an in vitro yeast reconstituted translation system, which is capable of synthesizing long polypeptides. Utilizing the system, we examined the role of eIF5A and its hypusine modification in translating polyproline sequence within long open reading frames. We found that polyproline motif inserted at the internal position of the protein arrests translation exclusively at low Mg2+ concentrations, and peptidylpolyproline-tRNA intrinsically destabilizes 80S ribosomes. We demonstrate that unmodified eIF5A essentially resolves such ribosome stalling; however, the hypusine modification drastically stimulates ability of eIF5A to rescue polyproline-mediated ribosome stalling and is particularly important for the efficient translation of the N-terminal or long internal polyproline motifs.

scholarly journals Engineering of Recombinant Sheep Pox Viruses Expressing Foreign Antigens

2021 ◽  
Vol 9 (5) ◽  
pp. 1005
Author(s):  
Olga Chervyakova ◽  
Elmira Tailakova ◽  
Nurlan Kozhabergenov ◽  
Sandugash Sadikaliyeva ◽  
Kulyaisan Sultankulova ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Viral Vector ◽  
Foot And Mouth Disease ◽  
Open Reading Frames ◽  
Foreign Gene ◽  
Mouth Disease Virus ◽  
Foreign Genes ◽  
Green Fluorescent ◽  
Reading Frames

Capripoxviruses with a host range limited to ruminants have the great potential to be used as vaccine vectors. The aim of this work was to evaluate attenuated sheep pox virus (SPPV) vaccine strain NISKHI as a vector expressing several genes. Open reading frames SPPV020 (ribonucleotide kinase) and SPPV066 (thymidine kinase) were selected as sites for the insertion of foreign genes. Two integration plasmids with expression cassette were designed and constructed. Recombinant SPPVs expressing an enhanced green fluorescent protein (EGFP) (rSPPV(RRΔ)EGFP and rSPPV(TKΔ)EGFP), Foot-and-mouth disease virus capsid protein (VP1), and Brucella spp. outer membrane protein 25 (OMP25) (rSPPV(RRΔ)VP1A-(TKΔ)OMP25) were generated under the transient dominant selection method. The insertion of foreign genes into the SPPV020 and SPPV066 open reading frames did not influence the replication of the recombinant viruses in the cells. Successful foreign gene expression in vitro was assessed by luminescent microscopy (EGFP) and Western blot (VP1 and OMP25). Our results have shown that foreign genes were expressed by rSPPV both in permissive (lamb testicles) and non-permissive (bovine kidney, saiga kidney, porcine kidney) cells. Mice immunized with rSPPV(RRΔ)VP1A-(TKΔ)OMP25 elicited specific antibodies to both SPPV and foreign genes VP1 and OMP25. Thus, SPPV NISKHI may be used as a potential safe immunogenic viral vector for the development of polyvalent vaccines.

scholarly journals Genomic Sequence of Rhesus Cytomegalovirus 180.92: Insights into the Coding Potential of Rhesus Cytomegalovirus

2006 ◽  
Vol 80 (8) ◽  
pp. 4179-4182 ◽  
Author(s):  
Pierre Rivailler ◽  
Amitinder Kaur ◽  
R. Paul Johnson ◽  
Fred Wang
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Rhesus Cytomegalovirus ◽  
Human Cmv ◽  
Coding Capacity ◽  
Coding Potential ◽  
Reading Frames ◽  
Genetic Rearrangements

ABSTRACT A pathogenic isolate of rhesus cytomegalovirus (rhCMV 180.92) was cloned, sequenced, and annotated. Comparisons with the published rhCMV 68.1 genome revealed 8 open reading frames (ORFs) in isolate 180.92 that are absent in 68.1, 10 ORFs in 68.1 that are absent in 180.92, and 34 additional ORFs that were not previously annotated. Most of the differences appear to be due to genetic rearrangements in both isolates from a region that is frequently altered in human CMV (hCMV) during in vitro passage. These results indicate that the rhCMV ORF repertoire is larger than previously recognized. Like hCMV, understanding of the complete coding capacity of rhCMV is complicated by genomic instability and may require comparisons with additional isolates in vitro and in vivo.

scholarly journals DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

2008 ◽  
Vol 190 (6) ◽  
pp. 2231-2238 ◽  
Author(s):  
Melanie Zaparty ◽  
Alexander Zaigler ◽  
Claudia Stamme ◽  
Jörg Soppa ◽  
Reinhard Hensel ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Dna Microarray ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Heterotrophic Growth ◽  
Thermoproteus Tenax ◽  
Central Carbohydrate Metabolism ◽  
Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

E1−E4+ Adenoviral Gene Transfer Vectors Function as a “Pro-Life” Signal to Promote Survival of Primary Human Endothelial Cells

Blood ◽  
1999 ◽  
Vol 93 (9) ◽  
pp. 2936-2944 ◽  
Author(s):  
Ramachandran Ramalingam ◽  
Shahin Rafii ◽  
Stefan Worgall ◽  
Douglas E. Brough ◽  
Ronald G. Crystal
Keyword(s):  
Endothelial Cells ◽  
Open Reading Frames ◽  
Adenoviral Gene Transfer ◽  
Vector Genome ◽  
Transfer Vectors ◽  
Reading Frames ◽  
Human Endothelium ◽  
Pro Life

Abstract Although endothelial cells are quiescent and long-lived in vivo, when they are removed from blood vessels and cultured in vitro they die within days to weeks. In studies of the interaction of E1−E4+ replication–deficient adenovirus (Ad) vectors and human endothelium, the cells remained quiescent and were viable for prolonged periods. Evaluation of these cultures showed that E1−E4+ Ad vectors provide an “antiapoptotic” signal that, in association with an increase in the ratio of Bcl2 to Bax levels, induces the endothelial cells to enter a state of “suspended animation,” remaining viable for at least 30 days, even in the absence of serum and growth factors. Although the mechanisms initiating these events are unclear, the antiapoptoic signal requires the presence of E4 genes in the vector genome, suggesting that one or more E4 open reading frames of subgroup C Ad initiate a “pro-life” program that modifies cultured endothelial cells to survive for prolonged periods.

scholarly journals Characterization of Endogenous Retroviruses in Sheep

2003 ◽  
Vol 77 (20) ◽  
pp. 11268-11273 ◽  
Author(s):  
Nikolai Klymiuk ◽  
Mathias Müller ◽  
Gottfried Brem ◽  
Bernhard Aigner
Keyword(s):  
Endogenous Retrovirus ◽  
Ovis Aries ◽  
Endogenous Retroviruses ◽  
Open Reading Frames ◽  
In Vivo Experiments ◽  
Pregnant Sheep ◽  
Reading Frames

ABSTRACT Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV β families and nine OERV γ families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV β family and two OERV γ families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.

scholarly journals Characterization of the Urease Operon of Brucella abortus and Assessment of Its Role in Virulence of the Bacterium

2006 ◽  
Vol 75 (2) ◽  
pp. 774-780 ◽  
Author(s):  
Félix J. Sangari ◽  
Asunción Seoane ◽  
María Cruz Rodríguez ◽  
Jesús Agüero ◽  
Juan M. García Lobo
Keyword(s):  
Brucella Abortus ◽  
Urease Activity ◽  
Strong Acid ◽  
Oral Route ◽  
Open Reading Frames ◽  
Human Brucellosis ◽  
Major Route

ABSTRACT Most members of the genus Brucella show strong urease activity. However, the role of this enzyme in the pathogenesis of Brucella infections is poorly understood. We isolated several Tn5 insertion mutants deficient in urease activity from Brucella abortus strain 2308. The mutations of most of these mutants mapped to a 5.7-kbp DNA region essential for urease activity. Sequencing of this region, designated ure1, revealed the presence of seven open reading frames corresponding to the urease structural proteins (UreA, UreB, and UreC) and the accessory proteins (UreD, UreE, UreF, and UreG). In addition to the urease genes, another gene (cobT) was identified, and inactivation of this gene affected urease activity in Brucella. Subsequent analysis of the previously described sequences of the genomes of Brucella spp. revealed the presence of a second urease cluster, ure2, in all them. The ure2 locus was apparently inactive in B. abortus 2308. Urease-deficient mutants were used to evaluate the role of urease in Brucella pathogenesis. The urease-producing strains were found to be resistant in vitro to strong acid conditions in the presence of urea, while urease-negative mutants were susceptible to acid treatment. Similarly, the urease-negative mutants were killed more efficiently than the urease-producing strains during transit through the stomach. These results suggested that urease protects brucellae during their passage through the stomach when the bacteria are acquired by the oral route, which is the major route of infection in human brucellosis.

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