scholarly journals ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

2017 ◽  
Author(s):  
Amy I. Gilson ◽  
Niamh Durfee ◽  
Rostam M. Razban ◽  
Hendrick Strobelt ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Protein Structure ◽  
Protein Evolution ◽  
Scale Effects ◽  
Structure Evolution ◽  
P Value ◽  
Sequence Evolution ◽  
Protein Chain ◽  
E Coli ◽  
Protein Properties ◽  
Web App

AbstractMotivationProtein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the S. cerevisiae and E. coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution is studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level.ResultsWe demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S. cerevisiae and E. coli oPCUGs are scale-free with scaling constants of 1.78 and 1.50, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution (Dokholyan et al., 2002). Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of −0.51 (p-value<10−10) and −0.46 (p-value<10−10) for S. cerevisiae and E. coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant (Zhang and Yang, 2015).AvailabilityProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu/proteomevis/[email protected] informationAvailable to download on bioRxiv.

scholarly journals ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

2018 ◽  
Vol 34 (23) ◽  
pp. 4140-4140
Author(s):  
Rostam M Razban ◽  
Amy I Gilson ◽  
Niamh Durfee ◽  
Hendrik Strobelt ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Sequence Evolution ◽  
Protein Properties ◽  
Web App

scholarly journals Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli

2017 ◽  
Author(s):  
Eric Girard ◽  
Pouria Dasmeh ◽  
Adrian W.R. Serohijos
Keyword(s):  
Protein Evolution ◽  
Protein Unfolding ◽  
Long Term Evolution ◽  
Fitness Cost ◽  
Sequence Evolution ◽  
E Coli ◽  
Term Evolution ◽  
Highly Expressed Genes

ABSTRACTEpistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation. Our results highlight the coupling between selection and epistasis in the long-term evolution of a proteome.

scholarly journals ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms’ proteomes

2018 ◽  
Vol 34 (20) ◽  
pp. 3557-3565 ◽  
Author(s):  
Rostam M Razban ◽  
Amy I Gilson ◽  
Niamh Durfee ◽  
Hendrik Strobelt ◽  
Kasper Dinkla ◽  
...  
Keyword(s):  
Sequence Evolution ◽  
Protein Properties ◽  
Web App

Penyelidikan KLB keracunan makanan acara ruwahan di desa Mulo, Gunung Kidul provinsi DIY

2018 ◽  
pp. 1
Author(s):  
Mur Prasetyaningrum ◽  
Z. Chomariyah ◽  
Trisno Agung Wibowo
Keyword(s):  
At Risk ◽  
Total Population ◽  
Total Coliform ◽  
Case Control ◽  
P Value ◽  
Common Source ◽  
Population At Risk ◽  
E Coli

Tujuan: Studi ini untuk mengetahui gambaran KLB keracunan pangan yang terjadi di desa Mulo menurut deskripsi epidemiologi, faktor risiko dan penyebab KLB keracunan makanan. Metode: Studi ini menggunakan studi analitik case control, dimana kasus adalah orang yang mengalami sakit pada tanggal 7 - 8 Mei 2017, tinggal di desa Mulo dan mengkonsumsi makanan olahan dari bapak S dan K. Instrument menggunakan kuesioner. Hasil: KLB terjadi di Desa Mulo RT 5 dan 6 dengan jumlah kasus sebanyak 18 orang dari total population at risk 112 orang dengan gejala utama diare (100%), mual (72,2%), demam (66,6%), pusing (66,6%) dan muntah (50%). Dari diagnosa banding menurut gejala, masa inkubasi dan agent penyebab keracunan, kecurigaan kontaminasi bakteri mengarah pada E. Coli (ETEC). Masa inkubasi 1-16 jam (rata-rata 9 jam) dan common source curve. Penyaji makanan ada dua (pak K dan pak S). Dari perhitungan AR, berdasarkan sumber makanan mengarah pada makanan dari pak S (AR=42,8%). Bedasarkan menu, perhitungan OR dan CI 95 % jenis makanan yang dicurigai sebagai penyebab KLB adalah urap/gudangan (OR=4,33; p value0,0071) dan sayur lombok (OR=6,31; p value 0,0071). Sampel yang didapatkan adalah sampel air bersih, feses, dan muntahan penderita, sampel makanan tidak didapatkan karena keterlambatan informasi dari masyarakat. Hasil laboratorium, Total Coliform sampel air bersih melebihi ambang batas, sampel feses dan muntahan mengandung bakteri Klebsiella pneumonia.Simpulan: Terdapat 3 (tiga) faktor yang diduga sebagai penyebab keracunan pada warga Desa Mulo yaitu air bersih untuk mengolah makanan tercemar bakteri patogen, pengolahan makanan tidak hygienis dan penyajian makanan pada suhu ruang lebih dari 1 jam.

scholarly journals Characterization of Escherichia coli Strains Derived from Cow Milk of Subclinical and Clinical Cases of Mastitis

2021 ◽  
Vol 11 (2) ◽  
pp. 541
Author(s):  
Katarzyna Grudlewska-Buda ◽  
Krzysztof Skowron ◽  
Ewa Wałecka-Zacharska ◽  
Natalia Wiktorczyk-Kapischke ◽  
Jarosław Bystroń ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Economic Problem ◽  
Cow Milk ◽  
P Value ◽  
Dairy Herds ◽  
E Coli ◽  
Bonferroni Test

Mastitis is a major economic problem in dairy herds, as it might decrease fertility, and negatively affect milk quality and milk yield. Out of over 150 bacterial species responsible for the udder inflammation, Escherichia coli is one of the most notable. This study aimed to assess antimicrobial susceptibility, resistance to dipping agents and biofilm formation of 150 E. coli strains isolated from milk of cows with subclinical and clinical mastitis. The strains came from three dairy herds located in Northern and Central Poland. The statistical analyses were performed with post-hoc Bonferroni test and chi-square test (including Yates correction). The data with a p value of <0.05 were considered significant. We found that the tested strains were mostly sensitive to antimicrobials and dipping agents. It was shown that 37.33% and 4.67% of strains were resistant and moderately resistant to at least one antimicrobial agent, respectively. No extended-spectrum beta-lactamases (ESBL)-producing E. coli were detected. The majority of strains did not possess the ability to form biofilm or formed a weak biofilm. The strong biofilm formers were found only among strains derived from cows with subclinical mastitis. The lowest bacteria number was noted for subclinical mastitis cows’ strains, after stabilization with iodine (3.77 log CFU × cm−2) and chlorhexidine (3.96 log CFU × cm−2) treatment. In the present study, no statistically significant differences in susceptibility to antibiotics and the ability to form biofilm were found among the strains isolated from cows with subclinical and clinical mastitis. Despite this, infections in dairy herds should be monitored. Limiting the spread of bacteria and characterizing the most common etiological factors would allow proper treatment.

scholarly journals The lytB Gene of Escherichia coli Is Essential and Specifies a Product Needed for Isoprenoid Biosynthesis

2001 ◽  
Vol 183 (24) ◽  
pp. 7403-7407 ◽  
Author(s):  
Sean McAteer ◽  
Andrew Coulson ◽  
Neil McLennan ◽  
Millicent Masters
Keyword(s):  
Escherichia Coli ◽  
Protein Structure ◽  
Cell Lysis ◽  
Isoprenoid Biosynthesis ◽  
Globular Protein ◽  
Limited Growth ◽  
E Coli ◽  
Nonmevalonate Pathway ◽  
Tim Barrel

ABSTRACT LytB and GcpE, because they are codistributed with other pathway enzymes, have been predicted to catalyze unknown steps in the nonmevalonate pathway for isoprenoid biosynthesis. We constructed a conditional Escherichia coli lytB mutant and found that LytB is essential for survival and that depletion of LytB results in cell lysis, which is consistent with a role for this protein in isoprenoid biosynthesis. Alcohols which can be converted to pathway intermediates beyond the hypothesized LytB step(s) support limited growth of E. coli lytB mutants. An informatic analysis of protein structure suggested that GcpE is a globular protein of the TIM barrel class and that LytB is also a globular protein. Possible biochemical roles for LytB and GcpE are suggested.

scholarly journals Chance, contingency, and necessity in the experimental evolution of ancestral proteins

2020 ◽  
Author(s):  
Victoria Cochran Xie ◽  
Jinyue Pu ◽  
Brian P.H. Metzger ◽  
Joseph W. Thornton ◽  
Bryan C. Dickinson
Keyword(s):  
Protein Evolution ◽  
Experimental Evolution ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Sequence Evolution ◽  
Protein Protein Interaction ◽  
Evolutionary Trajectories ◽  
Historical Moment ◽  
Related Proteins ◽  
Ancestral Protein

SUMMARYThe extent to which chance and contingency shaped the sequence outcomes of protein evolution is largely unknown. To directly characterize the causes and consequences of chance and contingency, we combined directed evolution with ancestral protein reconstruction. By repeatedly selecting a phylogenetic series of ancestral proteins in the B-cell lymphoma-2 family to evolve the same protein-protein interaction specificities that existed during history, we show that contingency and chance interact to make sequence evolution almost entirely unpredictable over the timescale of metazoan evolution. At any historical moment, multiple sets of mutations can alter or maintain specificity, and chance decides which ones occur. Contingency arises because historical sequence substitutions epistatically altered which mutations are compatible with new or ancestral functions. Evolutionary trajectories launched from different ancestors therefore lead to dramatically different outcomes over phylogenetic time, with virtually no mutations occurring repeatedly in distantly related proteins, even under identical selection conditions.

scholarly journals Lactic Acid Bacteria (Lactobacillus bulgaricus and Streptococcus thermophillus) in Yogurt Inhibit the Growth of Escherichia coli, Salmonella typhimurium, and Shigella sp. In Vitro

2021 ◽  
Vol 31 (4) ◽  
pp. 2
Author(s):  
IDSAP Peramiarti
Keyword(s):  
Escherichia Coli ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Salmonella Typhimurium ◽  
Pathogenic Bacteria ◽  
Test Method ◽  
P Value ◽  
E Coli ◽  
Significant Difference

Diarrhea is defecation with a frequency more often than usual (three times or more) a day (10 mL/kg/day) with a soft or liquid consistency, even in the form of water alone. Pathogenic bacteria, such as Escherichia coli, Salmonella typhimurium, and Shigella sp., play a role in many cases, to which antibiotics are prescribed as the first-line therapy. However, since antibiotic resistance cases are often found, preventive therapies are needed, such as consuming yogurt, which is produced through a fermentation process by lactic acid bacteria (LAB). This research aimed to determine the activity of lactic acid bacteria (Liactobacillus bulgaricus and Streptococcus thermophilus) in yogurt in inhibiting the growth of the pathogenic bacteria E. coli, S. typhimurium, and Shigella sp. The research applied in vitro with the liquid dilution test method and the true experimental design research method with post-test-only and control group design. The design was used to see the inhibitory effect of yogurt LAB on the growth of E. coli, S. typhimurium, and Shigell sp. to compare the effect of several different yogurt concentrations, namely 20%, 40%, 60%, and 80%. The results of the Least Significance Different analysis showed that there was a significant difference between yogurt with a concentration of 0% and that with various concentrations in inhibiting the growth of E. coli, S. typhimurium, and Shigella sp. with a p-value of &lt;0.05. Whereas, there was no significant difference in the various concentrations of yogurt in inhibiting the growth of the three kinds of bacteria with a p-value of &gt; 0.05.<p class="Default" align="center"> </p>

scholarly journals Housing Condition of Coastal Area in Bangladesh: A Case Study of Kutubdia, Cox’s Bazaar

2015 ◽  
Vol 6 (1) ◽  
pp. 15-20 ◽  
Author(s):  
M Mohiuddin ◽  
MB Latif
Keyword(s):  
Type A ◽  
P Value ◽  
Type B ◽  
Laboratory Examination ◽  
Chi Square ◽  
E Coli ◽  
Significant Difference ◽  
Different Types ◽  
Hygienic Measures

This study was conducted to determine the contamination of E. coli and Salmonella for different types of foods in Chittagong city area. In case of laboratory examination, almost half (49.58%) of the samples were contaminated where 28.75% positive for E. coli. and 20.83% for Salmonella. The positive cases for type A sample was 20 out of 96 constituting 20.83% whereas the positive cases for type B sample was 49 out of 144 constituting 34.03% for E. coli. The positive cases of type A sample was 15 out of 96 making up 15.63% and for type B sample was 35 out of 144 making up 24.31% for Salmonella.A chi-square (?2) test was used to examine the equality of observed proportions for E. coli and Salmonella of each item of both types of food where significant difference among the observed proportion for E. coli (p-value<0.01) and Salmonella (p-value=0.032) for different items of A type and for E. coli (p-value<0.01) for different items of B type were observed and an odds ratio (OR) was measured for association between exposure and outcome where the probability of contaminated by E. coli of type B food is higher than contaminated of type A food (OR= 1.96 and CI:1.07-3.58). The probability of contaminated by Salmonella of type B food was higher than type A food (OR= 1.73 and CI: 0.89-3.39).The comparatively high bacteria in type B samples indicated contamination from water, practice of inadequate hygienic measures, mishandling, improper storage, inadequate cooking and above all unhygienic condition of the retail shops.DOI: http://dx.doi.org/10.3329/jesnr.v6i1.22034 J. Environ. Sci. & Natural Resources, 6(1): 15-20 2013

Comparison of the Patient Diagnostic Yield of Fibre-optic Bronchoscopy with Conventional Tracheal Aspirate

2020 ◽  
Vol 3 (1) ◽  
pp. 66-72
Author(s):  
Subodh Sagar Dhakal ◽  
Navin Kumar Mishra ◽  
Karuna Bhatta ◽  
Milan Shrestha ◽  
Rohit Karna ◽  
...  
Keyword(s):  
Diagnostic Yield ◽  
Tracheal Aspirate ◽  
P Value ◽  
Infectious Agents ◽  
Single Center ◽  
Acinetobacter Baumanii ◽  
E Coli ◽  
Baseline Characteristics ◽  
Staphyloccus Aureus ◽  
Overall Health Status

Objective: To know the efficacy of Bronchoalveolar Lavage (BAL) in establishing diagnosis and its impact on overall health status of the patients. Methods: A single center, longitudinal study involving 40 patients aged > 18 years old with septic shock with similar baseline characteristics was conducted. Two study arms, 20 patients in intervention arm - patient with utilization of Bronchoscopy and BAL in aiding diagnosis and 20-patients in conservative- arm without Bronchoscopy were compared in terms of establishing diagnosis primarily and secondarily in terms of length of stay and 30-day mortality. We were able to identify following organisms in BAL sample: Mycobacterium tuberculosis- 4, Acinetobacter baumanii- 3, Pseudomonasaeruginosa- 2, Klebsiella oxytica- 2, E. coli- 2, Streptococcus pneumoniae- 2, Staphyloccus aureus- Results: We were able to identify various infectious agents as mentioned above 16/20 in BAL group compared to 8/20 in conventional arm; neoplasm in 4 out of 20 subjects in BAL group. In 80% of cases, BAL helped in identifying the organisms compared to only 40% in tracheal aspirate group. In addition, six cases in Intervention arm vs. nine cases in conventional arm had more than > 14 days hospital stay with the p-value 0 .492091. Interventional arm had lesser mortality 5 cases vs. 7 cases in Conventional arm with the p-value of 0.490153 which was not statistically significant. Conclusion: We conclude that the diagnostic bronchoscope and related procedures among critically ill patients are helpful in identifying the pathogens and in detecting malignancy.

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