scholarly journals Pb(II) Bio-Removal, Viability, and Population Distribution of an Industrial Microbial Consortium: The Effect of Pb(II) and Nutrient Concentrations

2020 ◽  
Vol 12 (6) ◽  
pp. 2511
Author(s):  
Carla Hörstmann ◽  
Hendrik G. Brink ◽  
Evans M.N. Chirwa
Keyword(s):  
Klebsiella Pneumoniae ◽  
Microbial Growth ◽  
Microbial Consortium ◽  
Population Distribution ◽  
Active Species ◽  
Sem Analysis ◽  
Nutrient Concentrations ◽  
Local Alignment ◽  
Factors Affecting ◽  
Search Tool

This study presents the effect of aqueous Pb(II) and nutrient concentrations on the Pb(II)-removal, biomass viability, active species identities, and population distribution of an industrial Pb(II) resistant microbial consortium. The studied consortium has previously shown to be highly effective at precipitating Pb(II) from solution. At all conditions tested (80 and 500 ppm Pb(II), and varying nutrients conditions) it was found that circa 50% of Pb(II) was removed within the first 3 h, with the absence of any visual changes, followed by a slower rate of Pb(II) removal accompanied by the formation of a dark precipitate. The Pb(II) removal was found to be independent of microbial growth, while growth was observed dependent on the concentration of Pb(II), nutrients, and nitrates in the system. SEM analysis indicated viable bacilli embedded in precipitate. These findings indicate that precipitation occurs on the surface of the biomass as opposed to an internal excretion mechanism. BLAST (Basic Local Alignment Search Tool) results indicated Klebsiella pneumoniae as the active species responsible for Pb(II) bioprecipitation for both the 80 and 500 ppm isolated colonies, while a diverse population distribution of organisms was observed for the streak plate analyses. A quicker microbial generation rate was observed than what was expected for Klebsiella pneumoniae, indicating that the overall consortial population contributed to the growth rates observed. This study provided insights into the factors affecting Pb(II) bio-removal and bioprecipitation by the investigated industrially obtained consortium, thereby providing invaluable knowledge required for industrial application.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

scholarly journals Insight into the Metabolic Profiles of Pb(II) Removing Microorganisms

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4008
Author(s):  
Carla Cilliers ◽  
Evans M. N. Chirwa ◽  
Hendrik G. Brink
Keyword(s):  
Liquid Chromatography ◽  
High Performance ◽  
Microbial Consortium ◽  
Luria Bertani ◽  
Nutrient Concentrations ◽  
Batch Experiments ◽  
Metabolic Study ◽  
Luria Bertani Broth ◽  
Tandem Mass Spectroscopy ◽  
Insight Into

The objective of the study was to gather insight into the metabolism of lead-removing microorganisms, coupled with Pb(II) removal, biomass viability and nitrate concentrations for Pb(II) bioremoval using an industrially obtained microbial consortium. The consortium used for study has proven to be highly effective at removing aqueous Pb(II) from solution. Anaerobic batch experiments were conducted with Luria-Bertani broth as rich growth medium over a period of 33 h, comparing a lower concentration of Pb(II) with a higher concentration at two different nutrient concentrations. Metabolite profiling and quantification were conducted with the aid of both liquid chromatography coupled with tandem mass spectroscopy (UPLC-HDMS) in a “non-targeted” fashion and high-performance liquid chromatography (HPLC) in a “targeted” fashion. Four main compounds were identified, and a metabolic study was conducted on each to establish their possible significance for Pb(II) bioremoval. The study investigates the first metabolic profile to date for Pb(II) bioremoval, which in turn can result in a clarified understanding for development on an industrial and microbial level.

scholarly journals Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ommer Mohammed Dafalla ◽  
Mohammed Alzahrani ◽  
Ahmed Sahli ◽  
Mohammed Abdulla Al Helal ◽  
Mohammad Mohammad Alhazmi ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Saudi Arabia ◽  
Parasite Clearance ◽  
Sub Saharan Africa ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Synonymous Mutations ◽  
Search Tool ◽  
Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

Organics and its Control in Reclaimed Water

2014 ◽  
Vol 507 ◽  
pp. 752-756
Author(s):  
Chao Xiang ◽  
Ping Xu ◽  
Jing Wang ◽  
Tao Wang ◽  
Ya Jun Zhang
Keyword(s):  
Water Supply ◽  
Indirect Effects ◽  
Microbial Growth ◽  
Treatment Process ◽  
Reclaimed Water ◽  
Limiting Factors ◽  
Supply Network ◽  
Water Supply Network ◽  
Factors Affecting ◽  
Comprehensive Study

Some forms of organic matter existing in the water have direct or indirect effects on microbial growth. By the investigation data over drinking water and reclaimed water, we summarized organic limiting factors that may affect the growth of microorganisms and factors affecting these water qualities in the reclaimed water supply network, such as a variety of treatment process and the residual disinfectants. Through its comprehensive study, we want to make a contribution of opinion to control the growth of microorganisms in reclaimed water supply network.

scholarly journals Lactobacillus fructivorans Spoilage of Tomato Ketchup

1997 ◽  
Vol 60 (5) ◽  
pp. 505-509 ◽  
Author(s):  
K. JOHANNA BJORKROTH ◽  
HANNU J. KORKEALA
Keyword(s):  
Gel Electrophoresis ◽  
Microbial Growth ◽  
Antimicrobial Agents ◽  
Growth And Survival ◽  
Factors Affecting ◽  
Physiological And Biochemical Characteristics ◽  
Gas Formation ◽  
Tomato Ketchup ◽  
Dna Fragment ◽  
Physiological And Biochemical

Spoilage characterized by bulging as a result of gas formation in bottled ketchup was studied, Samples produced microbial growth on MRS and Rogosa selective Lactobacillus agar. Seventy randomly selected isolates typed by using restriction endonuclease (ClaI, EcoRI, HindIII) analysis were found to have identical DNA fragment patterns in gel electrophoresis. The strain was identified as Lactobacillus fructivorans using morphological, physiological and biochemical characteristics, combined with the information obtained from ribotyping. Factors affecting growth and survival of this L. fructivorans strain in ketchup production were also studied. An L. fructivorans count of 105 CFU/g resulted in spoilage of inoculated ketchup samples. Spoilage occurred only in samples incubated at 15 to 30°C. The L. fructivorans implicated in causing spoilage demonstrated heat resistance with a D value of 1.2 min at 65°C. The strain did not show resistance to alkaline active chloride-containing detergent sanitizer; alkyldimethylbenzylammonium chloride and alkyldimethylethylbenzylammonium chloride-containing sanitizer were also found to be effective antimicrobial agents.

scholarly journals Analysis of determinant factors affecting retail business customer loyalty

2021 ◽  
Vol 5 (S3) ◽  
pp. 310-318
Author(s):  
Abdul Haris ◽  
Abdul Rahman ◽  
Yusriadi Yusriadi ◽  
Umi Farida
Keyword(s):  
Customer Satisfaction ◽  
Service Quality ◽  
Customer Loyalty ◽  
Structural Equation ◽  
Descriptive Analysis ◽  
Sem Analysis ◽  
Demographic Development ◽  
Five Dimensions ◽  
Factors Affecting ◽  
Goods And Services

Demographic development is the first field that influences the growth of retail stores. The rising population allows all goods and services to increase. To establish customer loyalty, the company must try to try to offer the highest quality in any product or service it must create a positive sense of quality in the minds of its customers. This research is a descriptive research type, trying to explain and describe each variable's conditions in detail and see the relationship or relationship between these variables. In the context of this study, the independent variables are Service Quality (X1), Relationship Marketing (X2), and Customer Satisfaction (Y), while the dependent variable is Customer Loyalty (Z). Quantitative data were analyzed using descriptive analysis and Structural Equation Modelling (SEM) analysis. Partially service quality has a significant influence on customer satisfaction in modern stores. In the sense that the quality of service provided by modern store management in Makassar City can contribute positively to customer satisfaction with the five dimensions of Tangible, Reliability, Empathy, Assurance, and Responsiveness. Direct service quality significantly influences customer loyalty, and indirect service quality has a significant effect on customer loyalty (LP) through customer satisfaction at modern stores in Makassar City.

scholarly journals Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

2021 ◽  
Vol 322 ◽  
pp. 01038
Author(s):  
Tuah N. M. Wulandari
Keyword(s):  
Phylogenetic Tree ◽  
Coi Gene ◽  
Local Alignment ◽  
Mtdna Sequences ◽  
Mitochondrial Coi ◽  
Search Tool ◽  
Very High ◽  
I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

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