Characterization Of Different Strains Research Articles

Surface-enhanced Raman spectroscopy (SERS) for the characterization of supernatants of bacterial cultures of bacterial strains causing sinusitis.

Sinusitis is defined as inflammation of the paranasal sinus mucous membrane lining caused by bacteria which usually invade the sinus by upper respiratory tract viral infections (UTI). In the present study, Surface-enhanced Raman spectroscopy (SERS) has been applied to differentiate and characterize supernatant samples, in triplicate, of three different types of bacteria which are considered leading cause of sinusitis disease. For this purpose, supernatant samples of three different strains of bacteria namely Staphylococcus aureus, Klebsiella pneumoniae and Enterococcus faecalis. The SERS has identified significant changes as a result of secretions of biomolecules by these bacteria in their supernatants which can be helpful to explore the potential of this technique for the identification and characterization of different strains of bacteria causing same disease. These differentiating characteristic SERS spectral features including 552cm-1 (C-S-S-C bonds), 951cm-1 (CN stretching), 1008cm-1 (Phenylalanine), 1032cm-1 (In plane CH bending mode Phenylalanine), 1280cm-1, 1320cm-1, 1329cm-1 (Amide III band), 1368cm-1, 1400cm-1, 1420cm-1 (COO-sym. stretching and CH bending), 1583cm-1 (Tyrosine) correspond to Proteins and 1051cm-1 (C-C, C-O, -C-OH def.) correspond to carbohydrates contents of these three different types of bacterial secretions in their respective supernatants. Furthermore, multivariate data analysis techniques like principal component analysis (PCA) and a supervised method partial least squares-discriminant analysis (PLS-DA) were found to be useful for the identification and characterization of different bacterial supernatants. Surface-enhanced Raman spectroscopy is proven to be a helpful approach for the characterization and discrimination of three bacterial supernatants including S. aureus, K. pneumonia and E. faecalis.

Physical characteristics of different strains of deoni cattle

Physical characteristics of different strains of deoni cattle

Production of commercial and Amazonian strains of Pleurotus ostreatus in plant waste / Produção de linhagens comerciais e amazônicas de Pleurotus ostreatus em resíduos de plantas

Pleurotus spp. have the ability to grow on a wide variety of lignocellulosic materials, which opens up a range of options to be explored. The use of locally available residues and native strains can reduce production costs, thus making fungiculture a potential economic activity in developing regions, such as northern Brazil. The aim of this research was to compare the production and nutritional characteristics of different strains of P. ostreatus, cultivated on lignocellulosic residues available in Amazonas state, Brazil. The native (474 and 1467) and commercial (542 and 885) strains were cultivated in marupá (Simarouba amara) and pine (Pinus sp.) sawdust, açaí (Euterpe oleracea) seeds and elephant grass (Pennisetum purpureum Schum.) straw. Productivity was evaluated according to biological efficiency, yield and loss of organic matter. Some physicochemical and nutritional parameters were also evaluated. In general, among the residues evaluated for mushroom cultivation, the elephant grass substrates (EG) showed better physicochemical properties in terms of moisture, ash content (minerals), hemicellulose and lignin. Additionally, the EG-based substrate resulted in the best productive parameters (yield and EB) for all strains studied, with emphasis on strain 1467, which is native to the Amazon. The basidiocarps of the native strains (474 and 1467) presented a nutritional composition that is similar to the commercial strains (885 and 542), and the mushrooms grown in EG-based residue, in general, presented the best nutritional compositions. Thus, strain 1467 of Pleurotus ostreatus, native to the Amazon, shows promise for commercial purposes, when cultivated in elephant grass residue.

Functional Analysis of the C-5 Sterol Desaturase PcErg3 in the Sterol Auxotrophic Oomycete Pathogen Phytophthora capsici

Although sterols play an important role in most eukaryotes, some oomycetes, including Phytophthora spp., have lost the sterol synthesis pathway. Nevertheless, the ERG3 gene encoding C-5 sterol desaturase in the sterol synthesis pathway is still present in the genomes of Phytophthora spp. Phytophthora capsici, a destructive pathogen with a broad range of plant hosts, poses a significant threat to the production of agriculture. This study focused on the ERG3 gene in P. capsici (PcERG3) and explored its function in this pathogen. It showed that the PcERG3 gene could be expressed in all tested developmental stages of P. capsici, with sporangium and mycelium displaying higher expression levels. A potential substrate of Erg3 (stellasterol) was used to treat the P. capsici wild-type strain and a PcERG3Δ transformant, and their sterol profiles were determined by GC-MS. The wild-type strain could convert stellasterol into the down-stream product while the transformant could not, indicating that PcErg3 retains the C-5 sterol desaturase activity. By comparing the biological characteristics of different strains, it was found that PcERG3 is not important for the development of P. capsici. The pathogenicity of the PcERG3Δ transformants and the wild-type strain was comparable, suggesting that PcERG3 is not necessary for the interaction between P. capsici and its hosts. Further investigations revealed that the PcERG3Δ transformants and the wild-type strain displayed a similar level of tolerance to external adversities such as unsuitable temperatures, high osmotic pressures, and intemperate pH, signifying that PcERG3 is not essential for P. capsici to cope with these environmental stresses.

Isolation and particle characterization of different strains of BmNPV isolated from south Indian region

Grasserie is a deadly viral disease which turns a clean creamy white silkworm into zombie worm. The nuclear polyhedrosis of B. mori caused by Nuclear Polyhedrosis Virus strain Bm (BmNPV) showing jaundice-like symptoms is collectively referred to as polyhedrosis. This DNA virus multiplies only in the nucleus of the host cells forming its complete structure in the host cell. The drawback of this disease is huge amount of crop loss. And to avoid this, the only way is prevention or the use of hazardous chemicals. To avoid all these, finding a new natural way is necessary. Before we think of controlling the virus, one should understand the detail characters of BmNPV. Light scattering is a fundamental analytical technique for the characterization of particulate materials and is most commonly applied to colloidal systems, nanoparticles and acromolecules in solution or dispersion to determine particle size and zeta Potential. This examination mainly focused on size and surface charge determination using SZ-100 nanoparticle series instrument. Further, the average OB size was found to be 150.7 nm, 138.8 nm, 143.8 nm, 140.0 nm and 140.5 nm in diameter for HRH, HSR, KNK, MSI and VKK BmNPV strain respectively. The zeta potential is often measured as a function of pH or other change in the chemistry to help formulators create new products with a long shelf life. The zeta-potentials of isolates were found to be more of negative because of the presence of PEP with the charge of - 29.0 mV, -35.4 mV, -45.0 mV, -28.1 mV and -23.5 mV for HRH, HSR, KNK, MSI and VKK BmNPV strain respectively. Thus, by exposing, these aspects may help to deduce in detail structural characteristics of different south Indian strains of BmNPV.

Genetic Diversity and Population Structure of Three Strains of Indigenous Tswana Chickens and Commercial Broiler Using Single Nucleotide Polymormophic (SNP) Markers

The Tswana chicken is native to Botswana and comprises strains such as the naked neck, normal, dwarf, frizzled, and rumples. The origins of the different strains of Tswana chicken remain unknown and it is not yet clear if the different strains represent distinct breeds within the large Tswana chicken population. Genetic characterization of different strains of Tswana chickens using SNP arrays can elucidate their genetic relationships and ascertain if the strains represent distinct breeds of Tswana chicken population. The aim of this study was therefore to investigate population structure and diversity and to estimate genetic distances/identity between the naked neck, normal and dwarf strains of Tswana chickens. A total of 96 chickens (normal strain (n = 39), naked neck strain (n = 32), dwarf strain (n = 13) and commercial broiler (n = 12)) were used in the study. SNP genotyping was carried out using the Illumina chicken iSelect SNP 60 Bead chip using the Infinium assay compatible with the Illumina HiScan SQ genotyping platform. The observed heterozygosity (Ho) values were 0.610 ± 0.012, 0.611 ± 0.014, 0.613 ± 0.0006 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.611 ± 0.016 across the three strains of Tswana chickens compared to Ho of 0.347 ± 0.023 in commercial broiler chicken. The expected heterozygosity (He) values were 0.613 ± 0.00012, 0.614 ± 0.00013, 0.608 ± 0.00021 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.612 ± 0.00015 across the three strains of Tswana chickens compared to He of 0.577 ± 0.00022 in commercial broiler chicken. Principal component analysis (PCA) was used to get an insight into the population structure of indigenous Tswana chickens. The first two principal components revealed a set of three clusters. The normal strain of Tswana chicken and commercial broiler clustered together in one group. The dwarf strain clustered separately in one group and the naked neck and normal strains clustered together in the last group. The separate clustering of the dwarf strain from the rest of Tswana chicken strains suggests significant genetic uniqueness of the dwarf strain and very close genetic similarities between the normal and naked neck strains. The clustering pattern was confirmed by less genetic differentiation and less genetic distances between the naked neck and normal strains of Tswana chicken than between the two strains and the dwarf strain of Tswana chicken.

Characterization of Clostridioides difficile Strains, the Disease Severity, and the Microbial Changes They Induce.

Background: Clostridioides difficile infection (CDI) is a major nosocomial disease. The characteristics of different strains, the disease severity they cause, their susceptibility to antibiotics, and the changes they inflict on gut microbiome, have not been comprehensively studied in Israel. Methods: A severity score was calculated for 70 patients. Stool samples were tested for toxins presence using a special kit. Bacteria were isolated, identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and antibiotic susceptibility tests were performed for several antibiotics. Strains were classified by Multi-locus sequence typing (MLST), and changes in gut microbiome were tested. Results: ST04 (22.5%) and ST37 (12.7%) were the most frequent strains. Clade (phylogenetic lineage) 1 was the most (81.4%) prevalent. We found significant associations between ST and age (p = 0.024) and between ST and moxifloxacin susceptibility (p = 0.001). At the clade level, we found significant associations with binary toxin gene occurrence (p = 0.002), and with susceptibility to both metronidazole and vancomycin (p = 0.024, 0.035, respectively). Differences in intestine microbiome were affected by age, clades’ distribution and STs. Conclusions: By defining the characteristics of the different strains and clades, clinicians can choose medical interventions based on the predicted response or disease severity associated with each strain, enabling new advances in the field of personalized medicine.

Genetic tools discriminate strains of Leishmania infantum isolated from humans and dogs in Sicily, Italy.

BackgroundLeishmaniasis is one of the most important vector-borne diseases and it represents a serious world health problem affecting millions of people. High levels of Leishmania infections, affecting both humans and animals, are recognized among Italian regions. Among these, Sicily has one of the highest prevalence of Leishmania infection.Methodology/Principal FindingsSeventy-eight Leishmania strains isolated from human and animal samples across Sicily, were analyzed for the polymorphic k26-gene and genotypes were assigned according to the size of the PCR products. A multilocus microsatellite typing (MLMT) approach based on the analysis of 11 independent loci was used to investigate populations structure and genetic diversity of the isolated strains. Six L. infantum reference strains were included in the analysis for comparison. Bayesian clustering analysis of microsatellite data showed that all the isolated strains clustered in two genetically distinct populations, corresponding to human and canine isolates respectively. A further subdivision was observed between the two main groups, giving a good correlation between human strains and their geographic origin, conversely canine population showed a great genetic variability diffused in the territory.Conclusions/SignificanceAmong the 78 Leishmania isolates, K26 analysis detected 71 samples (91%) as MON-1 zymodeme, confirming it as the predominant strain in Mediterranean area and 7 human samples (9%) as non-MON-1. MLMT gives important insights into the epidemiology of leishmaniases and allows characterization of different strains to a higher resolution than possible with zymodeme typing. Two main populations presented a strong correlation respect to the different hosts, exhibiting a co-circulation of two distinct populations of L. infantum. The population found in infected humans exhibited a correlation with geographic origin. These clusters could represent a geographically restricted population of strains with the same or related genotypes. This study can contribute to an understanding of Leishmania epidemiology, including the spread of reservoirs and sand fly vectors in the different foci of infection, characterizing parasites within the different hosts.

SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

Huanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

English

The fermentation characteristics of different strains of Saccharomyces cerevisiae isolated from sugar cane musts for the production of cachaca (Brazilian sugar cane spirit) and from beer musts were analyzed based on the kinetic parameters of alcoholic fermentation in mango pulp. The commercial pressed baker’s yeast was used as a standard inoculum. The results show that the yeast strains tested from sugar cane must and beer must had low fermentation performance when inoculated into mango pulp. They did not meet the selection criteria for fermentative cultures, such as productivity, efficiency, ethanol yield and ethanol production. It is observed that the commercial pressed baker’s yeast showed greater adaptability in the mango must than the other yeasts. Key words: Alcohol fermentation, industrial microbiology, mango, yeast.

Morphometric Characterization of Different Strains of Osmanabadi Goat at 0-3 and 4-6 Months of Age

Morphometric Characterization of Different Strains of Osmanabadi Goat at 0-3 and 4-6 Months of Age

New Insights into Various Production Characteristics of Streptococcus thermophilus Strains

Streptococcus thermophilus is one of the most valuable homo-fermentative lactic acid bacteria, which, for a long time, has been widely used as a starter for the production of fermented dairy products. The key production characteristics of S. thermophilus, for example the production of extracellular polysaccharide, proteolytic enzymes and flavor substances as well as acidifying capacity etc., have an important effect on the quality of dairy products. The acidification capacity of the strains determines the manufacturing time and quality of dairy products. It depends on the sugar utilization ability of strains. The production of extracellular polysaccharide is beneficial for improving the texture of dairy products. Flavor substances increase the acceptability of dairy products. The proteolytic activity of the strain influences not only the absorption of the nitrogen source, but also the formation of flavor substances. Different strains have obvious differences in production characteristics via long-time evolution and adaptation to environment. Gaining new strains with novel and desirable characteristics is an important long-term goal for researchers and the fermenting industry. The understanding of the potential molecular mechanisms behind important characteristics of different strains will promote the screening and breeding of excellent strains. In this paper, key technological and functional properties of different S. thermophilus strains are discussed, including sugar metabolism, proteolytic system and amino acid metabolism, and polysaccharide and flavor substance biosynthesis. At the same time, diversity of genomes and plasmids of S. thermophilus are presented. Advances in research on key production characteristics and molecular levels of S. thermophilus will increase understanding of molecular mechanisms of different strains with different important characteristics, and improve the industrialization control level for fermented foods.

Microsatellite Based Genetic Diversity and Differentiation of Common Carp, Cyprinus carpio in Rajasthan (India)

Five microsatellite loci (MFW1, MFW3, MFW4, MFW5 and MFW7) were used to study the genetic diversity and characterization of different strains (Maharashtra, Local, Koi and Amour) of common carp (Cyprinus carpio L.). The average number of alleles across all loci was highest in Koi (11.4) followed by Maharashtra (11.0) and Local strains (9.0). The amour had lowest (6.2) mean number of alleles. The mean observed heterozygosity (Ho) ranged between 0.45 and 0.62, while expected heterozygosity (He) 0.32–0.68. Polymorphic information content mean values varied from 0.58 to 0.74. The Nm and the FST values indicated a low level of gene flow and high level of differentiation. The highest genetic distance was observed between the Amour and the Local strains, while the lowest was between Maharashtra and Local strains. The FST value ranged between 0.028 and 0.207.

Approach to molecular characterization of different strains of Fasciola hepatica using random amplified polymorphic DNA polymerase chain reaction.

The aim of the present study was to genetically characterize Fasciola hepatica strains from diverse ecogeographical regions (America and Europe), susceptible and resistant to Triclabendazole, using the random amplified polymorphic DNA fragments (RAPDs-PCR) technique to elucidate genetic variability between the different isolates. Ten different oligonucleotide primers of 10 bases with GC content varying from 50-70% were used. A polymerase chain reaction (PCR) was carried out in 25 μl of total volume. Duplicate PCR reactions on each individual template DNA were performed to test the reproducibility of the individual DNA bands. The size of the RAPD-PCR fragments was determined by the reciprocal plot between the delay factors (Rf) versus the logarithm of molecular weight ladder. The phenogram obtained showed three main clusters, the major of which contained European Strains (Cullompton and Sligo) showing a genetic distance of 27.2 between them. The American strains (Cedive and Cajamarca) on the other hand formed each their distinctive group but clearly maintaining a closer genetic relationship among them than that to their European counterparts, with which showed a distance of 33.8 and 37.8, respectively. This polymorphism would give this species enhanced adaptability against the host, as well as the environment. The existence of genetically different populations of F. hepatica could allow, against any selection pressure, natural or artificial (for use fasciolicides products and/or control measures), one or more populations of F. hepatica to be able to survive and create resistance or adaptability to such selective pressure.

Type differentiation of porcine circovirus from tissues of sick pigs and replication characteristics of different strains of PCV2

PCR was conducted on tissues of pigs suspected to suffer from PCV2-associated diseases, and differentiation PCR for PCV1 and PCV2 was conducted on PCV positive samples. The results showed that 117 out of the 192 tissue samples were PCV positive, all of which harbored PCV2 genome, two of which harbored PCV1 simultaneously. PCV2 were cloned from the samples only harbored PCV2, and the sequences obtained all belonged to PCV2–1. Infectious clone viruses were constructed using two of these sequences, and the rescued viruses were named PCV2(2–1) and PCV2(4–1). Cultivation of these viruses showed that they replicated efficiently in cells maintained by alteration of culture medium.

Molecular characterization of Ralstonia solanacearum infecting Eucalyptus spp. in Brazil

SummaryAmong the bacterial pathogens of Eucalyptus in Brazil, Ralstonia solanacearum is considered one of the most important because of the characteristics of the pathogen, like the high diversity among the strains related to host range, high virulence, broad geographical distribution and its damage to the crop in recent years. Given its importance and the lack of research on this pathosystem, the present study aimed to perform a molecular characterization of different strains of infected Eucalyptus plants in Brazil. A total of 19 bacterial cultures isolated from Eucalyptus in different regions of Brazil were analysed. A 372‐bp product generated by multiplex‐PCR amplification using Nmult primers identified all the strains analysed as belonging to phylotype II. Eighteen strains were grouped into subclade IIA and one into subclade IIB. The phylogenetic tree generated from the gene sequences of endoglucanase (egl) confirmed the classification of the strains into phylotype II and separated the strains into sequevars. Strains AMC22, IBSBF2568 and IBSBF2576 were grouped into a single clade, as were strains UFV18 and UFV20, with 89% and 78% a posteriori probability, respectively, forming two new potential sequevars not yet defined. We also identified strains belonging to sequevars 41 (100% probability) and 37 (88% probability). However, most of the strains did not fit into any previously described sequevar and did not form distinct clades. The results of the analysis of fragments amplified using the ERIC‐PCR technique indicated the existence of genetic diversity among the strains studied, with a generally high correlation between similarity and the geographical origin of the strains.

Morphogenesis, Pathogenesis, Detection and Transmission Risks of White Spot Syndrome Virus in Shrimps

Among the important challenges to shrimp aquaculture worldwide are diseases caused by viruses, in particular by White Spot Syndrome Virus (WSSV) whose genome of 305 kb has been recently sequenced. WSSV, also dubbed White Spot Bacilliform Virus (WSBV), is a major shrimp pathogen with a high mortality rate and a wide host range. The sequencing and characterization of different strains of WSSV has begun to reveal aspects of its biology, virulence and pathogenesis. Knowledge on these aspects is critical for developing effective control methods. The socioeconomic impacts of the diseases caused by the WSSV have been catastrophic in some shrimp producing countries of Asia and the Americas. Thus, these diseases were listed by the World Animal Health Organization (or Office International des Epizootics, OIE) as posing a significant threat to cultured and wild crustaceans as a consequence of international trade or movement of infected organisms. The aim of this review is to present a state-of-the-art knowledge in different aspects of WSSV like morphogenesis, pathogenesis, transmission risks, detection, bio-inoculation studies, and international rules and standards.

Studying Fusion of Influenza to Supported Lipid Bilayers using Individual Virion Imaging Techniques

Influenza viruses are membrane-enveloped, negative-strand RNA viruses that employ membrane fusion to release its RNA into host cells and initiate replication. Influenza enters the cell via clathrin-mediated endocytosis. Fusion of the viral and endosomal membrane is facilitated by the conformational change of the viral protein hemagglutinin (HA) at low pH. Traditional bulk fusion assays rely on the fusion fluorescently labeled viruses to synthetic lipid vesicles to obtain kinetic data about the fusion pathway. However, fusion is a stochastic event and only ensemble averages of fusion kinetics are obtained from bulk measurements. To obtain more detail, we use fluorescence dequenching and total internal reflection microscopy (TIRFM) to track and quantify fusion of individual viruses to supported lipid membranes. Imaging individual virus fusion events enables hemifusion kinetics to be differentiated from pore formation kinetics. Our assays are carried out in high-throughput microfluidic devices where fusion is initiated by reducing the pH in the device. Hemifusion lag times are determined for each individual fusing virus and from this data we can determine hemfusion rate constants (kH) and the number of steps in the hemifusion pathway (N). By using a distinct two-fluorophore labeling approach, we can also measure the time to pore formation of individual viruses following the hemifusion event. In this work, we compare fusion characteristics of different strains of influenza, including seasonal and pandemic strains, and show that there are significant differences in kinetics among them.

Analysis of photosynthetic pigments and chlorophyll fluorescence characteristics of different strains of Porphyra yezoensis

The levels of photosynthetic pigments and chlorophyll fluorescence of Porphyra yezoensis strains selected from high-light environments were investigated. Sutong and Sulian strains originated from the same high-light environment but were selected from different sites on the Yellow Sea coast of Jiangsu Province, China. In January (a low temperature period), the Sulian strain and the WT (a widely cultivated strain) had higher levels of chlorophyll a, phycoerythrin, phycocyanin, and allophycocyanin, and higher actual photochemical efficiency of PSII (ΔF/Fm′) than the Sutong strain. This indicated that Sulian and the WT may have better adaptation to low temperature. In March (an optimal temperature period), Sutong had higher levels of photosynthetic pigments and higher ΔF/Fm′ than the WT and Sulian strains. This suggested that Sutong had higher light use efficiency at optimal temperatures and that most energy absorbed by PSII was used for photosynthetic electron transport. The differing areas of origin of these strains may have resulted in these differences in temperature adaptation.

Genetic diversity of Legionella pneumophila serogroup 1 in hospital water distribution systems in Shanghai

To classify Legionella pneumophila serogroup 1 (LP1) isolated from the water distribution systems in hospitals of Shanghai by using genotying methods, and therefore to explore the genetic relationship between different genotypes. LP1 was isolated from 8 hospitals in Shanghai, and strains of LP1 were subtyped using pulse field gel electrophoresis (PFGE). Genotyping results of PFGE were classified as dendrogram, and cluster analysis was used to compare the genetic characteristics of different strains. Twenty-four strains of LP1 were isolated from 193 water specimens. LP1 belonged to 6 PFGE genotypes, of which 21 belonged to 3 predominant genotypes. Different hospitals shared the same genotype, while some strains isolated from the same hospital had different genotypes. The genetic characteristics are stable in environmental LP1. Molecular biology techniques should be added to epidemiological study for hospital acquired legionellosis due to the genetic diversity in one hospital.