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Summary The increased consumption of minimally processed vegetables (MPV) in various countries is related to the continued interest of consumers in seeking practical and healthy food items. Due to multiple processing steps, MPV can be contaminated by several foodborne pathogens that pose significant health risks to consumers. The use of rapid techniques to detect pathogens in ready‐to‐eat (RTE) foods such as MPV is therefore essential to provide high quality and safe products. This review aims to provide a comprehensive description of molecular‐based techniques for rapid detection of pathogenic bacteria in MPV, and their occurrence reported in studies published in the last 10 years. The main pathogens detected using rapid methods were Salmonella spp., Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, Shigella spp., and Campylobacter jejuni. Molecular‐based techniques included real‐time polymerase chain reaction (PCR), multiplex PCR, matrix‐assisted laser desorption ionisation time of flight mass spectrometry (MALDI‐TOF MS), and denaturing gradient gel electrophoresis (DGGE). The data indicate high incidences of pathogenic bacteria in MPV, stressing the need for their rapid detection in these products to prevent associated health risks. Further studies should be carried out to increase the sensitivity of molecular‐based techniques and prevent false positives due to undesirable non‐specific PCR amplifications. [ABSTRACT FROM AUTHOR]

Mayflies, recognized for their hemimetabolous life cycle and ephemeral adult phase, exhibit diverse larval forms categorized as burrowing, flattened, swimming, and creeping. Ameletus inopinatus Eaton, 1887, a member of the Ameletidae family within the order Ephemeroptera, undergoes aquatic development and is commonly found in the tranquil stretches of small rivers or streams, particularly among stones and boulders. This study focused on A. inopinatus nymphs collected from Yarımca village in Eskişehir, Turkiye. Employing molecular techniques and culture-independent methods, rRNA-based analyses were conducted to characterize the archaeal and bacterial communities within the nymphs' gut. Microbial DNA was extracted from the gut, and PCR amplification targeted 16S rRNA genes for both Archaea and Bacteria domains. Denaturing gradient gel electrophoresis (DGGE) separated the amplified products, yielding six distinct bands with Bacteria-specific primers. The subsequent analysis of 16S rRNA sequencing from DGGE bands revealed a predominance of the Proteobacteria phylum within the gut lumen. Complementary investigations into prokaryotic diversity employed fluorescence in situ hybridization (FISH) and 4',6-diamidino-2-phenylindole (DAPI) staining. Total DAPI cell counts indicated a microbial cell population of approximately 106 ± 0.18 in the samples. The overarching conclusion derived from these findings is that the microbial community within the Ameletus inopinatus gut is predominantly associated with the Bacteria domain. Recognizing the ecological importance of this symbiotic relationship, the coexistence of mayflies with specific microbial communities is emphasized, underscoring the potential mutualistic roles played by these microorganisms in the life cycle and ecological dynamics of Ameletus inopinatus. This research not only contributes valuable insights into the microbial ecology of mayfly nymphs but also underscores the significance of understanding the intricate relationships between insects and their associated microorganisms for broader ecological perspectives and potential applications in environmental management. [ABSTRACT FROM AUTHOR]

The role of the gut microbiota and its interplay with host metabolic health, particularly in the context of type 2 diabetes mellitus (T2DM) management, is garnering increasing attention. Dipeptidyl peptidase 4 (DPP4) inhibitors, commonly known as gliptins, constitute a class of drugs extensively used in T2DM treatment. However, their potential interactions with gut microbiota remain poorly understood. In this study, we employed computational methodologies to investigate the binding affinities of various gliptins to DPP4-like homologs produced by intestinal bacteria. The 3D structures of DPP4 homologs from gut microbiota species, including Segatella copri, Phocaeicola vulgatus, Bacteroides uniformis, Parabacteroides merdae, and Alistipes sp., were predicted using computational modeling techniques. Subsequently, molecular dynamics simulations were conducted for 200 ns to ensure the stability of the predicted structures. Stable structures were then utilized to predict the binding interactions with known gliptins through molecular docking algorithms. Our results revealed binding similarities of gliptins toward bacterial DPP4 homologs compared to human DPP4. Specifically, certain gliptins exhibited similar binding scores to bacterial DPP4 homologs as they did with human DPP4, suggesting a potential interaction of these drugs with gut microbiota. These findings could help in understanding the interplay between gliptins and gut microbiota DPP4 homologs, considering the intricate relationship between the host metabolism and microbial communities in the gut. [ABSTRACT FROM AUTHOR]

This research investigated the physicochemical, microbiological, and bacterial diversity of Jben cheese, a popular artisanal variety in Morocco. The bacterial diversity was explored using culture-independent methods, including temporal temperature gel electrophoresis (TTGE), denaturing gradient gel electrophoresis (DGGE), and high-throughput sequencing (HTS). Significant intra-sample differences were observed for most physicochemical parameters within each milk type, while inter-sample differences occurred between cow and goat cheeses for dry matter and ash. Jben cheese exhibited distinct characteristics, with low pH values of 3.96, 4.16, and 4.18 for cow, goat, and mixed cheeses, respectively. Goat cheeses had higher fat (49.23 g/100 g), ash (1.91 g/100 g), and dry matter (36.39 g/100 g) than cow cheeses. All cheeses displayed high microbial counts, with a notable prevalence of the lactic acid bacteria (LAB) group, averaging 8.80 ± 0.92 log CFU/g. Jben cheese also displayed high contamination levels with total coliforms, faecal coliforms, yeast, and molds. Fatty acid profiling revealed fraudulent practices in Jben cheese marketing, with cow or mixed cheeses sold as goat cheese, as proven by low capric acid concentration. HTS analysis of Jben cheese identified ten genera and twenty-four species, highlighting Lactococcus lactis as predominant. TTGE and DGGE confirmed the presence of L. lactis but failed to provide the detailed profile achieved through HTS analysis. HTS has been demonstrated to be more reliable, whereas TTGE/DGGE methods, though informative, were more time-consuming and less reliable. Despite limitations, the combined use of TTGE, DGGE, and HTS provided a comprehensive view of indigenous bacterial communities in Jben cheese, identifying L. lactis as the main species. [ABSTRACT FROM AUTHOR]

Introduction: It is known that BRCA1 and BRCA2 genes' mutation carriers are predisposed to breast and ovarian cancers and other organ cancers such as prostate, colon and cervix. In the previous study performed at X University, all coding exons of both genes were screened by denaturing gradient gel electrophoresis (DGGE). In addition to various nonsense, missense mutations, polymorphisms and intronic region changes, seven novel missense mutations, including H513L, H816P and S1517Y in BRCA1 and S326R, G258P, E2903K and N2742S in BRCA2, had been identified. Methods: To determine whether these unclassified variants are pathogenic, DNA samples of 150 healthy individuals without a known cancer history in the family were screened in this study for these seven novel missense mutations. These DNA samples were recruited from archives of previous polymorphism studies. PCR performed DNA amplifications, and denaturing high-performance liquid chromatography (DHPLC) techniques did mutation screenings. Results: Peak patterns suggestive of a change in DNA fragments were considered for sequencing analyses. Analyses revealed that none of the 150 DNA samples had any change in the seven screened fragments. As a result, it is assumed that these seven mutations might be novel pathogenic mutations described in the Turkish population. Conclusion: In conclusion, these carriers must be informed about the mutation and given appropriate genetic counseling by their physicians. In addition, genetic testing must be offered to high-risk individuals (men/women) in the family so that it would be possible for other family members to have genetic counseling and contribute to disease prevention. On the other hand, these findings would contribute to current literature with novel results and shed light on future research. [ABSTRACT FROM AUTHOR]

Bacteriological studies of well water mainly focus on aerobic and facultative aerobic coliform bacteria. However, the presence of obligate anaerobic bacteria in well water, especially sulfate-reducing bacteria (SRB), possible causative agents of some diseases, is often ignored. In this study, the presence of SRB and coexisting anaerobic bacteria with SRB in sulfate-reducing enrichment cultures obtained from 10 well water samples in Istanbul was investigated. A nested polymerase chain reaction-denaturing gradient gel electrophoresis strategy was performed to characterize the bacterial community structure of the enrichments. The most probable number method was used to determine SRB number. Out of 10, SRB growth was observed in only one (10%) enrichment culture and the SRB number was low (,10 cells/mL). Community members were identified as Desulfolutivibrio sulfodismutans and Anaerosinus sp. The results show that SRB coexist with Anaerosinus sp., and this may indicate poor water quality, posing a risk to public health. Furthermore, Anaerosinus sp., found in the human intestinal tract, may be used as an alternative anaerobic fecal indicator. It is worth noting that the detection of bacteria using molecular analyzes following enrichment culture techniques can bring new perspectives to determine the possible origin and presence of alternative microbial indicators in aquatic environments. [ABSTRACT FROM AUTHOR]

The relationship between bacterial diversity and the bioavailability of nutrients, toxic metals and the herbicide oxyfluorfen in a tropical vegetable growing area was evaluated. The study was conducted in a vegetable growing area located in the mountainous region of Rio de Janeiro (Brazil), and samples were collected in areas of vegetable cultivation and areas of environmental reserve. Fertility analyses and determination of the pseudototal levels of toxic metals in the soil samples were performed. The profile of the soil bacterial community was determined by amplification of the 16S rRNA gene and separation by DGGE. The results showed that the levels of toxic metals and elements associated with soil fertility were higher in vegetable production areas. These differences in the physical and chemical characteristics of the soil favored the presence of a greater number of OTUs in the cultivation areas (17.3-27 OTUs) than in the areas of environmental reserve (13-22 OTUs). Therefore, this study demonstrates that the presence of toxic metals and the herbicide oxyfluorfen and the increase in fertility in soils in areas with intensive vegetable cultivation resulting from the intensive management adopted in these areas promotes a differentiation of the bacterial profiles in soils in tropical vegetable growing areas. [ABSTRACT FROM AUTHOR]

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation. [ABSTRACT FROM AUTHOR]

This study investigated the effect of upland crop rotation on soil bacterial community in bulk soil and rice straw residues in the alluvial soils. Soil samples and rice straw residues in two crop rotation models including triple rice and rice-upland crops were collected for incubation under anaerobic and aerobic conditions. Data were analyzed from Denaturing Gradient Gel Electrophoresis band patterns. The results showed that the composition and diversity of communities colonizing the rice straw residues differed from those inhabiting the bulk soil. The bacterial community composition and diversity were only moderately affected by rice straw residues in the bulk soil. Especially, this study indicated that the composition of the bacterial community associated with the bulk soil and rice straw residues was dynamic in two incubation conditions (aerobic or anaerobic) and the different crop rotation models. The findings of this study demonstrated that the bacterial diversity was not affected by the difference in continuous paddy rice cultivation compared to the upland crop rotation system. [ABSTRACT FROM AUTHOR]

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ABSTRACT Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is a traditional non-culture technique that can provide a fingerprint of the microbial community. In the field of gut microbiota analysis, PCR-DGGE still holds potential for development. In the present study, we utilized an improved nested PCR-DGGE approach targeting the V3 region of 16S ribosomal DNA to investigate the impact of whole grain highland hull-less barley (WHLB), a cereal known for its significant hypocholesterolemic effect, on the gut microbiota profiles of high-fat diet rats. Seventy-two male Sprague–Dawley rats were divided into four groups and fed a normal control diet, a high-fat diet, or a high-fat diet supplemented with a low or high dose of WHLB for 4 or 8 weeks. The results revealed that the dominant bands varied among different dose groups and further changed with different treatment times. The compositions of bacterial communities in feces and cecal content were similar, but the dominant bacterial bands differed. After performing double DGGE, extracting the bands, sequencing the DNA, and aligning the sequences, a total of 19 bands were classified under the Firmicutes and Bacteroidetes phyla, while two bands were identified as unclassified uncultured bacteria. The relative abundance of Lactobacillus gasseri, Uncultured Prevotella sp., and Clostridium sp. increased following the administration of WHLB. Illumina-based sequencing was employed to assess the reliability of DGGE, demonstrating its reliability in analyzing the dominant taxonomic composition, although it may have limitations in accurately detecting the alpha diversity of bacterial species.IMPORTANCEWhile next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.

Background and Objectives: Respiratory infections are the most serious condition in cystic fibrosis (CF) patients; therefore, a thorough comprehension of the diversity and dominant microbial species in CF airways has a crucial role in treatment. Our objective was to determine the antibiotic resistance profile of CF airways microbiota and compare culture methods and PCR-DGGE to evaluate bacterial diversity. Materials and Methods: Pharyngeal swabs from 121 CF patients were collected. The samples were then cultured, identified and antibiotic resistance testing was performed. Thirty samples were subjected to further molecular surveys. DNA contents of these samples were extracted and amplified using nested-PCR technique and their bacterial diversity was assessed by DGGE. The DGGE patterns were visualized and certain bands were excised and purified. Next, the DNA was amplified by another round of PCR and sent out for sequencing. Results: Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most prevalent species isolated using culture methods. S. aureus was the most common bacteria among 6 years and younger patients; while, P. aeruginosa had more prevalence among older ones. The PCR-DGGE results showed more diversity than culture methods, particularly in younger patients who exhibited more bacterial diversity than the older groups. Sequencing results unveiled the presence of certain bacterial species including Haemophilus parainfluenzae and Stenotrophomonas maltophilia which were completely missed in culture. Conclusion: Even though culture-dependent methods are cost-effective, PCR-DGGE appeared to be more efficient to determine bacterial diversity. PCR-DGGE detects less abundant species, though their viability could not be determined using this method. [ABSTRACT FROM AUTHOR]

Traditional dairy products, especially cheeses, represent part of the cultural food heritage of many countries. In addition, these cheeses constitute microbiological "reservoirs", of which many have been lost due to the introduction of the pasteurization of milk in the dairy industry. Increased awareness of the importance of microorganisms that make up the biodiversity of traditional cheeses, as well as the development of molecular methods in recent decades, have enabled efforts to identify and preserve them. Traditional Livno cheese is a full-fat hard cheese, considered one of the most famous traditional cheeses of Bosnia and Herzegovina and is seasonally produced from a mixture of raw sheep's milk supplemented with cow's milk. Often, Livno cheese has variable quality, due to microbial contamination and poor milk quality. In this study, traditional Livno cheese was studied during the ripening of cheeses produced by different producers during two seasons. Culture-dependent analyses were made during ripening using microbiological plating on suitable media. Likewise, culture-independent methods Denaturing Gradient Gel Electrophoresis (DGGE) and Automated Ribosomal Intergenic Spacer Analysis (ARISA) were used to elucidate the cheese microbiota. Results of analysis showed Lactococcus spp., Streptococcus spp., Lactobacillus spp., Pediococcus spp. and Leuconostoc spp. to be dominant species in traditional Livno cheese. However, when comparing the use of culture-dependent and culture-independent methods in the evaluation of Livno cheese microbiota, Enterococcus was not detected by culture-independent DGGE methods. The microbial population of both the milk and the environment determines the fermentation processes during cheese production and ripening, and thereby defines the quality of this cheese. The numbers of bacteria in the cheese were shown to be dependent on the manufacturer, the degree of ripening and the production season. [ABSTRACT FROM AUTHOR]

Aims: The inefficient lysis of recalcitrant bacterial cell wall and subsequent isolation of DNA from environmental samples can lead to a bias in the qualitative and quantitative assessment of bacteria present in the sample. Thus, the selection of an optimum DNA isolation method is the important first step for biosurveillance and metagenomic analyses. This study aims to determine the optimal DNA isolation method out of four commercial DNA isolation kits (A, B, C and D) and two conventional methods (E and F), for rodent faecal droppings. The key selection criterion is the general bacterial diversity contained in the isolated DNA, as evaluated by the Shannon-Weaver index based on the maximal number of PCRamplicons of partial 16S rRNA gene, derived from each method. The amplicons were separated in accordance with their difference in nucleotide sequences via DGGE. Methodology and results: Five faecal samples of wild rodents were collected from different sites and preserved in DNA/RNA shield reagent (Zymo Research). Each sample was extracted, and the DNA extracts were then subjected to amplification of the bacterial 16S rRNA and DGGE separation of the amplicons. Method E showed a higher yield of DNA (average 324.22 ng/µL) as compared to the other methods. However, the majority of the DNA extracts showed partial degradation. The DGGE profiles showed the highest number of amplicons were generated from DNA extracted from Method A and B with a total of 168 and 167 respectively. This is indicated by the Shannon-Weaver index which were 0.306 and 0.305, respectively. Conclusion, significance and impact of study: Method A is the optimum DNA isolation method for rodent faecal samples as its isolated DNA contains the most diverse bacteria. The isolated DNA can then be used for PCRbiosurveillance or metagenomic sequencing and analyses. [ABSTRACT FROM AUTHOR]

Calcium carbonate (CaCO3) is a widely used inorganic filling pigment used in coatings, and it is known for its nontoxicity, odorlessness, and environmental friendliness. The application of CaCO3 as a filler can effectively reduce raw material costs, and optimization of the filler formula enhances the coating film performance. In this study, oak planks were prepared as substrates for water-based inkjet printing. Three composite water-based primers with different TiO2-to-CaCO3 ratios and a polyurethane resin primer were used to prepare the substrate for the printing surface. The properties of the water-based primer coating and the water-based inkjet printing coating were characterized and analyzed via Fourier-transform infrared spectroscopy, video-based contact angle analysis, and environmental scanning electron microscopy. The aim was to investigate the effects of the composite waterborne primer coatings on the ink absorption and coloring properties of the interface between wood substrates and waterborne inkjet coatings. Sample WDCC-3#, with a TiO2-to-CaCO3 ratio of 15:35, exhibited the most comprehensive characteristics. The wood surface coated with 15 g/m2 of the polyurethane resin primer and 15 g/m2 of WDCC-3# exhibited a 5.8° contact angle of the water-based ink, first-grade adhesion, 4 H hardness, 70.52 whiteness value, and a roughness of ~2.33. The surface of the printed water-based inkjet-coated substrate was uniform and smooth, featuring rounded and transparent edges of the water-based ink droplets and a small CMYK color difference value. Therefore, the composite waterborne primer, incorporating TiO2 and CaCO3 in specific ratios, can be effectively combined with waterborne polyurethane primer coatings. This combination significantly improves the interfacial compatibility between the oak surface and waterborne inkjet coatings, leading to enhanced ink absorption on the oak plank surface during printing. This results in a high degree of color reproduction and clearer printed images. Overall, this study provides valuable insights for the development of primer programs for the industrial application of waterborne digital inkjet technology on wood products. [ABSTRACT FROM AUTHOR]

A conversion coating was formed on the surface of TC4 titanium alloy by sol--gel method in a solution comprising organic silane and zirconium alkoxide as main components with ethanol as solvent. The surface morphology and composition, and element distribution and valence state of oxygen along the depth direction of coating were analyzed by scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), glow discharge mass spectrometry (GDMS), and X-ray photoelectron spectroscopy (XPS). The electrochemical properties and structure of the conversion coating were examined by electrochemical impedance spectroscopy (EIS). The effect of zirconium alkoxide content on the adhesion of organic primer coat was studied by long-term damp-heat test. The results showed that the sol--gel conversion coating consisted of an inorganic layer, which was mainly composed of covalently bonded Ti-O-Zr/Si structure, and an organic layer, which was formed by the crosslinking reaction of carbon chains attached to the silane. The sol--gel conversion coating obtained with 2 000 mg/kg of zirconium alkoxide featured the best structure integrity, and the primer sprayed on it had excellent adhesion and durability. [ABSTRACT FROM AUTHOR]

Most studies focus on the "clockwise sequential" switching manner for a four-compartment periodic anaerobic baffled reactor (PABR), while the exploration of the "every second" option on the feasibility for real industrial wastewater treatment is rarely reported. Hence, a PABR-treating traditional Chinese medicine wastewater was run continuously in "every second" switching manner with both switching period T and hydraulic residence time of 48 h. Satisfactory start-up performance was achieved during the operation of a climbing average organic load rate at approximately 1, 2, 4, and 6 kg chemical oxygen demand (COD) m-3 d-1 for 12, 24, 24, and 6 days, respectively. The average COD removal was 87.20% after the second lifting of OLR and 89.98% after the third one. Denaturing gradient gel electrophoresis and its cluster analysis showed that the microbial communities in each compartment adapted their structure in response to the periodically changing micro-ecology conditions. Moreover, the residence time distribution test with tap water in the clean PABR was carried out in experiments and computational fluid dynamics (CFD) simulation, both of which were in good agreement. The CFD model output visualized the flow velocity field and hydrodynamic-mass transport inside the PABR. Optimization of operation pattern in PABR including switching manner and frequency depended on both the type of waste being treated and the flexibility of biomass to periodically changing micro-ecology conditions. [ABSTRACT FROM AUTHOR]

Lactococcosis, caused by Lactococcus garvieae, is an acute hemorrhagic septicemia in fish recorded in marine and freshwater aquaculture during the summer months. In 2020–2021, several sea cage Pompano farms recorded sudden fish mortality events. Based on the results of phenotypic and biochemical tests, L. garvieae was predicted to be the cause. PCR with L. garvieae specific primers (pLG1 and pLG2) targeting the 16S rRNA region further confirmed the etiological agent as L. garvieae after amplifying an 1100 base pairs (bp) product. Furthermore, the 16S rRNA sequences of the two representative strains (AOD109‐196‐2B and AOD110‐215‐2B) shared 99.81% identity with L. garvieae (GenBank accession number: MT597707.1). The genetic profiles of the strains were classified using pulsed‐field gel electrophoresis after digestion with SmaI and ApaI, which clustered our strains under the same pulsotype. Multiplex PCR targeting the capsule gene cluster and serotype‐specific PCR collectively showed that the strains were non‐capsulated; thus, they belonged to serotype I. An experimental infection was designed to fulfil Koch's postulates by infecting healthy Pompano with case‐driven L. garvieae strains (AOD109‐196‐2B and AOD110‐215‐2B) with a cumulative mortality of 70%. Overall, L. garvieae infection in Pompano emphasizes the need for better monitoring and control procedures in aquaculture settings. [ABSTRACT FROM AUTHOR]

Exploring the possibility of using agricultural waste as a substrate for the synthesis of cellulase enzymes for fuel and renewable energy is the main goal of this study, which is in line with the notions of sustainable development and environmental stewardship. The product of delignification of cocoa peel can be used as a substrate for cellulase enzymes producing by yeast isolated from Balinese palm wine. Cellulase enzymes made from yeast from Balinese palm wine can be produced using the delignified cocoa peel as a substrate. This study aims to analyze the cellulase enzyme activity of yeast from Bali's palm wine on delignified cocoa bark substrates. The tests carried out were delignification of cocoa bark (solvent variations: HCl, H2SO4 and NaOH; concentrations: 1, 1.5 and 2 %; biomass 1:15 and 1:20 (w/v)); screening of cellulolytic yeast from Balinese palm wine; molecular identification and morphological characteristics of yeast; and cellulase enzyme activity (variation of yeast isolates and fermentation time of 48, 72 and 96 h). The results of delignification of cocoa shells showed that the use of 1.5 % NaOH solvent with cocoa shell powder biomass of 1:15 (9.59 ± 0.11) significantly differed from the value of reducing sugar content. Based on the screening results of 6 yeast isolates, 3 yeast isolates with the highest cellulolytic index values were selected, namely UNJCC Y-83 (0.29 ± 0.01 mm), UNJCC Y-123 (0.24 ± 0.01 mm) and UNJCC Y-84 (0.23 ± 0.01 mm). For testing cellulase enzyme activity. S. cerevisiae UNJCC Y-83 (4.11 ± 0.41 U/mL); S. cerevisiae UNJCC Y-84 (4.11 ± 0.33 U/mL) and P. manshurica UNJCC Y-123 (4.06 ± 0.12 U/mL) at 96 h of fermentation had significantly different cellulase enzyme activity. The results of identification of yeast rDNA in the D1/D2 region with NL1/NL4 primers obtained the identity of Saccharomyces cerevisiae UNJCC Y-83; Saccharomyces cerevisiae UNJCC Y-84 (99.66 % homology); and Pichia manshurica (100 % homology). Theobroma cocoa rind can be used as a yeast substrate to produce cellulase enzymes for fuel and renewable energy. [ABSTRACT FROM AUTHOR]

The invasive insect pest known as the coconut rugose spiraling whitefly was discovered. Recently in 2018, the research was conducted to examine the variation of gut microbiota in Rugose Spiraling Whiteflies collected from three distinct locations in Karnataka where coconut is produced. Nine culturable bacteria were identified using molecular methods after being found in the gut of three populations of Rugose Spiraling Whiteflies. The nine isolates were found to produce chitinase, siderophores and proteases. The activity of chitinase, siderophore and protease ranged in the gut bacterial isolates of coconut rugose spiraling whitefly 0.023 to 0.44 nmol-1 min-1 mL-1, 8.27 to 35.63 per cent and 19.10 to 84.71 per cent, respectively. They have analysed for the presence of enzymase activity. An analysis of the 16S rRNA gene revealed that the gut of Aleurodicus rugioperculatus has a number of bacterial species. Includes Bacillus cereus, Lederbergia. Sp. Proteus vulgaris, Lysinibacillus fusiformis, Pseudomonas helleri, Pseudomonas fragi, Pseudomonas psychrophila, Hafinia paralvei. [ABSTRACT FROM AUTHOR]

Background and Objectives: Respiratory infections are the most serious condition in cystic fibrosis (CF) patients; therefore, a thorough comprehension of the diversity and dominant microbial species in CF airways has a crucial role in treatment. Our objective was to determine the antibiotic resistance profile of CF airways microbiota and compare culture methods and PCR-DGGE to evaluate bacterial diversity. Materials and Methods: Pharyngeal swabs from 121 CF patients were collected. The samples were then cultured, identified and antibiotic resistance testing was performed. Thirty samples were subjected to further molecular surveys. DNA contents of these samples were extracted and amplified using nested-PCR technique and their bacterial diversity was assessed by DGGE. The DGGE patterns were visualized and certain bands were excised and purified. Next, the DNA was amplified by another round of PCR and sent out for sequencing. Results: Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most prevalent species isolated using culture methods. S. aureus was the most common bacteria among 6 years and younger patients; while, P. aeruginosa had more prevalence among older ones. The PCR-DGGE results showed more diversity than culture methods, particularly in younger patients who exhibited more bacterial diversity than the older groups. Sequencing results unveiled the presence of certain bacterial species including Haemophilus parainfluenzae and Stenotrophomonas maltophilia which were completely missed in culture. Conclusion: Even though culture-dependent methods are cost-effective, PCR-DGGE appeared to be more efficient to determine bacterial diversity. PCR-DGGE detects less abundant species, though their viability could not be determined using this method.

In order to reveal the biological diversity and the evolution of microbial community structure in the process of sludge cultivation and acclimation at the start-up stage of simultaneous partial nitrification and denitrification (SNAD) process, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze the microbial community structure in different operating periods. And molecular cloning was used for species identification and phylogenetic analysis. The 16S rDNA sequence analysis of the characteristic bands of the DGGE profile of total bacteria showed that the bacterial populations in the sludge were rich in diversity, and β- proteobacteria were slightly more abundant and maintained a relatively stable dominant position. With the operation of the reactor, the secondary populations were strengthened and became new dominant communities, such as Firmicutes, γ- proteobacteria, Bacteroides and so on. The 16S rDNA sequence analysis of the characteristic bands of the DGGE profile of ammonia-oxidizing bacteria showed that the strains obtained by sequencing basically belonged to Nitrosomonas of β-proteobacteria. The fast growth rate of this genus made it the dominant ammonia-oxidizing bacteria (AOB) in the activated sludge systems. [ABSTRACT FROM AUTHOR]

After the collapse of Fundão Dam in Mariana‐MG, Brazil, the discharge of iron ore mining waste into the Doce River watershed negatively impacted the landscape. Monitoring the composition and species richness of soil microbiota may be useful bioindicators of ecosystem recovery. This study aimed to compare soil chemical properties, total fungal species, and arbuscular mycorrhizal fungi (AMF) in sites unaffected and affected by mining tailings in the first 3 years after the collapse of Fundão Dam. Soil and root samples were collected in dry and rainy seasons over 3 years in unaffected (adjacent forest and pasture) and affected areas (REC1, REC2, and PASTrec) by mine tailings. Changes in soil chemical properties over the sampling period were measured by routine chemical analyses. Total fungi in the soil was determined by high‐throughput sequencing. AMF community was evaluated using spore number, root colonization, and denaturing gradient gel electrophoresis. Affected sites had higher ranges of pH and lower soil organic matter than unaffected sites. Revegetation had a positive effect on soil fungal community. Increased similarity in AMF DGGE analysis was observed in the two sampling sites over time. A high similarity of total fungi and AMF was observed between REC and pasture areas, suggesting that revegetation strategy employed may be heading towards a pasture condition. Thus, post‐disturbance analysis of this study was important to evaluate of ecosystem recovery affected by the rupture of iron ore mining dam and demonstrated that the soil microbiota was a sensitive bioindicator in this long path of ecosystem recovery. [ABSTRACT FROM AUTHOR]

The Indian golden muga silkworm, Antheraea assamensis Helfer is an economically important wild silkworm endemic to Northeastern part of India. In recent years, climate change has posed a threat to muga silk production due to the requirement that larvae be reared outdoors. Since the muga silkworm larvae are exposed to the vagaries of nature, the changing climate has increased the incidence of microbial diseases in the rearing fields. Accurate diagnosis of the disease causing pathogens and its associated epidemiology are prerequisites to manage the diseases in the rearing field. Although conventional microbial culturing methods are widely used to identify pathogenic bacteria, they would not provide meaningful information on a wide variety of silkworm pathogens. The information on use of molecular diagnostic tools in detection of microbial pathogens of wild silk moths is very limited. A wide range of molecular and immunodiagnostic techniques including denaturing gradient gel electrophoresis (DGGE), random amplified polymorphism (RAPD), 16S rRNA/ITSA gene sequencing, multiplex polymerase chain reaction (M-PCR), fluorescence in situ hybridization (FISH), immunofluorescence, and repetitive-element PCR (Rep-PCR), have been used for detecting and characterizing the pathogens of insects with economic significance. Nevertheless, the application of these molecular tools for detecting and typing entomopathogens in surveillance studies of muga silkworm rearing is very limited. Here, we discuss the possible application of these molecular techniques, their advantages and major limitations. These methods show promise in better management of diseases in muga ecosystem. [ABSTRACT FROM AUTHOR]

Laccase enzyme is a ligninolytic enzyme which has an ability to oxidize phenolic compounds of lignocellulosic biomass. The aim of the study was to identify, optimize a thermo-tolerant isolate and laccase enzyme production using Response Surface Methodology- Box Behnken design respectively. The strain S3 was isolated from the compost soil pit and the crude laccase enzyme was extracted from the strain. The parameters such as pH, incubation period and CuSO4 concentration has been optimized using Box-Behnken design and the outcome shows that the enzyme with 4.71 U mL− 1 was stable at pH 6 and 8, the optimum CuSO4 concentration was 100 mM and the incubation period was 7 days at the temperature of 46֯ C. The genomic DNA of the strain was amplified using ITS-1 and 4 primers which showed a product size of 700 bp. The amplicon was sequenced and the blast analysis showed a sequence similarity of 96.6% with the Flammulina velutipes. The protein was isolated and the SDS analysis showed a molecular weight of 120 kDa.The crude laccase enzyme produced from the strain S3 Flammulina velutipes was formulated and optimized at varying parameters to increase the yield of laccase enzyme. We conclude that our results will assist to a wide application in bio-fuel production. [ABSTRACT FROM AUTHOR]

Foot-and-mouth disease virus (FMDV) causes Foot-and-mouth disease, which was listed as a reported disease by Office international des épizooties. It has caused great economic losses to the meat industry. Here, we developed a sensitive, rapid, and visible method based Reverse Transcriptase Enzyme-assisted recombinant isothermal amplification technique (RT-ERA) and CRISPR/Cpf1 for detecting FMDV. RT-ERA achieved simultaneous reverse transcription and amplification in a short time at 37 ℃. Moreover, CRISPR/Cpf1 specifically recognized the products and amplified the signals through the trans-cleavage activity, which converted the DNA signals into fluorescence signals and lateral flow assay strip. Within 30 min, the method detected FMDV as low as 10 copies·μL−1, making it 103 times more sensitive than gel electrophoresis and 10 times more sensitive than reverse transcription quantitative real-time PCR. Moreover, the method had good performance in actual samples. Therefore, this method realized visual detection without the large instruments and showed significant potential for FMDV assay. [Display omitted] • RT-ERA fulfills reverse transcription and amplification in 20 min to reduce time. • The role of the primers and crRNA improves the specificity of the method. • The method has high sensitivity by the trans-cleavage activity of Cpf1 and RT-ERA. • The method achieves visual detected by LFA without large equipment. [ABSTRACT FROM AUTHOR]

Lipase is one of the most important industrial enzymes, which has been widely used in the preparation of food additives, cosmetics and pharmaceuticals industries. High-level production of lipase, was achieved using a methylotrophic yeast Pichia pastoris X-33 expression system. The lipase gene of 1.4 kbp was cloned into integrative vector pPICZ&945A amplifying from pKNAPFL0812 construct and restriction digested by KpnI and NotI. The restricted gene and vector was ligated using T4 DNA ligase and transformed into E. coli DH5α cells. The recombinant colonies were selected by zeocin. Clones were confirmed by PCR using gene specific primers and confirmed clones were linearized by SacI restriction enzyme. The linearized recombinant pPICZαA vector was transformed into Pichia pastoris using electroporator and plated on YPD with zeocin. Positive clones were induced for lipase production using methanol as inducer and confirmed by SDS PAGE. The produced lipase can be utilized for various applications like biodiesel production. [ABSTRACT FROM AUTHOR]

Chinese strong-flavour liquor is produced via a traditional solid-state fermentation strategy facilitated by live microorganisms in pit mud-based cellars. For the present analysis, pit mud samples from different spatial locations within fermentation cellars were collected, and the yeast communities therein were assessed via culture-based and denaturing gradient gel electrophoresis (DGGE) approaches. These analyses revealed significant differences in the composition of yeast communities present in different layers of pit mud. In total, 29 different yeast species were detected, and principal component analyses revealed clear differences in microbial diversity in pit mud samples taken from different cellar locations. Culture-dependent strategies similarly detected 20 different yeast species in these samples. However, while Geotrichum silvicola, Torulaspora delbrueckii, Hanseniaspora uvarum, Saturnispora silvae, Issatchenkia orientalis, Candida mucifera, Kazachstania barnettii, Cyberlindnera jadinii, Hanseniaspora spp., Alternaria tenuissima, Cryptococcus laurentii, Metschnikowia spp., and Rhodotorula dairenensis were detected via a PCR-DGGE approach, they were not detectable in culture-dependent analyses. In contrast, culture-based approaches led to the identification of Schizosaccharomyces pombe and Debaryomyces hansenii in these pit mud samples, whereas they were not detected using DGGE fingerprints profiles. An additional HS-SPME-GC-MS-based analysis of the volatile compounds present in fermented grains samples led to the identification of 66 such compounds, with the highest levels of volatile acids, esters, and alcohols being detected in fermented grains from lower layer samples. A canonical correspondence analysis (CCA) suggested they were significant correlations between pit mud yeast communities and associated volatile compounds in fermented grains. [ABSTRACT FROM AUTHOR]

Simultaneous bioproduction of hydrogen and ethanol from cheaper waste feedstock has the potential for the development of a more cost-effective biofuel generation process. Crude glycerol (CG), a by-product of the biodiesel industry, is a renewable resource, abundant, sold at low prices and available worldwide. However, the main CG limitations in fermentation processes are mainly related to the presence of impurities and the lack of nitrogen sources, both acting on microbial activity. In this study, a fermentation process with CG was improved using a highly specific microbial consortium called GlyCeroL (GCL). The process was developed in fed-batch fermentation mode using not diluted substrate and carried out under non-sterile conditions and at increasing amounts of the substrate (from 20 to 80 gL−1 of glycerol). The results showed higher H2 (from 6 to 8 LL−1) and EtOH (from 13 to 20 gL−1) production by increasing glycerol concentration from 20 to 40 gL−1. On the other hand, a decrease in glycerol degradation efficiency (from 75 to 56%) was observed. Then, the nitrogen sparging strategy was applied. Using CG of 40 gL−1, process improvement was achieved, leading to the increased production of hydrogen (10 LL−1) but not that of ethanol (20 gL−1). A further increase to 60 gL−1 of glycerol produced a slight increment of EtOH (21 gL−1) and H2 (11 gL−1) but a sharp decrease in glycerol degradation efficiency (41%). Acetate, as the main impurity of CG, was an additional carbon source for GCL microorganisms contributing to EtOH production and increasing that of lactic acid to restore the redox balance. The Denaturing Gradient Gel Electrophoresis (DGGE) fingerprint at the end of all fed-batch fermentations supported the robustness of GCL functional units and their adaptability to fermentation conditions. [ABSTRACT FROM AUTHOR]

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The ecological balance of an ecosystem has a relation to its biodiversity. Although it has been established that biodiversity and ecological stability are related, generalization about the exact nature of this relation remains elusive and more so in microbial diversity. A growing volume of studies has indicated that anthropogenic activities impact biodiversity, but it is difficult to generalize the impact of anthropogenic activities on microbial diversity. Landfilling by municipal solid waste is one such activity where microbes play a major role, and leachates are released from the landfill, altering the soil's physical and chemical nature. Change in factors like carbon source, pH, and toxicity of the soil is most likely to affect the indigenous microflora of the soil. The present study was undertaken to compare the microbial diversity of soil receiving landfill leachate with that of the soil not receiving any landfill leachate to assess the impact of the landfilling activity on microbial diversity. The landfill site selected for the study was that of Kamrup Metro District of Assam, located at Boragaon, near the Ramsar wetland called Deeporbeel. By using the Denaturing Gradient Gel Electrophoresis (DGGE) method, it has been found that the microbial diversity of the soil receiving leachate was higher than that of the soil not receiving any leachate from the landfill. [ABSTRACT FROM AUTHOR]

Background: Modulating the microbiota is an emerging way to improve pig health. In-vitro bioreactor systems can be used to reproduce intestinal microbiota to study modulating avenues. In this study, a continuous feeding system to support a microbiota derived from piglet colonic contents, over 72 h, was developed. The microbiota from piglets was collected and used as inoculum. The culture media was derived from an artificial digestion of piglet feed. The microbiota diversity in time, the reproducibility between replicates and the diversity of the bioreactor microbiota compared to the inoculum was assessed. Essential oils were used as a proof of concept to assess the in vitro microbiota modulation. The microbiota diversity was assessed by 16S rRNA amplicon sequencing. Quantitative PCR was also used for total bacteria, lactobacilli and Enterobacteria. Results: At the start of the assay, the bioreactor microbiota diversity was similar to the inoculum. Time and replication affected the bioreactor microbiota diversity. Between 48 and 72 h, no statistical variation of the microbiota diversity was observable. After a 48 h running period, thymol and carvacrol were added at 200 ppm or 1000 ppm for 24 h. No microbiota modification was observed by sequencing. Quantitative PCR results showed a significant growth of lactobacilli when thymol was used at 1000 ppm, where only a trend was observed with the 16S analysis. Conclusions: This study presents a bioreactor assay that can be used as a tool for rapid screening of additives and suggests that the effects of essential oils on the microbiota are subtle, acting against a few bacterial genera. [ABSTRACT FROM AUTHOR]

Sulfate-rich effluents have been successfully treated in anaerobic reactors using sulfate-reducing bacteria (SRB). Many authors have demonstrated that these systems require nitrogen and phosphorous supplementation to achieve high sulfate removal rates. However, the resource ratio theory assumes that some species can be dominant according to the nutritional relations used or even without external nutrient supplementation. Thus, this study evaluated the SRB communities in batch reactors without external nitrogen and phosphorus sources based on most probable number (MPN) quantification, denaturing gradient gel electrophoresis (DGGE) analyses and sequencing. The sulfate and chemical oxygen demand (COD) removal and kinetic parameters were also determined. After 100 days of operation, the sulfate and COD removal achieved 71.8 ± 10% and 86.5 ± 10%, respectively. The SRB population increased from 8.106 to 4x1012 MPN 100mL-1, and the richness of SRB bands was much higher at the end of the experiment compared to the inoculum. In addition, the sequenced bands from SRB-DGGE showed similarities to Desulfacinum infernum, Desulfobulbus sp, Syntrophobacter and Desulfomicrobium aestuarii-related sequences. Therefore, biological treatment of acid mine drainage wastewater was effective in the absence of nutrients, lowering costs and providing high sulfate removal efficiency. [ABSTRACT FROM AUTHOR]

We analyse the dynamics of different routes to collapse of a constrained polyelectrolyte gel in contact with an ionic bath. The evolution of the gel is described by a model that incorporates non-linear elasticity, Stefan--Maxwell diffusion and interfacial gradient free energy to account for phase separation of the gel. A bifurcation analysis of the homogeneous equilibrium states reveals three solution branches at low ion concentrations in the bath, giving way to only one above a critical ion concentration. We present numerical solutions that capture both the spatial heterogeneity and the multiple timescales involved in the process of collapse. These solutions are complemented by two analytical studies. Firstly, a phase-plane analysis that reveals the existence of a depletion front for the transition from the highly swollen to the new collapsed equilibrium state. This depletion front is initiated after the fast ionic diffusion has set the initial condition for this time regime. Secondly, we perform a linear stability analysis about the homogeneous states that show that for a range of ion concentrations in the bath, spinodal decomposition of the swollen state gives rise to localized solvent-rich(poor) and, due to the electroneutrality condition, ion-poor(rich) phases that coarsen on the route to collapse. This dynamics of a collapsing polyelectrolyte gel has not been described before. [ABSTRACT FROM AUTHOR]

Background and Aim: Oral infections are common among people of any age and can trigger systemic inflammation. The microbiota is a diverse group of microorganisms that play important roles in metabolism, immune function, and homeostasis. Oral microbiota in human atherosclerotic plaques has been identified using various techniques. Therefore, the focus of this study was to determine the correlation between metabolic parameters and oral microbiota composition in patients with atherosclerosis using Denaturing Gradient Gel Electrophoresis (DGGE) assays. Materials and Methods: In this case-control study, saliva samples were collected from 139 patients with atherosclerosis and healthy individuals from Imam Ali Cardiovascular Hospital, Kermanshah, Iran. After DNA extraction, PCR products were examined and evaluated using DGGE assays. Results: The study included 89 (36%) patients with a history of atherosclerosis and 50 (36%) healthy individuals. There was a significant relationship between the mean total cholesterol, Low-Density Lipoprotein (LDL), Fasting Blood Sugar (FBS), and Blood Urea Nitrogen (BUN) in the two groups. However, there was no significant difference in the mean high-density lipoprotein (HDL) and Triglyceride levels between the study groups. Conclusion: Our results showed a relationship between metabolic parameters and oral microbiota composition in patients with atherosclerosis. Additionally, our results indicated that the DGGE assay is a useful method for diagnosing and comparing the oral microbiota of people with atherosclerosis and healthy individuals. Therefore, further examination of the oral microbiota is necessary to determine its potential as a biomarker for atherosclerosis. [ABSTRACT FROM AUTHOR]

Azoarcus sp. DN11 was previously isolated from gasoline-contaminated groundwater as an anaerobic benzene-degrading bacterium. Genome analysis of strain DN11 revealed that it contained a putative idr gene cluster (idrABP1P2), which was recently found to be involved in bacterial iodate (IO3-) respiration. In this study, we determined if strain DN11 performed iodate respiration and assessed its potential use to remove and sequester radioactive iodine (129I) from subsurface contaminated aquifers. Strain DN11 coupled acetate oxidation to iodate reduction and grew anaerobically with iodate as the sole electron acceptor. The respiratory iodate reductase (Idr) activity of strain DN11 was visualized on non-denaturing gel electrophoresis, and liquid chromatography--tandem mass spectrometry analysis of the active band suggested the involvement of IdrA, IdrP1, and IdrP2 in iodate respiration. The transcriptomic analysis also showed that idrA, idrP1, and idrP2 expression was upregulated under iodate-respiring conditions. After the growth of strain DN11 on iodate, silver-impregnated zeolite was added to the spent medium to remove iodide from the aqueous phase. In the presence of 200 μM iodate as the electron acceptor, more than 98% of iodine was successfully removed from the aqueous phase. These results suggest that strain DN11 is potentially helpful for bioaugmentation of 129I-contaminated subsurface aquifers. [ABSTRACT FROM AUTHOR]

Before osteoma cutis was fully developed, several diagnoses were considered, including elastic tissue nevus, focal dermal hypoplasia, anetoderma of prematurity, atrophic macules of neurofibromatosis, and infantile myofibromatosis. Primary osteoma cutis is a rare condition of intramembranous ossification as a result of differentiation of mesenchymal stem cells into bone without previous cartilage formation.[1] It is a hallmark of several genetic conditions appearing under different phenotypes, including Albright's hereditary osteodystrophy (AHO), osteomatosis cutis, progressive osseous heteroplasia (POH), and plate-like osteoma cutis.[2] There is considerable overlap between these conditions in relation to their skin and endocrinological manifestations. We present the case of a newborn who had multiple skin atrophic macules at birth that showed intramembranous ossification at 1 year of age, and report the histologic features of the pre-osseous stage of osteoma cutis. [Extracted from the article]

Genes of host plants and parasitic nematodes govern the plant–nematode interaction. The biological receptors and parasitism effectors are variable among plant species and nematode populations, respectively. In the present study, hatch testing and bioassays on cabbage, oilseed radish, and mustard were conducted to compare the biological characteristics among six populations of the beet cyst nematode Heterodera schachtii. Genetic patterns of the vap1 gene for the studied populations were distinct as shown by denaturing the gradient gel electrophoresis of PCR-amplified gene fragments. Concurrently, significant differences in the hatching rates, number of penetrated J2 in roots, and eggs/cyst ratios among the six nematode populations for the three cruciferous species were observed. In conclusion, analyzing the population genetic structure of H. schachtii plays a pivotal role in illustrating the variability in the plant–nematode interaction among its populations and plant species, which in its role leads to developing nematode management depending on plant resistance. [ABSTRACT FROM AUTHOR]

Chronic disease following Nocardia seriolae infection in a wide range of aquatic animals has been reported in many Asian countries and recently in America and Mexico. This study aimed to investigate the epidemiological relationship among N. seriolae isolates in Taiwan by investigating their genotype and enzymatic activities. A total of 66 strains isolated from 14 known and four unknown host fish from five sites in Taiwan were characterized using five combined methods. High genotypic diversity was recognized among the isolates with 10 pulsotypes being identified from the pulsed‐field gel electrophoresis method and 21 reptypes from the repetitive extragenic palindromic amplification method; however, no natural plasmids were detected in this bacterial population. Pulsotypes A8 and RI analysed by PFGE and repPCR, respectively, were found to be predominant within five sites in Taiwan over 17 years of isolation. Enzymatically, the majority of isolates displayed high leucine arylamidase, β‐glucosidase and α‐glucosidase activities but were negative for lipase, α‐galactosidase, β‐glucuronidase, N‐acetyl‐glucosaminidase, α‐mannosidase and α‐fucosidase activities. We identified a strong association between genotype and enzymatic activity since the majority of pulsotypes displayed the same type of enzymatic profile. This study provides comprehensive and potential epidemiological data, which will aid the fish farming activities and prevention method development. [ABSTRACT FROM AUTHOR]

The microbiota of dairy products is composed of starter and non-starter lactic acid bacteria, as well as other bacteria, yeasts and filamentous fungi that form secondary microbiota and play an important role in cheese ripening. The use of combined LAB strains based on compatibility and/or coexistence tests plays an important role in food production and preservation, while combinations of strains that exhibit mutually inhibitory properties must be avoided. For centuries, researchers have focused on the exploration of autochthonous LAB biodiversity from various ecological dairy niches in order to address its role in texture and flavour formation and to select strains for use as starter cultures. Recent advanced technological tools like next-generation sequencing machines have played a significant role in the fast and accurate characterization and isolation of microbial communities from dairy products. However, the characterization and isolation of LAB using culture-independent methods is also a reliable and cost-effective method for studying a bacterial community without prior cultivation. These methods include single-strand conformation polymorphism (SSCP-PCR), denaturing gradient gel electrophoresis (DGGE), thermal gradient gel electrophoresis (TGGE), real-time PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP), length heterogeneity PCR (LH-PCR), automated ribosomal intergenic spacer analysis (ARISA) and fluorescence in situ hybridization (FISH). Therefore the goal of this review is to compare and describe the most recent culture-independent molecular-based methods for the characterization and isolation of LAB in dairy products. [ABSTRACT FROM AUTHOR]

The present article deals with the diffusiophoresis of hydrophobic rigid colloids bearing arbitrary ζ-potential. We derived the generic expression for the diffusiophoretic velocity of such a colloid exposed in an externally applied concentration gradient of the general electrolyte solution. The derived expression takes into account the relaxation effect and is applicable for all values of surface ζ-potential and hydrodynamic slip length at large κa (κ a ≥ ca.50), where κ − 1 is the thickness of the electric double layer and a is the particle radius. We further derived several closed-form expressions for particle velocity derived under various electrostatic and hydrodynamic conditions when the particle is exposed in an applied concentration gradient of binary symmetric (e.g., z : z), asymmetric (1:2, 2:1, 3:1, 1:3), and a mixed electrolyte (mixture of 1:1 and 2:1 electrolytes). The results for diffusiophoretic velocity are further illustrated graphically to indicate the mutual interaction of chemiphoresis, induced electrophoresis due to unequal mobilities of cations and anions of the electrolyte, and the mechanism by which the sufficiently charged particle migrates opposite to the direction of the applied concentration gradient. The impact of hydrophobicity is further discussed. [ABSTRACT FROM AUTHOR]

Bacteria primarily live in structured environments, such as colonies and biofilms, attached to surfaces or growing within soft tissues. They are engaged in local competitive and cooperative interactions impacting our health and well-being, for example, by affecting population-level drug resistance. Our knowledge of bacterial competition and cooperation within soft matrices is incomplete, partly because we lack high-throughput tools to quantitatively study their interactions. Here, we introduce a method to generate a large amount of agarose microbeads that mimic the natural culture conditions experienced by bacteria to co-encapsulate two strains of fluorescence-labeled Escherichia coli. Focusing specifically on low bacterial inoculum (1–100 cells/capsule), we demonstrate a study on the formation of colonies of both strains within these 3D scaffolds and follow their growth kinetics and interaction using fluorescence microscopy in highly replicated experiments. We confirmed that the average final colony size is inversely proportional to the inoculum size in this semi-solid environment as a result of limited available resources. Furthermore, the colony shape and fluorescence intensity per colony are distinctly different in monoculture and co-culture. The experimental observations in mono- and co-culture are compared with predictions from a simple growth model. We suggest that our high throughput and small footprint microbead system is an excellent platform for future investigation of competitive and cooperative interactions in bacterial communities under diverse conditions, including antibiotics stress. [ABSTRACT FROM AUTHOR]

To engage sustainable forest management, understanding the impact of disturbances on the stability of soil microorganisms is important. This study reported the immediate effects of two-level thinning intensities on the soil microbial population, community composition and functions of a plantation forest over two years. Results showed that the thinning of Cryptomeria japonica forest significantly increased viable counts of soil bacteria from 7.7 × 106 to 1.4 × 107 or 1.6 × 107 in the 3rd month and the effect subsided in the 6th month post-thinning. The counts of actinobacteria, cellulolytic, nitrogen-fixing and phosphate-solubilizing bacteria groups maintained stable populations in the forest soils. Denaturing gradient gel electrophoresis profiles indicated that soil bacterial communities significantly differed among 25% thinning, 50% thinning and control treatment from the 12th to 18th month post-thinning, with no significant differences after 22 months. The community level physiological profiles were significantly different between control and thinning treatments in the 12th month post-thinning, the impacts of thinning then subsided by the 22nd month post-thinning as well. Soil bacteria were sensitive to thinning disturbances, but with resilience, their community and function approached to the control status in 2 years. This study demonstrates that the soil microbes of Taiwanese C. japonica forests are very sensitive to thinning disturbances, but recover stability after a relatively short period of time. [ABSTRACT FROM AUTHOR]

These were related to two uncultured microorganisms and belonged to the class I Halobacteria i ( I Archaea), i therefore demonstrating the great effort that still remains to be made to isolate new microorganisms in a pure culture. Culture-independent techniques, such as metagenomic and -omic studies, have been particularly interesting in recent years, providing valuable information regarding the diversity and biotechnological potential of these environments and the microorganisms that inhabit it [[4]]. The authors determinedthe biodiversity both through classical, culture-dependent studies and through culture-independent techniques using sequencing performed by by Illumina MiSeq platform. Hypersaline environments are mainly represented by aquatic systems, such as solar salt ponds or natural salt lakes, as well as by the sediments of these hypersaline aquatic ecosystems and soils with high salt content [[1]]. [Extracted from the article]

The feasibility of microbial enhancing oil recovery (MEOR) by biogas in Qinghai oil field with hypersalinity was studied. Different nutrient packages (molasses, coin milk, and starch) for biogas production were evaluated, respectively. The indigenous microorganisms preferentially use carbon source (molasses) to produce gas, and 0.9% molasses promoted the gas production effectively, the gas/liquid ratio came up to 0.775, the biogases was composed of CO2 (54.37%), N2 (45.03%), and H2 (0.60%), and pressure reached to 0.64 MPa. The effect of nitrate addition on microbial H2S production was also investigated. Addition of 0.2% nitrate led to complete elimination of sulfate-reducing bacteria. Because the microbial community significantly influences the results of the application of MEOR, so the microbial community structure dynamics was also analyzed by denaturing gradient gel electrophoresis (DGGE). Species were confirmed mainly to Halomonas sp. and some uncultured bacteria. In sand pack experiment, the acetate concentration in the experimental group achieved to 15.8 mM, and the residual oil recovery was 7.27% which exhibited a great potential to enhance oil recovery. [ABSTRACT FROM AUTHOR]

Objective: Minimal residual disease (MRD) is considered the greatest prognostic factor in acute lymphoblastic leukemia (ALL). MRD is a valuable tool for anticipating impending relapse and treatment response assessment. The objective of the present study was to investigate whether the detection of IgH gene rearrangement using polymerase chain reaction (PCR)-based GeneScan analysis could be a complementary method to monitor MRD along with the quantitative realtime PCR (qPCR). Materials and Methods: In this cross-sectional study, we valued the MRD levels, based on the GeneScanning analysis (GSA), and then compared the data with quantitative real-time polymerase chain reaction at different time points in peripheral blood (PB) samples of adult B-lineage ALL patients (n=35). The specific polymerase chain reaction (PCR) primers for IGH gene FR-1 and fluorescence-labeled J-primer were used and analyzed by capillary gel electrophoresis on a sequencer. The results of this study were compared with the previously reported MRD results obtained by the IGH rearrangements allele-specific oligonucleotide (ASO) -qPCR methods. Results: The total concordance rate was 86.7%, with a P<0.001. MRD results obtained by GSA and ASO-qPCR methods were concordant in all diagnostic samples and samples on the 14th and 28th days of induction therapy. The results of these 2.5 years’ follow-ups demonstrated a significant correlation between the two techniques (r=0.892, P<0.001). Conclusion: It seems that the PCR-based GeneScan analysis of IGH gene rearrangement detection may be a valuable molecular technique to distinguish monoclonality from polyclonality. And also, it may be a precise tool to detect the residual leukemic DNA in the PB follow-up samples of patients. [ABSTRACT FROM AUTHOR]

Semen Sojae Preparatum is one of the fermentｅｄ products with a unique flavor and delicious taste, applied in the food industry and traditional Chinese medicine over one thousand seven hundred years. It has notable benefits of human health. Nevertheless, knowledge about it is very fragmented and unsystematic, which made less know. To promote a comprehensive understanding, this review summarizes the fermentation procedures, microbiology research, bioactive compounds, and medicinal importance, quality, and safety. Finally, we provide with some perspectives. Hopefully, it will deserve more attention and lay a foundation for utilizing Semen Sojae Preparatum on industrialization. ABBREVIATIONS: SSP, Semen Sojae Preparatum; TCM, Ｔraditional Chinese Ｍedicine; Ch. P, Chinese Pharmacopoeia; PCR-DGGE, Polymerase Chain Reaction-denaturing gradient gel electrophoresis; SOD: Superoxide Dismutase; T2DM: Type 2 Diabetes Mellitus; VEC: vascular endothelial cell; AFT, Aflatoxin; Nrf2: Nuclear factor E2-related factor 2; HO-1: Heme oxygenase 1 [ABSTRACT FROM AUTHOR]

Broad‐range‐response pressure‐sensitive wearable electronics are urgently needed but their preparation remains a challenge. Herein, we report unprecedented bioinspired wearable electronics based on stretchable and superelastic reduced graphene oxide/polyurethane nanocomposite aerogels with gradient porous structures by a sol‐gel/hot pressing/freeze casting/ambient pressure drying strategy. The gradient structure with a hot‐pressed layer promotes strain transfer and resistance variation under high pressures, leading to an ultrabroad detection range of 1 Pa–12.6 MPa, one of the broadest ranges ever reported. They can withstand 10 000 compression cycles under 1 MPa, which can't be achieved by traditional flexible pressure sensors. They can be applied for broad‐range‐response electronic skins and monitoring various physical signals/motions and ultrahigh pressures of automobile tires. Moreover, the gradient aerogels can be used as high‐efficient gradient separators for water purification. [ABSTRACT FROM AUTHOR]