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The article discusses the importance of biological control methods for managing difficult-to-control plant diseases and pests in sustainable agriculture. It highlights research on antimicrobial substance-producing bacteria, endophytic bacteria, and classical biological control methods. The study emphasizes the need for innovative biological control strategies to reduce reliance on chemical pesticides and promote environmentally friendly agricultural practices. The research also addresses safety evaluations of biocontrol bacterial agents and collaborative efforts to control invasive weeds like Japanese knotweed. [Extracted from the article]

This study is on fly ash (FA) concrete admixed with TiO2 nanoparticles (FAT), CaCO3 nanoparticles (FAC), and an equal ratio of TiO2 and CaCO3 nanoparticles (FATC) were exposed to seawater for 365 days in order to find the attachment of macrofoulants on their surface. The pH reduction studies were carried out in order to determine concrete deterioration in seawater, the results showed that FA specimens had more pH reduction than FAT, FAC and FATC. Total viable count, epifluorescence microscopy and denaturing gradient gel electrophoresis (DGGE) analysis confirmed the intensity of bacterial attachment and its diversity on FA, FAT, FAC, and FATC specimens. A systematic and comparative analysis predicted the overall relationship in terms of the dominant bacterial species on the different fly ash concrete specimens. To determine the biodeterioration of the fly ash concrete specimens in seawater, we used thermography experiments to evaluate the regions affected by bacteria on mortar specimens and confirmed that FA and FAC had more degradation and that FAT and FATC were the least degraded. Laser Raman Spectroscopy was interesting to find the white micron-sized particles of sulphur on FAC, FAT, and FATC specimens after 365 days immersed in seawater. We used a confocal laser scanning microscope to estimate the thickness of biofilm growth on FAT (13.91 0.38 mm), FATC (21.64 0.22 mm), FAC (33.56 0.26 mm), and FA (43.36 0.10 mm) specimens. The results showed that FAT and FATC specimens were the superior specimens, with enhanced biofouling and biodeterioration resistance in a seawater environment. Practical Applications: Fly ash is a waste material from thermal power plants and is used as a supplementary cementitious material in the construction industry. However, fly ash concrete has a slow hydration process and early strength problems. To overcome these problems, we used TiO2 and CaCO3 nanoparticles to enhance the properties of fly ash concrete. Nanoparticles have a high surface area and unique functional properties such as maintaining concrete pH, reducing porosity, enhancing pozzolanic activity, and so forth. In this study, we used TiO2 and CaCO3 nanoparticles to improve the strength of fly ash concrete and provide it with antibacterial properties. This study is significant in advancing our knowledge of fly ash concrete modified with nanoparticles and exposed to seawater with respect to its mechanical properties, durability, and antibacterial properties. Addition of nanoparticles upgraded the fly ash concrete towards its practical applications. [ABSTRACT FROM AUTHOR]

Background: Ghee, known as "roghane heiwâni," or "Kermanshahi oil" is a traditional fermented butter-like product highly esteemed for its nutritional value. Ghee is prepared using traditional methods and has substantial potential as a reservoir of probiotic microorganisms. Previous research delved into isolating and identifying lactic acid bacteria (LAB) in Kermanshahi through culture and PCR sequencing. This study seeks to elucidate the microbial profiles and diversity within Kermanshahi using culture, Denaturing Gradient Gel Electrophoresis (DGGE), and sequencing methodologies. Methods: Twenty samples of Kermanshahi oil were meticulously gathered from diverse locales across Kermanshah province. These samples were cultivated under specialized conditions in MRS and M17 environments spanning 24 to 72 h. Following DNA extraction, amplification of the 16SrRNA gene sequences was performed, culminating in sequencing for conclusive identification of the isolates. Furthermore, the DGGE technique was directly employed to separate and identify various species present in the oil samples utilizing bioinformatics software. Results: Sequencing outcomes revealed a diverse array of microorganisms among the isolates, with Lactobacillus constituting 43%, Streptococcus comprising 27.6%, Enterococcus at 4.61%, and yeasts at 7.6%. Other species exhibited lower frequencies, encompassing Rhizobium, Bacillus coagulans, and Staphylococcus hominis. Conclusions: The isolation of a diverse spectrum of probiotic microorganisms underscores their potential utility in the realm of industrial dairy product production. These findings allude to the possibility of integrating these valuable microorganisms, which have historically been associated with traditional products, into the contemporary dairy industry. As consumer interest in probiotic-enriched products surges, the insights gained from this study pave the way for harnessing the benefits of Kermanshahi-derived probiotics. [ABSTRACT FROM AUTHOR]

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]

Abstract Background Ghee, known as “roghane heiwâni,” or “Kermanshahi oil” is a traditional fermented butter-like product highly esteemed for its nutritional value. Ghee is prepared using traditional methods and has substantial potential as a reservoir of probiotic microorganisms. Previous research delved into isolating and identifying lactic acid bacteria (LAB) in Kermanshahi through culture and PCR sequencing. This study seeks to elucidate the microbial profiles and diversity within Kermanshahi using culture, Denaturing Gradient Gel Electrophoresis (DGGE), and sequencing methodologies. Methods Twenty samples of Kermanshahi oil were meticulously gathered from diverse locales across Kermanshah province. These samples were cultivated under specialized conditions in MRS and M17 environments spanning 24 to 72 h. Following DNA extraction, amplification of the 16SrRNA gene sequences was performed, culminating in sequencing for conclusive identification of the isolates. Furthermore, the DGGE technique was directly employed to separate and identify various species present in the oil samples utilizing bioinformatics software. Results Sequencing outcomes revealed a diverse array of microorganisms among the isolates, with Lactobacillus constituting 43%, Streptococcus comprising 27.6%, Enterococcus at 4.61%, and yeasts at 7.6%. Other species exhibited lower frequencies, encompassing Rhizobium, Bacillus coagulans, and Staphylococcus hominis. Conclusions The isolation of a diverse spectrum of probiotic microorganisms underscores their potential utility in the realm of industrial dairy product production. These findings allude to the possibility of integrating these valuable microorganisms, which have historically been associated with traditional products, into the contemporary dairy industry. As consumer interest in probiotic-enriched products surges, the insights gained from this study pave the way for harnessing the benefits of Kermanshahi-derived probiotics.

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]

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.

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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Oral infections can activate local and systemic inflammation. The inflammatory response plays a main role in atherosclerosis. several studies have reported a relation between oral pathogen infection and Atherosclerosis. Recently it was indicated that some oral microbiome has a significant role in triggering atherosclerosis. Denaturing Gradient Gel Electrophoresis (DGGE) is an acceptable assay for identification of uncultivable bacteria. Therefore, we compared the bacterial population diversity in the oral microbiota between atherosclerosis patients and healthy people. Oral microbiota profiling was performed for 139 individuals including 89 patients with CAD and 50 healthy individuals. After DNA extracted from saliva, PCR products were examined and evaluated using DGGE assay. We found that significant relationship between the increased risk of atherosclerosis and the presence of Actinomyces oris, Enterococcus faecalis, Bacterium strain sulresv, Bacterium Culaenoe, NC4, NC7, and NC5 in atherosclerosis patients and healthy individuals. There was also a significant relationship between reducing the risk of atherosclerosis in the presence of NC3 and Entreococcus munotii in atherosclerosis patients and healthy individuals.  In conclusion, presence of some oral microbiota increases the risk of atherosclerosis and the presence of some oral microbiota reduces the risk, so the oral microbiota should be further examined to determine its potential as a biomarker for atherosclerosis.

The Minas artisanal cheese from the Serra da Canastra (MAC-CM) microregion is a traditional product due to its production and ripening process. Artisanal chesses manufactured with raw cow's milk and endogenous dairy starters ("also known as pingo") have distinctive flavors and other sensory characteristics because of the unknown microbiota. The aim of this study was to evaluate the microbiota during 30 days of ripening, the physicochemical changes, and their relation in MACs produced in two different microregions located in the Serra da Canastra microregion through culture-dependent and culture-independent methods. The MACs were collected in the cities of Bambuí (MAC-CMB) and Tapiraí (MAC-CMT) in the Canastra microregion (n = 21). Cheeses uniqueness was demonstrated with the multivariate analysis that joined the microbiota and physicochemical characteristics, mainly to the proteolysis process, in which the MAC-CMT showed deeper proteolysis (DI -T0:14.18; T30: 13.95), while the MAC-CMB reached only a primary level (EI -T0:24.23; T30: 31.10). Abiotic factors were responsible for the differences in microbial diversity between the cheese farms. Different microbial groups: the prokaryotes, like Corynebacterium variabile, Lactococcus lactis, and Staphylococcus saprophyticus; and the eukaryotes, like Kluyveromyces lactis and Diutina catenulata dominated ripening over time. The microbial community and proteolysis were responsible for the predominance of volatile groups, with alcohols predominating in MAC-CMB and free fatty acids/acids and esters in MAC-CMT., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

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., Importance: While 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., Competing Interests: The authors declare no conflict of interest.

NsrR from Streptomyces coelicolor is a bacterial nitric oxide (NO) sensor/nitrosative stress regulator as its primary function, and has been shown to have differential response at low, mid, and high levels of NO. These must correspond to discrete structural changes at the protein-bound [4Fe-4S] cluster in response to stepwise nitrosylation of the cluster. We have investigated the effect of the monohapto carboxylate ligand in the site differentiated [4Fe-4S] cluster cofactor of the protein NsrR on modulating its reactivity to NO with a focus on indentifying mechanistic intermediates. We have prepared a synthetic model [4Fe-4S] cluster complex with tripodal ligand and one single site differentiated site occupied by either thiolate or carboxylate ligand. We report here the mechanistic details of sequential steps of nitrosylation as observed by ESI MS and IR spectroscopy. Parallel non-denaturing mass spectrometry analyses were performed using site-differentiated variants of NsrR with the native aspartic acid, cysteine, or alanine in the position of the forth ligand to the cluster. A mono-nitrosylated synthetic [4Fe-4S] cluster was observed for the first time in a biologically-relevant thiolate-based coordination environment. Combined synthetic and protein data give unprecedented clarity in the modulation of nitrosylation of a [4Fe-4S] cluster. This manuscript describes an investigation of the role played by the unusual carboxylate ligand in the nitrosylation of the [4Fe-4S] cluster of the NO-sensing bacterial protein NsrR. A two-pronged approach, following the reaction of NO with: 1. variants of NsrR from Streptomyces coelicolor varied at the ligand site, and 2. biomimetic synthetic model cluster complexes, showed greater control of the mechanism of nitrosylation, and longer lived intermediates, in the site-differentiated cluster. [Display omitted] • Side-by-side study of nitrosylation of protein- and synthetic cluster model [4Fe-4S] species • Understanding of mechanistic control in NO-sensor NsrR from Streptomyces coelicolor • Effect of cluster coordination sphere on nitrosylation mechanism / mechanistic control • Observation of a thiolate-bound mononitrosylated synthetic [4Fe-4S] cluster as key intermediate [ABSTRACT FROM AUTHOR]

[Display omitted] • The controlled domain gels promote bone regeneration and suppress tumor recurrence. • The gels with a large wide stiffness gradient differentially regulate migration of MSCs and tumor cell. • Domian design allows for selectively inducing tumor cell apoptosis and promoting osteogenic differentiation. • The DAPK-mediated signaling cascades are involved in the selected apoptosis of tumor cell. The reconstruction of bone defects following bone tumor resection pose significant challenges, including high risks for tumor recurrence. To address these challenges, we designed controlled-domain gels that possessed exceptional anti-tumorigenic effectiveness and osteogenic activity. This was achieved through the selection of an amino-acid-based low-molecular-weight gels (LMWGs) with superior biocompatibility and antitumor efficacy, and further construction of three-domain structure with a large-range stiffness gradient, through the assembly/disassembly of LMWGs inside a stable methacrylated alginate (AlgMA) network using photopolymerization. Such layered design not only constructed a top anti-tumorigenic domain at 0.6 kPa and a bottom osteogenic domain at 500 kPa, allowing for selectively inducing tumor cell apoptosis and promoting osteogenic differentiation of mesenchymal stem cells (MSCs), but also generated a gradient selectively confining the migration of tumor cells along soft-to-hard direction, without affecting the recruiting of MSCs toward the injury sites. In particular, the critical involvement of the DAPK-mediated signaling cascades might lead to the selected apoptosis of tumor cells on LMWG domain. The in-vivo results further suggested that multi-domain gel effectively inhibited tumor growth and displayed excellent bone-forming activity. Overall, such strategies could advance our fundamental understanding of the bone tumor postoperative treatment, in addition to offering new therapeutic opportunities. [ABSTRACT FROM AUTHOR]

To optimize real-time PCR assays for diagnosis of Bacterial Vaginosis (BV) and determine cut-off loads by ROC analysis for Gardnerella vaginalis, Atopobium vaginae and Lactobacillus spp. as compared to Nugent scoring (Gold standard) in clinical samples. Out of 125 women, 34 were positive, 26 intermediate and 65 negative for BV by Nugent scoring. All three real-time PCR assays were found to be highly sensitive & specific and AUC suggested excellent diagnostic accuracy. An optimal cut-off was >9.45 × 103 copies/ ml, >3.34 × 103 copies/ ml & ≤ 18.63 × 103 copies/ ml for G. vaginalis, A. vaginae and Lactobacillus spp. respectively, in BV positives. Gram staining and qPCR were discordant only in patients with intermediate scores (n = 26) where qPCR identified 15 (57.69%) as positive and 11 (42.3%) as negative. PCR-based molecular BV diagnosis is more accurate and can be used for deciphering intermediate Nugent scores. [ABSTRACT FROM AUTHOR]

Background: The accurate and expeditious detection of SARS-CoV-2 mutations is critical for monitoring viral evolution, assessing its impact on transmission, virulence, and vaccine efficacy, and formulating public health interventions. In this study, a detection system utilizing micro temperature gradient gel electrophoresis (μTGGE) was developed for the identification of the D614 and G614 variants of the SARS-CoV-2 spike protein., Methods: The in vitro synthesized D614 and G614 gene fragments of the SARS-CoV-2 spike protein were amplified via polymerase chain reaction and subjected to μTGGE analysis., Results: The migration patterns exhibited by the D614 and G614 variants on the polyacrylamide gel were distinctly dissimilar and readily discernible by μTGGE. In particular, the mid-melting pattern of D614 was shorter than that of G614., Conclusions: Our results demonstrate the capability of μTGGE for the rapid, precise, and cost-effective detection of SARS-CoV-2 spike protein D614 and G614 variants without the need for sequencing. Therefore, this approach holds considerable potential for use in point-of-care mutation assays for SARS-CoV-2 and other pathogens., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

DGGE (denaturing gradient gel electrophoresis) is a nucleic acid separation technique applied to the evaluation of microbial biodiversity. This technique is quite rapid and cheap compared to other types of analysis. Here we describe the comparison of nematode communities inhabiting different ecosystems. After an ecologically representative sampling collection and the nematode extraction from soil, nematodes are centrifuged in Eppendorf tubes to facilitate DNA extraction. DNA from the whole community of each type of soil is extracted, amplified with primers for 18 S rDNA and used in DGGE analysis. The profiles of DGGE can be analyzed with appropriate software, and biodiversity indices can be estimated., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)