CONCEPT PAPER | doi:10.20944/preprints202107.0546.v1
Subject: Biology, Anatomy & Morphology Keywords: Bacterial nomenclature; taxonomy; microbial genomics
Online: 23 July 2021 (14:22:59 CEST)
The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names, while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice, while minimising difficulties. Adoption of linguistic pragmatism, obeying the rules while treating recommendations as merely optional will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed, while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.
Subject: Life Sciences, Microbiology Keywords: Rhodococcus equi; Rhodococcus hoagii; bacterial nomenclature; bacterial taxonomy; bacterial systematics
Online: 2 February 2020 (06:56:32 CET)
A recent taxonomic study confirmed the synonymy of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and Corynebacterium hoagii (Morse 1912) Eberson 1918. As a result, both R. equi and C. hoagii were reclassified to Rhodococcus hoagii comb. nov. in application of the principle of priority of the Prokaryotic Code. Being R. equi a well-known animal and zoonotic human pathogen, and the name solidly established in the veterinary and medical literature, we and others argued that the nomenclatural change may cause error and confusion and be potentially perilous. We have now additionally found that the nomenclatural type of the basonym C. hoagii, ATCC 7005T, does not correspond with the original description of C. hoagii in the early literature. Its inclusion as the C. hoagii type on the Approved Lists 1980 results in a change in the characters of the taxon and in C. hoagii clearly designating two different bacteria. Moreover, ATCC 7005, the only strain in circulation under the name C. hoagii, does not have a well documented history; it is unclear why it was deposited as C. hoagii and a possible mixup with a Corynebacterium (Rhodococcus) equi isolate is a reasonable assumption. We therefore request the rejection of Rhodococcus hoagii as a nomen ambiguum, nomen dubium and nomen perplexum in addition to nomen periculosum, and conservation of the name Rhodococcus equi, according to Rules 56ab of the Code.
CASE REPORT | doi:10.20944/preprints201912.0170.v1
Subject: Medicine & Pharmacology, Dermatology Keywords: sphingomonas; gram-negative bacterial infection; skin disease; bacterial
Online: 12 December 2019 (10:01:35 CET)
Sphingomonas paucimobilis is an opportunist pathogen bacillus gram-negative aerobic with a rare occurrence. We present a case in an immunocompetent man successfully treated by surgical debridement, purulent drainage and with an associated course of antibiotics. A large necrotic infection, approximately 5 cm x 3 cm, in a 74-year-old man was identified. Empirical antibiotic therapy with ciprofloxacin 400mg EV 12/12 hours, associated with clindamycin 600mg EV 6/6 hours and pain control was done through dipyrone 1gr, tramadol 400 mg. Deep venous thrombosis was prevented through the prescription of enoxaparin 40mg subcutaneous once a day during hospitalization. The case was well illustrated with pictures throughout treatment. Complete healing was achieved after 90 days. Herein, we present a case of cutaneous contamination. The presented case is the third cutaneous contamination case reported in the literature and the first reported case in the Amazonia region in Brazil.
REVIEW | doi:10.20944/preprints202103.0358.v1
Subject: Life Sciences, Biochemistry Keywords: Nanoparticle; Bacterial; Biotechnology; Biomedical; Application
Online: 13 March 2021 (00:17:05 CET)
On estimation scales ranging from 0.1 nm to 100 nm, the nanoscale is part of the capacitance components of the physical-synthetic and natural environment. Dimensionality, morphology, structure, uniformity, and agglomeration are all used to classify nanoparticles. Its functionality and effect on the environment and species are influenced by its shape and morphology. The priority research is to determine the effects of nanoparticles on any biological entity that is necessary when designing nanotechnology-based biotechnological and biomedical products. Bacteria have a remarkable ability to reduce metal ions, making them one of the most promising candidates for nanoparticle biosynthesis. Nanoparticles have been researched in the biomedical field for antimicrobial, biosensor, diagnostic imaging, and drug delivery applications. These natural technologies appear to be capable of producing stable nanoparticles with well-defined dimensions, morphologies, and compositions by optimizing reaction conditions and selecting the best bacteria. This work includes a list of the most commonly used microorganisms and associated Nanoparticles, as well as a discussion of current biotechnology and biomedical developments.
Subject: Life Sciences, Microbiology Keywords: actin cytoskeleton; chlamydia; bacterial pathogenesis
Online: 9 December 2019 (03:53:26 CET)
The actin cytoskeleton is crucially important to maintenance of cellular structure, cell motility and endocytosis. Accordingly, bacterial pathogens often co-opt the actin-restructuring machinery of host cells to access or create a favorable environment for their own replication. The obligate intracellular organism Chlamydia trachomatis and related species exemplify this dynamic: by inducing actin polymerization at the site of pathogen-host attachment, Chlamydiae induce their own uptake by the typically non-phagocytic epithelium they infect. The interaction of chlamydial adhesins with host surface receptors has been implicated in this effect, as has the activity of the chlamydial effector TarP (translocated actin recruitment protein). Following invasion, C. trachomatis dynamically assembles and maintains an actin-rich cage around the pathogen’s membrane-bound replicative niche, the chlamydial inclusion. Through further induction of actin polymerization and modulation of the actin-crosslinking protein myosin II, C. trachomatis promotes egress from the host via extrusion of the inclusion. In this review, we present the experimental findings that inform our understanding of actin-dependent chlamydial pathogenesis, discuss lingering questions, and identify potential avenues of future study.
ARTICLE | doi:10.20944/preprints201810.0698.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: optic biosensor; fluorescence; bacterial detection
Online: 30 October 2018 (03:44:11 CET)
The importance of detecting bacteria in various food products is ever-increasing, due to recent food trends that lend themselves to food contamination. Additionally, the detection of probiotics in food products is of increasing importance to consumers, who realize the benefits of probiotics on one’s diet. Existing technologies for detection of bacteria in food are accurate, but most are slow, increasingly costly and unsuitable for applications outside of research laboratories. Optic approaches have recently emerged as an alternative, allowing rapid detection of bacterial presence. This study employs a portable kinetics fluorometer, fabricated in-house, in conjunction with NADH sensitive fluorescence reporter for analysis of various food products. The presence of bacteria is detected in 5 minutes. Both pathogenic and probiotic bacteria were detected in food products, such as raw chicken and beef, spoiled lettuce and contaminated water, yogurt, and kombucha tea. The cellular activity of two probiotic pills was also verified. All samples displayed varying levels of bacterial activity. The study indicates the viability of biosensors being used as an alternate method to detect bacteria in food products – and the viability of a fluorescence-based biosensor to detect viable bacteria. The approach is suitable for both laboratory and field determinations.
ARTICLE | doi:10.20944/preprints202209.0131.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: bacterial vaginosis; recurrent vaginitis; biofilm; polycarbophil
Online: 9 September 2022 (07:33:38 CEST)
Recurrent bacterial vaginosis (RBV) after antibiotic treatments has a relapse rate of 35% within 3 months and 60% within 12 months. Products containing polycarbophil (PLGG), that inhibits bacterial growth and mucoadhesive property, can impair biofilm formation. Here are shown the results of the POLARIS (Polybactum® to assess Recurrent Bacterial Vaginosis) study. The first phase was an interventional, open-label, non-controlled, and multicentre trial enrolling 56 women in Italy and Romania. The second phase was an observational 10-month follow-up without treatment conducted only in Romania. After 3 cycles with PLGG, only 8 BV recurrences out of 54 evaluable patients were identified (rate 14.81%) and for 26 out of 39 patients (66.67%) was evidenced positive effect on Lactobacilli in the vaginal secretions. In the follow-up 35 patients were observed after PLGG stopping treatment; 1 RBV (2.86%) at the 4th month and an additional 6 cases (17.14%) were evidenced at the end of the follow-up period. Therefore, no recurrence was evidenced in 12 subjects (34.28%) at 10th ± 2 months after the end of the PLGGtreatment. The use of PLGG vaginal ovules in the treatment of BV reduces the rate of relapses and improves the microbiological parameters (positive effect on Lactobacilli in 66.7 % of cases).
REVIEW | doi:10.20944/preprints202204.0309.v1
Subject: Life Sciences, Microbiology Keywords: bacteriophages; biocontrol; food production; bacterial resistance
Online: 29 April 2022 (15:49:21 CEST)
Bacteriophages have been recognized as potential biocontrol agents in the food industry. Bacteriophages have been proposed for a variety of applications within this industry including bio preservation, pathogen detection, and as an alternative treatment method to antibiotics in animal health. The potential applications of bacteriophages are widespread throughout the entire food production process and serve to enhance food quality, prevent foodborne illnesses, and enhance the efficiency of production. The ability of bacteriophages to lyse bacterial targets with high specificity and pose no threat to mammalian cells or natural microbiota is unique and relevant in terms of suitability for food safety. This review will outline potential and current applications of bacteriophages and their respective impacts on the field.
ARTICLE | doi:10.20944/preprints202111.0031.v1
Subject: Earth Sciences, Environmental Sciences Keywords: aquaponics; metabarcoding; bacterial communities; carbohydrases; phytases
Online: 2 November 2021 (10:12:35 CET)
Aquaponics are efficient systems that associate aquatic organisms’ production and plants by recirculating water and nutrients between aquaculture and hydroponic tanks. In this study, we have characterised the bacterial communities in the fresh water aquaponics system that can mineralise polysaccharides and phytate by producing carbohydrate degrading enzymes and phytases, by 16S rRNA gene sequencing and in vitro culture techniques. Around 20% of the operational taxonomic units (OTUs) identified were previously reported to carry fibre-degrading enzymes putative genes, namely β-glucanase (1%), xylanase (5%) or cellulases (17%). Ten % of the OTUs were previously reported to carry putative genes of phytases with different catalytic mechanisms, namely β-propeller (6%), histidine acid phytases (3%) and protein tyrosine phytase (<1%). Thirty-eight morphologically different bacteria were isolated from biofilms accumulated in fish and plant compartments, and identified to belong to the Bacilli class. Among these, seven could produce xylanase, 8 produced β-glucanase, 14 produced cellulase, and 11 isolates could secrete amylases. In addition, Staphylococcus sp. and Rossellomorea sp. could produce consistent extracellular phytate-degrading activity. The PCR amplification of β-propeller genes both in environmental samples and in the isolates obtained showed that this is the most ecologically relevant phytase type in the aquaponics systems used. In summary, the aquaponics system is abundant with bacteria carrying enzymes responsible for plant-nutrient mineralisation.
ARTICLE | doi:10.20944/preprints202106.0639.v1
Subject: Life Sciences, Biochemistry Keywords: Microscopy; Bacterial cell biology; Nanofabrication; Microfluidics
Online: 28 June 2021 (10:38:11 CEST)
Light microscopy is indispensable for analysis of bacterial spatial organization. However, imaging in bacteria is difficult due to their small sizes and the fact that most species are non-spherical, meaning they typically lie horizontally on a microscope coverslip. This is especially problematic when considering that many essential bacterial processes—such as cell division—occur along the short axes of these cells, and so are viewed side-on by standard microscopy. We recently developed a pair of methods to overcome this problem by forcing cells to stand vertically during imaging, named VerCINI (Vertical Cell Imaging by Nanostructured Immobilisation) and µVerCINI (Microfluidic VerCINI). The concept behind both methods is that cells are imaged while confined vertically inside cell traps made from a nanofabricated mould. By doing so, the short axes of the cells are rotated parallel to the microscope imaging plane and are imaged with high resolution. μVerCINI combines the vertical cell confinement with microfluidics so that vertical imaging can be done during fluid exchange, such as during antibiotic perturbations. Here, we provide a practical guide to implementing both VerCINI and µVerCINI, with detailed protocols and experience-based tips so that interested researchers can easily use one or both imaging methods to complement their current approaches.
COMMUNICATION | doi:10.20944/preprints202009.0134.v1
Subject: Materials Science, Biomaterials Keywords: Bacterial cellulose; Nisin; Antimicrobial activity; Stability
Online: 5 September 2020 (08:52:11 CEST)
Nisin is a 3.4 kDa antimicrobial peptide, produced by Lactococcus lactis (ATCC 11454). This bacteriocin can inhibit spores gemination and gram-positive bacteria development and has gained visibility in therapeutic use. The bacterial cellulose (CB) has been considered an ideal material and with high quality applied in food and medical-pharmaceutical inputs. Because of all this benefits, it is important to know the system proceeding of CB with nisin. Therefore, it was realize nisin release profile analysis of CBs was performed; analysis of the minimum inhibitory concentration (MIC) of nisin against Escherichia coli ATCC 25922, Pseudomonas aeuroginosa ATCC 9721 and Staphylococus aureus ATCC 10390; antimicrobial stability test, for 100 days at different temperatures of 4º, 25º and 37 ° C against microorganisms: S. aureus e L. sakei. The results show that nisin is released by the CB in 4 hours of contact with medium and the MIC of nisin is 78 µg/mL for S. aureus, doesn’t have gram-negative inhibition. It had stability until 100 days against L. sakei and 60 days for S. aureus. The system proved to be efficient and CB potentiated the antimicrobial action of nisin, acting as a selective barrier for other compounds present in the standard solution, serving as protection of the peptide at different temperatures. The CB loading system can be an ideal antimicrobial stability system for nisin.
REVIEW | doi:10.20944/preprints202009.0405.v1
Subject: Life Sciences, Microbiology Keywords: horizontal gene transfer; bacterial conjugation; phenotypic conversion; drug-resistance dissemination; bacterial biofilms; mobile plasmids; F plasmid
Online: 17 September 2020 (12:00:29 CEST)
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism where the DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic life-style, virulence, biofilm formation, or resistance to heavy metals and, most importantly, resistance to antibiotics. These properties make of conjugation a fundamentally important process at the center of extensive study. Here, we review the key steps of conjugation by following the life-cycle of the F plasmid during transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms.
REVIEW | doi:10.20944/preprints202203.0042.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: antimicrobial resistance; bacterial vaginosis; refractory; recurrent; treatment
Online: 2 March 2022 (10:11:03 CET)
Bacterial vaginosis (BV), the most common cause of vaginal discharge, is characterized by a shift in the vaginal microbiota from lactobacillus dominance to a diverse array of facultative and strict anaerobic bacteria which form a multi-species biofilm on vaginal epithelial cells. The rate of recurrence after therapy is high, often >60%. While the BV biofilm itself likely contributes to recurrent and/or refractory disease after treatment by reducing antimicrobial penetration, antimicrobial resistance in BV-associated bacteria including those, both within the biofilm and the vaginal canal, may be the result of independent, unrelated bacterial properties which are discussed in this paper. Our current recommendations for the treatment of refractory and recurrent BV are also provided.
ARTICLE | doi:10.20944/preprints202110.0140.v1
Subject: Chemistry, Applied Chemistry Keywords: performance; biodegradation; bacterial consortium; marine sponge; PAHs
Online: 8 October 2021 (12:09:30 CEST)
Every petroleum processing industry produces sewage sludge containing several types of poly-cyclic aromatic hydrocarbon (PAHs) components. The degradation of PAH components by physical, biological and chemical methods is not efficient. The use of marine sponge symbiont bacteria is considered an alternative method in the degradation and reduction of PAHs com-pared to the previous method. This study aims to explore the potential and performance of a consortium of sponge symbiont bacteria in degrading anthracene and pyrene. There are three types of bacteria (Bacillus pumilus strain GLB197, Pseudomonas stutzeri strain SLG510A3-8, Acineto-bacter calcoaceticus strain SLCDA 976) were mixed to form a consortium. The interaction between the bacterial consortium suspension and PAH components was measured at 5-day intervals for 25 days. The biodegradation performance of bacteria on PAHs samples was determined based on five biodegradation parameters. The analysis results showed a decrease in the concentration of anthracene (21.89%) and pyrene (7.71%), equivalent to a ratio of 3: 1. The data was followed by a decrease in the abundance of anthracene (60.30%) and pyrene (27.52%), an equivalent ratio of 2: 1. The level of degradation of the pyrene component is lower than that of the anthracene compo-nent, presumably due to the higher toxicity of pyrene and the more stable molecular structure, making it difficult for bacterial cells to destroy it. The biodegradation products are organic compounds of alcohol, aldehyde, carboxylic acids and a small proportion of aromatic hydrocarbon components. Keywords: performance; biodegradation; bacterial consortium; marine sponge; PAHs
REVIEW | doi:10.20944/preprints202103.0595.v1
Subject: Biology, Anatomy & Morphology Keywords: germination, bacterial cell wall, sporulation, germination, morphology
Online: 24 March 2021 (14:56:55 CET)
A fundamental question in biology is how cell shapes are genetically encoded and enzymatically generated. Prevalent shapes among walled bacteria include spheres and rods. These shapes are chiefly determined by the peptidoglycan (PG) cell wall. Bacterial division results in two daughter cells, whose shapes are predetermined by the mother. This makes it difficult to explore the origin of cell shapes in healthy bacteria. In this review, we argue that the Gram-negative bacterium Myxococcus xanthus is an ideal model for understanding PG assembly and bacterial morphogenesis because it forms rods and spheres at different life stages. Rod-shaped vegetative cells of M. xanthus can thoroughly degrade their PG and form spherical spores. As these spores germinate, cells rebuild their PG and reestablish rod shape without preexisting templates. Such a unique sphere-to-rod transition provides a rare opportunity to visualize de novo PG assembly and rod-like morphogenesis in a well-established model organism.
REVIEW | doi:10.20944/preprints202209.0048.v1
Subject: Chemistry, Chemical Engineering Keywords: removal; PAHs; heavy metals; marine sponges; bacterial consortium
Online: 5 September 2022 (07:43:34 CEST)
Toxic materials in waste generally contain several components of global trending pollutant categories, especially PAHs and heavy metals. Bioremediation technology for managing waste utilizing microorganisms (bacteria) has not been fully capable of breaking down these toxic materials simple and environmentally friendly chemical products. This study examines the potential application of a marine sponge symbiont consortium with high performance and efficiency in removing PAHs and heavy metal contaminants. The method is carried out through a review of some related research articles by the author and published by other re-searchers. The study results concluded that bioremediation technology development GTP, can be carried out to improve remediation efficiency. Several types of marine sponge symbiont bacteria, hydrocarbonoclastic (R-1), metalloclastic (R-2), and metallohydro-carbonoclastic (R-3), have the potential to be applied to improve the removal performance of waste. Bacterial screening be done to find and categorize R-1 bacteria, R-2; R-3 to remediate GTP. Develop of R-1 bacteria, R-2; R-3 forms of the mobile formulation are needed in the future. A crystalline consortium of bacteria preparations is needed so that they can be quickly mobilized to locations exposed to GTP. Marine sponge symbiont bacteria be traced mainly to marine sponges whose body surface is covered with mucus.
REVIEW | doi:10.20944/preprints202103.0424.v1
Subject: Medicine & Pharmacology, Allergology Keywords: vaginal probiotics; reproductive dysbiosis; bacterial vaginosis; VVC; IVF
Online: 16 March 2021 (12:28:32 CET)
The use of probiotics in reproductive-related dysbiosis is an area of continuous progress due to the growing interest from clinicians and patients suffering recurrent reproductive microbiota disorders. An imbalance in the natural colonization sites related to reproductive health: vaginal, cervicovaginal, endometrial and also pregnancy-related altered microbiota could play decisive role in reproductive outcomes. Oral and vaginal administrations are in continuous discussion regarding the clinical effect pursued, but probiotics as oral supplement therapy is the route administration better studied. To complement and summarise with qualitative and quantitative information of vaginal probiotics clinical studies, the main objective of this work was to retrieve the standardised protocols commonly used and their microbiota modulation capacities. The studies selected were related to treat bacterial vaginosis (BV) as the most commonly disorder, few studies on vulvovaginal candidiasis (VVC) and also administration to stabilise microbiota before in vitro fertilisation (IVF). Probiotic doses administered were similar to oral probiotics protocols, ranging from ≥ 107 CFU/day to 2.5 x 1010 CFU/day, and variable regarding posology duration from 1 day to 12 weeks, being 1 week commonly applied. Moderate modulation was achieved regarding the relative abundance decrease of abnormal microbiota, coinciding with parallel increase in Lactobacillus species.
ARTICLE | doi:10.20944/preprints202010.0573.v1
Subject: Medicine & Pharmacology, Allergology Keywords: implant; bacterial cellulose; patch; myocardial infarction; cell; delivery
Online: 28 October 2020 (08:59:09 CET)
Biologic scaffolds have become an attractive approach for repairing the infarcted myocardium and have been shown to facilitate constructive remodeling in injured tissues. This study aimed to investigate the possible utilization of bacterial cellulose membrane patch containing cocultured cells to limit the myocardium's post-infarction pathology. Myocardial infarction was induced by ligating the left anterior descending coronary artery in 45 Wistar rats, and patches with or without cells were attached to the hearts. After one week, the animals underwent echocardiography for assessing ejection fraction and left ventricular end-diastolic and end-systolic volumes. Following the patch formation, cocultured cells retained viability of >90% over 14 days in culture. The patch was applied to the myocardial surface of the infarcted area after staying 14 days in culture. Interestingly, the bacterial cellulose membrane without cellular treatment showed higher preservation of cardiac dimensions; however, we did not observe improvement in the left ventricular ejection fraction of this group compared to coculture treated membranes. Our results demonstrated an important role for bacterial cellulose in supporting cells known to produce cardioprotective soluble factors and may thus provide effective future therapeutic outcomes for patients suffering from ischemic heart disease.
ARTICLE | doi:10.20944/preprints202001.0069.v1
Subject: Biology, Ecology Keywords: DEHP; biochemical pathways; immobilization; MBR; bacterial community dynamics
Online: 9 January 2020 (05:00:48 CET)
A bacterial strain that could effectively degrade DEHP was isolated from the activated sludge and identified as Bacillus sp. by DNA sequencing. The biochemical degradation pathway of DEHP was further analyzed by GC-MS, and the results showed that DEHP was first decomposed into phthalates (DBP). Diuretic sylycol (DEP) was then generated, and phthalates (PA) were generated by a continuous de-ehelateization reaction. Phthalic acid (PA) was oxidized, dehydrogenated, and decarboxylated into protocatechins. Protocatechins enter the TCA cycle through orthotopic ring opening. To enhance DEHP degradation, sodium alginate and calcium chloride were used as embedding and cross-linking materials, and the strain was immobilized. The immobilization conditions were optimized via an orthogonal experiment, and the results showed that the optimal immobilization conditions were SA mass fraction of 4%, CaCl2 mass fraction of 5%, ratio of bacteria to SA of 1:1, and the crosslinking time of 6 hours. The immobilized bacteria agent was further applied to MBR systems. The results showed that the removal rate of DEHP (5mg/L) in the system by immobilized bacteria was 91.9%, which is significantly higher than that of free bacteria. The 3, 4-dioxygenase gene and microbial community dynamics were analyzed by q-PCR and Illumina Miseq sequencing. The q-PCR results showed that the number of copies of 3, 4-dioxygenase gene in the immobilized system was significantly higher than that of free bacteria. Illumina Miseq sequencing results showed that Micromonospora, Rhodococcus, Bacteroides and Pseudomonas were the dominant generas in the MBR system. The analysis of bacterial community structure indicated that immobilization technology had a positive impact on the system stability. The results implied that this immobilized technique had potential applications in DEHP wastewater treatment.
REVIEW | doi:10.20944/preprints201708.0093.v1
Subject: Life Sciences, Microbiology Keywords: bacterial pathogens; host-pathogen interaction; infection biology; omics
Online: 27 August 2017 (11:18:27 CEST)
By providing useful tools to study host-pathogen interactions, next-generation omics has recently enabled the study of gene expression changes in both pathogen and infected host simultaneously. However, since great discriminative power is required to study pathogen and host simultaneously throughout the infection process, the depth of quantitative gene expression profiling has proven to be unsatisfactory when focusing on bacterial pathogens, thus preferentially requiring specific strategies or the development of novel methodologies based on complementary omics approaches. In this review, we focus on the difficulties encountered when making use of omics approaches to study bacterial pathogenesis. Besides, we review different omics strategies (i.e. transcriptomics, proteomics and secretomics) and their applications for studying interactions of pathogens with their host.
ARTICLE | doi:10.20944/preprints202209.0143.v1
Subject: Life Sciences, Microbiology Keywords: Salmonella; novel antibacterial agents; cannabidiol; co-therapy; bacterial genetics
Online: 12 September 2022 (09:55:22 CEST)
New generation antibiotics are needed to combat the development of resistance to antimicrobials. One of the most promising new classes of antibiotics is cannabidiol (CBD). It is a non-toxic and low-resistance chemical that can be used to treat bacterial infections. The antibacterial activity of Cannabis sativa L. byproducts, specifically CBD, has been of growing interest in the field of novel therapeutics. As research continues to define and characterize the antibacterial activity that CBD possesses against a wide variety of bacterial species it is important to examine potential interaction between CBD and common therapeutics such as broad-spectrum antibiotics. Here, we show that CBD-antibiotic co-therapy can effectively fight S. typhimurium via membrane integrity disruption. This research serves to examine the potential synergy between CBD and three broad-spectrum antibiotics for potential antibiotic-CBD co-therapy. In this study, we reveal that Salmonella typhimurium (S. typhimurium) growth is inhibited at very low dosages of CBD-antibiotic. This interesting finding demonstrates that CBD and CBD-antibiotic co-therapies are viable novel alternatives to combating Salmonella typhimurium.
ARTICLE | doi:10.20944/preprints202208.0191.v1
Subject: Life Sciences, Molecular Biology Keywords: bacterial genomics; de novo assembly; Oxford Nanopore Technologies; Snakemake
Online: 10 August 2022 (04:37:01 CEST)
With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run all these programs, I developed two workflows for the workflow management system Snakemake for bacterial genome assembly and evaluation of assemblies, which provide end users with an easy-to-run method for both tasks. The workflows are available as open source software under the MIT license at https://github.com/pmenzel/ont-assembly-snake and https://github.com/pmenzel/score-assemblies.
ARTICLE | doi:10.20944/preprints202112.0127.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: plant pathogenic bacterium; phage; bacterial wilt; biological control; lyophilization
Online: 8 December 2021 (14:12:11 CET)
Ralstonia solanacearum is a pathogen that causes bacterial wilt producing severe damage in staple solanaceous crops. Traditional control has low efficacy and/or environmental impact. Recently, the bases of a new biotechnological method by lytic bacteriophages vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 with specific activity against R. solanacearum were established. However, some aspects remain unknown, such as the survival and maintenance of the lytic activity after submission to a preservation method as the lyophilization. To this end, viability and stability of lyophilized vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 and their capacity for bacterial wilt biocontrol have been determined against one pathogenic Spanish reference strain of R. solanacearum in susceptible tomato plants in different conditions and making use of various cryoprotectants. The assays carried out have shown satisfactory results with respect to the viability and stability of the bacteriophages after the lyophilization process, maintaining high titres throughout the experimental period, also with respect to the capacity of the bacteriophages for the biological control of bacterial wilt, controlling this disease in more than 50% of the plants. The results offer good prospects for the use of lyophilization as a conservation method for the lytic bacteriophages of R. solanacearum in view of their commercialization as biocontrol agents.
ARTICLE | doi:10.20944/preprints202111.0348.v1
Online: 19 November 2021 (12:23:16 CET)
Antibiotic-sparing treatments are required to prevent the further emergence of anti-microbial resistance in Neisseria gonorrhoeae. Commensal Neisseria species have previously been found to inhibit the growth of pathogenic Neisseria species. For example, a previous study found that 3 out of 5 historical isolates of Neisseria mucosa could inhibit the growth of N. gonorrhoeae. In this study, we used agar overlay assays to assess if 24 circulating and historical isolates of Neisseria mucosa could inhibit the growth of 28 circulating and historical isolates of N. gonorrhoeae. Although pitting around each colony of N. mucosa created an optical illusion of decreased growth of N. gonorrhoeae, we found no evidence of inhibition (n=24). In contrast, positive controls of Streptococcus pneumoniae and Escherichia coli demonstrated a strong inhibitory effect against the growth of N. gonorrhoeae.
REVIEW | doi:10.20944/preprints202101.0517.v1
Subject: Life Sciences, Biochemistry Keywords: Gram-negative bacterial; Metabolite transporter; pathways; metabolic engineering approaches
Online: 25 January 2021 (15:49:13 CET)
Metabolite transport across cellular membranes is a key feature of living organisms. Specialized proteins or protein complexes mediate such transport processes and are accessible to genetic engineering approaches. This special issue will reflect on the different transport between cellular compartments. It will provide an overview about different transporter classes and metabolic engineering approaches in different organisms ranging from Bacteria to Eukarya. The transport mechanisms energetics of these compounds were thought little of, and most consideration was given to the designing of metabolic pathways. Gram-negative microbes discharge a wide scope of proteins whose capacities incorporate biogenesis of organelles, for example, pilli and flagella, supplement securing, destructiveness, and efflux of medications and different poisons. Six particular emission frameworks have been appeared to intervene protein send out through the inward and external layers of Gram-negative microbes. These pathways are exceptionally monitored all through the Gram-negative bacterial species. In Gram-positive microscopic organisms, discharged proteins are usually moved across the single layer by the Sec pathway or the two-arginine (Tat) pathway. Recently efforts focused on transporter and metabolite engineering, visualize the improvement and enhancement of microbial cell to pass such metabolites these metabolite carrier proteins are inserted into the inner membrane of mitochondria across the inner membrane, specialized carrier proteins are necessary that mediate the transport into and out of the mitochondrial matrix. Two main strategies for metabolic engineering in plants: the introduction of genes encoding new enzymes and the use of TFs controlling specialized metabolic pathways
ARTICLE | doi:10.20944/preprints202007.0092.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Bacterial resistance; Animal venom; Purification; Antibacterial and antibiofilm activity
Online: 6 July 2020 (04:00:43 CEST)
Introduction: Bacterial resistance is a worldwide public health problem, requiring new therapeutic options. An alternative approach to this problem is the use of animal toxins, such as phospholipases (PLA2) isolated from snake venom, which have important biological activities. Bothrops erythromelas is one of the snake species in the Northeast of Brazil that attracts great medical-scientific interest. Here we aimed to purify and characterize a PLA2 from B. erythromelas, searching for heterologous activities against bacterial biofilm. Methods: Venom extraction and quantification were followed by RP-HPLC in C18 column, MALDI-ToF mass spectrometry and sequencing by Edman degradation. All experiments were monitored by specific activity using 4-nitro-3 (octanoyloxy) benzoic acid (4N3OBA) substrate. In addition, hemolytic tests and anti-bacterial tests including action against Escherichia coli, Staphylococcus aureus and Acinetobacter baumannii, were carried out. Moreover, tests of antibiofilm action against A. baumannii were also performed. Results: PLA2, after one purification step, presented 31 N-terminal amino acid residues, and molecular weight of 13656.4 Da with enzymatic activity confirmed in 0.06 µM concentration. Antibacterial activity against S. aureus (IC50 = 30.2 µM) and antibiofilm activity against A. baumannii (IC50 = 1.1 µM) were observed. Conclusions: This is the first time that PLA2 purified from B. erythromelas venom has appeared as an alternative candidate in studies of new antibacterial medicines.
ARTICLE | doi:10.20944/preprints201804.0349.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: bacterial infections; sensitivity; specificity; immature granulocytes; Latvia; child; sepsis
Online: 27 April 2018 (06:09:47 CEST)
Background: Detection of small proportion of serious bacterial infections (SBI) with potentially life threating course in a large group of children with fever admitted to emergency department (ED) is still complicated. Measurement of immature granulocytes (IG) percentage may be used as a marker of bacterial infections. The aim of the study was to evaluate whether the IG percentage is a useful additional predictive marker of SBI. Methods: This study included 258 children with febrile infections admitted to the ED. Clinical follow-up, microbiological and radiological tests were used as reference standards for the definition of SBI. Study population was categorized into two groups: (i) infected patients with no suspicion of SBI (n = 75); (ii) patients with suspicion of SBI (n = 183). IG percentage, white blood cell count (WBC) and C-reactive protein (CRP) levels were analyzed from the first routine blood samples at hospital admission. Results: A statistically significant difference in IG percentage levels was observed in children with SBI and those without - the mean IG percentage was 1.2% for the SBI group, 0.3% for those without SBI. The cutoff level of IG percentage to predict SBI was 0.45 (84% specificity, 66% sensitivity, 90% positive predictive value). We combine variables and evaluate their additive values. The sensitivity of WBC to detected SBI improved from 74% to 85% when IG percentage was added to the prediction models. When CRP, WBC and IG percentage were combined, the sensitivity to predict SBI increased to 93%, the specificity to 86%. (95% CI 77–93%). Receiver operator characteristic analysis to predict SBI showed an area under the curve (AUC) of 0.80 for IG percentage. Conclusion: Addition of IG percentage to traditionally used markers of SBI as WBC and CRP may help to identify children with serious bacterial infections. Furthermore IG percentage can be rapidly obtained from the traditional full blood count without any extra sampling and costs.
ARTICLE | doi:10.20944/preprints201711.0202.v1
Subject: Life Sciences, Biotechnology Keywords: bacterial inactivation; drinking water; electromagnetic fields; electroporation; Escherichia coli
Online: 30 November 2017 (11:22:25 CET)
Bacteria play a key role in both human health and disease. One of the most prevalent harmful bacteria is E. coli which is responsible for several illnesses ranging from diarrhea, stomach cramp and fever. In this work we explore the application of moderate electric or magnetic fields for treating deionized water that is contaminated with E. coli. We found that moderate alternating electric (AC) fields (10 V/cm to 1kV/cm) and moderate static magnetic fields (10 to 65 mT) can significantly inactivate E. coli by up to 90% or more. This provides the possibilities of developing a low cost and a practical bacteria inactivation technique using electric or magnetic fields.
ARTICLE | doi:10.20944/preprints201701.0071.v1
Subject: Life Sciences, Biotechnology Keywords: C-type lectin; agglutination; CRD; bacterial detection; E. coli
Online: 13 January 2017 (13:17:13 CET)
Lectins are carbohydrate-interacting proteins playing a pivotal role in multiple physiological and developmental aspects of all organisms. They can specifically interact with different bacterial and viral pathogens through the carbohydrate-recognition domains (CRD). In addition, lectins are also of biotechnological interest because of their potential use as biosensor for capturing and identification of bacterial species. In this work, we have characterized the bacterial agglutination properties of three C-type lectins from the Lepidoptera Spodoptera exigua. One of these lectins, BLL2, was able to agglutinate cells from a broad range of bacterial species at an extremely low concentration, becoming a very interesting protein to be used as biosensor or other biotechnological applications involving bacterial capturing.
ARTICLE | doi:10.20944/preprints202204.0005.v1
Subject: Medicine & Pharmacology, Other Keywords: genome mining; marine environments; molecular networking; bacterial extremophiles; secondary metabolites
Online: 1 April 2022 (10:21:11 CEST)
Understanding extremophiles and their usefulness in biotechnology involves studying their habitat, physiology and biochemical adaptations , as well as their ability to produce biocatalysts, in environments that are still poorly explored. In northwestern Peru, which saline lagoons of marine origin Pacific Ocean, the other site from the coast of Brazil of the Atlantic Ocean. Both environments are considered extreme. The objective of the present work was to compare two different strains isolated from these extreme environments at the metabolic level using molecular network methodology through the Global Natural Products Molecular Social Network (GNPS). In our study, the MS/MS spectra from the network were compared with GNPS spectral libraries, where the metabolites were annotated. Differences were observed in the molecular network presented in the two strains of Streptomyces spp. coming from these two different environments. Within the annotated compounds from marine bacteria, the metabolites characterized for Streptomyces sp. B-81 from Peruvian marshes were lobophorins A (1) and H (2), as well as divergolides A (3), B (4) and C (5). Streptomyces sp. 796.1 produced different compounds, such as glucopiericidin A (6) and dehydro-piericidin A1a (7). The search for new metabolites in underexplored environments may therefore reveal new metabolites with potential application in different areas of biotechnology.
ARTICLE | doi:10.20944/preprints202111.0557.v1
Subject: Biology, Other Keywords: Bacterial nomenclature; archaeal nomenclature; genome taxonomy; shotgun metagenomics; Candidatus names
Online: 30 November 2021 (10:53:50 CET)
Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.
ARTICLE | doi:10.20944/preprints202107.0596.v1
Subject: Medicine & Pharmacology, Allergology Keywords: schizophrenia; neuro-immune; inflammation; physiological stress; bacterial translocation; psychiatry; LPS
Online: 27 July 2021 (09:16:54 CEST)
There is evidence that schizophrenia is characterized by activation of the immune-inflammatory response (IRS) and compensatory immune-regulatory (CIRS) systems and lowered neuroprotection. Studies performed on antipsychotic-naïve first episode psychosis (AF-FEP) and schizophrenia (FES) patients are important as they may disclose the pathogenesis of the disease. However, the interactome of FEP/FES is not well delineated. The aim of the current study was to delineate the characteristics of the protein-protein interaction (PPI) network of AN-FEP and its transition to FES and the biological functions, pathways, and molecular patterns, which are over-represented in FEP/FES. PPI network analysis shows that FEP and FEP/FES are strongly associated with a response to a bacterium, TNF, NFκB, RELA, SP1, JAK-STAT, death receptor and TLR4 signaling, and tyrosine phosphorylation of STAT proteins. Specific molecular complexes of the peripheral immune response are associated with microglial activation, neuroinflammation and gliogenesis. FEP/FES is accompanied by lowered protection against inflammation in part attributable to dysfunctional miRNA maturation, deficits in neurotrophin/Trk, RTK and Wnt/catenin signaling and adherens junction organization. Lowered neuroprotection due to reduced neurotrophin/Trk and Wnt/catenin signaling, and DISC1 expression and multiple interactions between lowered BDNF, CDH1, CTNNB, and DISC1 expression, increase the vulnerability to the neurotoxic effects of immune products including cytokines and complement factors. All pathways or molecular patterns enriched in the interactome of FEP/FES are directly or indirectly affected by LPS. In summary: FEP appears to be triggered by a biotic stimulus (e.g. Gram-negative bacteria) which may induce neuro-immune toxicity cascades especially when anti-inflammatory and neurotrophic protections are deficient.
ARTICLE | doi:10.20944/preprints202105.0556.v1
Subject: Life Sciences, Biochemistry Keywords: Alzheimer’s disease; amyloid-beta; amyloid plaques; bacterial DNA; protein aggregation
Online: 24 May 2021 (10:33:22 CEST)
Alzheimer’s disease is associated with prion-like aggregation of the amyloid β (Aβ) peptide and the subsequent accumulation of misfolded neurotoxic aggregates in the brain. Therefore, it is critical to clearly identify the factors that trigger the cascade of Aβ misfolding and aggregation. Numerous studies have pointed out the association between microorganisms and their virulence factors and Alzheimer’s disease; however, their exact mechanisms of action remain unclear. Recently, we discovered a new pathogenic role of bacterial extracellular DNA, triggering the formation of misfolded Tau aggregates. In this study, we investigated the possible role of DNA extracted from different bacterial and eukaryotic cells in triggering Aβ aggregation in vitro. Interestingly, we found that the extracellular DNA of some, but not all, bacteria is an effective trigger of Aβ aggregation. Furthermore, the acceleration of Aβ nucleation and elongation can vary based on the concentration of the bacterial DNA and the bacterial strain from which this DNA had originated. Our findings suggest that bacterial extracellular DNA might play a previously overlooked role in the Aβ protein misfolding associated with Alzheimer’s disease pathogenesis. Moreover, it highlights a new mechanism of how distantly localized bacteria can remotely contribute to protein misfolding and diseases associated with this process. These findings might lead to the use of bacterial DNA as a novel therapeutic target for the prevention and treatment of Alzheimer’s disease.
ARTICLE | doi:10.20944/preprints202105.0207.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Suture material; Third molar surgery; Surgical wound infection; Bacterial adhesion
Online: 10 May 2021 (15:08:53 CEST)
Background: Selection and application of suture materials, has gained more importance especially with the increasing number of patients seeking oral surgeries. Since lying in a bacterial-filled environment, sutures make the tissue prone to infection. Suture material plays an important role in the reduction of the risk of infection. This study aimed to assess the success rate of an antibacterial suture named Vicryl Plus in preventing bacterial growth in the surgical site of the mandibular third molar. Methods: 27 patients were included in this double-blinded randomized clinical trial study. Surgical Extraction of the mandibular wisdom tooth was done and the incision was managed by randomly using Vicryl Plus and Vicryl sutures. After 7 days, sutures were removed and assessed microbiologically. Predominant species of Streptococcus mutans and Lactobacillus were assessed as well as the total number of colonies on each suture. Results: There was a significant difference between two suture materials in colony number-length ratio of lactobacillus (p-value= 0.031) and total bacterial colonies (p-value=0.016); but not for S. mutans species (p-value=0.201). Conclusion: Antibacterial Vicryl suture can be a useful tool for the reduction in the rate of surgical site infection in high-risk cases and situations.
HYPOTHESIS | doi:10.20944/preprints202104.0516.v1
Subject: Medicine & Pharmacology, Allergology Keywords: spontaneous regression; tumors; cancer; bacterial therapy; Coley; immunotherapy; hyperthermia; oncology
Online: 19 April 2021 (21:03:16 CEST)
Neither tumor growth nor regression is truly spontaneous, but both may under special circumstances be driven by similar events. We describe a sequence of processes that typically leads to tumor progression but may on occasion inadvertently result in regression. A possible procedure for reducing tumor mass through a controlled intervention is also outlined.
ARTICLE | doi:10.20944/preprints202101.0623.v1
Subject: Medicine & Pharmacology, Allergology Keywords: depression; neuroimmune; inflammation; oxidative and nitrosative stress; autoimmune; bacterial translocation
Online: 29 January 2021 (13:17:48 CET)
The approach towards myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS) remains in a permanent state of crisis with fierce competition between the psychosocial school, which attributes ME/CFS to the perception of effort, and the medical approach (Maes and Twisk, BMC Med, 2010,8,35). The aim of this paper is to review how to construct a nomothetic model of ME/CFS using Partial Least Squares (PLS) path analysis and ensembling causome (bacterial translocation as assessed with IgM/IgA responses to LPS), protectome (lowered coenzyme Q10), adverse outcome pathways (AOP) including increased lysozyme, CD38+ T cell activation, cell-mediated immune activation (CMI), and IgM responses to oxidative specific epitopes and NO-adducts (IgM OSENO). Using PLS, we trained, tested and validated this knowledge- and data-driven causal ME/CFS model, which showed adequate convergence, construct and replicability validity. This bottom-up explicit data model of ME/CFS objectivates the descriptive narratives of the ME/CFS phenome, using causome-protectome-AOP data, whereby the abstract concept ME/CFS is translated into pathways, thereby securing the reification of the ME/CFS phenome. We found that 31.6% of the variance in the physiosomatic symptom dimension of ME/CFS was explained by the cumulative effects of CMI and CD38+ activation, IgM OSENO, IgA LPS, lysozyme (all positive) and coenzyme Q10 (inversely). Cluster analysis performed on the PLS-generated latent vector scores of all feature sets exposed three distinct immune groups of ME/CFS, namely one with increased lysozyme, one with increased CMI + CD38 activation + depressive symptoms, and another with increased bacterial translocation + autoimmune responses to OSENO.
BRIEF REPORT | doi:10.20944/preprints202010.0039.v1
Subject: Medicine & Pharmacology, Allergology Keywords: peritoneal catheter; PleurX, liver cirrhosis, refractory ascites, spontaneous bacterial peritonitis,
Online: 2 October 2020 (10:39:07 CEST)
Background and objectives: Refractory ascites markedly worsens prognosis in cirrhosis. Large volume paracentesis (LVP) is standard treatment, but complications are common. In a randomized controlled case-series, we assessed a permanent tunneled peritoneal catheter versus LVP in patients with cirrhosis and ascites. Materials and Methods: Random allocation was computer-generated, and concealment used opaque envelopes. Patients were included from 01-2017 to 12-2018. Inclusion criteria were cirrhosis and recurrent ascites and expected survival of more than 3 months. Results: Thirteen patients were enrolled (PleurX =6 versus LVP =7). Seven were female, age range 51 to 80 years. No procedure-related complications occurred. Two patients died due to variceal bleeding (PleurX-group) and sepsis (LVP-group). One patient was withdrawn due to hyponatremia (PleurX-group). Two patients were withdrawn due to bacterial peritonitis and infection of unknown origin (Control-group). In the PleurX-group, all patients colonized the catheter, two developed bacterial peritonitis. The most common bacterial colonization was Staph. Epidermidis (n=4). Conclusions: In selected patients, the PleurX catheter mobilizes ascites and may be an alternative to LVP. The risk of infection should be considered in each case. The impact of colonization and risk of infections needs further investigation. Trial Registration: EudraCT: CIV-16-10-017324; clinicaltrials.gov: NCT 03027635; Scientific Ethics Committee journal no: H-1604179
ARTICLE | doi:10.20944/preprints201912.0286.v1
Subject: Materials Science, Biomaterials Keywords: Moringa oleifera; bismuth nanoparticles; polyphenolics; anti-bacterial; anti-fungal; antioxidant
Online: 21 December 2019 (12:28:21 CET)
The use of plant extracts in the synthesis of metal nanoparticles is a very attractive approach in the field of green synthesis. To benefit from the potential synergy between the biological activities of the Moringa oleifera leaves extract and metallic bismuth, our study aimed at synthesizing bismuth nanoparticles using a hydroalcoholic extract of M. oleifera leaves as a means of green synthesis that yields nontoxic products and reduces the production of wasteful material. To this end, the M. oleifera leaves extract was treated with a bismuth nitrate pentahydrate solution. A color change from light brown to dark brown indicates the synthesis of bismuth nanoparticles. The total phenolic content in the M. oleifera leaves extract used was 23.0 ± 0.3 mg gallic acid equivalent/g of dried M. oleifera leaves powder. Antioxidant property of MO synthesised bismuth Nanoparticles was evaluated and in line with the extract used in the synthesis of NPs. The physical properties of the synthesized bismuth nanoparticles were characterized using UV-Vis spectrophotometer, FT-IR spectrometer, TEM, SEM, and XRD. The synthesized bismuth nanoparticles have a size in the range of 40.4-57.8 nm with amorphous morphology. Using DPPH and phosphomolybdate assays, our findings revealed that the M. oleifera leaves extract and the synthesized bismuth nanoparticles possess antioxidant properties. Using resazurin microtiter assay, we also demonstrate that the M. oleifera leaves extract and the synthesized bismuth nanoparticles exert potent anti-bacterial activity against Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus and Enterococcus faecalis, similarly to the inhibition exerted by Moringa extract, especially against Enterococcus faecalis (MIC values for the extract: 500, 250, 250, and 250 µg/mL; MIC values for the bismuth nanoparticles: 500, 500, 500, and 250 µg/mL, respectively). Similarly, the M. oleifera leaves extract and the synthesized bismuth nanoparticles display relatively stronger anti-fungal activity against Aspergillus niger, Aspergillus flavus, Candida albicans, and Candida glabrata (MIC values for the extract: 62.5, 62.5, 125, and 250 µg/mL; MIC values for the bismuth nanoparticles: 250, 250, 62.5, and 62.5 µg/mL, respectively). Thus, the hydroalcoholic extract of M. oleifera leaves was successfully used in the synthesis of bismuth nanoparticles, showing a positive antioxidant, anti-bacterial, and anti-fungal activity. Therefore, the synthesized bismuth nanoparticles can potentially be employed in the alleviation of symptoms associated with oxidative stress and in the topic treatment of Candida infections.
ARTICLE | doi:10.20944/preprints201911.0305.v1
Subject: Life Sciences, Microbiology Keywords: Moringa oleifera; copper nanoparticles; polyphenolics; anti-bacterial; anti-fungal; antioxidant
Online: 26 November 2019 (03:45:52 CET)
The synthesis of metal nanoparticles using plant extracts is a very promising method in green synthesis. The medicinal value of Moringa oleifera leaves and the anti-microbial activity of metallic copper were combined in the present study to synthesize copper nanoparticles having a desirable added-value inorganic material. The use of a hydroalcoholic extract of M. oleifera leaves for the green synthesis of copper nanoparticles is an attractive method as it leads to the production of harmless chemicals and reduces waste. The total phenolic content in the M. oleifera leaves extract was 23.0 ± 0.3 mg gallic acid equivalent/g of dried M. oleifera leaves powder. The M. oleifera leaves extract was treated with a copper sulphate solution. A color change from brown to black indicates the formation of copper nanoparticles. Characterization of the synthesized copper nanoparticles was performed using UV-Vis spectrophotometer, FT-IR spectrometer, TEM, SEM, and XRD. The synthesized copper nanoparticles have an amorphous nature and particle size of 35.8-49.2 nm. We demonstrate that the M. oleifera leaves extract and the synthesized copper nanoparticles display considerable antioxidant activity. Moreover, the M. oleifera leaves extract and the synthesized copper nanoparticles exert potent anti-bacterial activity against Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus faecalis (MIC values for the extract: 500, 250, 250, and 250 μg/mL; MIC values for the cooper nanoparticles: 500, 500, 500, and 250 μg/mL, respectively). Similarly, the M. oleifera leaves extract and the synthesized copper nanoparticles exert relatively more potent anti-fungal activity against Aspergillus niger, Aspergillus flavus, Candida albicans, and Candida glabrata (MIC values for the extract: 62.5, 62.5, 125, and 250 μg/mL; MIC values for the cooper nanoparticles: 125, 125, 62.5, and 31.2 μg/mL, respectively). Our study reveals that the green synthesis of copper nanoparticles using a hydroalcoholic extract of M. oleifera leaves was successful. In addition, the synthesized copper nanoparticles can be potentially employed in the treatment of various microbial infections due to their potent antioxidant, anti-bacterial, and anti-fungal activities.
ARTICLE | doi:10.20944/preprints201810.0113.v1
Subject: Chemistry, Food Chemistry Keywords: Sea Squirts; Metabolites; GC-MS; Anti-bacterial; Zika vector; larvicidal
Online: 6 October 2018 (11:18:31 CEST)
In this present study, we conducted untargeted metabolic profiling using Gas Chromatography-Mass Spectrometry (GC-MS) analysis of ascidian Didemnum bistratum to assess the chemical constituents by searching in NIST library with promising biological properties against anti-bacterial and Zika virus vector mosquitocidal Properties. Metabolites, steroids and fatty acids are abundant in crude compounds of ascidian D. bistratum and showed potential zone growth inhibition against bacterial strains Kluyvera ascorbate (10 mm). The active crude compounds of D. bistratum exhibited prominent larvicidal activity against the Zika vector mosquitoes of Aedes aegypti and Cluex quinquefasciatus (LC50 values of 0.4436 to 2.23 mg/mL). The findings of this study provide a first evidence of the biological properties exhibited by D. bistratum extracts, thus increasing the knowledge about the Zika virus vector mosquitocidal properties of ascidian. Overall, ascidian D. bistratum are promising and biocontrol or eco-friendly tool against A. aegypti and C. quinquefasciatus with prospective toxicity against non-target organisms.
REVIEW | doi:10.20944/preprints201807.0091.v1
Subject: Medicine & Pharmacology, Other Keywords: bacterial infection; antibiotic resistance; bacteriophage; antibiotic therapy; phage therapy; review
Online: 5 July 2018 (10:09:09 CEST)
Bacteriophages, viruses that are widespread throughout the world, are highly specific for bacteria, usually of a single species and often of a particular strain. After being discovered and isolated 100 years ago, their use, called phage therapy, was instituted in medicine two years later and quickly used around the world to treat various bacterial infections. In the West, phage therapy was overshadowed in the second half of the 20th century by antibiotic therapy, which was then thought to be the definitive solution. But because of the increase in bacterial resistance to antibiotics, the idea of using bacteriophages in medicine has been reawakened. The innumerable observations reported over the years in the literature constitute an invaluable experience. We and some of our colleagues have, in the last decade treated some patients compassionately. With the available documentation and our own experience we discuss the potential indications and limitations of phage therapy. The observation of the increasing number of therapeutic failures in the announced perspective of a post-antibiotic era, we believe, that the introduction of bacteriophages into the therapeutic arsenal seems conceivable today to two preconditions: that their production as biologic drug meets current regulatory standards and that the benefit-risk assessment was conducted in a modern setting. Phage therapy could be applied as a substitution or supplement to antibiotic therapy under multiple circumstances in different modes, precise indications and limits.
ARTICLE | doi:10.20944/preprints201804.0128.v1
Subject: Biology, Plant Sciences Keywords: bacterial artificial chromosomes; RNAseq; genetic map; transposable element; gene density
Online: 10 April 2018 (10:49:41 CEST)
Many dioecious plants have sex chromosomes that are cytologically heteromorphic, but about half of species lack cytological differences between males and females and are thus homomorphic. Very little is known about the size and content of the non-recombining sex-determining region (SDR) in these species. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, which has homomorphic sex chromosomes and shows signatures of mild Y-chromosome degeneration. We used RNAseq to identify new Y-linked markers for M. annua. Twelve of 24 transcripts with male-specific and male-biased expression could only be PCR-amplified from males and are thus Y-linked. We found a further six Y-linked sequences that were present in males but not females using genome capture data from multiple populations. We used the Y-linked sequences to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequence, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests it is enriched for repeats, has a low gene density and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which is estimated to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, especially given the small genome size of M. annua. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
ARTICLE | doi:10.20944/preprints202111.0158.v1
Subject: Biology, Forestry Keywords: Cinnamomum camphora; chemotype; soil nutrient; soil bacterial community diversity and structure
Online: 8 November 2021 (15:20:35 CET)
Abstract: Plant types and soil bacterial communities had a close relationship, understanding the profound association between them contributes to better learn bacterial ecological function for plant growth. In this study, rhizosphere soil of six different chemotype Cinnamomum camphora trees were collected, including C. bodinieri var. citralifera, [C. camphora (Linn.) Presl], camphora-type, cineole-type, linalool-type and isoborneol-type. Soil properties content and bacterial communities were analyzed. Two chemotype C. camphora, including [C. camphora (Linn.) Presl] and linalool-type, shaped similar bacterial community structure, decreased Firmcutes relative abundance. richness estimators (Chao1 index and Ace index) of [C. camphora (Linn.) Presl] were decreased compared with the others. Furthermore, soil bacterial community structure was also similar among bodinieri var. citralifera, camphora-type, cineole-type and isoborneol-type. Hence, different chemotype C. camphora altered soil nutrient and shaped rhizosphere bacterial communities.
REVIEW | doi:10.20944/preprints202107.0182.v1
Subject: Life Sciences, Biochemistry Keywords: CRISPR-Cas9; Genome editing; plant editing; bacterial immune system; genetic disease
Online: 8 July 2021 (09:50:22 CEST)
Clustered regularly interspaced short palindromic repeats or CRISPR, one of the major technological tools from nature's toolbox, has revolutionized the scientific world with its potential use in humans and plants. CRISPR Cas9 was first known as an adaptive immune system of bacteria. It is a system that cleaves foreign DNA. It has been exploited to be used as a genome editing tool for correcting genetic diseases in humans, for plants to create stress-resistant plants, and for a variety of different purposes. This review provides a basic overview of its applications in different areas of biological research. It has immense potential for a variety of researches, but it's still a mystery for science. It feels like scientists just know a tip of an iceberg.
Subject: Life Sciences, Biochemistry Keywords: 16S rRNA gene; bacterial diversity; catabolic activity; cultivation; Pannonian steppe; pyrosequencing
Online: 22 June 2021 (14:26:55 CEST)
In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils at different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analysed by MicroResp method, the bacterial diversity was assessed by cultivation and next generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes changed also mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.
ARTICLE | doi:10.20944/preprints202106.0434.v1
Subject: Life Sciences, Biochemistry Keywords: bacterial community composition; metabolic activity; microbial diversity; soil erosion; soil quality
Online: 16 June 2021 (10:23:06 CEST)
Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).
ARTICLE | doi:10.20944/preprints202007.0162.v1
Subject: Engineering, Other Keywords: Heterotrophic denitrification; Granular activated carbon (GAC); Bacterial Community; 3D-BER system
Online: 9 July 2020 (01:51:11 CEST)
In this study, a three-dimensional bioelectrochemical reactor system (3D-BERs) with granular activated carbon (GAC) epitomizes a novel treatment technology for treating nitrate-polluted water. The conventional denitrification process faces many challenges, including the huge demand for organic carbon, long-term accumulation of intermediate products, and the adaptation period. Results shown that under the optimal conditions of the COD/NO3--N ratio was 1.5, the denitrification efficiency reached 98.62%, when compared to 81.12% at COD/ NO3--N ratio of 3.5, and the initial pH of 7.5 ± 0.5, NO3--N was entirely removed at 2.2 h without accumulation of nitrite. The high initial ratio of NO2--N/NO3--N is mainly to accelerate the denitrification rate by accelerating the reduction of nitrite. Denitrification process followed by zero-order kinetics linear model for at different concentrations of inlet NO3--N, and achieved higher denitrification rate at greater inlet NO3--N concentration. High-throughput sequencing shows that the community structure and relative abundance of bacteria changed significantly, especially at the genes and the phyla level in immobilized GAC particles. Microbial composition enhanced the removal of nitrogen at the inner surface (IS) and bottom surface (BS) of immobilized GAC carriers. Therefore, this system is expected to be a more efficient and useful supplement or a cost-effective alternative compared to the traditional low carbon to nitrogen wastewater treatment system.
ARTICLE | doi:10.20944/preprints201912.0373.v1
Subject: Life Sciences, Molecular Biology Keywords: bacterial flagellar motility; flagellin; Salmonella; FljB; FliC; electron cryomicroscopy; viscosity; infection
Online: 29 December 2019 (07:47:57 CET)
The bacterial flagellum is a motility organelle, consisting of a long helical filament as a propeller and a rotary motor that drives rapid filament rotation to produce thrust. Salmonella enterica serovar Typhimurium has two genes of flagellin, fljB and fliC, for flagellar filament formation and autonomously switches their expression at a frequency of 10-3–10-4 per cell per generation. We report here differences in their structures and motility functions under high viscosity conditions. A Salmonella strain expressing FljB showed a higher motility than the one expressing FliC under high viscousity. To examine the reasons for this motility difference, we carried out structural analyses of the FljB filament by electron cryomicroscopy and found that the structure is nearly identical to that of the FliC filament except for the position and orientation of the outermost domain D3 of flagellin. The density of domain D3 was much lower in FljB than FliC, suggesting that domain D3 of FljB is more flexible and mobile than that of FliC. These differences suggest that domain D3 plays an important role not only in changing antigenicity of the filament but also in optimizing motility function of the filament as a propeller under different conditions.
ARTICLE | doi:10.20944/preprints202112.0049.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: bacterial wilt; biological control; phage; microscopy; sequencing; molecular characterization; genomic characterization; depolymerase
Online: 3 December 2021 (10:36:47 CET)
Ralstonia solanacearum is the causative agent of bacterial wilt, one of the most destructive plant diseases. While chemical control has an environmental impact, biological control strategies can allow sustainable agrosystems. Three lytic bacteriophages (phages) of R. solanacearum with biocontrol capacity in environmental water and plant were isolated from river water in Europe but not fully characterized, their genomic characterization being fundamental to understand their biology. In this work, the phage genomes were sequenced and subjected to bioinformatic analysis. The morphology was also observed by electron microscopy. Phylogenetic analyses were performed with a selection of phages able to infect R. solanacearum and the closely related phytopathogenic species R. pseudosolanacearum. The results indicated that the genomes of vRsoP-WF2, vRsoP-WM2 and vRsoP-WR2 range from 40,688 to 41,158 bp with almost 59% GC-contents, 52 ORFs in vRsoP-WF2 and vRsoP-WM2, and 53 in vRsoP-WR2 but, with only 22 or 23 predicted proteins with functional homologs in databases. Among them, two lysins and one exopolysaccharide (EPS) depolymerase, this type of depolymerase being identified in R. solanacearum phages for the first time. These three European phages belong to the same novel species within the Gyeongsanvirus, Autographiviridae family (formerly Podoviridae). These genomic data will contribute to a better understanding of the abilities of these phages to damage host cells and, consequently, to an improvement in the biological control of R. solanacearum.
REVIEW | doi:10.20944/preprints202108.0383.v1
Subject: Chemistry, Analytical Chemistry Keywords: Bacterial carotenoids; Cell disruption; HPLC separation; MS analysis; Food and textile applications
Online: 18 August 2021 (14:09:35 CEST)
Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory and anti-cancer properties. These types of compounds are in high demand by pharmaceutical, cosmetic, textile and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses much of this information. To understand the diversity of these carotenoids, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use of bacterial carotenoids. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.
ARTICLE | doi:10.20944/preprints202108.0312.v1
Subject: Life Sciences, Microbiology Keywords: Komagataeibacter rhaeticus; Bacterial cellulose; Crude glycerol; Minimal medium; Whole-genome analysis; Acetate
Online: 16 August 2021 (08:32:19 CEST)
Komagataeibacter spp. have been used for the bioconversion of industrial wastes and lignocellulosic hydrolysates to bacterial cellulose (BC). Recently studies have demonstrated the capacity of Komagataeibacter spp. in the biotransformation of inhibitors found in lignocellulosic hydrolysates, aromatic lignin-derived monomers (LDMs) and acetate. In general, detoxification and BC synthesis from lignocellulosic inhibitors requires a carbon flow from acetyl-coA towards tricarboxylic acid and gluconeogenesis, respectively. However, the related molecular aspects have not yet been identified in Komagataeibacter spp. In this study, we isolated a cellulose producing bacteria capable of synthesizing BC in a minimal medium containing crude glycerol, a by-product from biodiesel production process. The isolate, affiliated to Komagataeibacter genus, synthesized cellulose in minimal medium containing glucose (3.3±0.3 g/L), pure glycerol (2.2±0.1 g/L) and crude glycerol (2.1±0.1 g/L). Genome assembly and annotation identified four copies of bacterial cellulose synthase operon and genes for redirecting the carbon from central metabolic pathway to gluconeogenesis. According to the genome annotations, a BC production route from acetyl-CoA, a central metabolic intermediate, was hypothesized and was validated using acetate. We identified that when K. rhaeticus ENS9b was grown in minimal medium supplemented with acetate, BC production was not observed. However, in presence of readily utilizable substrate, such as spent yeast hydrolysate, acetate supplementation improved BC synthesis.
ARTICLE | doi:10.20944/preprints202105.0182.v1
Subject: Medicine & Pharmacology, Allergology Keywords: chronic fatigue syndrome; Myalgic encephalomyelitis; oxidative stress; neuro-immune; inflammation; bacterial translocation
Online: 10 May 2021 (12:27:45 CEST)
Background: A meaningful part of schizophrenia patients suffer from physiosomatic symptoms (formerly named psychosomatic) which are reminiscent of chronic fatigue syndrome and fibromyalgia (FF) and are associated with signs of immune activation and increased levels of tryptophan catabolites (TRYCATs). Aims: To examine whether FF symptoms in schizophrenia are associated with breakdown of the paracellular pathway, zonulin, lowered natural IgM responses to oxidative specific epitopes (OSEs); and whether FF symptoms belong to the behavioral-cognitive-physical-psychosocial-(BCPS)-worsening index consisting of indices of a general cognitive decline (G-CoDe), symptomatome of schizophrenia, and quality of life (QoL)-phenomenome. Methods: FF symptoms were assessed using the Fibromyalgia and Chronic Fatigue Rating scale in 80 schizophrenia patients and 40 healthy controls and serum cytokines/chemokines, IgA levels to TRYCATs, IgM to OSEs, zonulin and transcellular/paracellular (TRANS/PARA) molecules were assayed using ELISA methods. Results: A large part (42.3%) of the variance in the total FF score was explained by the regression on the PARA/TRANS ratio, pro-inflammatory cytokines, IgM to zonulin, IgA to TRYCATs (all positively) and IgM to OSEs (inversely). There were highly significant correlations between the total FF score and G-CoDe, symtopmatome, QoL phenomenome and BCPS-worsening score. FF symptoms belong to a common core shared by G-CoDe, symtopmatome, and QoL phenomenome. Discussion: The physio-somatic symptoms of schizophrenia are driven by various pathways including increased zonulin, breakdown of the paracellular tight-junctions pathway, immune activation with induction of the TRYCAT pathway, and consequent neurotoxicity. It is concluded that FF symptoms are part of the phenome of schizophrenia and BCPS-worsening as well.
ARTICLE | doi:10.20944/preprints202101.0437.v1
Subject: Materials Science, Biomaterials Keywords: Candida albicans biofilm; Mixed salivary bacterial biofilm; Phosphated PMMA; Antimicrobials; Salivary pellicle
Online: 22 January 2021 (09:34:24 CET)
Biofilms play a crucial role in the development of Candida-associated denture stomatitis. Inhibition of microbial adhesion to PMMA and phosphate containing PMMA has been examined in this work. C. albicans and mixed salivary microbial biofilms were compared on naked and salivary pre-conditioned PMMA surfaces in the presence or absence of antimicrobials (cetyl pyridinium chloride [CPC], KSL-W, histatin 5 [his 5]). Polymers with varying amounts of phosphate (0-25%) were tested using four C. albicans oral isolates as well as mixed salivary bacteria and 24 h biofilms were assessed for metabolic activity and confirmed using Live/Dead staining and confocal microscopy. Biofilm metabolism was reduced as phosphate density increased (15%: P=0.004; 25%: P=0.001). Loading of CPC on 15% phosphated disks showed a substantial decrease (P=0.001) in biofilm metabolism in the presence or absence of a salivary pellicle. Salivary pellicle on uncharged PMMA enhanced the antimicrobial activity of CPC only. CPC also demonstrated remarkable antimicrobial activity on mixed salivary bacterial biofilms under different conditions displaying the potent efficacy of CPC (350 µg/ml) when combined with an artificial protein pellicle (Biotene half strength).
ARTICLE | doi:10.20944/preprints202010.0441.v2
Subject: Engineering, Automotive Engineering Keywords: coronavirus; wastewater treatment techniques; mathematical model; statistical procedures; bacterial reactors, anaerobic ponds
Online: 8 January 2021 (13:22:36 CET)
This paper presents multidisciplinary and innovative research concerning fighting against coronavirus through wastewater collection and treatment. Studies suggest that coronavirus exists in the wastewaters. Untreated wastewater is proved to spread the virus. Coronavirus is attacking people globally and shrinking the economy. This paper highlights the idea that the coronavirus shall be defeated with the help of wastewater collection and treatment as well. The question addressed by this paper is will communities defeat the coronavirus without well-collected and treated wastewaters? This research aims to display the role of wastewaters in the spread of coronavirus in cities and to require their collection. The methods to achieve the goals are theoretical surveys, case study strategy, mathematical modeling, statistical procedures, forecasting of future, and dialectical discussions. The findings of this research demonstrate the need for carefully collected and treated wastewaters to overcome the coronavirus. This paper gives suitable techniques to collect and treat wastewater such as wastewater stabilization ponds, bacterial reactors, and anaerobic ponds. The innovative idea of this paper, its suggested indicators to select a certain wastewater treatment technique in every city, and its outcome will assist the global community to fight the coronavirus more effectively.
ARTICLE | doi:10.20944/preprints202012.0116.v1
Subject: Materials Science, Biomaterials Keywords: antibacterial coating; antimicrobial peptide; plasma polymer; LL 37; Magainin; Parasin; bacterial attachment
Online: 4 December 2020 (14:56:18 CET)
To combat infections on biomedical devices, antimicrobial coatings have attracted considerable attention, including coatings comprising naturally occurring antimicrobial peptides (AMPs). In this study the aim was to explore performance upon extended challenge by bacteria growing in media above samples. The AMPs LL37, Magainin 2, and Parasin 1 were covalently grafted onto a plasma polymer platform, which enables application of this multilayer coating strategy to a wide range of biomaterials. Detailed surface analyses were performed to verify the intended outcomes of the coating sequence. Samples were challenged by incubation in bacterial growth media for 5 and 20 hrs. Compared with the control plasma polymer surface, all three grafted AMP coatings showed considerable reductions in bacterial colonization even at the high bacterial challenge of initial seeding at 1x107 CFU, but there were increasing numbers of dead bacteria attached to the surface. All three grafted AMP coatings were found to be non-toxic to primary fibroblasts. These coatings thus could be useful to produce antibacterial surface coatings for biomaterials, though possible consequences arising from the presence of dead bacteria need to be studied further, and compared to non-fouling coatings that avoid attached dead bacteria.
ARTICLE | doi:10.20944/preprints202008.0677.v1
Subject: Life Sciences, Microbiology Keywords: Nasal microbiota; Illumina sequencing; nanopore sequencing; 16S rRNA gene; Bacterial species; Corynebacterium
Online: 30 August 2020 (16:04:50 CEST)
Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME and an in house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 and R9.2 were compared.
ARTICLE | doi:10.20944/preprints201808.0214.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: immunomagnetic separation (IMS); bacterial pathogen; 3D printing; preconcentration; DNA purification; molecular diagnostics
Online: 12 August 2018 (19:26:04 CEST)
Molecular detection of pathogens in clinical samples often requires pretreatment techniques, including immunomagnetic separation and magnetic silica bead (MSB)-based DNA purification to obtain the purified DNA of pathogens. These two techniques usually rely on handling small tubes containing a few millilitres of the sample and manual operation, implying that an automated system encompassing both techniques is needed for larger quantities of the samples. Here, we report a 3D-printed microfluidic platform that enables bacterial preconcentration and genomic DNA (gDNA) purification for improving the molecular detection of target pathogens in blood samples. The device consists of two microchannels and one chamber, which can be used to preconcentrate pathogens bound to antibody-conjugated magnetic nanoparticles (Ab-MNPs) and subsequently extract gDNA using magnetic silica beads (MSBs) in a sequential manner. The device was able to preconcentrate very low concentrations of pathogens and extract their genomic DNA in 10 mL of 10% blood within 30 min, and thus allowed polymerase chain reaction (PCR) and quantitative PCR to detect 1 colony forming unit of Escherichia coli O157:H7 in 10% blood. The results suggest that the 3D-printed microfluidic platform is highly useful for lowering the limitations on molecular detection in blood by preconcentrating the target pathogen and isolating its DNA in a large volume of the sample.
ARTICLE | doi:10.20944/preprints201805.0356.v1
Subject: Life Sciences, Microbiology Keywords: Scoprion Venoms; Hos Defence Peptides; antimicrobial activity; antibiofilm activity; synergism; bacterial resistance
Online: 25 May 2018 (09:26:11 CEST)
Current research in the field of antimicrobials is focused on the development of novel antibiotics and antimicrobial agents to counteract the huge dilemma that the human population is mainly facing in regards to the rise of bacterial resistance and biofilm infections. Host Defense peptides (HDPs) are a promising group of molecules for antimicrobial development as they share unique characteristics suitable for antimicrobial activity including their broad spectrum of activity and potency against bacteria. AamAP1 is a novel HDP that was identified through molecular cloning from the venom of the North African scorpion Androctonus amoeruxi. In vitro antimicrobial assays revealed that the peptide displays moderate activity against different strains of Gram-positive and Gram-negative bacteria. Additionally, the peptide proved to be highly hemolytic and displaying significantly high toxicity against mammalian cells. In our study, a novel synthetic peptide analogue named A3 was designed from the naturally occurring scorpion venom host defense peptide. The design strategy depended on modifying the amino acid sequence of the parent peptide in order to increase its net positive charge, percentage helicity and optimize other physico-chemical parameters involved theoretically in HDPs activity. Accordingly, A3 was evaluated for its in vitro antimicrobial and anti-biofilm activity individually and in combination with four different types of conventional antibiotics against clinical isolates of multi-drug resistant (MDR) Gram-positive bacteria. A3 was also evaluated for its cytotoxicity against mammalian cells. A3 displayed potent and selective in vitro antimicrobial activities against a wide range of MDR Gram-positive bacteria. Our results also showed that combining A3 with conventional antibiotics displayed a synergistic mode of action which resulted in decreasing the MIC value for A3 peptide as low as 0.125 µM. These effective concentrations were associated with negligible toxicities on mammalian cells. In conclusion, A3 exhibits enhanced activity and selectivity when compared with the parent natural scorpion venom peptide. The combination of A3 with conventional antibiotics may be pursued as a potential novel treatment strategy against MDR and biofilm forming bacteria.
ARTICLE | doi:10.20944/preprints202208.0489.v1
Subject: Chemistry, Organic Chemistry Keywords: pyrazolo[3,4-b]pyridine; triazole; in vitro; anti-bacterial; S. Aureus; K. Pneumoniae
Online: 29 August 2022 (10:51:23 CEST)
Antimicrobial resistance is on the rise, and there aren't enough new treatments to combat it. This might send the modern world back to the pre-antibiotic age. The molecular hybrids of pyrazolo[3,4-b]pyridine and triazole have been designed, synthesized, and analyzed for their drug-like molecule nature and in vitro analyses for their inhibition potentials against S. Aureus and K. Pneumoniae. The compounds CY-R2-25 and CY-R2-28 have been identified as the high potential molecules in this series based on in vitro experiments. CY-R2-25 has zone of inhibition values of 15 0.82 and 14 0.7, whilst CY-R2-28 has the zone of inhibition values of 18 0.95 and 16 0.82 against S. Aureus and K. Pneumoniae, respectively. MIC and MIB values for CY-R2-25 and CY-R2-28 against S. Aureus and K. Pneumoniae are 0.25 and 0.5, respectively.
ARTICLE | doi:10.20944/preprints202104.0026.v1
Subject: Life Sciences, Biochemistry Keywords: chloramphenicol; alkyl(triphenyl)phosphonium; bacterial ribosome; molecular dynamics simulations; antibiotic activity; antiproliferative activity
Online: 1 April 2021 (14:38:19 CEST)
In the current work, in continuation of our recent research  we synthesized and studied new chimeric compounds comprising the ribosome-targeting antibiotic chloramphenicol (CHL) and the membrane-penetrating cation triphenylphosphonium (TPP) connected by alkyl linkers of different lengths. Using various biochemical assays, we showed that these CAM-Cn-TPP compounds bind to the bacterial ribosome, inhibit protein synthesis in vitro and in vivo in a way similar to that of the parent CHL, and significantly decrease membrane potential. Similar to CAM-C4-TPP, the mode of action of CAM-C10-TPP and CAM-C14-TPP on bacterial ribosomes differ from that of CHL. By simulating the dynamics of complexes of CAM-Cn-TPP with bacterial ribosomes, we have proposed a possible explanation for the specificity of the action of these analogs on the translation process. CAM-C10-TPP and CAM-C14-TPP stronger inhibit the growth of the Gram-positive bacteria in comparison to the CHL and suppress some strains of CHL-resistant bacteria. Thus, we have shown that TPP derivatives of CHL are dual-acting compounds that target the ribosomes and the cellular membranes of bacteria. The TPP fragment of CAM-Cn-TPP compounds contributes to the inhibitory effect on bacteria. Moreover, since the mitochondria of eukaryotic cells have qualities similar to those of their prokaryotic ancestors, we demonstrate the possibility of targeting chemoresistant cancer cells with these compounds.
ARTICLE | doi:10.20944/preprints202007.0591.v1
Subject: Mathematics & Computer Science, Artificial Intelligence & Robotics Keywords: Bacterial -Viral Pneumonia; COVID-19; X-ray Image; Deep Learning; Convolution Neural Network
Online: 24 July 2020 (14:02:07 CEST)
The paper demonstrates the analysis of Corona Virus Disease based on a CNN probabilistic model. It involves a technique for classification and prediction by recognizing typical and diagnostically most important CT images features relating to Corona Virus. The main contributions of the research include predicting the probability of recurrences in no recurrence (first time detection) cases at applying our proposed Convolution neural network structure. The Study is validated on 2002 chest X-ray images with 60 confirmed positive covid19 cases and (650 bacterial – 412 viral -880 normal) x-ray images. The proposed CNN compared with traditional classifiers with proposed CHFS feature extraction model. The experimental study has done with real data demonstrates the feasibility and potential of the proposed approach for the said cause. The result of proposed CNN structure has been successfully done to achieve 98.20% accuracy of covid19 potential cases with comparable of traditional classifiers.
ARTICLE | doi:10.20944/preprints201907.0293.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: depression; bipolar disorder; gut; bacterial translocation; LPS; oxidative stress; neuro-immune; immunology; psychiatry
Online: 26 July 2019 (00:38:09 CEST)
Major depression (MDD) is accompanied by higher serum IgM/IgA responses to LPS of Gram-negative bacteria, suggesting increased bacterial translocation and gut dysbiosis. Gut dysbiosis may occur in bipolar disorder (BD) and there are differences between MDD and BD type 1 (BP1) and -2 (BP2) in nitro-oxidative stress biomarkers associated with leaky gut. This study examines serum IgM/IgA responses directed to LPS of 6 Gram-negative bacteria in 29 BP1, 37 BP2, 44 MDD and 30 healthy individuals. MDD plus BD was best discriminated from controls by increased IgM/IgA responses to Pseudomonas aeruginosa. BP1 patients showed higher IgM responses to Morganella morganii as compared with MDD and BP2 patients. Patients with melancholia showed higher IgA responses to Citrobacter koseri as compared to controls and non-melancholic depression. The total score on the Hamilton Depression Rating Scale was significantly associated with IgA responses, especially C. koseri. IgG responses to oxidized low-density lipoprotein were significantly associated with signs of increased bacterial translocation. In conclusion, not only MDD but also BP1 and BP2 are accompanied by an immune response due to the increased load of plasma LPS of gut commensal bacteria while these aberrations in the gut-brain axis are most pronounced in BP1 and patients with melancholic features. Activated oxidative stress pathways and autoimmune responses to oxidative specific epitopes in mood disorders may be driven by a breakdown in gut paracellular, transcellular and/or vascular pathways. If replicated, drugs that protect the integrity of the gut barrier may offer novel therapeutic opportunities for BP1 and MDD.
Subject: Life Sciences, Biochemistry Keywords: continuous cropping obstacles; Panax quinquefolius L.; phenolic acids; soil bacterial community composition; soil nutrients
Online: 5 January 2021 (11:46:53 CET)
This study aims to verify the time-variant feature of American ginseng (AG) continuous cropping obstacles and to explore the factors impeding continuous cropping. We verified the feature with a plant-soil feedback pot experiment and then investigated the factors by comparing the properties of control soils that had not been previously used for growing ginseng (CS) with those of soils with a 10-year-crop-rotation cycle following the growth of AG (RS). It’s found that the survival rate of AG in RS was lower than that in CS. The RS had lower pH, available potassium content, and urease activity. Additionally, p-coumaric, p-hydroxybenzoic, vanillic, caffeic, and cinnamic acid levels were lower in RS than in CS, but salicylic acid levels showed the opposite pattern. RS had higher Rhodanobacter and lower Acidothermus, Sphingomonas relative abundances in bacterial community. It’s also found that many bacteria were substantially correlated with phenolic acids and soil physiochemical properties. Results indicate that even after 10-year crop rotation, the negative effects of prior continuous cropping of AG has not been eliminated. The growth of AG can be affected negatively with deterioration of soil physicochemical properties and with lower levels of phenolic acids which promote pathogen reproduction. Probiotics reduction also weighs. Moreover, biotic factors are interrelated with abiotic ones. Therefore, it can be inferred that the comprehensive change of soil properties is the main obstacle for continuous cropping.
ARTICLE | doi:10.20944/preprints202012.0297.v1
Subject: Life Sciences, Biochemistry Keywords: Rhizobium; species complex; bacterial taxonomy; core genes; housekeeping genes; average nucleotide identity; speciation; genospecies
Online: 12 December 2020 (11:51:22 CET)
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at around 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterise isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterising the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
ARTICLE | doi:10.20944/preprints201905.0207.v1
Subject: Biology, Horticulture Keywords: bacterial wilt; Ralstonia solanacearum; genotype-by-sequencing; disease resistance; quantitative trait loci; Solanum lycopersicum
Online: 16 May 2019 (10:35:18 CEST)
Bacterial wilt (BW), caused by Ralstonia solanacearum is one of the major biotic factors limiting tomato production in the humid tropics. Pyramiding of resistance genes through marker-assisted selection is an efficient way to develop durable BW resistant cultivars. Tomato line ‘Hawaii 7996’ (H7996) is a stable and robust resistance source against various R. solanacearum strains. Major BW resistance quantitative trait loci (QTLs) Bwr-12 and Bwr-6, and several minor or strain specific QTLs have been coarse-mapped in this line, but none has been fine-mapped and validated. The objective of the current study was to construct a high density genetic map using single-nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing, fine-map Bwr-12 and Bwr-6 and determine the effects of these QTLs using a near isogenic line (NIL) population. A high density genetic map using 1,604 SNP markers with an average distance of 0.82 cM was developed for 188 F9 recombinant inbred lines derived from the cross H7996 × WVa700. A total of seven QTLs associated with BW resistance to race 1-phylotype I or/and race 3-phylotype II strains were located on chromosomes 6 (Bwr-6.1, 6.2, 6.3 and 6.4) and 12 (Bwr-12.1, Bwr-12.2 and Bwr-12.3) with logarithm of odds (LOD) scores of 6.2-15.6 and 6.2-31.1, explaining 14.2-33.4% and 15.9-53.9% of the total phenotypic variation contributed from H7996, respectively. To validate the genetic effects of the two QTL regions, a set of 80 BC3F3 NILs containing different sections of Bwr-6 with or without Bwr-12 was phenotyped for disease severity after challenge with either race 1-phylotype I Pss4 or race 3-phylotype II Pss1632 BW strains over two seasons. Bwr-6.1 specific to Pss4 and Bwr-6.3 specific to Pss1632 were mapped to an interval of 5.0 cM (P < 0.05) between 6_33,444,000_SLM6-47 and 6_33,868,000_SLM6-124 SNP marker, and to 2.7 cM (P < 0.01) between positions 6_35,949,000 _SLM6-107 to 6_36,750,000_SLM6-82 marker, respectively. In addition, the specific effect of Bwr-12 for resistance to Pss4 (LOD score of 5.8-16.1, P < 0.01) was confirmed and markers for this QTL have already been made available previously.
ARTICLE | doi:10.20944/preprints201704.0070.v1
Subject: Life Sciences, Microbiology Keywords: genistein; soy isoflavone extracts; anti-menopausal dietary supplements; bacterial growth; viability of human cells
Online: 13 April 2017 (05:33:06 CEST)
Flavonoids, compounds present in many dietary supplements, affect growth of different bacterial species when tested as purified or synthetic substances. Here, we asked if soy isoflavone extracts, commonly used in many products sold as anti-menopausal dietary supplements, influence bacterial growth similarly to synthetic isoflavone, genistein. Four commercially available products were tested in amounts corresponding to genistein concentrations causing inhibition of growth of Vibrio harveyi (a model bacterium sensitive to this isoflavone) and Escherichia coli (a model bacterium resistant to genistein). Differential effects of various extracts on V. harveyi and E. coli growth, from stimulation, through no changes, to inhibition, were observed. Moreover, contrary to genistein, tested extracts caused a decrease (to different extends) in viability of human dermal fibroblasts. These results indicate that effects of various soy isoflavone extracts on bacterial growth and viability of human cells are different, despite similar declared composition of the commercially available products.
ARTICLE | doi:10.20944/preprints202108.0177.v1
Subject: Medicine & Pharmacology, Dentistry Keywords: Antibacterial composites; Antiadhesive composites; Poly-Pore; Split-mouth; Clinical trial; Live/dead staining; Bacterial viability
Online: 9 August 2021 (07:53:57 CEST)
The purpose of the study was to investigate the bacterial viability of the initial biofilm on the surface of experimental modified dental resin composites. Twenty-five healthy individuals with good oral hygiene were included in this study. In a split-mouth design, they received acrylic splints with five experimental composite resin specimens. Four of them were modified with either a novel polymeric hollow beads delivery system or methacrylated polymerizable Irgasan (Antibacterial B), while one specimen served as unmodified control (ST). The delivery system based on Poly-Pore® was loaded with one of the active agents Tego® Protect 5000 (Antiadhesive A), Dimethicone (Antiadhesive B) or Irgasan (Antibacterial A). All study subjects refrained from toothbrushing during the study period. Specimens were detached from the splints after 8h and given a live/dead staining before fluorescence microscopy. Friedman test and post-hoc Nemenyi test were applied with significance level at p < 0.05. In summary all materials but Antibacterial B showed a significant antibacterial effect compared to ST. In conclusion dental resin composites with Poly-Pore loaded active agents show antibacterial effectiveness in situ.
ARTICLE | doi:10.20944/preprints202101.0045.v1
Subject: Life Sciences, Biochemistry Keywords: Kombucha tea; microbial diversity; bacterial cellulose; Komagataeibacter xylinus; repetitive elements sequence-based rep-PCR; typing
Online: 4 January 2021 (13:24:41 CET)
Bacterial cellulose (BC) is receiving great attention due to its unique properties such as high purity, water retention capacity, high mechanical strength, and biocompatibility. However, the production of BC has been limited because of high cost and low productivity. In this light, the isolation of new BC producing bacteria and selection of high productive strains became a promising issue. Kombucha tea is a fermented beverage in which the bacteria fraction of the microbial community is composed mostly by strains belonging to the genus Komagataeibacter. In this study Kombucha tea production trials were performed starting from a previous batch, and bacterial isolation was conducted along cultivation time. From the whole microbial pool, 46 isolates were tested for their ability in producing BC. The obtained BC yield ranged from 0.59 g/L, for the isolate K2G36, to 23 g/L for K2G30 used as the reference strain. The genetic intraspecific diversity of the 46 isolates was investigated using two repetitive-sequence-based PCR typing methods, which are the enterobacterial repetitive intergenic consensus (ERIC) elements and the (GTG)5 sequences, respectively. The results obtained using two different approaches revealed the suitability of the fingerprints techniques, showing a discrimination power, calculated as D index, of 0.94 for (GTG)5 rep-PCR and 0.95 for ERIC rep-PCR. In order to improve the sensitivity of the applied method, a combined model from the two genotyping experiments was performed, allowing to discriminate among strains.
ARTICLE | doi:10.20944/preprints202101.0018.v1
Subject: Engineering, Automotive Engineering Keywords: conjunctive use; cropping pattern; genetic algorithm; bacterial foraging optimization; ant colony optimization; hybrid optimization; productivity
Online: 4 January 2021 (11:31:59 CET)
Increasing demand for food production with limited available water resources pose the threat to agricultural activities. The conjunctive allocation of water resources maximizes the net benefit of farmers efficiently. In this study, a novel hybrid optimization model was developed based on a genetic algorithm (GA), bacterial foraging optimization (BFO) and ant colony optimization (ACO) to maximize the net benefit of water deficit Sathanur reservoir command. The GA-based opti-mization model considered crop-related physical and economical parameters to derive optimal cropping patterns for three different conjunctive use policies and further allocation of surface and groundwater for different crops are enhanced with the BFO. The allocation of surface and groundwater for the head, middle and tail reach obtained from BFO is considered as input to ACO as a guiding mechanism to attain an optimal cropping pattern. Comparing the average produc-tivity values Policy 3 (3.665 Rs/m3) has better values relating to Policy 1 (3.662 Rs/m3) and Policy 2 (3.440 Rs/m3). Thus, the developed novel hybrid optimization model (GA-BFO-ACO) is very promising to enhance the farmer's net income as well as for the command area water conservation and can be replicated in other irrigated regions of the globe to overcome chronic land and water problems.
ARTICLE | doi:10.20944/preprints201711.0135.v1
Subject: Life Sciences, Microbiology Keywords: rice; endophyte; sustainable agriculture; plant microbiome; simplified bacterial community; syncom; taxonomic profiling; core plant microbiome
Online: 21 November 2017 (03:33:00 CET)
Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed the isolation of bacterial strains from the endorhizosphere of two rice cultivars from Venezuela. The validation of plant-growth promoting bacterial activities in vitro has led us to select and characterize 15 isolates for in planta studies such as germination test, endophytism ability and plant growth promotion. Consequently, a set of 10 isolates was selected for the set-up of an endophytic consortium as a simplified model of the natural rice bacterial endomicrobiota. Upon inoculation, the colonization and abundance of each strain within the rice roots was tracked by a culture-independent technique in gnotobiotic conditions in a 30 days period. Four strains belonging to Pseudomonas, Agrobacterium and Delftia genera have shown a promising capacity for colonizing and coexistence in root tissues. On the other hand, a bacterial community taxonomic profiling of the rhizosphere and the endorhizosphere of both cultivars were obtained and are discussed. This study is part of a growing body of research on core crops microbiome and simplified microbiomes, which strengthens the formation process of the endophytic community leading to a better understanding of the rice microbiome.
ARTICLE | doi:10.20944/preprints201709.0031.v1
Subject: Biology, Other Keywords: rice; endophyte; sustainable agriculture; plant microbiome; simplified bacterial community; syncomm; taxonomic profiling; core plant microbiome
Online: 8 September 2017 (14:02:56 CEST)
Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed the isolation of hundreds bacterial isolates obtained from endorhizosphere of two rice cultivars from Venezuela. The validation of plant-growth promoting bacterial activities in vitro has led us to select and characterize 15 isolates for in planta studies such as germination test, endophytism ability and plant growth promotion. Consequently, a set of 10 isolates was selected for the set-up of an endophytic consortium as a simplified model of the natural rice bacterial endomicrobiota. Upon inoculation, the colonization and abundance of each strain within the rice roots was tracked by a culture-independent technique in gnotobiotic conditions in a 30 days period. Four strains belonging to Pseudomonas, Agrobacterium and Delftia genera have shown a promising capacity for colonizing and coexistence in root tissues. On the other hand, a bacterial community taxonomic profiling of the rhizosphere and the endorhizosphere of both cultivars were obtained and are discussed. This study is part of a growing body of research on core crops microbiome and simplified microbiomes, which strengthens the formation process of the endophytic community leading to a better understanding of the rice microbiome.
Subject: Life Sciences, Biochemistry Keywords: continuous evolution; protein design; protein engineering; phage; bacterial one-hybrid; plaque assay; mutational analysis; DNA sequencing
Online: 5 November 2019 (02:19:01 CET)
Directed evolution methods are becoming increasingly popular, as they are extremely powerful toward developing new biomolecules with altered/novel activities, e.g., proteins with new catalytic functions or substrate specificities, and nucleic acids that recognize an intended target. Especially useful are systems that have incorporated continuous evolution, where the protein to be evolved undergoes continuous mutagenesis to evolve a desired trait with little to no input from the researcher once the system is started. However, continuous evolution methods can be challenging to implement in the lab and daunting for researchers to invest time and resources. Our intent is to provide basic information and helpful suggestions that we have gained from our experience with bacterial phage-assisted continuous evolution (PACE). Specifically, we review factors to consider before adopting PACE for a given evolution scheme, different types of selection circuits that can be utilized with particular focus on the PACE-B1H selection system, what optimization of a PACE selection circuit may look like using directed evolution of ME47 as a case study, and additional techniques that may be incorporated into a PACE experiment. With this information, researchers will be better equipped to determine if PACE is a valid strategy to use to evolve their proteins and how to set up a valid selection circuit.
REVIEW | doi:10.20944/preprints201908.0221.v1
Subject: Keywords: luminescence bioassays; bacterial cells; enzymes; fluorescent protein; low-intensity factors; hormesis; radiation; bioactive compounds; antioxidant activity
Online: 21 August 2019 (09:02:20 CEST)
Current paper reviews applications of luminescence bioassays for monitoring low-intensity factors, namely, radioactivity of different types (alpha, beta and gamma), and bioactive compounds (humic substances and fullerenols). Luminescence intensity is taken as a physiological parameter of luminous organisms. High rates of luminescence response can provide (1) a proper number of experiments under comparable conditions and, therefore, proper statistical processing, with this being highly important for ‘noisy’ low-dose exposures; (2) non-genetic, i.e. biochemical and physicochemical mechanisms of cellular response, in accordance to “exposome” concept. Bioassays based on luminous marine bacteria, their enzymes, and fluorescence coelenteramide-containing proteins were used to compare results of low-intensity exposures at cellular, biochemical and physicochemical levels, respectively. Results of the cellular exposures were discussed in terms of hormesis concept. Bioluminescence time dependence under low-dose radiation exposures corresponded to hormesis or threshold models; no bioluminescence monotonic dependency on intensity of exposure (dose rate, radioactivity, concentration) was found. Bioluminescence activation and absence of its dependency on intensity of exposure can be accepted as features of cellular adaptive response. Changes of biological luminescence were analyzed and discussed for bioassays of lower organization level – enzymes and florescent protein.
ARTICLE | doi:10.20944/preprints202105.0608.v3
Subject: Materials Science, Biomaterials Keywords: nanocomposites; bacterial cellulose; ceria nanoparticles; thermal properties; swelling; mechanical behavior; biomedical applications; stem cells proliferation; gene expression
Online: 17 June 2021 (10:02:24 CEST)
A technique for fabrication of bacterial cellulose-based films with CeO2 nanofiller has been developed. The structural and morphological characteristics of the materials have been studied, their thermal and mechanical properties in dry and swollen states having been determined. The preparation methodology makes it possible to obtain composites with a uniform distribution of nanoparticles. The catalytic effect of ceria regarding the thermal oxidative destruction of cellulose has been confirmed by TGA and DTA methods. An increase in CeO2 content led to an increase in the elastic modulus (a 1.27-fold increase caused by the introduction of 5 wt.% of the nanofiller into the polymer) and strength of the films. This effect is explained by the formation of additional links between polymer macro-chains via the nanoparticles’ surface. The materials fabricated were characterised by a limited ability to swell in water. Swelling caused a 20- to 30-fold reduction in the stiffness of the material, the mechanical properties of the films in a swollen state remaining germane to their practical use. The application of the composite films in cell engineering as substrates for the stem cells’ proliferation has been studied. The increase in CeO2 content in the films enhanced the proliferative activity of embryonic mouse stem cells. The cells cultured on the scaffold containing 5 wt.% of ceria demonstrated increased cell survival and migration activity. An analysis of gene expression confirmed improved cultivation conditions on CeO2-containing scaffolds.
ARTICLE | doi:10.20944/preprints202009.0273.v1
Subject: Life Sciences, Microbiology Keywords: Chromobacterium vaccinii; biofilm; sharing goods; social cheater; bog microbiome; bacterial genome, violacein, cold adaptation, IDBac, QS mutant
Online: 12 September 2020 (12:04:38 CEST)
Chromobacterium species are common in tropical and subtropical zones in environmental water samples and believed to «tropical» species. Here we describe an environmental case of resident Chromobacterium vaccinii in biofilms associated with Carex spp. roots in Moscow region, Russia (warm-summer humid continental climate zone). We performed broad characterization of individual properties as well as surrounding context for better understanding the premise of C. vaccinii survival during winter season. Genome properties of isolated strains propose some insights into adaptation to habit and biofilm mode of life, including social cheaters carrying ΔluxR mutation. Isolated C. vaccinii differs with previously described strains in some biochemical properties and some basic characteristics like fatty acid composition as well as unique genome features. Despite potential to modulate membrane fluidity and presence of several genes responsible for cold shock response, isolated C. vaccinii didn`t survive during exposure to 4 °C, while in initial complex biofilm it was able to survive for months in vitro at 4 °C. Surrounding bacterial community within the same biofilm with C. vaccinii represented a series of psychrophilic bacterial species which may share resistance to low temperatures with other species within biofilm and provide C. vaccinii opportunity to survive during cold winter season.
SHORT NOTE | doi:10.20944/preprints202008.0663.v1
Subject: Keywords: Mask; PPE; Bacteria; Nasal; Breath; Bacterial Culture; bioaerosols; COVID-19; SARS-CoV-2; hygiene behavior; face mask
Online: 30 August 2020 (11:41:33 CEST)
Many individuals are wearing face masks improperly at ‘half mask’ and potentially breathing out microbes that can contaminate the air as well as anything below the nose. This note provides the first report that bacteria and fungi breathed out during nasal air exhalation are able to be cultured after landing on blood agar plates. The CFU’s are higher after both 10 breaths and extremely significant for 20 breaths compared to the control plates exposed to the air. Implications of this finding are that going ‘nose commando’ may be able to continue the spread of respiratory diseases such as COVID-19.
ARTICLE | doi:10.20944/preprints201911.0130.v1
Subject: Biology, Ecology Keywords: bacterial calcium-carbonate precipitation (BCP); calcifying bacteria selection; calcifying mixed cultures; imagej software; biolog ecoplates; sand biocementation
Online: 12 November 2019 (16:06:06 CET)
Bacterial Calcium-carbonate Precipitation (BCP) has been studied for multiple applications such as remediation, consolidation and cementation. Isolation and screening of strong calcifying bacteria is the main task of BCP-technique. In this paper we studied CaCO3 precipitation by different bacteria isolated from a rhizospheric soil in both solid and liquid media. It has been found, through culture-depending studies, that bacteria belonging to Actinobacteria, Gammaproteobacteria and Alphaproteobacteria are the dominant bacteria involved in CaCO3 precipitation in this environment. Pure and mixed cultures of selected strains were applied for sand biocementation experiments. Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray Spectroscopy (EDS) analyses of the biotreated samples revealed the biological nature of the cementation and the effectiveness of the biodeposition treatment by mixed cultures. X-ray diffraction (XRD) analysis confirmed that all the calcifying strains selected for sand biocementation precipitated CaCO3, mostly in the form of calcite. In this study Biolog® Eco-plate is evaluated as a useful method for a more targeted choice of the sampling site with the purpose of obtaining interesting candidates for BCP applications. Furthermore, ImageJ software was investigated, for the first time to our knowledge, as a potential method to screen high CaCO3 producer strains.
ARTICLE | doi:10.20944/preprints201809.0452.v1
Subject: Life Sciences, Biotechnology Keywords: Microbial fuel cell; polymer matrix; immobilization of bacterial cells; interaction of cell membranes with carbon nanotubes, boostconverter accumulation
Online: 24 September 2018 (11:06:23 CEST)
The anode of a microbial fuel cell (MFC) was formed on a graphite electrode and immobilized Gluconobacter oxydans VKM-1280 bacterial cells. Immobilization was performed in chitosan, poly(vinyl alcohol) or N-vinylpyrrolidone-modified poly(vinyl alcohol). Ethanol was used as substrate. The anode was modified using multiwalled carbon nanotubes. The aim of the modification was to create a conductive network between cell lipid membranes, containing exposed PQQ-dependent alcoholdehydrogenases, and the electrode to facilitate electron transfer in the system. The bioelectrochemical characteristics of modified anodes at various cell/polymer ratios were assessed via current density, power density, polarization curves and impedance spectres. MFCs based on chitosan at a matrix/cell volume ratio of 5:1 produced maximal power characteristics of the system (8.3 μW/cm2) at a minimal resistance (1111 Ohm cm2). Modification of the anode by multiwalled carbon nanotubes led to a slight decrease of internal resistance (down to 1078 Ohm cm2) and to an increase of generated power density up to 10.6 μW/cm2. We explored the possibility of accumulating electric energy from an MFC on a 6,800-μF capacitor via a boost converter. Generated voltage was increased from 0.3 V up to 3.2 V. Accumulated energy was used to power a Clark-type biosensor and a bluetooth transmitter with three sensors, a miniature electric motor and a light-emitting diode.
ARTICLE | doi:10.20944/preprints202202.0265.v1
Subject: Life Sciences, Cell & Developmental Biology Keywords: adult neurogenesis; dentate gyrus; diet; microglia; bacterial endotoxin lipopolysaccharide; LPS; Omega 3; polyunsaturated fatty acids; sexual dimorphism; systemic inflammation
Online: 22 February 2022 (09:44:55 CET)
Maternal intake of the polyunsaturated fatty acids omega-3 (n-3 PUFA) and omega-6 (n-6 PUFA) impacts hippocampal neurogenesis during development, an effect that may extend to adulthood by altering adult hippocampal neurogenesis (AHN). n-3 PUFA and n-6 PUFA are precursors of inflammatory regulators that potentially affect AHN and glia. Additionally, n-3 PUFA dietary supplementation may present a sexually dimorphic action in the brain. Therefore, we postulated that dietary n-6/n-3 PUFA balance shapes the adult DG in a sex-dependent manner influencing AHN and glia. We test our hypothesis by feeding adult female and male mice with n-3 PUFA balanced or deficient diets. To analyze the immunomodulatory potential of the diets, we injected mice with the bacterial endotoxin lipopolysaccharide (LPS). LPS reduced neuroblast number, and its effect was exacerbated by the n-3 PUFA deficient diet. The n-3 PUFA deficient diet reduced the DG volume, AHN, microglia number and surveilled volume. Diet effect on most mature neuroblasts was exclusively significant in female mice. Colocalization and multivariate analysis revealed an association between microglia and AHN, and the sexual dimorphic effect of diet. Our study reveals that female mice are more susceptible than males to the effect of dietary n-6/n-3 PUFA ratio on AHN and microglia.
REVIEW | doi:10.20944/preprints202011.0156.v1
Subject: Materials Science, Nanotechnology Keywords: Bacterial detection; Biosensors; Clinical pathogen; COVID-19; Electrospun nanofibers; Nano-biosensors; Point-of-care; SARS-CoV-2; Viral detection.
Online: 3 November 2020 (14:15:34 CET)
Biosensors are measurement devices that can sense several biomolecules, and are widely used for the detection of relevant clinical pathogens such as bacteria and viruses, showing outstanding results. Because of the latent existing risk of facing another pandemic like the one we are living due to COVID-19, researchers are constantly looking forward to developing new technologies for diagnosis and treatment of infections caused by different bacteria and viruses. Regarding that, nanotechnology has improved biosensors design and performance through the development of materials and nanoparticles that enhance their affinity, selectivity, and efficacy in detecting these pathogens, such as employing nanoparticles, graphene quantum dots, and electrospun nanofibers. Therefore, this work aims to present a comprehensive review that exposes how biosensors work in terms of bacterial and viral detection, and the nanotechnological features that are contributing to achieving a faster yet still efficient COVID-19 diagnosis at the point-of-care.
REVIEW | doi:10.20944/preprints202007.0375.v1
Subject: Medicine & Pharmacology, Other Keywords: bacterial infection; non-healing wounds; antimicrobial resistance; multidrug resistance; antimicrobial peptides (AMPs); AMP conjugates; AMP carriers and delivery systems
Online: 17 July 2020 (09:26:21 CEST)
Bacterial infections occur when wound healing fails to reach the final stage of healing, usually hindered by the presence of different pathogens. Different topical antimicrobial agents are used to inhibit bacterial growth due to antibiotic failure in reaching the infected site accompanied very often by an increased drug resistance and other side effects. In this review, we focus on antimicrobial peptides (AMPs), especially those with a high potential of efficacy against multidrug-resistant and biofilm-forming bacteria and fungi present in wound infections. Currently, different AMPs undergo preclinical and clinical phase to combat infection-related diseases. AMP dendrimers (AMPDs) have been mentioned as potent microbial agents. Various AMP delivery strategies, such as polymers, scaffolds, films and wound dressings, organic and inorganic nanoparticles, to combat infection and modulate the healing rate have been discussed as well. New technologies such as CRISPR-Cas are taken into consideration as potential future tools for AMP delivery in skin therapy.
ARTICLE | doi:10.20944/preprints202111.0558.v1
Subject: Life Sciences, Microbiology Keywords: Yersinia pestis; vaccine; guinea pigs; bubonic plague; inactivated vaccine; phage; bacterial ghost; protection; protein-E-mediated lysis, holin-endolysin system
Online: 30 November 2021 (11:08:18 CET)
To develop a modern plague vaccine, we used hypo-endotoxic Yersinia pestis bacterial ghosts (BGs) with combinations of genes encoding the bacteriophage ɸX174 lysis-mediating protein E and/or holin-endolysin systems from λ or L-413C phages. Expression of the protein E gene resulted in the BGs that retained the shape of the original bacterium. Co-expression of this gene with genes coding for holin-endolysin system of the phage L-413C caused formation of structures resembling collapsed sacs. Such structures, which have lost their rigidity, were also formed as a result of the expression of only the L-413C holin-endolysin genes. Similar holin-endolysin system from phage λ containing mutated holin gene S and intact genes R-Rz coding for the endolysins caused generation of mixtures of BGs that had (i) practically preserved and (ii) completely lost their original rigidity. The addition of protein E to the work of this system shifted the equilibrium in the mixture towards the collapsed sacs. The collapse of the structure of BGs can be explained by endolysis of peptidoglycan sacculi. Immunizations of laboratory animals with the variants of BGs followed by infection with a wild-type Y. pestis strain showed that bacterial envelopes protected only cavies. BGs with peptidoglycan maximally hydrolyzed had a greater protectivity compared to BGs with preserved peptidoglycan skeleton.
REVIEW | doi:10.20944/preprints201812.0170.v1
Subject: Life Sciences, Biotechnology Keywords: bacterial nanocellulose; nanofibrillated nanocellulose; animal nanocellulose; algal nanocellulose; tissue engineering; tissue repair; wound dressing; cell delivery; drug delivery; antimicrobial properties
Online: 14 December 2018 (06:44:53 CET)
Nanocellulose is cellulose in the form of nanostructures, i.e. features not exceeding 100 nm at least in one dimension. These nanostructures include nanofibrils, e.g. in bacterial cellulose; nanofibers, e.g. in electrospun matrices; nanowhiskers and nanocrystals. These structures can be further assembled into bigger 2D and 3D nano-, micro- and macro-structures, such as nanoplatelets, membranes, films, microparticles and porous macroscopic matrices. There are four main sources of nanocellulose: bacteria (Gluonacetobacter), plants (trees, shrubs, herbs), algae (Cladophora) and animals (Tunicata). Nanocellulose has emerged for a wide range of industrial, technology and biomedical applications, e.g. for adsorption, ultrafiltration, packaging, conservation of historical artifacts, thermal insulation and fire retardation, energy extraction and storage, acoustics, sensorics, controlled drug delivery, and particularly for tissue engineering. Nanocellulose is promising for use in scaffolds for engineering of blood vessels, neural tissue, bone, cartilage, liver, adipose tissue, urethra and dura mater, for repairing connective tissue and congenital heart defects, and for constructing contact lenses and protective barriers. This review is focused on applications of nanocellulose in skin tissue engineering and wound healing as a scaffold for cell growth, for delivering cells into wounds, and as a material for advanced wound dressings coupled with drug delivery, transparency and sensorics. Potential cytotoxicity and immunogenicity of nanocellulose are also discussed.
ARTICLE | doi:10.20944/preprints201809.0065.v1
Subject: Physical Sciences, Applied Physics Keywords: AFM, photothermal excitation, off-resonance tapping, high-speed atomic force microscopy, live cell imaging, antimicrobial peptide, thrombocytes, bacterial imaging, cell lysis
Online: 4 September 2018 (12:25:20 CEST)
Imaging living cells by atomic force microscopy (AFM) promises not only high-resolution topographical data, but additionally, mechanical contrast, which are not obtainable with other microscopy techniques. Such imaging is however challenging, as cells need to be measured with low interaction forces to prevent either deformation or detachment from the surface. Off-resonance modes which periodically probe the surface have been shown to be advantageous, as they provide excellent force control combined with large amplitudes, which help reduce lateral force interactions. However, the low actuation frequency in traditional off-resonance techniques limits the imaging speed significantly. Using photothermal actuation, we probe the surface by directly actuating the cantilever. Due to the much smaller mass that needs to be actuated, the achievable measurement frequency is increased by two orders of magnitude. Additionally, photothermal off-resonance tapping retains the precise force control of conventional off-resonance modes and is therefore well suited to gentle imaging. Here we show how photothermal off-resonance tapping can be used to study live cells by AFM. As an example of imaging mammalian cells, the initial attachment, as well as long term detachment of a human thrombocytes are presented. The membrane disrupting effect of the antimicrobial peptide CM-15 is shown on the cell wall of E. coli. Finally, the dissolution of the cell wall of B. subtilis by lysozyme is shown. Taken together, these evolutionarily disparate forms of life exemplify the usefulness of PORT for live cell imaging in a multitude of biological disciplines.
Subject: Biology, Animal Sciences & Zoology Keywords: feminine hygiene; feminine gel wash; lactic acid; vulvar skin pH; vulvar microbiome; skin microflora; vulvovaginal environment; bacterial 16S rRNA gene; fungal ITS
Online: 9 December 2019 (03:53:52 CET)
Background: While intimate feminine hygiene products are widely used by women as part of daily cleansing routines, little is known about how these products impact the vulvovaginal area and its microbiome stability. A novel gel wash containing lactic acid (pH 4.2) for external daily use was formulated to provide gentle cleansing, freshness, and antimicrobial protection to maintain a healthy balance of the vulvar skin area. This 4-week clinical study assessed tolerance of the gel wash when used on the external genital area and its effects on skin hydration, vulvar skin pH, and the vulvar microbiome. After a 7-day pre-study conditioning period, 36 healthy females in 3 balanced age groups (18-29, 30-44, and 45-55 years) used the gel wash to cleanse their external genital area (mons pubis and vulva) and entire body at least once per day for 28 days. The primary endpoint wasSkin tolerance of the gel wash was assessed by the gynecologist. Effects of the gel wash on vulvar skin microbiota were studied by performing bacterial 16S rRNA and fungal ITS microbial richness and diversity analysis. Results: Based on gynecologic assessment after 28 days of use, the gel wash showed acceptable tolerance, with no signs of increased dryness, redness, edema, itching, stinging, or burning. Use of the gel wash was associated with a significant increase in both short-term (single application) and longer-term (daily use for 28 days) skin moisturization. There was no significant change in vulvar skin pH over time with daily product use, and the gel wash did not significantly affect the natural vulvar microbiome species richness or diversity for bacteria or fungi. Conclusions: Results of the study showed that this new gel wash is a mild, moisturizing cleanser that does not harm and instead maintains the natural pH and microbial diversity of vulvar skin. To our knowledge, this was the first study to assess the effect of an antimicrobial feminine gel wash on the natural pH and vulvar microbiome habitat of the skin using bacterial 16S rRNA and fungal ITS genetic sequencing techniques, thereby providing a better understanding of the bacterial and fungal communities that inhabit the external vulvar area in healthy women.
REVIEW | doi:10.20944/preprints201609.0050.v1
Subject: Engineering, Biomedical & Chemical Engineering Keywords: DCMS, DCMSP, and sputtering; highly ionized pulse plasma magnetron sputtering (HIPIMS); bacterial inactivation kinetics; Cu and TiO2 synergic effects; interfacial charge transfer
Online: 16 September 2016 (13:31:00 CEST)
This review focuses on Cu/TiO2 sequentially and Cu-TiO2 co-sputtered catalytic/photocatalytic surfaces leading to bacterial inactivation discussing their stability, synthesis, adhesion and antibacterial kinetics. The intervention of TiO2, Cu and the synergic effect of Cu and TiO2 on films prepared by a colloidal approach and other techniques is also reviewed leading to bacterial inactivation. Processes in aerobic media and anaerobic media leading to bacterial loss of viability on multidrug resistant (MDR) pathogens, Gram-negative (-) and Gram-positive(+) bacteria are described. Insight is provided for the interfacial charge transfer mechanism under solar irradiation occurring between TiO2 and Cu. surface properties of 2D TiO2/Cu and TiO2-Cu films are correlated with the bacterial inactivation kinetics observed in the dark and under light. The intervention of these antibacterial sputtered surfaces in health-care facilities leading to MRSA-isolates is described in the dark and under the actinic light. The synergic intervention of the Cu and TiO2 films leading to bacterial inactivation prepared by direct current magnetron sputtering (DCMS), pulsed direct current magnetron sputtering (DCMSP) and highly ionized pulse plasma magnetron sputtering (HIPIMS) is reported in a detailed way.
ARTICLE | doi:10.20944/preprints201608.0162.v1
Subject: Life Sciences, Microbiology Keywords: bacterial ghosts (BGs); Vibrio parahaemolyticus; chemically induced lysis; minimum inhibition concentration (MIC); sodium hydroxide (NaOH); lipopolysaccharides (LPS); endotoxic activity; macrophages; cytotoxicity; cytokine
Online: 17 August 2016 (10:26:00 CEST)
Acellular bacterial ghosts (BGs) are empty non-living bacterial cell envelopes, commonly generated by controlled expression of the cloned lysis gene E of bacteriophage PhiX174. In this study, Vibrio parahaemolyticus ghosts (VPGs) were generated by chemically induced lysis and the method is based on minimum inhibitory concentration (MIC) of sodium hydroxide (NaOH), acetic acid, boric acid, citric acid, maleic acid, hydrochloric acid and sulfuric acid. The MIC values of the respective chemicals were 3.125, 6.25, < 50.0, 25.0, 6.25, 1.56 and 0.781 mg/ml. Except boric acid, the lysis efficiency was reached more than 99.99% at 5 min after treatment of all chemicals. Among those chemicals, NaOH-induced VPGs showed completely DNA-free that was confirmed by quantitative real-time PCR. Besides, lipopolysaccharides (LPS) extracted from the NaOH-induced VPGs showed no distinctive band on SDS-PAGE gel after silver staining. On the other hand, LPS extracted from wild-type bacterial cells as well as the organic acids-induced VPGs showed triple major bands and LPS extracted from the inorganic acids-induced VPGs showed double bands. It suggests that some surface structures in LPS of the NaOH-induced VPGs may be lost, weakened or modified by the MIC of NaOH. Nevertheless, Limulus amoebocyte lysate assay revealed that there is no significant difference in endotoxic activity between the NaOH-induced VPGs and wild-type bacterial cells. Macrophages exposed to the NaOH-induced VPGs at 0.5 × 106 CFU/mL showed cell viability of 97.9%, however the MIC of NaOH did not reduce the cytotoxic effect of wild-type bacterial cells. Like Escherichia coli LPS, the NaOH-induced VPGs are an excellent activator of pro-inflammatory cytokines (IL-1β and iNOS), anti-inflammatory cytokine (IL-10) and dual activities (IL-6) in the stimulated macrophage cells. On the other hand, the induction of TNF-α mRNA was remarkable in the macrophages exposed with wild-type cells. Scanning electron microscopy showed the formation of trans-membrane lysis tunnel structures in the NaOH-induced VPGs. SDS-PAGE and agarose gel electrophoresis also confirmed that cytoplasmic proteins and genomic DNA released from the VPGs to culture medium through the lysis tunnel structures. Taken together, all these results indicated that the NaOH-induced VPGs show the potency of safe, economical and effective inactivated bacterial vaccine candidate.
ARTICLE | doi:10.20944/preprints202008.0056.v1
Subject: Life Sciences, Microbiology Keywords: Cornu aspersa mucus; antimicrobial peptides; antibacterial activity; bacterial strains; Pseudomonas aureofaciens AP9; Escherichia coli NBIMCC 8785; Brevibacillus laterosporus strain BT-271; Clostridium perfringens NBIMCC 8615
Online: 3 August 2020 (00:25:22 CEST)
Natural products have long played a major role in medicine and science. The garden snail Cornu aspersa is a rich source of biologically active natural substances which might be an important source for new drugs to treat human disease. Based on our previous studies seven fractions containing compounds with Mw <3 kDa, <10 kDa, <20 kDa, >20 kDa, and between 3-5 kDa, 5-10 kDa, and 10-30 kDa were purified from the mucus of C. aspersa and analyzed by tandem mass spectrometry (MALDI-TOF/TOF). Seventeen novel peptides with potential antibacterial activity have been identified by de novo MS/MS sequencing using tandem mass spectrometry. The different fractions were tested for antibacterial activity against Gram─ (Pseudomonas aureofaciens and Escherichia coli) and Gram+ (Brevibacillus laterosporus) bacterial strains as well anaerobic bacterium Clostridium perfringens. These results revealed that the peptide fractions exhibit a predominant antibacterial activity against B. laterosporus, the fraction with Mw 10 – 30 kDa against E. coli, another peptide fraction <20 kDa against P. aureofaciens, and the protein fraction >20 kDa against the bacterial strain C. perfringens. The discovery of new antimicrobial peptides (AMPs) from natural sources is of great importance for public health due to their effective antimicrobial activities and low resistance rates.
ARTICLE | doi:10.20944/preprints201812.0236.v2
Subject: Life Sciences, Biochemistry Keywords: bacterial toxin; cholera toxin; Escherichia coli heat-labile enterotoxin; lectin; N-acetyllactosamine binding; neutral glycosphingolipids; protein-carbohydrate interactions; surface plasmon resonance spectroscopy; X-ray crystal structure
Online: 28 January 2019 (15:23:24 CET)
Diarrhoea caused by enterotoxigenic Escherichia coli is one of the leading causes of mortality in children under five years of age and is a great burden on developing countries. The major virulence factor of the bacterium is the heat-labile enterotoxin (LT), a close homologue of the cholera toxin. The toxins bind to carbohydrate receptors in the gastrointestinal tract, leading to toxin uptake and, ultimately, to severe diarrhoea. Previously, LT from human- and porcine-infecting ETEC (hLT and pLT, respectively) were shown to have different carbohydrate-binding specificities, in particular with respect to N-acetyllactosamine-terminating glycosphingolipids. Here, we probed eleven single-residue variants of the heat-labile enterotoxin with surface plasmon resonance spectroscopy and compared the data to the parent toxins. In addition we present a 1.45 Å crystal structure of pLTB in complex with branched Lacto-N-neohexaose (Galbeta4GlcNAcbeta6[Galbeta4GlcNAcbeta3]Galbeta4Glc). The largest difference in binding specificity is caused by mutation of residue 94, which links the primary and secondary binding sites of the toxins. Residue 95 (and to a smaller extent also residues 7 and 18) also contribute, whereas residue 4 shows no effect on monovalent binding of the ligand and may rather be important for multivalent binding and avidity.
ARTICLE | doi:10.20944/preprints201706.0016.v1
Subject: Mathematics & Computer Science, Other Keywords: pumped storage hydro unit; guide vane closing schemes; multi-objective optimization; enhanced multi-objective bacterial-foraging chemotaxis gravitational search algorithm (EMOBCGSA); hydraulic and mechanical constraints
Online: 2 June 2017 (07:56:05 CEST)
The optimization of guide vane closing schemes (OGVCS) of pumped storage hydro unit (PSHU) is the research field of cooperative control and optimal operation of pumped storage, wind power and solar power generation. This paper presents a OGVCS model of PSHU considering the rise rate of the unit rotational speed and the specific node pressure of each hydraulic unit, as well as various complicated hydraulic and mechanical constraints. OGVCS model is formulated as a multi-objective optimization problem to optimize conflictive objectives, i.e., unit rotational speed and water hammer pressure criteria. In order to realize the efficient solution of the OGVCS model, an enhanced multi-objective bacterial-foraging chemotaxis gravitational search algorithm (EMOBCGSA) is proposed to solve this problem, which adopts population reconstruction, adaptive selection chemotaxis operator of local searching strategy and Elite archive set to efficiently solve the multi-objective problem. Especially, novel constraints-handling strategy with eliminating and local search based on violation ranking is used to balance various hydraulic and mechanical constraints. Finally, simulation cases of complex extreme operating conditions (i.e., load rejection and pump outage) of ‘single tube-double units’ type PSHU system are conducted to verify the feasibility and effectiveness of the proposed EMOBCGSA in solving OGVCS problem. The simulation results indicate that the proposed EMOBCGSA can provide lower rise rate of the unit rotational speed and smaller water hammer pressure than other method established recently while considering various complex constraints in OGVCS problem.
REVIEW | doi:10.20944/preprints202009.0182.v1
Subject: Biology, Plant Sciences Keywords: Ralstonia solanacearum species complex; taxonomy; phylogenomic; plant bacteria; tomato wilt; bacterial wilt; brown rot of potato; Granville Wilt of tobacco; moko disease of banana; Bugtok disease; spewy eye
Online: 8 September 2020 (10:19:34 CEST)
The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separation of Ralstonia solanacearum into three genomic species. Frequent name changes occurred as methodology transitioned from phenotypic, biochemical, and molecular studies, to genomics and functional genomics. The diversity, wide host range and geographical distribution of R. solanacearum has resulted in its inclusion in a “species complex” as genomic analyses of elucidated phylogenetic relationships among strains. Current advances in phylogenetics and functional genomics now open new avenues for research into the epidemiology and control of the devastating bacterial wilt disease.