scholarly journals The Integration of Metagenomics and Chemical Physical Techniques Biodecoded the Buried Traces of the Biodeteriogens of Parchment Purple Spots

2020 ◽  
Vol 11 ◽  
Author(s):  
Nicoletta Perini ◽  
Fulvio Mercuri ◽  
Silvia Orlanducci ◽  
Maria Cristina Thaller ◽  
Luciana Migliore
Keyword(s):  
High Throughput ◽  
Multidisciplinary Approach ◽  
Complex Dynamics ◽  
Light Transmission ◽  
Molecular Techniques ◽  
Trace Back ◽  
Microbiological Methods ◽  
Unequivocal Identification ◽  
Level Of Knowledge ◽  
Ancient Documents

Ancient parchments record an immense part of our cultural heritage, having been used as the main written support material for centuries. Parchment easily undergoes biodeterioration, whose main signs are the so-called purple spots, which often lead to detachment of the superficial written layer. Up to recent years, several studies have been analyzing damaged parchments from different world’s archives, trying to trace back the culprit of the purple spots. However, standard cultivation and early molecular techniques have been demonstrated to be unsuccessful, leading the parchment damage issue remaining unsolved for many years. Nowadays, some studies have explored the parchment biodeterioration dynamics by adopting a multidisciplinary approach combining standard microbiological methods with high-throughput molecular, chemical and physical techniques. This approach allowed an unprecedented level of knowledge on the complex dynamics of parchment biodeterioration. This mini review discusses the application of the combination of basic and high-throughput techniques to study historical parchments, highlighting the strengths and weaknesses of this approach. In particular, it focuses on how metagenomics has been paramount for the unequivocal identification of the microbial main actors of parchment biodeterioration and their dynamics, but also on how metagenomics may suffer the distortion inflict by the historical perspective on the analysis of ancient specimens. As a whole, this mini review aims to describe the scenario of information on parchment biodeterioration obtained so far by using the integration of metagenomic with recent chemical (Raman spectroscopy) and physical (Light Transmission Analysis) approaches, which might have key implications in the preservation of many ancient documents.

scholarly journals Effect of Chlorination on Microbiological Quality of Effluent of a Full-Scale Wastewater Treatment Plant

Life ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 68
Author(s):  
Ioanna Zerva ◽  
Nikolaos Remmas ◽  
Ifigeneia Kagalou ◽  
Paraschos Melidis ◽  
Marina Ariantsi ◽  
...  
Keyword(s):  
High Throughput ◽  
Treatment Plant ◽  
Microbiological Quality ◽  
Amplicon Sequencing ◽  
Molecular Techniques ◽  
Fecal Coliforms ◽  
Biological Phosphorus Removal ◽  
Effluent Quality ◽  
Microbiological Methods ◽  
Wastewater Quality

The evaluation of effluent wastewater quality mainly relies on the assessment of conventional bacterial indicators, such as fecal coliforms and enterococci; however, little is known about opportunistic pathogens, which can resist chlorination and may be transmitted in aquatic environments. In contrast to conventional microbiological methods, high-throughput molecular techniques can provide an accurate evaluation of effluent quality, although a limited number of studies have been performed in this direction. In this work, high-throughput amplicon sequencing was employed to assess the effectiveness of chlorination as a disinfection method for secondary effluents. Common inhabitants of the intestinal tract, such as Bacteroides, Arcobacter and Clostridium, and activated sludge denitrifiers capable of forming biofilms, such as Acidovorax, Pseudomonas and Thauera, were identified in the chlorinated effluent. Chloroflexi with dechlorination capability and the bacteria involved in enhanced biological phosphorus removal, i.e., Candidatus Accumulibacter and Candidatus Competibacter, were also found to resist chlorination. No detection of Escherichia indicates the lack of fecal coliform contamination. Mycobacterium spp. were absent in the chlorinated effluent, whereas toxin-producing cyanobacteria of the genera Anabaena and Microcystis were identified in low abundances. Chlorination significantly affected the filamentous bacteria Nocardioides and Gordonia, whereas Zoogloea proliferated in the disinfected effluent. Moreover, perchlorate/chlorate- and organochlorine-reducing bacteria resisted chlorination.

scholarly journals Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

2020 ◽  
Author(s):  
Emily N. Junkins ◽  
Bradley S. Stevenson
Keyword(s):  
High Throughput ◽  
Drug Targets ◽  
High Throughput Sequencing ◽  
Multidrug Resistant ◽  
Molecular Techniques ◽  
Bioactive Metabolites ◽  
Plate Count ◽  
Molecular Tools ◽  
Vast Number ◽  
Sequencing Studies

AbstractMolecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.ImportanceCultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.

scholarly journals Diagnóstico laboratorial das meningites bacterianas

2011 ◽  
Vol 10 (1) ◽  
pp. 77
Author(s):  
Fernanda Machado Fonseca ◽  
Synara Cecília De Santana ◽  
Marcela Machado Fonseca ◽  
Ana Paula Sarreta Terra ◽  
Ronaldo Rodrigues Sarmento
Keyword(s):  
Bacterial Meningitis ◽  
Molecular Techniques ◽  
Bacteriological Examination ◽  
Font Size ◽  
Neurological Sequelae ◽  
Worldwide Distribution ◽  
Technological Advances ◽  
Microbiological Methods ◽  
Microbiologic Diagnosis ◽  
Important Disease

<p class="MsoNormal" style="text-align: justify; text-indent: 36pt; margin: 0cm 0cm 0pt;"><span style="font-family: 'Times New Roman'; font-size: x-small;">A despeito dos avanços tecnológicos em relação ao diagnóstico, à patogênese e ao tratamento, a meningite bacteriana ainda permanece como importante doença de distribuição mundial, cujo diagnóstico se apoia, principalmente, no exame bacteriológico. Mesmo com o avanço das técnicas moleculares, o diagnóstico microbiológico continua sendo amplamente utilizado e, portanto, merece atenção especial. O objetivo deste trabalho foi realizar um levantamento bibliográfico sobre os principais métodos microbiológicos para o diagnóstico das meningites bacterianas e seus principais agentes causadores, visto que a identificação precisa do agente etiológico permite a correta utilização da terapia farmacológica, o que diminui significativamente os riscos de desenvolvimento de sequelas neurológicas. </span><span style="font-family: 'Times New Roman'; font-size: small; text-indent: 36pt;">Abstract:</span></p><span style="font-size: small;"><span style="font-family: Times New Roman;"><span style="mso-ansi-language: PT-BR;"><p class="MsoNormal" style="text-align: justify; margin: 0cm 0cm 0pt; vertical-align: top;"><span style="color: black; mso-ansi-language: EN;" lang="EN">Despite technological advances in the diagnosis, pathogenesis and treatment, bacterial meningitis still remains an important disease of worldwide distribution in which the diagnosis relies mainly on bacteriological examination. Even with the advances in molecular techniques, microbiologic diagnosis is still widely used and therefore deserves special attention. The aim of this study was a literature review on the main microbiological methods for diagnosis of bacterial meningitis and its main agents, since the precise identification of the agent allows the correct use of drug therapy which significantly reduces the risk of developing neurological sequelae.</span></p></span></span></span>

scholarly journals What Have We Learned about the Microbiomes of Indoor Environments?

mSystems ◽  
2016 ◽  
Vol 1 (4) ◽  
Author(s):  
Brent Stephens
Keyword(s):  
Built Environment ◽  
Microbial Communities ◽  
Knowledge Base ◽  
Human Health ◽  
High Throughput ◽  
Indoor Environment ◽  
Molecular Techniques ◽  
Indoor Environments ◽  
Advanced Knowledge ◽  
The Way

ABSTRACT The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or have not advanced knowledge in each area beyond what we already knew from over 100 years of applying culture-based methods to building samples. The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or have not advanced knowledge in each area beyond what we already knew from over 100 years of applying culture-based methods to building samples. I propose that while we have added tremendous complexity to the rich existing knowledge base, the practical implications of this added complexity remain somewhat elusive. It remains to be seen how this new knowledge base will change how we design, build, and operate buildings. Much more research is needed to better understand the complexity with which indoor microbiomes may affect human health in both positive and negative ways.

scholarly journals High-Throughput Analysis of Ovarian Granulosa Cell Transcriptome

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Ewa Chronowska
Keyword(s):  
Reproductive Biology ◽  
High Throughput ◽  
Granulosa Cells ◽  
Cumulus Cell ◽  
Cumulus Cells ◽  
Molecular Techniques ◽  
Embryo Morphology ◽  
Embryo Viability ◽  
High Throughput Analysis ◽  
Developmental Potential

The quality of follicular oocytes depends on interactions with surrounding granulosa cells. Development of molecular techniques and methods enables better understanding of processes underlying mammalian reproduction on cellular level. The success in reproductive biology and medicine in different species depends on reliable assessment of oocyte and embryo viability which presently mainly bases on embryo morphology. Although successful pregnancies have been achieved using this approach, its precision still should be improved and completed with other, more objective, and accurate assessment strategies. Global profiling of gene expression in follicular cumulus cells using microarrays is continuously leading to the establishment of new biomarkers which can be used to select oocytes with highest developmental potential. Even more potential applications and greater precision could be achieved using next generation sequencing (NGS) of granulosa and cumulus cell RNA (RNA-seq). However, due to the high cost, this method is not used as frequently as microarrays at the moment. In any case, high-throughput technologies offer the possibilities and advantages in ovarian somatic cell analysis on scale that has not been noted so far. The aim of this work is to present current directions and examples of global molecular profiling of granulosa cells and underline its impact on reproductive biology and medicine.

scholarly journals Improved phenotyping procedure for evaluating resistance in rice against gall midge (Orseolia oryzae, Wood-Mason)

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Ling Cheng ◽  
Fugang Huang ◽  
Zhe Jiang ◽  
Baiyi Lu ◽  
Xiaohui Zhong ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Resistance Gene ◽  
High Throughput ◽  
Gall Midge ◽  
Screening Method ◽  
Molecular Techniques ◽  
Orseolia Oryzae ◽  
Mutant Screening ◽  
Biological Studies ◽  
High Throughput Phenotyping

Abstract Background The rice gall midge (RGM, Orseolia oryzae, Wood-Mason), an important stem-feeding pest worldwide, has caused serious production losses over the past decades. Rice production practices indicate that the most reliable method for managing RGM is the deployment of cultivars that incorporate host resistance. However, the conventional phenotypic screening method of rice resistance to RGM suggested by the International Rice Research Institute (IRRI) has been used for approximately 30 years, and only 12 rice varieties/lines (including controls) can be evaluated in one tray. It is not suitable for high-throughput phenotyping of rice germplasm. Moreover, a suitable method to prepare samples for molecular biological studies of rice resistance against RGM is imperative with the rapid development of modern molecular techniques. Results The proper density of seedlings/RGM was determined for four seeding arrangements. A high-throughput phenotyping method (HTPM) for 60 lines/varieties infested with 36 female RGM adults in one tray, as described by method 4–3 (seeded 60 lines/varieties), was developed and verified using mutant screening. Furthermore, one RGM resistance gene flanked by markers 12RM28346 and 12RM28739 on chromosome 12 was simultaneously detected using method 2–2 (seeded 30 lines/varieties in one tray) treated with 24 RGM and analyzed using conventional and simplified grading systems. Genetic analysis of the RGM resistance gene was confirmed using a method identical to that suggested by IRRI. Finally, one bucket with 24 seedlings treated with at least five female RGM adults was efficacious and could offer adequate samples for insect development observation or molecular biological studies. Conclusion A highly efficient and reliable procedure for evaluation of resistance in rice to RGM was developed and improved, and was verified through mutant screening, gene mapping, genetic analysis, and insect growth and development observations.

scholarly journals Molecular enrichment for detection of S. aureus in recreational waters

2012 ◽  
Vol 66 (11) ◽  
pp. 2305-2310 ◽  
Author(s):  
F. Valeriani ◽  
S. Giampaoli ◽  
L. Buggiotti ◽  
G. Gianfranceschi ◽  
V. Romano Spica
Keyword(s):  
Pcr Primers ◽  
Molecular Techniques ◽  
Universal Primers ◽  
Recreational Water ◽  
Recreational Waters ◽  
Low Concentrations ◽  
Microbiological Methods ◽  
Microbiological Parameters ◽  
Specific Amplification ◽  
Polymerase Chain

The identification of rapid methods for the control of recreational water and of aquatic environments with similar characteristics is necessary to provide adequate levels of health safety for users. Molecular techniques have been proposed in recent years as a viable alternative to traditional microbiological methods, as they offer various advantages and are less time consuming than traditional tests. An innovative protocol based on molecular enrichment that allows the identification of low concentrations of Staphylococcus aureus in recreational water has been developed. The method is based on the specific amplification of prokaryotic genomic DNA by the usage of universal primers for 23S rDNA; subsequently, a second amplification step is performed with specific real-time polymerase chain reaction (PCR) primers and probe. This approach shows sensitivity levels similar to those observed with microbiological tests, with the additional benefits of the specificity typical of nucleic acids techniques. This methodology is easily applicable also to other microbiological parameters, representing an important milestone in hygiene monitoring by the detection of specific pollution indicators.

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