Identification of medically relevant microorganisms by vibrational spectroscopy

In the recent years, vibrational spectroscopies (infrared and Raman spectroscopy) have been developed for all sorts of analyses in microbiology. Important features of these methods are the relative ease with which measurements can be performed. Furthermore, in order to obtain infrared or Raman spectra, there is only a limited amount of sample handling involved without the need for expensive chemicals, labels or dyes. Here, we review the potential application of vibrational spectroscopies for the use in medical microbiology. After describing some of the basics of the techniques, considerations on reproducibility and standardisation are presented. Finally, the use of infrared and Raman spectroscopy for the (rapid) identification of medically relevant microorganisms is discussed. It can be concluded that vibrational spectroscopies show high potential as novel methods in medical microbiology.     

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group

In this article we present the Reporting Structure for Biological Investigation (RSBI), a working group under the Microarray Gene Expression Data (MGED) Society umbrella. RSBI brings together several communities to tackle the challenges associated with integrating data and representing complex biological investigations, employing multiple OMICS technologies. Currently, RSBI includes environmental genomics, nutrigenomics and toxicogenomics communities, where independent activities are underway to develop databases and establish data communication standards within their respective domains. The RSBI working group has been conceived as a "single point of focus" for these communities, conforming to general accepted view that duplication and incompatibility should be avoided where possible. This endeavour has aimed to synergize insular solutions into one common terminology between biologically driven standardisation efforts and has also resulted in strong collaborations and shared understanding between those in the technological domain. Through extensive liaisons with many standards efforts, several threads have been woven with the hope that ultimately technology-centered standards and their specific extensions into biological domains of interest will not only stand alone, but will also be able to function together, as interchangeable modules.     

The Role of Informatics in the Coordinated Management of Biological Resources Collections

The term 'biological resources' is applied to the living biological material collected, held and catalogued in culture collections: bacterial and fungal cultures; animal, human and plant cells; viruses; and isolated genetic material. A wealth of information on these materials has been accumulated in culture collections, and most of this information is accessible. Digitalisation of data has reached a high level; however, information is still dispersed. Individual and coordinated approaches have been initiated to improve accessibility of biological resource centres, their holdings and related information through the Internet. These approaches cover subjects such as standardisation of data handling and data accessibility, and standardisation and quality control of laboratory procedures. This article reviews some of the most important initiatives implemented so far, as well as the most recent achievements. It also discusses the possible improvements that could be achieved by adopting new communication standards and technologies, such as web services, in view of a deeper and more fruitful integration of biological resources information in the bioinformatics network environment.     

Aspergillus fumigatus and aspergillus niger in two potted ornamental plants,cactus (epiphyllum truncatum) and clivia (clivia miniata). Biological and epidemiological aspects

The presence and growth of Aspergillus fumigatus and Aspergillus niger in the soil of ornamental plants have been demonstrated. The ecological conditions in the soil of such plants as influenced by temperature, humidity, desiccation, fertilization and ventilation obviously influence such fungal growth. The epidemiological significance of these findings is of interest with a view to the present efforts to control aspergillosis in the environment of susceptible persons.Observations of a preferential growth of certain Aspergillus species in the soil of defined plants under defined conditions raise problems of soil microbiology.     

Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins

Recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a "consensus" set of experimental conditions (25 degrees C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two-state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self-consistent data set that will aid ongoing efforts to understand the folding process.     

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components of an experimental activity that are common across different technologies, including protocols, samples and data. FuGE provides a foundation for describing entire laboratory workflows and for the development of new data formats. The Microarray Gene Expression Data society and the Proteomics Standards Initiative have committed to using FuGE as the basis for defining their respective standards, and other standards groups, including the Metabolomics Standards Initiative, are evaluating FuGE in their development efforts. Adoption of FuGE by multiple standards bodies will enable uniform reporting of common parts of functional genomics workflows, simplify data-integration efforts and ease the burden on researchers seeking to fulfill multiple minimum reporting requirements. Such advances are important for transparent data management and mining in functional genomics and systems biology.     

Development of soil microbiology methods: from respirometry to molecular approaches

This review deals with techniques and methods used in the study of the function and development of microorganisms occurring in soil with emphasis on the contributions of Czech Academician Ivan Málek and his coworkers or fellows (Jiří Macura, František Kunc) to the development of basic techniques used in soil microbiology. Early studies, including batch cultivation and respirometric techniques, as well as later developments of percolation and continuous-flow methods of cultivation of soil microorganisms are discussed. Recent developments in the application of analytical chemistry (HPLC or GC) and of molecular biological techniques to ecological questions that have revolutionized concepts in soil microbiology and microbial ecology are also briefly mentioned, including denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), phospholipid fatty acid analysis (PLFA) and others. The shift of soil microbiology from the study of individual microorganisms to entire microbial communities, including nonculturable species, is briefly discussed.     

树种多样性对土壤微生物群落结构和元素生物地球化学循环的影响研究进展

森林是陆地生态系统的重要组成部分,其巨大的生产力和生态服务功能对人类的生存和发展至关重要。森林树种多样性增加能够显著提高森林生产力,关于树种多样性如何影响地下生物多样性及生态功能逐渐受到国内外学者的广泛关注。从土壤微生物及其介导的元素生物地球化学循环这一视角出发,综述了树种多样性对土壤细菌和真菌多样性、群落结构及功能的影响,提出需要进一步深入研究的方向。总体来说,树种多样性有利于增加土壤细菌生物量和多样性,是预测病原性真菌和菌根真菌多样性及群落结构的重要生物因子。树种多样性能增加土壤有机碳储量,增强森林土壤的甲烷氧化能力,并提高土壤磷周转速率及有效磷含量。关于树种多样性对森林土壤氮循环的影响需考虑多样性假说和质量比假说的相对贡献。今后应加强树种多样性对多个营养级之间相互作用的研究;关注树种多样性对生态系统多功能的影响;加强学科交叉,引入微生物种群动态模型和气候模型等模型预测方法,研究树种多样性对全球气候变化的应对机制,以期促进地上植物多样性与地下生态系统功能关系的研究,增强森林生态系统应对未来全球环境变化的能力。     

Ecohydrological effects of grazing‐induced degradation in the Patagonian Monte,Argentina

Water‐limited ecosystems have undergone rapid change as a consequence of changing land use and climate. The consequences of these changes on soil quality and vegetation dynamics have been documented in different regions of the world. In contrast, their effects on soil water, the most limiting resource in these environments, have received less attention, although in recent years increasing efforts have been made to relate grazing, soil water and vegetation functioning. In this paper, we present the results of field observations of plant phenology and soil water content carried out during two successive years at four sites along a degradation gradient caused by grazing in the Patagonian Monte, Argentina. We also developed a simplified soil water balance model to evaluate how changes in plant cover could affect water balance. Our field observations showed that the soil water content in the soil layer where roots of grasses are abundant (0–25 cm) was higher and the growing cycles were longer in degraded than in preserved sites. Similarly, our modelling approach showed that the deep soil (depth > 10 cm) was wetter in the degraded than in the preserved situation. Simulation also suggested a switch from transpiration to a direct evaporation dominance of water losses with degradation. Although reductions in plant cover related to grazing degradation were associated with a decrease in annual transpiration, the simulated soil water loss by transpiration was higher during summer in the degraded than in the well preserved situation. Thus, our field observations seem to be a consequence of ecohydrological changes causing an accumulation of water in the soil profile during the cold season and its transpiration during summer. In conclusion, our results showed that changes in plant cover caused by grazing disturbance can alter the soil water balance, which in turn can affect vegetation function.     

Remote sensing data predict indicators of soil functioning in semi-arid steppes,central Spain

A substantial part of current research efforts on desertification are devoted to establish monitoring systems to evaluate the status of natural resources and the onset of desertification processes. Methodologies based on ground-collected soil and plant indicators are being increasingly used for this aim because they are affordable yet do not compromise accuracy. Despite their inherent value, these methods have limitations regarding the extent of the area that can be monitored using them. Such limitations can be overcome combining field-based approaches with remote sensing data, which allow the establishment of monitoring programs over large areas. In this article we tested the relationship between a field methodology based on indicators of ecosystem functioning, the landscape function analysis (LFA), and a vegetation index (NDVI) obtained from satellite images of the ASTER sensor using data gathered in Stipa tenacissima steppes from central Spain. LFA uses soil surface indicators to assess the condition of a given ecosystem by producing three numerical indices (stability, infiltration and nutrient cycling) reflecting the status of basic soil functions. We found a significant positive linear relationship between the NDVI, the three LFA indices and some key structural attributes of vegetation related to the cover of perennial plants. Our results indicate that NDVI can be used as a surrogate of ecosystem functioning in semi-arid Mediterranean steppes, and thus can be a helpful index to monitor the functional status of large areas in these ecosystems, and the possible onset of desertification processes.     

Actual Problems of Physiology of Microorganisms

Physiology of microorganisms is traditionally considered as one of branches of microbiology. Fundamental works in this field, the last of which were written almost 40 years ago, included such issues, as chemical composition, physico-chemical properties, metabolism, respiration, reproduction, and growth of microorganisms. For the last few decades, the main efforts of scientists in these fields were concentrated on decoding molecular-genetic mechanisms underlying functioning of microbial cells. At the same time, the accumulated scientific data in adjacent fields of biological science require insistently the necessity of new understanding and systematization of results of study of processes of vital activity of all species of living organisms, based on general integrative physiological principles. By the present time, it has been convincingly proved that the existence of higher organisms is impossible without constant interaction with the world of microbes and, hence, physiology of human, animals or plants is inextricably connected with physiological processes of their inhabiting microorganisms. In the present work the main actual problems of modern physiology of microorganisms are considered, and the necessity of separation of this branch of knowledge as an autonomous part of physiology is emphasized.     

Sterile Products: Advances and Challenges in Formulation,Manufacturing and Regulatory Aspects—A Regulatory Review Perspective

For several decades, the FDA has undertaken many initiatives to improve the quality and safety of sterile drug products. In recent years, efforts have also been undertaken to accelerate the rate for application approval by adding earlier involvement of microbiology reviewers in drug development. Product and manufacturing process development, as well as safe use and product design, are among the elements of enhanced technical involvement. An overview of the product quality microbiology aspects for sterile drugs is provided.     

On the standardisation of the twinning rate.

In many studies the twinning rate, being strongly dependent on maternal age (and parity), has been standardised according to the maternal age distribution. The direct method requires very informative twinning data for the target population. The indirect method is used when the data for the target population is not sufficiently informative or when the target population is small. We have earlier introduced an alternative indirect technique for standardising the twinning rate. Our technique requires even less of the twinning data. Besides maternal age, parity is an influential factor, and should, if possible, be taken into account. In this study we present the traditional standardisation methods based on both maternal age and parity, we propose a new direct standardisation method and we develop our standardisation methods so that they take into account both maternal age and parity. We apply these standardisation methods to data from Finland, 1953-1964, from St. Petersburg, Russia, 1882-92, from Canada 1952-1967, and from Denmark, 1896-1967. These methods all give results very similar to those for the Finnish data, but the effect of parity is strongest with the direct methods. This may be due to the fact that, among extramarital maternities, parity has a strongly increasing effect on the twinning rate. This may be attributed to a higher reproduction capacity among unmarried mothers. Standardisations of the Canadian and the Danish data also give reliable results. With the St. Petersburg data, however, the different standardisations show notable discrepancies. These discrepancies are compared with Allen's findings.     

The proposed benefits of incorporating non-human animals into preventative efforts for Conduct Disorder

Abstract

Conduct disorder (CD) is among the most intractable mental health problems and has been found to be increasingly prevalent throughout childhood, and into adolescence. Although many of the behaviors that comprise CD have been researched, there has been limited focus on preventative interventions for childhood conduct problems. This article reviews risk factors for the development of CD, which include the characteristics of early-starting conduct-disordered children, their parents and families. I then discuss directions for future preventative efforts with particular focus on the promotion of concern for others, and the development of positive interpersonal relationships. To this end, I provide a detailed rationale for the proposal that animal-assisted preventative efforts are an optimal vehicle for promoting positive functioning, and thereby interrupting the development of CD.     

Impact of standardization on clinical cell analysis by flow cytometry

The evolution of flow cytometry from a research tool to a pivotal technology for clinical diagnostic purposes has required significant efforts to standardize methods. The great advantage of flow cytometry is that it's applications are highly amenable to standardization. Here, we review the efforts that have been made for flow cytometric applications in four major fields of clinical cell analysis: CD4+ T-cell enumeration, CD34+ hematopoietic stem and progenitor cell enumeration, screening for the HLA-B27 antigen and leukemia/lymphoma immunophenotyping. These standardization efforts have been parallelled by the establishment of external quality assessment (EQA) schemes in many countries worldwide. The goal of these EQA exercises has been primarily educa-tional, but their results will increasingly serve as a basis for laboratory accreditation. This important development requires that the EQA schemes, in particular the quality of the distributed samples and the procedures for evaluating the results, meet the highest standards.     

The Role of Microbes in Agriculture: Sergei Vinogradskii’s Discovery and Investigation of Chemosynthesis, 1880–1910

In 1890, Sergei Nikolaevich Vinogradskii (Winogradsky) proposed a novel life process called chemosynthesis. His discovery that some microbes could live solely on inorganic matter emerged during his physiological research in 1880s in Strassburg and Zurich on sulfur, iron, and nitrogen bacteria. In his nitrification research, Vinogradskii first embraced the idea that microbiology could have great bearing on agricultural problems. His critique of agricultural chemists and Kochian-style bacteriologists brought this message to the broader agricultural community, resulting in an heightened interest in biological, rather than chemical methods to investigate soil processes. From 1891 to 1910, he directed the microbiological laboratory at the Imperial Institute of Experimental Medicine in St. Petersburg, Russia, where he expanded his chemosynthesis research to a broad investigation of the manifold significance of autotrophic organisms in soil processes. This work and that of his students attracted the serious attention of agricultural chemists and soil scientists in Russia and abroad, changing essentially the way they understood and investigated the role of microbes in the soil. His student, Vasilii Omelianskii, effectively integrated Vinogradskii’s approach into Russian and Soviet, and international agricultural microbiology. Vinogradskii’s activities in the late 19th century reflect the changes occurring more broadly in science. At that time, microbiologists such as Louis Pasteur, Eugenius Warming, and Martianus Beijerinck were contributing new laboratory methods and theoretical perspectives to incipient disciplines closely related to agriculture: ecology, soil science, and soil microbiology.     

The urgent need for microbiology literacy in society: children as educators

Microbes and their activities have pervasive influence and deterministic roles in the functioning and health of the geosphere, atmosphere and biosphere, i.e. in nature. Microbiology can be considered a language of nature. We have argued that the relevance of microbes for everyday personal decisions and collective policies requires that society attains microbiology literacy, through the introduction of child-relevant microbiology topics into school curricula. That is: children should learn the microbiology language of nature. Children can be effective transmitters of new and/or rapidly evolving knowledge within families and beyond, where there is a substantive information asymmetry (witness digital technology, social media, and new languages in foreign countries). They can thus be key disseminators of microbiology knowledge, where there will be information asymmetry for the foreseeable future, and thereby contribute to the attainment of microbiology literacy in society. The education of family and friends can be encouraged/stimulated by home assignments, family leisure projects, and school-organised microbiology-centric social-education events. Children are key stakeholders in family decisions. Their microbiology knowledge, and their dissemination of it, can help inform and increase the objectivity of such decisions.     

Effects of Plant Diversity,Functional Group Composition,and Fertilization on Soil Microbial Properties in Experimental Grassland

BackgroundLoss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization.Conclusions/SignificanceOur study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and nutrient inputs for soil processes.