Microbiology

HCV is a leading cause of hepatocellular carcinoma and cirrhosis all over the world. Claudins belong to family of tight junction's proteins that are responsible for establishing barriers for controlling the flow of molecules around cells. For therapeutic strategies, regulation of viral entry into the host cells holds a lot of promise. During HCV infection claudin-1 is highly expressed in liver and believed to be associated with HCV virus entry after HCV binding with or without co-receptor CD81. The claudin-1 assembly with tight junctions is regulated by post translational modifications. During claudins assembly and disassembly with tight junctions, phosphorylation is required at C-terminal tail. In cellular proteins, interplay between phosphorylation and O-b-GlcNAc modification is believed to be functional switch, but it is very difficult to monitor these functional and vibrant changes in vivo. Netphos 2.0 and Disphos 1.3 programs were used for potential phosphorylation; NetPhosK 1.0 and KinasePhos for kinase prediction; and YinOYang 1.2 and OGPET to predict possible O-glycosylation sites. We also identified Yin Yang sites that may have potential for O-b-GlcNAc and phosphorylation interplay at same Ser/Thr residues. We for the first time proposed that alternate phosphorylation and O-b-GlcNAc modification on Ser 192, Ser 205, Ser 206; and Thr 191 may provide an on/off switch to regulate assembly of claudin-1 at tight junctions. In addition these phosphorylation sites may be targeted by novel chemotherapeutic agents to prevent phosphorylation lead by HCV viral entry complex.

Batch experiments were carried out to investigate the stoichiometry and kinetics of microbial degradation of toluene under denitrifying conditions. The inoculum originated from a mixture of sludges from sewage treatment plants with alternating nitrification and denitrification. The culture was able to degrade toluene under anaerobic conditions in the presence of nitrate, nitrite, nitric oxide, or nitrous oxide. No degradation occurred in the absence of Noxides. The culture was also able to use oxygen, but ferric iron could not be used as an electron acceptor. In experiments with 14C-labeled toluene, 34% 4-8% of the carbon was incorporated into the biomass, while 53% 4-10% was recovered as t4CO2, and 6% + 2% remained in the medium as nonvolatile water soluble products. The average consumption of nitrate in experiments, where all the reduced nitrate was recovered as nitrite, was 1.3 :t: 0.2 mg of nitrate-N per mg of toluene. This nitrate reduction accounted for 70% of the electrons donated during the oxidation of toluene. When nitrate was reduced to nitrogen gas, the consumption was 0.7 4-0.2 nag per mg of toluene, accounting for 97% of the donated electrons. Since the ammonia concentration decreased during degradation, dissimilatory reduction of nitrate to ammonia was not the reductive process. The degradation of toluene was modelled by classical Monod kinetics. The maximum specific rate of degradation, k, was estimated to be 0.71 mg toluene per mg of protein per hour, and the Monod saturation constant, Ks, to be 0.2 mg toluene/1. The maximum specific growth rate,/~,~ax, was estimated to be 0.1 per hour, and the yield coefficient, Y, was 0.14 mg protein per mg toluene.

Detection of the Mycobacterium tuberculosis cell wall antigen lipoarabinomannan (LAM) in urine permits diagnoses of tuberculosis (TB) to be made in HIV-infected patients with advanced immunodeficiency. This can be achieved at the point-of-care within just 30 minutes using the Determine TB-LAM, which is a commercially available, lateral-flow urine 'strip test' assay. The assay has been shown to have useful diagnostic accuracy in patients enrolling in antiretroviral treatment services or in HIV-infected patients requiring admission to hospital medical wards in sub-Saharan Africa. Such patients have high mortality risk and have most to gain from rapid diagnosis of TB and immediate initiation of treatment. However, few studies using this assay have yet been reported and many questions remain concerning the correct use of the assay, interpretation of results, the role of the assay as an add-on test within existing diagnostic algorithms and the types of further studies needed. In this paper we address a series of questions with the aim of informing the design, conduct and interpretation of future studies. Specifically, we clarify which clinical populations are most likely to derive benefit from use of this assay and how patients enrolled in such studies might best be characterised. We describe the importance of employing a rigorous microbiological diagnostic reference standard in studies of diagnostic accuracy and discuss issues surrounding the specificity of the assay in different geographical areas and potential cross-reactivity with non-tuberculous mycobacteria and other organisms. We highlight the importance of careful procedures for urine collection and storage and the critical issue of how to read and interpret the test strips. Finally, we consider how the assay could be used in combination with other assays and outline the types of studies that are required to build the evidence base concerning its use.

Symptoms of decline have been observed on dying coast live oak (Quercus agrifolia) trees in areas throughout southern California that are both infested and uninfested by the gold-spotted oak borer (GSOB). The purpose of this study was to identify and assess the pathogenicity of several anamorph species of the Botryosphaeriaceae, including Diplodia corticola, Dothiorella iberica and Diplodia agrifolia sp. nov., that were recovered consistently from symptomatic tissues. Species were identified morphologically and by phylogenetic analyses of the complete sequence of the internal transcribed spacer (ITS) of the rDNA and partial sequences of b-tubulin and elongation factor (EF1-a) genes. Results from morphological assessments and phylogenetic analyses support the erection of a new species closely related to D. mutila, described herein as Diplodia agrifolia sp. nov. Pathogenicity of all species was verified by wound inoculation of 1 y old coast live oak seedlings under controlled conditions. Isolates of D. corticola were the most aggressive tested, and isolates of D. agrifolia were the second most aggressive. Both species caused bleeding symptoms on inoculated seedlings. Seedlings inoculated with D. corticola died within 4 wk, with the pathogen progressing up and down through the xylem in advance of living phloem and moving throughout the taproot in 70% of inoculated seedlings. Colonization and re-isolation was successful for all species. All three fungal species represent newly recorded fungal pathogens of coast live oak in California. Results from the pathogenicity test suggest that these fungi play a role in the decline of coast live oaks throughout southern California.

Conventional methods to detect and assess the viability of plant pathogenic bacteria are usually based on plating assays or serological techniques. Plating assays provide information about the number of viable cells, expressed as colony-forming units, but are time-consuming and laborious. Serological methods, such as the enzyme-linked immunosorbent assay (ELISA) and immunofluorescence microscopy (IF), can be performed in a shorter timespan than most plating assays, but they do not discriminate between live and dead cells. Flow cytometry (FCM) in combination with fluorescent probe technology is a rapid, sensitive, and quantitative technique to detect microorganisms and assess their viability. Quantitative information on the presence and viability of plant pathogenic microorganisms is valuable for risk assessment regarding disease transmission and disease development. FCM has been applied successfully in the fields of food microbiology, veterinary science, and medical research to dete...

This study compared growth, nodulation, nitrogen fixation, and nodular enzyme activities in response to salinity in some common bean-rhizobia symbiotic combinations. Seeds of Paulista and Efequince, two varieties of the common bean (Phaseolus vulgaris) were germinated and seedlings were transferred to pots containing vermiculite inoculated with the reference Rhizobium strain CIAT899 or with RhM11 or RhM14, two local strains. Plants were grown in a temperature-controlled glasshouse at 28°C and irrigated with a nutrient solution without NaCl (control) or supplemented with 25 mM NaCl (stressed). Plants were harvested at the flowering stage. The results showed that in controls, inoculation with RhM11 improved plant and nodule growth compared with those inoculated with RhM14 and CIAT 899. NaCl treatment generally had a negative affect on plant and nodule growth. Under the saline treatment, symbiotic nitrogen fixation was not significantly affected in the CIAT899-Paulista, CIAT899-Efequince and RhM11-Paulista combinations. Plant mineral nutrition was negatively affected under salt treatment for all of the tested symbiotic combinations. Inoculation with CIAT899 and RhM11 conferred more plant tolerance to salinity than inoculation with RhM14. The nodular phosphoenolpyruvate carboxylase (PEPC) and malate dehydrogenase (MDH) exhibited higher activities and were less affected by salinity in plants inoculated with the reference strain CIAT899 than those inoculated with local strains. We conclude that plants inoculated with CIAT899 and RhM11 showed more salinity stress tolerance than those inoculated with RhM14.

In recent years, outbreaks of infections associated with raw and minimally processed fruits and vegetables have been reported. The objective of this study was to analyse the growth/survival of Salmonella Enteritidis at spot-inoculated or stem-injected cherry tomatoes during passive modified atmosphere packaging (MAP), controlled atmosphere (CA) and to compare the results with those of air storage at 7 and 22 1C. During MAP, the gas composition equilibrated to 6% O 2 /4% CO 2 . CO 2 level was maintained as 5% through the term of CA storage at 7 and 22 1C. The results demonstrate that S. Enteritidis can survive and/or grow during the storage of tomatoes depending on the location site of the pathogen on fruit, suspension cell density and storage temperature. During MAP, CA and air storage, S. Enteritidis with initial population of 7.0 log 10 cfu/tomato survived on tomato surfaces with an approximate decrease of 4.0-5.0 log 10 cfu/ tomato in population within the storage period; however, in the case of initial population of 3.0 log 10 cfu/tomato, cells died completely on day 4 during MAP storage and on day 6 during both CA and air storage. The death rate of S. Enteritidis on the surfaces of tomatoes that were stored in MAP was faster than that of stored in air and in CA. Storage temperature was effective on the survival of S. Enteritidis for the samples stored at ambient atmosphere; cells died completely on day 6 at 7 1C and on day 8 at 22 1C. Stem scars provided protective environments for Salmonella; an approximate increase of 1.0 log 10 cfu/tomato in stem-scar population was observed during MAP, CA and air storage at 22 1C within the period of 20 days. Cells survived with no significant change in number at 7 1C. During the research, the effect of ozone treatment (5-30 mg/l ozone gas for 0-20 min) was also considered for surface sanitation before storage. Gaseous ozone treatment has bactericidal effect on S. Enteritidis, inoculated on the surface of the tomatoes and can be used for surface sanitation of S. Enteritidis on tomatoes before storage at different conditions. Ten mg/l ozone gas treatment with different time intervals of 5 and 15 min was found to be effective respectively on low and high dose inoculum levels of S. Enteritidis attached for 1 h. Another variable considered during ozone treatment was the 4 h attachment time.

Inoculation of maize silage with Lactobacillus buchneri (5 x 10(5) c.f.u. g(-1) of maize silage) prior to ensiling results in the formation of aerobically stable silage. After 9 months, lactic acid bacterium counts are approximately 10(10) c.f.u. g(-1) in these treated silages. An important subpopulation (5.9 x 10(7) c.f.u. g(-1)) is able to degrade 1,2-propanediol, a fermentation product of L. buchneri, under anoxic conditions to 1-propanol and propionic acid. From this group of 1,2-propanediol-fermenting, facultatively anaerobic, heterofermentative lactobacilli, two rod-shaped isolates were purified and characterized. Comparative 16S rDNA sequence analysis revealed that the newly isolated bacteria have identical 16S rDNA sequences and belong phylogenetically to the L. buchneri group. DNA-DNA hybridizations, whole-cell protein fingerprinting and examination of phenotypic properties indicated that these two isolates represent a novel species, for which the name Lactobacillus diolivo...

Trichoderma species are ubiquitous soil fungi that hold enormous potential for the development of credible alternatives to agrochemicals and synthetic fertilizers in sustainable crop production. In this paper, we show that substantial improvements in plant productivity can be met by genetic modification of a plant-growth-promoting and biocontrol strain of Trichoderma hamatum, but that these improvements are obtained in the absence of disease pressure only. Using a quantitative monoclonal antibody-based ELISA, we show that an N-acetyl-b-D-glucosaminidase-deficient mutant of T. hamatum, generated by insertional mutagenesis of the corresponding gene, has impaired saprotrophic competitiveness during antagonistic interactions with Rhizoctonia solani in soil. Furthermore, its fitness as a biocontrol agent of the pre-emergence damping-off pathogen Sclerotinia sclerotiorum is significantly reduced, and its ability to promote plant growth is constrained by the presence of both pathogens. This work shows that while gains in T. hamatummediated plant-growth-promotion can be met through genetic manipulation of a single beneficial trait, such a modification has negative impacts on other aspects of its biology and ecology that contribute to its success as a saprotrophic competitor and antagonist of soil-borne pathogens. The work has important implications for fungal morphogenesis, demonstrating a clear link between hyphal architecture and secretory potential. Furthermore, it highlights the need for a holistic approach to the development of genetically modified Trichoderma strains for use as crop stimulants and biocontrol agents in plant agriculture.

Bacterial endotoxin is the lipopolysaccharide component of the cell wall of Gram-negative bacteria, together with other cellular material that combines to form an endotoxin complex. Endotoxin is pyrogenic and it presents a risk to patients who are administered intravenous and intramuscular preparations.1Thus bacterial endotoxins pose a risk to many pharmaceutical processes and, where not controlled, to the finished products. There are different methods for endotoxin removal. These include depyrogenation,2 such as dry-heat processes applied to glassware, and rinsing,3 as might be applied to closures. These areas receive reasonable coverage within the pharmaceutical sector. Areas that are actively discussed within biotechnology fields but which receive less attention in the wider pharmaceutical context are steps to remove endotoxin bound to protein. This article considers some of the biotechnological applications for endotoxin removal.

Waikato Environment for Knowledge Analysis (WEKA) is a comprehensive suite of Java class libraries that implement many state-of-the-art machine learning/data mining algorithms. Non-programmers interact with the software via a user interface component called the Knowledge Explorer.

Although truffles are cultivated since decades, their life cycle and the conditions stimulating ascocarp formation still remain mysterious. A role for bacteria in the development of several truffle species has been suggested but few is known regarding the natural bacterial communities of Périgord Black truffle. Thus, the aim of this study was to decipher the structure and the functional potential of the bacterial communities associated to the Black truffle in the course of its life cycle and along truffle maturation. A polyphasic approach combining 454-pyrosequencing of 16S rRNA gene, TTGE, in situ hybridization and functional GeoChip 3.0 revealed that Black truffle ascocarps provide a habitat to complex bacterial communities that are clearly differentiated from those of the surrounding soil and the ectomycorrhizosphere. The composition of these communities is dynamic and evolves during the maturation of the ascocarps with an enrichment of specific taxa and a differentiation of the gleba and peridium-associated bacterial communities. Genes related to nitrogen and sulphur cycling were enriched in the ascocarps. Together, these data paint a new picture of the interactions existing between truffle and bacteria and of the potential role of these bacteria in truffle maturation.

The concept that the gut microbiota serves as a virtual endocrine organ arises from a number of important observations. Evidence for a direct role arises from its metabolic capacity to produce and regulate multiple compounds that reach the circulation and act to influence the function of distal organs and systems. For example, metabolism of carbohydrates results in the production of short chain fatty acids (SCFAs), such as butyrate and propionate, which provide an important source of nutrients as well as regulatory control of the host digestive system. This influence over host metabolism is also seen in the ability of the prebiotic inulin is to influence production of relevant hormones such as glucagon like peptide-1 (GLP-1), peptide YY (PYY), ghrelin and leptin. Moreover, the probiotic L. rhamnosus PL60, which produces conjugated linoleic acid, has been shown to reduce body weight gain and white adipose tissue without effects on food intake. Manipulating the microbial composition of the gastrointestinal tract modulates plasma concentrations of tryptophan, an essential amino acid and precursor to serotonin, a key neurotransmitter within both the enteric and central nervous systems. Indirectly and through as yet unknown mechanisms, the gut microbiota exerts control over the hypothalamic-pituitary-adrenal axis (HPA). This is clear from studies on animals raised in a germ-free environment, who show exaggerated responses to psychological stress, which normalises following monocolonisation by certain bacterial species including B. infantis. It is tempting to speculate that therapeutic targeting of the gut microbiota may be useful in treating stress-related disorders and metabolic diseases.

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Whole-genome nucleotide sequencing has revolutionized the genetic, biochemical and molecular biology research on bacteria and indeed, many higher organisms. The genome sequences of the strains of two subspecies of Lactococcus lactis, L. lactis subsp. lactis and L. lactis subsp. cremoris, have been determined. These genomic sequences have permitted two important new approaches to be applied in the research of L. lactis. The analysis of the regulation of expression of all genes under specific circumstances at a given point in time is now possible by DNA microarray technology. The elucidation of the full protein complement of the organism as a function of intrinsic or external factors has been made possible by high-throughput protein identification and analysis techniques combined with the gene-derived know-how of the total protein encoding capacity of the genome. These techniques from the genomics arena, transcriptomics and proteomics, have been recently implemented in the study of various aspects of growth and functioning of L. lactis. In this paper we discuss a number of similarities and differences between the two lactococcal genome sequences and review the current status of genomics research in L. lactis. We also propose future directions with respect to both answering fundamental questions more quickly and more completely, as well as opening new avenues for biotechnological applications.

The gastrointestinal tract is a complex ecosystem that associates a resident microbiota and cells of various phenotypes lining the epithelial wall expressing complex metabolic activities. The resident microbiota in the digestive tract is a heterogeneous microbial ecosystem containing up to 1 Â 10 14 colony-forming units (CFUs) of bacteria. The intestinal microbiota plays an important role in normal gut function and maintaining host health. The host is protected from attack by potentially harmful microbial microorganisms by the physical and chemical barriers created by the gastrointestinal epithelium. The cells lining the gastrointestinal epithelium and the resident microbiota are two partners that properly and/or synergistically function to promote an efficient host system of defence. The gastrointestinal cells that make up the epithelium, provide a physical barrier that protects the host against the unwanted intrusion of microorganisms into the gastrointestinal microbiota, and against the penetration of harmful microorganisms which usurp the cellular molecules and signalling pathways of the host to become pathogenic. One of the basic physiological functions of the resident microbiota is that it functions as a microbial barrier against microbial pathogens. The mechanisms by which the species of the microbiota exert this barrier effect remain largely to be determined. There is increasing evidence that lactobacilli and bifidobacteria, which inhabit the gastrointestinal microbiota, develop antimicrobial activities that participate in the host's gastrointestinal system of defence. The objective of this review is to analyze the in vitro and in vivo experimental and clinical studies in which the antimicrobial activities of selected lactobacilli and bifidobacteria strains have been documented.

Consumers are becoming increasingly health conscious and therefore more discerning in their food choices. The production of fermented food products with elevated levels of B-vitamins increase both their commercial and nutritional value, and eliminate the need for subsequent fortification with these essential vitamins. Such novel products could reduce the incidence of inadequate vitamin intake which is common in many parts of the world, not only in developing countries, but also in many industrialised countries. Moreover, the concept of in situ fortification by bacterial fermentation opens the way for development of food products targeted at specific groups in society such as the elderly and adolescents. This review looks at how vitamin overproduction strategies have been developed, some of which have successfully been tested in animal models. Such innovative strategies could be relatively easily adapted by the food industry to develop novel vitamin-enhanced functional foods with enhanced consumer appeal.

Both normal and diseased cells continuously shed extracellular vesicles (EVs) into extracellular space, and the EVs carry molecular signatures and effectors of both health and disease. EVs reflect dynamic changes that are occurring in cells and tissue microenvironment in health and at a different stage of a disease. EVs are capable of altering the function of the recipient cells. Trafficking and reciprocal exchange of molecular information by EVs among different organs and cell types have been shown to contribute to horizontal cellular transformation, cellular reprogramming, functional alterations, and metastasis. EV contents may include tumor suppressors, phosphoproteins, proteases, growth factors, bioactive lipids, mutant oncoproteins, oncogenic transcripts, microRNAs, and DNA sequences. Therefore, the EVs present in biofluids offer unprecedented, remote, and non-invasive access to crucial molecular information about the health status of cells, including their driver mutations, cl...

Sesbania grandiflora L. an indigenous species native to Asian, South-Asian nations widely used for innumerable purpose. The plant is accepted for its vast use for an economic benefit from environmental valuation to human livelihood. Nation such as Indonesia, Philippines cultivate this plant for economical purpose. The plant is also known to be useful for manufacture of paper and pulp. Thus, cellulose and fibres generated from various sources from this plant is highly valued in developing the economy. Moreover, the seeds of Sesbania are indeed utilized for consumption purpose. The current research is carried out to testify the amount of Dietary fibre in the seeds of Sesbania grandiflora L. Researches have shown the plant leaves enriched with high amount of nutrient content, hence the seed of the plant too forms an attractive theme to search out and study experimentally for the various nutritional sources. The research carried out for evaluation of dietary fibre successfully concludes the quantity and its consumption on a daily basis in a diet.

The central dogma of molecular biology defines the major route for the transfer of genetic information from genomic DNA to messenger RNA to three-dimensional proteins that affect structure and function. Like alternative splicing, the post-transcriptional conversion of adenosine to inosine (A-to-I) by RNA editing can dramatically expand the diversity of the transcriptome to generate multiple, functionally distinct protein isoforms from a single genomic locus. While RNA editing has been identified in virtually all tissues, such post-transcriptional modifications have been best characterized in RNAs encoding both ligand-and voltage-gated ion channels and neurotransmitter receptors. These RNA processing events have been shown to play an important role in the function of the encoded protein products and, in several cases, have been shown to be critical for the normal development and function of the nervous system.

The systematic review focused on the prognosis, mortality, medications, and promising vaccines for COVID-19. COVID-19 severity varies. Mild cases often recover within two weeks, while people with severe diseases may take 3 – 6 weeks to recover. Among people who died, the time from the onset of symptom to death ranged from 2 – 8 weeks. Children constitute a small percentage of reported cases, with around 1% of cases under 10 years and 4% aged 10 to 19 years. The risk of death is below 0.5% in those younger than 50 years, while more than 8% in those older than 70. Most of the people who die of COVID-19 have pre-existing conditions, including diabetes mellitus, cardiovascular disease, and hypertension. The impact of COVID-19 and its rate of mortality are different for both men and women; mortality rate is higher in men. As of May 2020, it is not known if past infection provides long-term and effective immunity in those who recover from the viral disease. Some of the infected people were reported to develop protective antibodies; the acquired immunity is presumed possible, based on other coronaviruses’ behaviour. The total infection fatality rate (IFR) is estimated to be 0.66%. No approved vaccine to treat the disease yet. International research on medicines and vaccines in COVID-19 is underway by academic groups, industry researchers, and government organizations. As of May 2020, there are over 300 active clinical trials underway. Many existing medications are under evaluation for COVID-19 treatment, including remdesivir, chloroquine, lopinavir/ritonavir, hydroxychloroquine, and lopinavir/ritonavir combined with interferon beta; as of May 2020, there is tentative evidence for remdesivir efficacy. Other candidates in trials are vasodilators, immune therapies, lipoic acid, corticosteroids, recombinant angiotensin-converting enzyme 2, bevacizumab, etc. Preliminary evidence suggests hydroxychloroquine might have anti-cytokine storm properties. Transferring concentrated and purified antibodies produced by immune systems of those who recovered from COVID-19 to those who need them is being investigated as non-vaccine method of passive immunization.

In the natural T. melanosporum truffle regions of Southern Europe, fine-textured soils present unique challenges to prospective cultivators. With reference to the edaphic and climatic conditions encountered at a hazel plantation in Piedmont, Italy, this study examines these challenges in great detail, and presents a novel phytosociological approach to the analysis of suitable truffle habitat. Ellenberg Indicator Values for T. melanosporum are derived, and then used to quantitatively explain the link between Vitis vinifera, the common grape vine, and T. melanosporum habitats. The significance of a locally-udic moisture regime for T. melanosporum development is also explored. Important new cultural procedures, including the potential of host tree early-season defruiting to achieve enhanced mycelial and ascocarp growth, are introduced. The latest version discusses the significance of humus forms, and of the 'mesoMull/oligoMull boundary' in particular, in greater detail.

Committee in Charge 2014 ii Acknowledgements I would be remiss not to acknowledge the many people who have made this work possible, more or less chronologically: My parents, Martha Jurchak and Larry Johnson, for encouraging and pushing my intellectual, scientific, and creative development from an early age; my brother and sister, Eban and Adriana Johnson; my Grandmother, Marie Jurchak, for planting the seed of bon vivantism and supplying the younger me with plenty of cookbooks to read; to my de-facto in-laws Alice Meadows and Pete, Grace, Jack and Joe Pold for welcoming me into their family. From the early days of what would turn out to be my career, Kent Kirshenbaum, for letting me stand in the back of the room at the first Experimental Cuisine Collective meeting and giving me the space and support to start developing ideas about how to do scientific research on culinary questions; and Dave Arnold for taking my half-developed ideas seriously and giving me a lot of challenging questions about smell and chemistry to figure out. At UC Davis, my advisor, Susan Ebeler, for providing the tools and space to develop as an analytical chemist and learn the hard work of a writing, lecturing scientist, and putting up with my scientific wanderings; Hildegarde Heymann, for teaching me everything I know about sensory science and experimental design, cultivating my ideas about how science should be dealing with questions of flavor, chemistry, and cuisine, and freely offering profound words of encouragement when I needed them. Carolyn Doyle, for invaluable instrumentation help. My lab and office mates, for their support and friendship, Larry Lerno, Helene Hopfer, Ellie King, Maya Hood White and especially Anna Hjelmeland, a stalwart friend both in and outside of work. Roger Boulton, for introducing me to the technology of distilled beverages and being a valuable and enjoyably challenging presence on both my qualifying exam and dissertation committees. Alyson Mitchell and Doug Adams for their presence on my qualifying exam committee and help with academic issues and conference travel. Harold McGee, first as a role model, then as a QE committee member, and now as a dear friend and colleague. iii Related to the University of Copenhagen, Line Holler Mielby for being an early scientific role model and encouraging me to go to Denmark, Michael Bom Frøst, for enabling my coming to the Nordic Food Lab and KU, my sensory panel at KU, and Wender Bredie, Belinda Nielsen, and Charlotte Dandanell of the sensory science group.

Environmental monitoring is a programme which evaluates the cleanliness of the manufacturing environment; the effectiveness of cleaning and disinfection programmes; and the operational performance of environmental controls. As such, pharmaceutical manufacturers of both sterile and non-sterile products, as well as medical devices, are required to demonstrate that manufacturing processes and procedures minimise any potential contamination to the product from the manufacturing environment. Contamination can arise from a number of sources: water, air, surfaces and personnel, each of which poses a potential risk to product.

Biocontamination refers to biological contamination of products by bacteria and/or fungi, as well as the toxic by-products of these microorganisms, such as endotoxin and mycotoxins from Gram-negative bacteria and fungi, respectively. When designing a biocontamination control strategy, which is based on the manufacturing process, there are three components to take into consideration, each of which requires risk assessment: 1) designing process systems to avoid contamination; 2) monitoring process systems to detect contamination; and 3) reacting to contamination events and putting proactive measures in place. The design of process systems is where maximal effort should be placed.

Surface monitoring by using swabs forms a regular part of environmental monitoring of cleanrooms. There are different factors that affect swab recovery, from tip type to enumeration method. One factor, for swabs where the microorganisms are detached from the swab tip and which are then membrane filtered, is the period of vortex mixing. This paper discusses microbial surface sampling, and the factors that affect swab recovery. The paper presents some experimental data where vortex times are considered for a range of microorganisms. The study outcome indicates that 15 seconds vortex mixing is sufficient to obtain microbial recoveries from the swab tip above 50%.

Cleanroom contamination can arise from a number of sources. Most contamination within the pharmaceutical facility can be traced to humans working in cleanrooms. The paper discusses staff gowning and personnel behavior in pharmaceutical cleanrooms, and how cleanroom risk can be minimized. The human skin ecosystem is discussed. The Human Microbiome Project (HMP) from the US NIH characterized microorganisms found in association with both healthy and diseased humans. Information from this project has great impact on cleanroom activities including gowning practices. Topics associated with cleanroom garments are discussed including fabric types,

Compressed gas sampling for microorganisms is an important part of contamination control assessment.  This paper addresses topics related to microbial assessment of compressed gases.  These include gas purity including moisture considerations, sterile filtration, compressed gas standards, microbial contamination, microbial survival, sampling and testing requirements, instrumentation, and various sampling considerations including growth medium choice and frequency, and reporting requirements.

Cleanrooms are highly controlled environments, defined by
the air quality, and where certain physical and microbiological
requirements need to be met. Air quality is achieved through
a combination of airborne particulate control, such as through
high efficiency particulate air filters; high fresh air rates (air
movement and air changes); clean-up (or ‘recovery’) times;
pressure differentials, which concerns air direction;
temperature and humidity control (where necessary); cleaning
and disinfection; and staff behaviours and gowning. The
requirements for air quality, and the associated physical
aspects designed to achieve this, are contained within the
international standard ISO 14644.

© 2021 Soniya Shetty et al. This is an open access article under the CC BY license (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Abstract Probiotics are defined as nonpathogenic living microorganisms, that have beneficial effects on host health. The most important and frequently used functional food compounds are probiotics and fermented foods. Functional foods have numerous beneficial nutritional effects. Probiotics dairy foods, idli, dhokla, pickles etc are traditional Indian foods that beneficially affect the host. They improve survival and implantation of live microbial supplements. In our study, probiotics were isolated from Fermented Idli batter. There is a difference observed in the pH of fermented idli batter. It decreases from 6 to 4.3-...

Herbaspirillum seropedicae is an endophytic diazotrophic bacterium that associates with economically important crops. NifA protein, the transcriptional activator of nif genes in H. seropedicae, binds to nif promoters and, together with RNA polymerase-s 54 holoenzyme, catalyzes the formation of open complexes to allow transcription initiation. The activity of H. seropedicae NifA is controlled by ammonium and oxygen levels, but the mechanisms of such control are unknown. Oxygen sensitivity is attributed to a conserved motif of cysteine residues in NifA that spans the central AAAþ domain and the interdomain linker that connects the AAAþ domain to the C-terminal DNA binding domain. Here we mutagenized this conserved motif of cysteines and assayed the activity of mutant proteins in vivo. We also purified the mutant variants of NifA and tested their capacity to bind to the nifB promoter region. Chimeric proteins between H. seropedicae NifA, an oxygen-sensitive protein, and Azotobacter vinelandii NifA, an oxygen-tolerant protein, were constructed and showed that the oxygen response is conferred by the central AAAþ and C-terminal DNA binding domains of H. seropedicae NifA. We conclude that the conserved cysteine motif is essential for NifA activity, although single cysteine-to-serine mutants are still competent at binding DNA.