bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rhodobacter sphaeroides Protein Mechanistically Similar to Escherichia coli DksA Regulates Photosynthetic Growth
Authors: Lennon Christopher W. , Lemmer Kimberly C. , Irons Jessica L. , Sellman Max I. , Donohue Timothy J. , Gourse Richard L. , Ross Wilma 
Published: April 2014

ABSTRACT

DksA is a global regulatory protein that, together with the alarmone ppGpp, is required for the “stringent response” to nutrient starvation in the gammaproteobacterium
Escherichia coli
and for more moderate shifts between growth conditions. DksA modulates the expression of hundreds of genes, directly or indirectly. Mutants lacking a DksA homolog exhibit pleiotropic phenotypes in other gammaproteobacteria as well. Here we analyzed the DksA homolog RSP2654 in the more distantly related
Rhodobacter sphaeroides
, an alphaproteobacterium. RSP2654 is 42% identical and similar in length to
E. coli
DksA but lacks the Zn finger motif of the
E. coli
DksA globular domain. Deletion of the RSP2654 gene results in defects in photosynthetic growth, impaired utilization of amino acids, and an increase in fatty acid content. RSP2654 complements the growth and regulatory defects of an
E. coli
strain lacking the
dksA
gene and modulates transcription
in vitro
with
E. coli
RNA polymerase (RNAP) similarly to
E. coli
DksA. RSP2654 reduces RNAP-promoter complex stability
in vitro
with RNAPs from
E. coli
or
R. sphaeroides
, alone and synergistically with ppGpp, suggesting that even though it has limited sequence identity to
E. coli
DksA (DksA
Ec
), it functions in a mechanistically similar manner. We therefore designate the RSP2654 protein DksA
Rsp
. Our work suggests that DksA
Rsp
has distinct and important physiological roles in alphaproteobacteria and will be useful for understanding structure-function relationships in DksA and the mechanism of synergy between DksA and ppGpp.

IMPORTANCE
The role of DksA has been analyzed primarily in the gammaproteobacteria, in which it is best understood for its role in control of the synthesis of the translation apparatus and amino acid biosynthesis. Our work suggests that DksA plays distinct and important physiological roles in alphaproteobacteria, including the control of photosynthesis in
Rhodobacter sphaeroides
. The study of DksA
Rsp
, should be useful for understanding structure-function relationships in the protein, including those that play a role in the little-understood synergy between DksA and ppGpp.
Bacterial Toxins—Staphylococcal Enterotoxin B
Authors: Fries Bettina C. , Varshney Avanish K. 
Published: April 2014

ABSTRACT
Staphylococcal enterotoxin B is one of the most potent bacterial superantigens that exerts profound toxic effects upon the immune system, leading to stimulation of cytokine release and inflammation. It is associated with food poisoning, nonmenstrual toxic shock, atopic dermatitis, asthma, and nasal polyps in humans. Currently, there is no treatment or vaccine available. Passive immunotherapy using monoclonal antibodies made in several different species has shown significant inhibition in in vitro studies and reduction in staphylococcal enterotoxin B-induced lethal shock in in vivo studies. This should encourage future endeavors to develop these antibodies as therapeutic reagents.
Plant-Derived Monoclonal Antibodies for Prevention and Treatment of Infectious Disease
Authors: Hiatt Andrew , Whaley Kevin J. , Zeitlin Larry 
Published: April 2014

ABSTRACT

Numerous monoclonal antibodies (MAbs) that recognize and neutralize infectious pathogens have been isolated and developed over the years. The fact that infectious diseases can involve large populations of infected individuals is an important factor that has motivated the search for both cost-effective and scalable methods of antibody production. The current technologies for production of antibodies in plants allow for very rapid expression and evaluation that can also be readily scaled for multikilogram production runs. In addition, recent progress in manipulating glycosylation in plant production systems has allowed for the evaluation of antibodies containing glycans that are nearly homogeneous, are mammalian in structure, and have enhanced neutralizing capabilities. Among the anti-infectious disease antibodies that have been produced in plants are included those intended for prevention or treatment of anthrax,
Clostridium perfringens
, Ebola virus, human immunodeficiency virus, herpes simplex virus, rabies, respiratory syncytial virus, staphylococcal enterotoxin, West Nile virus, and tooth decay. Animal and human efficacy data for these MAbs are discussed.
Probing Antibody-Antigen Interactions
Authors: Yang Guocheng , Velgos Stefanie N. , Boddapati Shanta P. , Sierks Michael R. 
Published: April 2014

ABSTRACT
Antibodies are biological molecules generated by the host immune system in response to the invasion of foreign bodies or antigens. Therefore, antibodies must possess high specificity toward target antigens in order for the antigen to be recognized and subsequently destroyed. Because of this specificity, antibodies or antibody fragments that maintain binding specificity are heavily used in diagnostic assays and are becoming increasingly important in many therapeutic applications. Classical immunoassays such as radioimmunoassay and enzyme-linked immunosorbent assay are effective analytical techniques that have been widely used to screen and determine antibody specificity. Because of increased demands for antibodies with well-defined specificities, other techniques have been developed that facilitate generation and characterization of antibody-binding specificities under different conditions, such as when the protein is expressed on a cell surface or the target antigen is hard to isolate. Here, we describe three alternate techniques that provide unique abilities to characterize antibody-antigen binding events: (i) surface plasmon resonance, (ii) fluorescence activated cell sorting, and (iii) atomic force microscopy. These different techniques take advantage of various changes in physical and/or chemical properties of the analytes that occur upon binding, such as refractive index, surface charge, and changes in structure. These techniques provide unique powerful advantages over traditional immunoassays including real-time and label-free detection, low sample volume and concentration requirements, and molecular-level detection sensitivity. This article provides an overview of how these alternate approaches to studying antibody-antigen interactions can be used to facilitate rapid development of new antibody-based reagents for diagnostic and therapeutic applications.
Rotavirus
Authors: Franco Manuel A. , Greenberg Harry B. 
Published: April 2014

ABSTRACTRotaviruses (RV) are ubiquitous, highly infectious, segmented double-stranded RNA genome viruses of importance in public health because of the severe acute gastroenteritis they cause in young children and many animal species. They are very well adapted to their host, with symptomatic and asymptomatic reinfections being virtually universal during the first 3 years of life. Antibodies are the major arm of the immune system responsible for protecting infants from RV reinfection. The relationship between the virus and the B cells (Bc) that produce these antibodies is complex and incompletely understood: most blood-circulating Bc that express RV-specific immunoglobulin (Ig) on their surface (RV-Ig) are naive Bc and recognize the intermediate capsid viral protein VP6 with low affinity. When compared to non-antigen-specific Bc, RV-Bc are enriched in CD27+memory Bc (mBc) that express IgM. The Ig genes used by naive RV-Bc are different than those expressed by RV-mBc, suggesting that the latter do not primarily develop from the former. Although RV predominantly infects mature villus enterocytes, an acute systemic viremia also occurs and RV-Bc can be thought of as belonging to either the intestinal or systemic immune compartments. Serotype-specific or heterotypic RV antibodies appear to mediate protection by multiple mechanisms, including intracellular and extracellular homotypic and heterotypic neutralization. Passive administration of RV-Ig can be used either prophylactically or therapeutically. A better understanding of the Bc response generated against RV will improve our capacity to identify improved correlates of protection for RV vaccines.
From Pasteur to Probiotics: A Historical Overview of Cheese and Microbes
Authors: Donnelly Catherine W. 
Published: April 2014

ABSTRACT

Cheese is a food which has been produced for centuries. While cheese was originally developed as a product which extended the shelf life of milk, over time distinct cheese varieties arose, being shaped by geographic, climate, cultural, and economic factors. Global demand for artisan cheeses is creating new economic opportunities. Consumers seeking distinctive products with regional flavor, or
terroir
, are becoming connoisseurs of hand-crafted cheeses with distinctive tastes and character. These demands have spurred new inquiry into microorganisms used as starter cultures and adjunct cultures, as well as the microbiological consortia of finished cheeses. Such demands have also created new concerns for food safety and international trade. New bacterial pathogens such as
Escherichia coli
O157:H7 and
Salmonella enterica
serovar Typhimurium DT104 have emerged in the food supply, causing a reevaluation of the efficacy of traditional cheesemaking procedures to control these pathogens. Similarly, pathogens such as
Listeria monocytogenes
pose problems to susceptible human populations, and cheese can be a vehicle of transmission for this deadly pathogen. With changes in sanitary requirements due to the globalization of the food industry, governments around the world are increasingly requiring assurances of cheese safety. While many governments recognize the safety of traditional artisan cheeses manufactured from raw milk, others are demanding pasteurization of all milk intended for cheesemaking to provide assurance of microbiological safety. In response, new technologies are being proposed to increase cheese safety, but these technologies fundamentally alter the traditional artisan practices and may not enhance microbiological safety. A reevaluation of the safety of traditional artisan practices, validation thereof, and communication of the scientific principles which promote safety will be necessary to enable the continued production of traditional artisan cheeses in global commerce. This also affords the opportunity to more fully explore the microbial diversity and microbial ecology of the great cheeses of the world.
Mesophilic and Thermophilic Cultures Used in Traditional Cheesemaking
Authors: Johnson Mark E. 
Published: April 2014

ABSTRACT
Most cheese varieties require acidification of milk by a select group of bacteria called starters. They ferment lactose to lactic acid and in so doing aid the cheesemaker in developing the desired texture as well as acidity of the cheese. However, while other microorganisms play the major role in flavor development of cheese, it is the starter that sets the stage for quality cheese manufacture. Starters were traditionally derived from the native microflora of the milk, but this practice is almost unheard of today. With the advent of better hygienic milking practices and industrialized cheesemaking, there was a need for more uniformity and reliable sources of the starter culture. Today’s starters are produced by companies specializing in their production as well as in the development of new strains for cheesemakers. The choice of starter for the manufacture of a specific cheese is dictated by the cheesemaking protocol, but it is also governed by the need to produce cheese with desired physical attributes. The properties of the starter that make it possible to do so help drive innovation in developing new potential choices in starter cultures. Indeed, the demands for predictable and reliable rates and extent of acidification of milk for cheesemaking and flavor development are as key for successful cheesemaking today with artisanal cheesemakers as they are for larger, more industrial-scale cheesemakers.
The Good, the Bad, and the Ugly: Tales of Mold-Ripened Cheese
Authors: Marcellino O.S.B. Sister Noëlla , Benson David R. 
Published: April 2014

ABSTRACT

The history of cheese manufacture is a “natural history” in which animals, microorganisms, and the environment interact to yield human food. Part of the fascination with cheese, both scientifically and culturally, stems from its ability to assume amazingly diverse flavors as a result of seemingly small details in preparation. In this review, we trace the roots of cheesemaking and its development by a variety of human cultures over centuries. Traditional cheesemakers observed empirically that certain environments and processes produced the best cheeses, unwittingly selecting for microorganisms with the best biochemical properties for developing desirable aromas and textures. The focus of this review is on the role of fungi in cheese ripening, with a particular emphasis on the yeast-like fungus
Geotrichum candidum
. Conditions that encourage the growth of problematic fungi such as
Mucor
and
Scopulariopsis
as well as Arachnida (cheese mites), and how such contaminants might be avoided, are discussed. Bethlehem cheese, a pressed, uncooked, semihard, Saint-Nectaire-type cheese manufactured in the United Sates without commercial strains of bacteria or fungi, was used as a model for the study of stable microbial succession during ripening in a natural environment. The appearance of fungi during a 60-day ripening period was documented using light and scanning electron microscopy, and it was shown to be remarkably reproducible and parallel to the course of ripening of authentic Saint-Nectaire cheese in the Auvergne region of France.
Geotrichum candidum
,
Mucor
, and
Trichothecium roseum
predominate the microbiotas of both cheese types.
Geotrichum
in particular was shown to have high diversity in different traditional cheese ripening environments, suggesting that traditional manufacturing techniques selected for particular fungi. This and other studies suggest that strain diversity arises in relation to the lore and history of the regions from which these types of cheeses arose.
Wooden Tools: Reservoirs of Microbial Biodiversity in Traditional Cheesemaking
Authors: Lortal Sylvie , Licitra Giuseppe , Valence Florence 
Published: April 2014

ABSTRACT
Today, wooden shelves are used for the ripening of about 500,000 tons of cheese per year in Europe, including about 350,000 tons in France, such as most of the famous cheeses with the protected designation of origin (PDO), e.g., Comté, Reblochon, Beaufort, Munster, Cantal, and Roquefort. For some PDO cheeses, the use of wooden tools is mandatory. Many cheesemakers believe that wooden tools improve the organoleptic and typical characteristics of their final products. Wood is a natural and sustainable material which has been used for centuries in traditional cheese production in a wide variety of forms (vats, shelves, and packaging). Wood is important in the cheesemaking process, interacting with the milk in vats or with the cheeses placed on shelves for ripening. Wood is viable due to its ability to exchange water but, above all, because it is covered by a rich microbial biofilm. As wood is porous and difficult to clean, the European Commission regularly highlights the question of its safety when in contact with food and calls for deeper scientific investigation. In this review, knowledge about the multiple technological roles of wood in dairy technology is discussed. The crucial role of wood as a reservoir of microbial biodiversity for traditional cheeses is reviewed, along with results of safety assessments. As a conclusion, the numerous questions remaining about this natural inoculating system are discussed.
The Microfloras of Traditional Greek Cheeses
Authors: Litopoulou-Tzanetaki Evanthia , Tzanetakis Nikolaos 
Published: April 2014

ABSTRACT
Many traditional cheeses are made in Greece. Some of them are, in fact, types of the same cheese variety, whether or not they have different cheesemaking technologies, but are known by different local names. Twenty of them have been granted protected designation of origin status. In the 8th century BCE, Homer described a cheese thought to be the ancestor of feta, the main cheese manufactured in Greece from the ancient times until today. Meanwhile, various cheese types evolved through the centuries, and almost every area in Greece has its own cheesemaking tradition. Some cheese varieties are local, handcrafted products whose production has been handed down from generation to generation, and without interest in their continued production, these varieties will disappear. Other local varieties are made at small factories from pasteurized milk and commercial rennet and starter and are very different from the traditional versions. However, some milk producers still make their cheeses at home or at small dairies from raw milk, without any starter, or sometimes from thermized milk, with traditional yogurt as the starter. Their cheeses are the basis for the information presented in this review.
Microbiological Quality and Safety Issues in Cheesemaking
Authors: D'amico Dennis J. 
Published: April 2014

ABSTRACT
As the manufacture of cheese relies in part on the select outgrowth of microorganisms, such conditions can also allow for the multiplication of unwanted contaminants. Milk ultimately becomes contaminated with microorganisms originating from infection, the farm environment, and feedstuffs, as well as milking and processing equipment. Thus, poor sanitation, improper milk handling, and animal health issues can result in not only decreased yield and poor quality but also sporadic cases and outbreaks of dairy-related disease. The entry, establishment, and persistence of food-borne pathogens in dairy processing environments also present a considerable risk to products postprocessing. Food safety management systems coupled with regulatory policies and microbiological standards for milk and milk products currently implemented in various nations work to reduce risk while improving the quality and safety of cheese and other dairy products. With that, cheese has enjoyed an excellent food safety record with relatively few outbreaks of food-borne disease considering the amount of cheese produced and consumed worldwide. However, as cheese production and consumption continue to grow, we must remain vigilant in ensuring the continued production of safe, high-quality cheese.
Sigma Factors: Key Molecules in
Mycobacterium tuberculosis
Physiology and Virulence
Authors: Manganelli Riccardo 
Published: April 2014

ABSTRACT

Rapid adaptation to changing environments is one of the keys to the success of microorganisms. Since infection is a dynamic process, it is possible to predict that
Mycobacterium tuberculosis
adaptation involves continuous modulation of its global transcriptional profile in response to the changing environment found in the human body. In the last 18 years several studies have stressed the role of sigma (σ) factors in this process. These are small interchangeable subunits of the RNA polymerase holoenzyme that are required for transcriptional initiation and that determine promoter specificity. The
M. tuberculosis
genome encodes 13 of these proteins, one of which—the principal σ factor σ
A
—is essential. Of the other 12 σ factors, at least 6 are required for virulence. In this article we review our current knowledge of mycobacterial σ factors, their regulons, the complex mechanisms determining their regulation, and their roles in
M. tuberculosis
physiology and virulence.
Two-Component Regulatory Systems of Mycobacteria
Authors: Parish Tanya 
Published: April 2014

ABSTRACT

Two-component regulatory systems (2CRSs) are widely used by bacteria to sense and respond to environmental stimuli with coordinated changes in gene expression. Systems are normally comprised of a sensory kinase protein that activates a transcriptional regulator by phosphorylation. Mycobacteria have few 2CRSs, but they are of key importance for bacterial survival and play important roles in pathogenicity.
Mycobacterium tuberculosis
has 12 paired two-component regulatory systems (which include a system with two regulators and one sensor, and a split sensor system), as well as four orphan regulators. Several systems are involved in virulence, and disruption of different systems leads to attenuation or hypervirulence. PhoPR plays a major role in regulating cell wall composition, and its inactivation results in sufficient attenuation of
M. tuberculosis
that deletion strains are live vaccine candidates. MprAB controls the stress response and is required for persistent infections. SenX3-RegX3 is required for control of aerobic respiration and phosphate uptake, and PrrAB is required for adaptation to intracellular infection. MtrAB is an essential system that controls DNA replication and cell division. The remaining systems (KdpDE, NarL, TrcRS, TcrXY, TcrA, PdtaRS, and four orphan regulators) are less well understood. The structure and binding motifs for several regulators have been characterized, revealing variations in function and operation. The sensors are less well characterized, and stimuli for many remain to be confirmed. This chapter reviews our current understanding of the role of two-component systems in mycobacteria, in particular
M. tuberculosis.
Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria
Authors: Derbyshire Keith M. , Gray Todd A. 
Published: April 2014

ABSTRACT

The past decade has seen an explosion in the application of genomic tools across all biological disciplines. This is also true for mycobacteria, where whole-genome sequences are now available for pathogens and nonpathogens alike. Genomes within the
Mycobacterium tuberculosis
complex (MTBC) bear the hallmarks of horizontal gene transfer (HGT). Conjugation is the form of HGT with the highest potential capacity and evolutionary influence. Donor and recipient strains of
Mycobacterium smegmatis
actively conjugate upon coculturing in biofilms and on solid media. Whole-genome sequencing of the transconjugant progeny demonstrated the incredible scale and range of genomic variation that conjugation generates. Transconjugant genomes are complex mosaics of the parental strains. Some transconjugant genomes are up to one-quarter donor-derived, distributed over 30 segments. Transferred segments range from ∼50 bp to ∼225,000 bp in length and are exchanged with their recipient orthologs all around the genome. This unpredictable genome-wide infusion of DNA sequences is called distributive conjugal transfer (DCT), to distinguish it from traditional
oriT
-based conjugation. The mosaicism generated in a single transfer event resembles that seen from meiotic recombination in sexually reproducing organisms and contrasts with traditional models of HGT. This similarity allowed the application of a genome-wide association study approach to map the donor genes that confer a donor mating identity phenotype. The mating identity genes map to the
esx1
locus, expanding the central role of ESX-1 function in conjugation. The potential for DCT to instantaneously blend genomes will affect how we view mycobacterial evolution and provide new tools for the facile manipulation of mycobacterial genomes.