bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity to the two‐peptide bacteriocin lactococcin G is dependent on UppP, an enzyme involved in cell‐wall synthesis
Authors: Kjos Morten , Oppegård Camilla , Diep Dzung B. , Nes Ingolf F. , Veening Jan‐Willem , Nissen‐Meyer Jon , Kristensen Tom 
Published: April 2014

SummaryMost bacterially produced antimicrobial peptides (bacteriocins) are thought to kill target cells by a receptor‐mediated mechanism. However, for most bacteriocins the receptor is unknown. For instance, no target receptor has been identified for the two‐peptide bacteriocins (class IIb), whose activity requires the combined action of two individual peptides. To identify the receptor for the class IIb bacteriocin lactococcin G, which targets strains of Lactococcus lactis, we generated 12 lactococcin G‐resistant mutants and performed whole‐genome sequencing to identify mutations causing the resistant phenotype. Remarkably, all had a mutation in or near the gene uppP (bacA), encoding an undecaprenyl pyrophosphate phosphatase; a membrane protein involved in peptidoglycan synthesis. Nine mutants had stop codons or frameshifts in the uppP gene, two had point mutations in putative regulatory regions and one caused an amino acid substitution in UppP. To verify the receptor function of UppP, it was shown that growth of non‐sensitive Streptococcus pneumoniae could be inhibited by lactococcin G when L. lactis uppP was expressed in this bacterium. Furthermore, we show that the related class IIb bacteriocin enterocin 1071 also uses UppP as receptor. The approach used here should be broadly applicable to identify receptors for other bacteriocins as well.
Frequency and distribution of the brown rust resistance gene Bru1 and implications for the Louisiana sugarcane breeding programme
Authors: Parco Arnold S. , Avellaneda Mavir C. , Hale Anna H. , Hoy Jeffrey W. , Kimbeng Collins A. , Pontif Michael J. , Gravois Kenneth A. , Baisakh Niranjan 
Published: April 2014

AbstractBrown rust, caused by the fungus Puccinia melanocephala, poses an increasing threat to sugarcane industries worldwide. Recently, markers R12H16 and 9020‐F4 were developed for a major resistance gene Bru1 that contributes to a significant proportion of brown rust resistance in multiple sugarcane industries. Marker‐assisted screening of Louisiana sugarcane germplasm showed a low frequency (4.3%, five out of 117 clones) of Bru1 among sugarcane cultivars and elite breeding clones. Likewise, among progeny of crosses involving wild/exotic germplasm, only 14 of 208 clones (6.7%) tested Bru1 positive. However, Bru1 frequency was higher (28.7%, 52 of 181 clones) in wild/exotic germplasm, which indicated that diverse genetic resources are available for Bru1 introgression. Commercial Bru1‐positive cultivar, ‘L 01‐299', was resistant to brown rust. However, Bru1‐positive cultivar, ‘L 10‐146’, was susceptible while Bru1‐negative cultivars, such as ‘L 99‐233’, showed resistance to brown rust. Bru1‐negative clones with brown rust resistance offer an opportunity to identify alternate sources of resistance, which can be pyramided with Bru1 for effective and durable resistance in sugarcane against the changing pathogen.
A phylogenetic study of the generic relationships within the subtribe Leucophoropterina Schuh (Miridae: Phylinae: Leucophoropterini)
Authors: MENARD KATRINA L. , WOOLLEY JAMES B. 
Published: April 2014

AbstractThe subtribe Leucophoropterina (Miridae: Phylinae: Leucophoropterini) is a relatively small lineage of mirids comprising 23 genera and 104 species. Most of the species are endemic to the Indo‐Pacific and Australia, and many are considered ant mimics. A phylogenetic analysis including both the Australian and the Indo‐Pacific taxa was conducted for the first time with a dataset of 137 morphological characters coded for all but two known species of Leucophoropterina. The hypothesis by Schuh () of at least two major lineages of ant‐mimicking taxa based on his analysis of the Indo‐Pacific taxa continues to be supported with our inclusion of Australian taxa. The Australian taxa and Indo‐Pacific taxa of Leucophoropterina do not form independent, geographically based lineages, but instead comprise several lineages containing taxa from both regions. This study provides a basis for future detailed studies of biogeography and ant mimicry in the group.
Integrated management of Bromus diandrus in dryland cereal fields under no‐till
Authors: García A L , Royo‐Esnal A , Torra J , Cantero‐Martinez C , Recasens J 
Published: April 2014

SummaryAs herbicides have limited effect in controlling Bromus diandrus in no‐till dryland cereal fields, the integration of chemical and cultural methods needs to be investigated. A field study was carried out in Lleida (Spain) during 2008–09, 2009–10 and 2010–11 seasons, in a no‐till winter cereal field integrating delayed crop sowing with herbicides in a barley–wheat–wheat rotation. Three crop sowing dates were considered: D1, mid‐October; D2, mid‐November; and D3, early December, and the herbicides mesosulfuron‐methyl plus iodosulfuron‐methyl‐sodium were applied in wheat. Weed density, cumulative emergence and fecundity were estimated for each sowing date. In all three seasons, a significant reduction in the cumulative emergence of B. diandrus as compared to D1 was observed in D2 (82.0, 97.5 and 98.1%) and D3 (80.8, 98.7 and 97.2%). In addition, a significant decrease in weed density and seed rain was observed across all sowing dates and seasons. The herbicide used in wheat was more effective under delayed sowing, due to lower weed density and presence of less developed weed seedlings. After three seasons, the populations of B. diandrus were completely depleted in D2 and D3. This study demonstrates the possibility of eliminating brome infestations in dryland cereal fields in no‐till systems through the integration of cultural and chemical strategies.
Extraction of Virgin Coconut (Cocos nucifera) Oil Using Supercritical Fluid Carbon Dioxide
Authors: Che Yunus Mohd Azizi , Rozak Muhammad Naim , Nian-Yian Lee , Ruslan Muhammad Syafiq Hazwan , Mohd-Setapar Siti Hamidah , Ahmad Zaini Muhammad Abbas 
Published: April 2014

Bioactive compound is an important component in health care to a majority of the world’s population. Virgin Coconut (Cocos nucifera) oil is used in Southeast Asia for treating various diseases and is well-known of its rich nutrients. In this study, supercritical fluid extraction (SFE), an environmental friendly technique was used to extract the interest compounds from crude virgin coconut. The extracted virgin coconut oil is free from organic solvent and safe to be consumed. This is because the solvent used in the extraction process is carbon dioxide which is inert and no solvent residue inside the extracted oil. The layout of the experiment was developed via Statistica 8.0 using the Box-Behnken experimental design model. The oil yield, antioxidant activity and total phenolic content were calculated while the comparison of the experimental results and the statistical data was done using response surface methodology (RSM). Therefore, the optimum conditions of temperature and pressure for the extraction of virgin coconut oil was obtained through the statistical study which is 47°C and 20MPa respectively.
Alterations in Cholesterol Metabolism Restrict HIV-1
Trans
Infection in Nonprogressors
Authors: Rappocciolo Giovanna , Jais Mariel , Piazza Paolo , Reinhart Todd A. , Berendam Stella J. , Garcia-Exposito Laura , Gupta Phalguni , Rinaldo Charles R. 
Published: April 2014

ABSTRACT

HIV-1-infected nonprogressors (NP) inhibit disease progression for years without antiretroviral therapy. Defining the mechanisms for this resistance to disease progression could be important in determining strategies for controlling HIV-1 infection. Here we show that two types of professional antigen-presenting cells (APC), i.e., dendritic cells (DC) and B lymphocytes, from NP lacked the ability to mediate HIV-1
trans
infection of CD4
+
T cells. In contrast, APC from HIV-1-infected progressors (PR) and HIV-1-seronegative donors (SN) were highly effective in mediating HIV-1
trans
infection. Direct
cis
infection of T cells with HIV-1 was comparably efficient among NP, PR, and SN. Lack of HIV-1
trans
infection in NP was linked to lower cholesterol levels and an increase in the levels of the reverse cholesterol transporter ABCA1 (ATP-binding cassette transporter A1) in APC but not in T cells. Moreover,
trans
infection mediated by APC from NP could be restored by reconstitution of cholesterol and by inhibiting ABCA1 by mRNA interference. Importantly, this appears to be an inherited trait, as it was evident in APC obtained from NP prior to their primary HIV-1 infection. The present study demonstrates a new mechanism wherein enhanced lipid metabolism in APC results in remarkable control of HIV-1
trans
infection that directly relates to lack of HIV-1 disease progression.

IMPORTANCE
HIV-1 can be captured by antigen-presenting cells (APC) such as dendritic cells and transferred to CD4 helper T cells, which results in greatly enhanced viral replication by a mechanism termed
trans
infection. A small percentage of HIV-1-infected persons are able to control disease progression for many years without antiretroviral therapy. In our study, we linked this lack of disease progression to a profound inability of APC from these individuals to
trans
infect T cells. This effect was due to altered lipid metabolism in their APC, which appears to be an inherited trait. These results provide a basis for therapeutic interventions to control of HIV-1 infection through modulation of cholesterol metabolism.
The Triphenylethylenes, a Novel Class of Antifungals
Authors: Odom Audrey R. 
Published: April 2014

ABSTRACT
New antifungals are needed, particularly in the developing world, to treat life-threatening fungal infections, such as cryptococcosis. Drug repurposing is one strategy to identify new drug-like compounds, but it is often difficult to identify a mechanism of action. Here we discuss the outstanding effort by Butts et al. to identify calmodulin as an antifungal target of repurposed estrogen receptor antagonists [A. Butts, K. Koselny, Y. Chabrier-Roselló, C. P. Semighini, Y. C. S. Brown, et al., mBio 5(1):e00765-13, 2014, doi:10.1128/mBio.00765-13]. The authors show that these compounds bind to and directly inhibit fungal calmodulin and also reduce fungal burden in an animal disease model. These studies thus establish both the key preclinical efficacy and the antifungal mechanism of action, which will allow these compounds to progress toward development of novel antifungal therapies.
Immunotherapeutic Approaches To Prevent Cytomegalovirus-Mediated Disease
Authors: Seedah Edith A. , Frye Zachary P. , Maynard Jennifer A. 
Published: April 2014

ABSTRACT

Human cytomegalovirus (CMV) is the major cause of congenital neurological defects in the United States and also causes significant morbidity and mortality for hematopoietic and solid organ transplant patients. Primary infection in immunocompetent individuals rarely causes disease but resolves as a life-long latent infection, characterized by sustained antibody and cellular responses. Despite considerable efforts over the last 40 years to develop live attenuated and subunit vaccines, none is close to receiving regulatory approval. However, there is evidence that antibodies can prevent primary infection and cytotoxic T cells can suppress secondary infection. Prior maternal infection decreases the risk a fetus will contract CMV, while adoptive transfer of virus-specific CD8
+
T cells is highly protective against CMV disease in hematopoietic stem cell transplant recipients. As a result, three polyclonal immunoglobulin preparations are approved for clinical use and one monoclonal antibody has reached phase III trials. Enhanced understanding of the viral life cycle from a biochemical perspective has revealed additional targets for neutralizing antibodies in the gH/gL/UL128-131 pentamer. Until an effective vaccine is licensed, passive immunotherapeutics may present an alternative to maintain viral loads and prevent CMV disease in susceptible populations. This review summarizes the progress and potential of immunotherapeutics to treat CMV infection.
The Basics of Cheesemaking
Authors: Kindstedt Paul S. 
Published: April 2014

ABSTRACT
All cheeses have a common set of principles that involve a complex web of chemical, biochemical, and microbiological changes. These changes first transform milk into fresh or unripened cheese. Although some cheeses are consumed immediately after manufacture, most are subsequently aged or ripened for weeks to years depending on the variety. During aging or ripening, a cheese's sensory characteristics undergo multifaceted and often dramatic changes. The steps performed during the earliest days of the cheesemaking process are especially critical because they establish the chemical characteristics of the cheese at the start of ripening, and these characteristics in turn affect the ripening process. For most cheeses, the key process on the first day of cheesemaking is the fermentation of lactose to lactic acid by bacteria. The rate at which lactic acid is produced profoundly affects the initial chemical characteristics of the cheese, which selectively influence the complex microbial populations that find their way from the milk and surrounding environment into the cheese. This article discusses the basics of cheesemaking by integrating the practical steps that all cheesemakers use with the scientific principles on which those practices are based. The aim is to paint a conceptual picture in which the microbiology of cheese “fits together” with the basic practices of cheesemaking and the scientific principles that underlie them.
The Microbiology of Traditional Hard and Semihard Cooked Mountain Cheeses
Authors: Beuvier Eric , Duboz Gabriel 
Published: April 2014

ABSTRACT
Traditional cheeses originate from complex systems that confer on them specific sensory characteristics. These characteristics are linked to various factors of biodiversity such as animal feed, the use of raw milk and its indigenous microflora, the cheese technology, and the ripening conditions, all in conjunction with the knowledge of the cheesemaker and affineur. In Europe, particularly in France, the preservation of traditional cheesemaking processes, some of which have protected designation of origin, is vital for the farming and food industry in certain regions. Among these cheeses, some are made in the Alps or Jura Mountains, including Comté, Beaufort, Abondance, and Emmental, which are made from raw milk. The principle of hard or semihard cooked cheese, produced in the Alps and Jura Mountains, was to make a product during the summer—a period during which the animals feed more and milk production is high—with a shelf life of several months that could be consumed in winter. Today, these traditional cheeses are produced according to a specific approach combining science and tradition in order to better understand and preserve the elements that contribute to the distinctiveness of these cheeses. To address this complex problem, a global approach to the role of the raw milk microflora in the final quality of cheeses was initially chosen. The modifications resulting from the elimination of the raw milk microflora, either by pasteurization or by microfiltration, to the biochemistry of the ripening process and ultimately the sensory quality of the cheeses were evaluated. This approach was achieved mainly with experimental hard cooked cheeses. Other types of traditional cheese made with raw and pasteurized milk are also considered when necessary. Besides the native raw milk microflora, traditional lactic starters (natural or wild starters) also participate in the development of the characteristics of traditional hard and semihard cooked mountain cheeses. After an initial description, their roles are described, mainly for Comté.
Regulated Expression Systems for Mycobacteria and Their Applications
Authors: Schnappinger Dirk , Ehrt Sabine 
Published: April 2014

ABSTRACT

For bacterial model organisms like
Escherichia coli
and
Bacillus subtilis
, genetic tools to experimentally manipulate the activity of individual genes have existed for decades. But for genetically less tractable yet medically important bacteria such as
Mycobacterium tuberculosis
, such tools have rarely been available. More recently, several groups developed genetic switches that function efficiently in
M. tuberculosis
and other mycobacteria. Together these systems utilize six transcription factors, eight regulated promoters, and three regulatory principles. In this chapter we describe their design features, review their main applications, and discuss the advantages and disadvantages of regulating transcription, translation, or protein stability for controlling gene activities in bacteria.

Genetic elements that enable specific and quantitative control over the activity of individual genes are irreplaceable components of the modern genetic toolbox. They facilitate not only the purification of proteins for biochemical, structural, or immunological studies but can also be applied to improve our understanding of
in vivo
gene functions. Until recently, only one such tool was available for use in mycobacteria, and its applicability in slowly growing mycobacteria was limited. But during the last decade at least a dozen new systems have been developed. In this chapter we review the design, components, and regulatory mechanisms of the different systems and discuss their main applications.
Mycobacterium tuberculosisin the Proteomics Era
Authors: Gengenbacher Martin , Mouritsen Jeppe , Schubert Olga T. , Aebersold Ruedi , Kaufmann Stefan H. E. 
Published: April 2014

ABSTRACTThe emerging field of proteomics has contributed greatly to improving our understanding of the human pathogenMycobacterium tuberculosisover the last two decades. In this chapter we provide a comprehensive overview of mycobacterial proteome research and highlight key findings. First, studies employing a combination of two-dimensional gel electrophoresis and mass spectrometry (MS) provided insights into the proteomic composition, initially of the whole bacillus and subsequently of subfractions, such as the cell wall, cytosol, and secreted proteins. Comparison of results obtained under various culture conditions, i.e., acidic pH, nutrient starvation, and low oxygen tension, aiming to mimic facets of the intracellular lifestyle ofM. tuberculosis,provided initial clues to proteins relevant for intracellular survival and manipulation of the host cell. Further attempts were aimed at identifying the biological functions of the hypotheticalM. tuberculosisproteins, which still make up a quarter of the gene products ofM. tuberculosis, and at characterizing posttranslational modifications. Recent technological advances in MS have given rise to new methods such as selected reaction monitoring (SRM) and data-independent acquisition (DIA). These targeted, cutting-edge techniques combined with a public database of specific MS assays covering the entire proteome ofM. tuberculosisallow the simple and reliable detection of any mycobacterial protein. Most recent studies attempt not only to identify but also to quantify absolute amounts of single proteins in the complex background of host cells without prior sample fractionation or enrichment. Finally, we will discuss the potential of proteomics to advance vaccinology, drug discovery, and biomarker identification to improve intervention and prevention measures for tuberculosis.
Structural Annotation of the
Mycobacterium tuberculosis
Proteome
Authors: Chandra Nagasuma , Sandhya Sankaran , Anand Praveen 
Published: April 2014

ABSTRACT

Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen's proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins, making up nearly 70% of the
Mycobacterium tuberculosis
proteome, are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of the
M. tuberculosis
genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site–based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.
Public Health Disease Surveillance Networks
Authors: Morse Stephen S. 
Published: April 2014

ABSTRACTZoonotic infections are important sources of human disease; most known emerging infections are zoonotic (e.g., HIV, Ebola virus, severe acute respiratory syndrome, Nipah virus, and enteropathogenicEscherichia coli) and originated as natural infections of other species that acquired opportunities to come in contact with humans. There are also serious infectious diseases classically considered zoonotic, such as influenza, rabies, bubonic plague, brucellosis, and leptospirosis. More recently, it has been recognized that wildlife constitutes a particularly important source of novel zoonoses. With all this microbial movement, surveillance is considered the first line of public health defense. The zoonotic origin of many human and livestock infections argues strongly for the synergistic value of a One Health approach, which provides the capability to identify pathogens crossing into new species and could provide earlier warning of potential epidemics. This article discusses public health surveillance and major recent surveillance initiatives and reviews progress toward implementing a One Health surveillance framework. Networks discussed include global intergovernmental organizations and recent combined efforts of these organizations; Web-based nongovernmental systems (e.g., ProMED, the Program for Monitoring Emerging Diseases); and networks of bilateral or multilateral government programs (e.g., the CDC's Global Disease Detection [GDD] platform; the U.S. Department of Defense's Global Emerging Infections Surveillance and Response System [GEIS]; regional and subregional networks; and the U.S. Agency for International Development's Emerging Pandemic Threats [EPT] program and its surveillance component, PREDICT). Syndromic surveillance also has potential to complement existing systems. New technologies are enabling revolutionary capabilities for global surveillance, but in addition to serious technical needs, both sustainability and data-sharing mechanisms remain challenges.