bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of evolvability in microRNA target sites in vertebrates
Authors: Xu Jin , Zhang Rui , Shen Yang , Liu Guojing , Lu Xuemei , Wu Chung-I
Published: September 2013

The lack of long-term evolutionary conservation of microRNA (miRNA) target sites appears to contradict many analyses of their functions. Several hypotheses have been offered, but an attractive one—that the conservation may be a function of taxonomic hierarchy (vertebrates, mammals, primates, etc.)—has rarely been discussed. For such an analysis, we cannot use evolutionary conservation as a criterion of target identification, and hence, have used high confidence target sites in the cross-linking immunoprecipitation (CLIP) data. Assuming that a proportion, p, of target sites in the CLIP data are conserved, we define the evolvability of miRNA targets as 1-p. Genomic data from vertebrate species show that the evolvability between human and fish is very high, at more than 90%. The evolvability decreases to 50% between birds and mammals, 20% among mammalian orders, and only 6% between human and chimpanzee. Within each taxonomic hierarchy, there is a set of targets that are conserved only at that level of evolution. Extrapolating the evolutionary trend, we find the evolvability in any single species to be close to 0%. Thus, all miRNA target sites identified by the CLIP method are evolutionarily conserved in one species, but the conservation is lost step by step in larger taxonomic groups. The changing evolvability of miRNA targets suggests that miRNA-target interactions may play a role in the evolution of organismal diversity.
Live Imaging of Neuroblast Lineages within Intact Larval Brains in Drosophila
Authors: Cabernard Clemens , Doe Chris Q.
Published: October 2013

Neuroblasts are the precursors of the Drosophila central nervous system and undergo repeated physical and molecular asymmetric cell divisions. Live imaging of neuroblast lineages within intact Drosophila larval brains has dramatically improved our current understanding of basic cellular processes such as the establishment of cell polarity, spindle orientation, and cytokinesis. The analysis of mutant phenotypes using live imaging can enlarge our understanding of asymmetric neuroblast division and self-renewal. Although much live neuroblast imaging is performed using green fluorescent protein only, the generation of improved fluorescent proteins has led to an increase in the use of two-color imaging. Here we present a simple protocol for isolating and imaging larval brain neuroblasts. We describe procedures for the dissection and mounting of brains from third-instar Drosophila larvae in explant solution and their subsequent live imaging. The method provides a close approximation to the in vivo environment and produces data with high temporal and spatial resolutions. We also discuss potential problems and pitfalls and provide examples of how this technique is used.
Tracking Individual Membrane Proteins Using Quantum Dots
Authors: Courty Sébastien , Dahan Maxime
Published: October 2013

Single-particle tracking of individual membrane molecules is now the method of choice to decipher the molecular organization of the plasma membrane. By labeling proteins or lipids with latex beads, 40-nm gold nanoparticles, or small organic fluorophores, it is possible to analyze the mechanisms controlling their lateral dynamics. Semiconductor quantum dots (QDs) provide several advantages for tracking membrane molecules: (1) Their size, which is intermediate between those of organic dyes (1–4 nm) and large beads (100 nm to 1 µm), remains close to the molecular scale; (2) their photostability allows observation over long durations; (3) parallel detection of multiple spots in a field of view is easy; and (4) multicolor imaging is facilitated by their absorption properties. In general, the labeling of membrane molecules is based on the targeting of an extracellular epitope by a tagged antibody or ligand. By progressively decreasing the concentration of markers, a regime is reached where isolated tags can be detected and tracked. We present here a protocol based on the successive use of biotinylated primary antibodies and streptavidin-coated QDs.
Miniaturization of Two-Photon Microscopy for Imaging in Freely Moving Animals
Authors: Helmchen Fritjof , Denk Winfried , Kerr Jason N.D.
Published: October 2013

This article describes the development and application of miniaturized two-photon-excited fluorescence microscopes (“two-photon fiberscopes”). Two-photon fiberscopes have been developed with the aim of enabling high-resolution imaging of neural activity in freely behaving animals. They use fiber optics to deliver laser light for two-photon excitation. Their small front piece typically contains a miniature scanning mechanism and imaging optics. Two-photon fiberscopes can be made sufficiently small and lightweight to be carried by rats and mice and to allow virtually unrestricted movement within a behavioral arena. Typically mounted to the animal’s skull above a cranial window, two-photon fiberscopes permit imaging of cells down to at least 250 µm below the brain surface (e.g., in rat neocortex). In freely exploring animals, action-potential-evoked calcium transients can be imaged in individual somata of visual cortex neurons bulk-labeled with a calcium indicator. Two-photon fiberscopes thus enable high-resolution optical recording of neural activity with cellular resolution during natural behaviors.
Crystal landscape in the orcinol:4,4′-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters
Authors: Dubey Ritesh , Pavan Mysore S. , Guru Row Tayur N. , Desiraju Gautam R
Published: October 2013

Polymorphism in the orcinol:4,4′-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing theSynthon Based Fragments Approach(SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O—H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O—H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.
Clustering of Lifestyle Risk Factors and Poor Physical Function in Older Adults: The Hertfordshire Cohort Study
Authors: Robinson Siân M. , Jameson Karen A. , Syddall Holly E. , Dennison Elaine M. , Cooper Cyrus , Aihie Sayer Avan ,   The Hertfordshire Cohort Study Group
Published: October 2013

Objectives

To examine the relationship between number of lifestyle risk factors (out of low physical activity, poor diet, obesity, smoking) and physical function in older community‐dwelling men and women.

Design

Cross‐sectional study, Hertfordshire, United Kingdom.

Participants

Men (n = 1,682) and women (n = 1,540) aged 59 to 73.

Measurements

Physical activity was assessed using an administered questionnaire with a score from 0 to 100; low activity was defined as a score of 50 or less. Diet was assessed using a food frequency questionnaire; diet quality was assessed according to a score for a principal component analysis‐defined “healthy” dietary pattern. Poor diet was categorized as a dietary pattern score in the lowest quarter of the distribution. Obesity was defined as a body mass index of 30.0 kg/m2 or more. Physical function was assessed according to self‐report (SF‐36); poor function was defined as a score in lowest quarter of the distribution. A subgroup of participants had objective assessments of physical function (Timed Up‐and‐Go Test, timed 3‐m walk, chair rises, one‐legged standing balance).

Results

There was a graded increase in prevalence of poor self‐reported physical function in men and women with increasing number of risk factors (men, adjusted odds ratio (AOR) for 3 or 4 risk factors vs none = 3.79, 95% confidence interval (CI) = 2.31–6.21; women, AOR = 5.37, 95% CI = 2.66–10.84). With the exception of balance, the objective assessments also showed graded relationships with number of risk factors, such that more risk factors was associated with poorer physical function.

Conclusion

These modifiable lifestyle risk factors are linked to marked differences in risk of poorer physical function in older adults. Efforts to encourage healthy lifestyles have the potential to improve physical function and to promote healthier ageing.
Large Eddy Simulation for Turbines: Methodologies, Cost and Future Outlooks
Authors: Tyacke James , Tucker Paul , Jefferson-Loveday Richard , Rao Vadlamani Nagabushana , Watson Robert , Naqavi Iftekhar , Yang Xiaoyu
Published: October 2013

Flows throughout different zones of turbines have been investigated using large eddy simulation (LES) and hybrid Reynolds-averaged Navier–Stokes-LES (RANS-LES) methods and contrasted with RANS modeling, which is more typically used in the design environment. The studied cases include low and high-pressure turbine cascades, real surface roughness effects, internal cooling ducts, trailing edge cut-backs, and labyrinth and rim seals. Evidence is presented that shows that LES and hybrid RANS-LES produces higher quality data than RANS/URANS for a wide range of flows. The higher level of physics that is resolved allows for greater flow physics insight, which is valuable for improving designs and refining lower order models. Turbine zones are categorized by flow type to assist in choosing the appropriate eddy resolving method and to estimate the computational cost.
Multimode Fluid Elastic Instability of Heat Exchanger Tubes
Authors: Blevins R. D.
Published: October 2013

Multimode fluid elastic instability analysis is made of heat exchanger tubes in cross flow. The stability analysis predicts that the flow velocity for onset of tube instability in nonuniform flow is lowered by participation of multiple tube modes with similar natural frequencies.
An introduction to molecular imaging in radiation oncology: A report by the AAPM Working Group on Molecular Imaging in Radiation Oncology (WGMIR)
Authors: Munley Michael T. , Kagadis George C. , McGee Kiaran P. , Kirov Assen S. , Jang Sunyoung , Mutic Sasa , Jeraj Robert , Xing Lei , Bourland J. Daniel
Published: October 2013

Molecular imaging is the direct or indirect noninvasive monitoring and recording of the spatial and temporal distribution ofin vivomolecular, genetic, and/or cellular processes for biochemical, biological, diagnostic, or therapeutic applications. Molecular images that indicate the presence of malignancy can be acquired using optical, ultrasonic, radiologic, radionuclide, and magnetic resonance techniques. For the radiation oncology physicist in particular, these methods and their roles in molecular imaging of oncologic processes are reviewed with respect to their physical bases and imaging characteristics, including signal intensity, spatial scale, and spatial resolution. Relevant molecular terminology is defined as an educational assist. Current and future clinical applications in oncologic diagnosis and treatment are discussed. National initiatives for the development of basic science and clinical molecular imaging techniques and expertise are reviewed, illustrating research opportunities in as well as the importance of this growing field.
Depletion of the 26
S
Proteasome Adaptor Ecm29 Increases Toll-Like Receptor 3 Signaling
Authors: Gorbea Carlos , Rechsteiner Martin , Vallejo Jesús G. , Bowles Neil E.
Published: October 2013

Responses to viral infection involve both proteasomal and autophagy-mediated degradation events.
4-(1
H
)-Quinolones and 1,2,3,4-Tetrahydroacridin-9(10
H
)-Ones Prevent the Transmission of Plasmodium falciparum to Anopheles freeborni
Authors: Sáenz Fabián E. , LaCrue Alexis N. , Cross R. Matthew , Maignan Jordany R. , Udenze Kenneth O. , Manetsch Roman , Kyle Dennis E.
Published: October 2013

Malaria kills approximately 1 million people a year, mainly in sub-Saharan Africa. Essential steps in the life cycle of the parasite are the development of gametocytes, as well as the formation of oocysts and sporozoites, in the
Anopheles
mosquito vector. Preventing transmission of malaria through the mosquito is necessary for the control of the disease; nevertheless, the vast majority of drugs in use act primarily against the blood stages. The study described herein focuses on the assessment of the transmission-blocking activities of potent antierythrocytic stage agents derived from the 4(1
H
)-quinolone scaffold. In particular, three 3-alkyl- or 3-phenyl-4(1
H
)-quinolones (P4Qs), one 7-(2-phenoxyethoxy)-4(1
H
)-quinolone (PEQ), and one 1,2,3,4-tetrahydroacridin-9(10
H
)-one (THA) were assessed for their transmission-blocking activity against the mosquito stages of the human malaria parasite (
Plasmodium falciparum
) and the rodent parasite (
P. berghei
). Results showed that all of the experimental compounds reduced or prevented the exflagellation of male gametocytes and, more importantly, prevented parasite transmission to the mosquito vector. Additionally, treatment with ICI 56,780 reduced the number of sporozoites that reached the
Anopheles
salivary glands. These findings suggest that 4(1
H
)-quinolones, which have activity against the blood stages, can also prevent the transmission of
Plasmodium
to the mosquito and, hence, are potentially important drug candidates to eradicate malaria.
Emergence of Staphylococcus aureus Carrying Multiple Drug Resistance Genes on a Plasmid Encoding Exfoliative Toxin B
Authors: Hisatsune Junzo , Hirakawa Hideki , Yamaguchi Takayuki , Fudaba Yasuyuki , Oshima Kenshiro , Hattori Masahira , Kato Fuminori , Kayama Shizuo , Sugai Motoyuki
Published: October 2013

We report the complete nucleotide sequence and analysis of pETB
TY825
, a
Staphylococcus aureus
TY825 plasmid encoding exfoliative toxin B (ETB).
S. aureus
TY825 is a clinical isolate obtained from an impetigo patient in 2002. The size of pETB
TY825
, 60.6 kbp, was unexpectedly larger than that of the archetype pETB
TY4
(∼30 kbp). Genomic comparison of the plasmids shows that pETB
TY825
has the archetype pETB
TY4
as the backbone and has a single large extra DNA region of 22.4 kbp. The extra DNA region contains genes for resistance to aminoglycoside [
aac
(
6′
)/
aph
(
2″
)], macrolide (
msrA
), and penicillin (
blaZ
). A plasmid deletion experiment indicated that these three resistance elements were functionally active. We retrospectively examined the resistance profile of the clinical ETB-producing
S. aureus
strains isolated in 1977 to 2007 using a MIC determination with gentamicin (GM), arbekacin (ABK), and erythromycin (EM) and by PCR analyses for
aac
(
6
′)/
aph
(
2″
) and
msrA
using purified plasmid preparations. The ETB-producing
S. aureus
strains began to display high resistance to GM, which was parallel with the detection of
aac
(
6′
)/
aph
(
2″
) and
mecA
, after 1990. Conversely, there was no significant change in the ABK MIC during the testing period, although it had a tendency to slightly increase. After 2001, isolates resistant to EM significantly increased; however,
msrA
was hardly detected in ETB-producing
S. aureus
strains, and only five isolates were positive for both
aac
(
6′
)/
aph
(
2″
) and
msrA
. In this study, we report the emergence of a fusion plasmid carrying the toxin gene
etb
and drug resistance genes. Prevalence of the pETB
TY825
carrier may further increase the clinical threat, since ETB-producing
S. aureus
is closely related to more severe impetigo or staphylococcal scalded-skin syndrome (SSSS), which requires a general antimicrobial treatment.
GRL-04810 and GRL-05010, Difluoride-Containing Nonpeptidic HIV-1 Protease Inhibitors (PIs) That Inhibit the Replication of Multi-PI-Resistant HIV-1
In Vitro
and Possess Favorable Lipophilicity That May Allow Blood-Brain Barrier Penetration
Authors: Salcedo Gómez Pedro Miguel , Amano Masayuki , Yashchuk Sofiya , Mizuno Akira , Das Debananda , Ghosh Arun K. , Mitsuya Hiroaki
Published: October 2013

We designed, synthesized, and identified two novel nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs), GRL-04810 and GRL-05010, containing the structure-based designed privileged cyclic ether-derived nonpeptide P2 ligand,
bis
-tetrahydrofuranylurethane (
bis
-THF), and a difluoride moiety, both of which are active against the laboratory strain HIV-1
LAI
(50% effective concentrations [EC
50
s], 0.0008 and 0.003 μM, respectively) with minimal cytotoxicity (50% cytotoxic concentrations [CC
50
s], 17.5 and 37.0 μM, respectively, in CD4
+
MT-2 cells). The two compounds were active against multi-PI-resistant clinical HIV-1 variants isolated from patients who had no response to various antiviral regimens. GRL-04810 and GRL-05010 also blocked the infectivity and replication of each of the HIV-1
NL4-3
variants selected by up to 5 μM lopinavir (EC
50
s, 0.03 and 0.03 μM, respectively) and atazanavir (EC
50
s, 0.02 and 0.04 μM, respectively). Moreover, they were active against darunavir (DRV)-resistant variants (EC
50
in 0.03 to 0.034 μM range for GRL-04810 and 0.026 to 0.043 μM for GRL-05010), while DRV had EC
50
s between 0.02 and 0.174 μM. GRL-04810 had a favorable lipophilicity profile as determined with the partition (log
P
) and distribution (log
D
) coefficients of −0.14 and −0.29, respectively. The
in vitro
blood-brain barrier (BBB) permeability assay revealed that GRL-04810 and GRL-05010 may have a greater advantage in terms of crossing the BBB than the currently available PIs, with apparent penetration indexes of 47.8 × 10
−6
and 61.8 × 10
−6
cm/s, respectively. The present data demonstrate that GRL-04810 and GRL-05010 exert efficient activity against a wide spectrum of HIV-1 variants
in vitro
and suggest that two fluorine atoms added to their
bis
-THF moieties may well enhance their penetration across the BBB.
IreB, a Ser/Thr Kinase Substrate, Influences Antimicrobial Resistance in Enterococcus faecalis
Authors: Hall Cherisse L. , Tschannen Michael , Worthey Elizabeth A. , Kristich Christopher J.
Published: October 2013

Enterococcus faecalis
is a Gram-positive bacterium that is a major cause of hospital-acquired infections, in part due to its intrinsic resistance to cephalosporins. The mechanism that confers intrinsic cephalosporin resistance in enterococci remains incompletely defined. Previously, we have shown that the Ser/Thr protein kinase and phosphatase pair IreK and IreP act antagonistically to regulate cephalosporin resistance in
E. faecalis
. We hypothesize that IreK senses antibiotic-induced cell wall damage and activates a signaling pathway leading to antibiotic resistance. However, the factors downstream of IreK have not yet been identified. To discover such factors, suppressor mutations that restored resistance to a Δ
ireK
kinase mutant were identified. Mutations were found in IreB, a highly conserved gene of unknown function that is widespread among low-GC Gram-positive bacteria. We show that IreB plays a negative regulatory role in cephalosporin resistance and is an endogenous substrate of both IreK and IreP. IreB is phosphorylated on conserved threonine residues, and mutations at these sites impair cephalosporin resistance. Our results are consistent with a model in which the activity of IreB is modulated by IreK-dependent phosphorylation in a signaling pathway required for cephalosporin resistance and begin to shed light on the function of this previously uncharacterized protein.
Genotypic Analysis of the V3 Region of HIV from Virologic Nonresponders to Maraviroc-Containing Regimens Reveals Distinct Patterns of Failure
Authors: Swenson Luke C. , Chui Celia K. S. , Brumme Chanson J. , Chan Dennison , Woods Conan K. , Mo Theresa , Dong Winnie , Chapman Doug , Lewis Marilyn , Demarest James F. , James Ian , Portsmouth Simon , Goodrich James , Heera Jayvant , Valdez Hernan , Harrigan P. Richard
Published: October 2013

Changes in HIV tropism from R5 to non-R5 or development of drug resistance is often associated with virologic failure in patients treated with maraviroc, a CCR5 antagonist. We sought to examine changes in HIV envelope sequences and inferred tropism in patients who did not respond to maraviroc-based regimens. We selected 181 patients who experienced early virologic failure on maraviroc-containing therapy in the MOTIVATE trials. All patients had R5 HIV by the original Trofile assay before entry. We used population-based sequencing methods and the geno2pheno algorithm to examine changes in tropism and V3 sequences at the time of failure. Using deep sequencing, we assessed whether V3 sequences observed at failure emerged from preexisting subpopulations. From population genotyping data at failure, 90 patients had R5 results, and 91 had non-R5 results. Of the latter group, the geno2pheno false-positive rate (FPR) value fell from a median of 20 at screening to 1.1 at failure. By deep sequencing, the median percentage of non-R5 variants in these patients rose from 1.4% to 99.5% after a median of 4 weeks on maraviroc. In 70% of cases, deep sequencing could detect a pretreatment CXCR4-using subpopulation, which emerged at failure. Overall, there were two distinct patterns of failure of maraviroc. Patients failing with R5 generally had few V3 substitutions and low non-R5 prevalence by deep sequencing. Patients with non-R5 HIV who were failing developed very-high-prevalence non-R5 HIV (median, 99%) and had very low geno2pheno values.
Interactions between Bifidobacterium and Bacteroides Species in Cofermentations Are Affected by Carbon Sources, Including Exopolysaccharides Produced by Bifidobacteria
Authors: Rios-Covian David , Arboleya Silvia , Hernandez-Barranco Ana M. , Alvarez-Buylla Jorge R. , Ruas-Madiedo Patricia , Gueimonde Miguel , de los Reyes-Gavilan Clara G.
Published: September 2013

Cocultures of strains from two
Bifidobacterium
and two
Bacteroides
species were performed with exopolysaccharides (EPS) previously purified from bifidobacteria, with inulin, or with glucose as the carbon source.
Bifidobacterium longum
NB667 and
Bifidobacterium breve
IPLA20004 grew in glucose but showed poor or no growth in complex carbohydrates (inulin, EPS E44, and EPS R1), whereas
Bacteroides
grew well in the four carbon sources tested. In the presence of glucose, the growth of
Bacteroides thetaiotaomicron
DSM-2079 was inhibited by
B. breve
, whereas it remained unaffected in the presence of
B. longum
.
Ba. fragilis
DSM-2151 contributed to a greater survival of
B. longum
, promoting changes in the synthesis of short-chain fatty acids (SCFA) and organic acids in coculture with respect to monocultures. In complex carbohydrates, cocultures of bifidobacterium strains with
Ba. thetaiotaomicron
did not modify the behavior of
Bacteroides
nor improve the poor growth of bifidobacteria. The metabolic activity of
Ba. fragilis
in coculture with bifidobacteria was not affected by EPS, but greater survival of bifidobacteria at late stages of incubation occurred in cocultures than in monocultures, leading to a higher production of acetic acid than in monocultures. Therefore, cocultures of
Bifidobacterium
and
Bacteroides
can behave differently against fermentable carbohydrates as a function of the specific characteristics of the strains from each species. These results stress the importance of considering specific species and strain interactions and not simply higher taxonomic divisions in the relationship among intestinal microbial populations and their different responses to probiotics and prebiotics.
Risk Factors Associated with Salmonella and Listeria monocytogenes Contamination of Produce Fields
Authors: Strawn Laura K. , Gröhn Yrjo T. , Warchocki Steven , Worobo Randy W. , Bihn Elizabeth A. , Wiedmann Martin
Published: September 2013

Identification of management practices associated with preharvest pathogen contamination of produce fields is crucial to the development of effective Good Agricultural Practices (GAPs). A cross-sectional study was conducted to (i) determine management practices associated with a
Salmonella
- or
Listeria monocytogenes
-positive field and (ii) quantify the frequency of these pathogens in irrigation and nonirrigation water sources. Over 5 weeks, 21 produce farms in New York State were visited. Field-level management practices were recorded for 263 fields, and 600 environmental samples (soil, drag swab, and water) were collected and analyzed for
Salmonella
and
L. monocytogenes
. Management practices were evaluated for their association with the presence of a pathogen-positive field.
Salmonella
and
L. monocytogenes
were detected in 6.1% and 17.5% of fields (
n
= 263) and 11% and 30% of water samples (
n
= 74), respectively. The majority of pathogen-positive water samples were from nonirrigation surface water sources. Multivariate analysis showed that manure application within a year increased the odds of a
Salmonella
-positive field (odds ratio [OR], 16.7), while the presence of a buffer zone had a protective effect (OR, 0.1). Irrigation (within 3 days of sample collection) (OR, 6.0), reported wildlife observation (within 3 days of sample collection) (OR, 6.1), and soil cultivation (within 7 days of sample collection) (OR, 2.9) all increased the likelihood of an
L. monocytogenes
-positive field. Our findings provide new data that will assist growers with science-based evaluation of their current GAPs and implementation of preventive controls that reduce the risk of preharvest contamination.
Glycerol-3-Phosphate Acyltransferase Contributes to Triacylglycerol Biosynthesis, Lipid Droplet Formation, and Host Invasion in Metarhizium robertsii
Authors: Gao Qiang , Shang Yanfang , Huang Wei , Wang Chengshu
Published: September 2013

Enzymes involved in the triacylglycerol (TAG) biosynthesis have been well studied in the model organisms of yeasts and animals. Among these, the isoforms of glycerol-3-phosphate acyltransferase (GPAT) redundantly catalyze the first and rate-limiting step in glycerolipid synthesis. Here, we report the functions of mrGAT, a GPAT ortholog, in an insect-pathogenic fungus,
Metarhizium robertsii
. Unlike in yeasts and animals, a single copy of the mrGAT gene is present in the fungal genome and the gene deletion mutant is viable. Compared to the wild type and the gene-rescued mutant, the Δ
mrGAT
mutant demonstrated reduced abilities to produce conidia and synthesize TAG, glycerol, and total lipids. More importantly, we found that mrGAT is localized to the endoplasmic reticulum and directly linked to the formation of lipid droplets (LDs) in fungal cells. Insect bioassay results showed that
mrGAT
is required for full fungal virulence by aiding fungal penetration of host cuticles. Data from this study not only advance our understanding of GPAT functions in fungi but also suggest that filamentous fungi such as
M. robertsii
can serve as a good model to elucidate the role of the glycerol phosphate pathway in fungal physiology, particularly to determine the mechanistic connection of GPAT to LD formation.
Impaired Innate Mucosal Immunity in Aged Mice Permits Prolonged Streptococcus pneumoniae Colonization
Authors: Krone Cassandra L. , Trzciński Krzysztof , Zborowski Tomasz , Sanders Elisabeth A. M. , Bogaert Debby
Published: October 2013

Streptococcus pneumoniae
is a frequent asymptomatic colonizer of the nasopharyngeal niche and only occasionally progresses toward infection. The burden of pneumococcal disease is particularly high in the elderly, and the mechanisms behind this increased susceptibility are poorly understood. Here we used a mouse model of pneumococcal carriage to study immunosenescence in the upper respiratory tract (URT). Nasal mucosa-associated lymphoid tissue (NALT) showed increased expression of Toll-like receptor 1, interleukin-1β, NLRp3 inflammasome, and CCL2 in naive elderly compared to young animals. This suggests an increased proinflammatory expression profile in the NALT of aged mice at baseline. Simultaneously, we observed a more tolerogenic profile in respiratory epithelia of naive elderly compared to young adult mice with upregulation of the NF-κβ pathway inhibitor peroxisome proliferator-activated receptor gamma (PPARγ). After nasal instillation of pneumococci, pneumococcal colonization was prolonged in elderly mice compared to in young adults. The delay in clearance was associated with absent or delayed upregulation of a proinflammatory mediator(s) in the NALT, diminished influx of macrophages into the URT niche, and absent downregulation of PPARγ in respiratory epithelium, accompanied by diminished expression of cathelicidin (CRAMP) at the site of colonization. These findings suggest that unresponsiveness to pneumococcal challenge due to altered mucosal immune regulation is the key to increased susceptibility to disease in the elderly.
Surface Charge of Streptococcus pneumoniae Predicts Serotype Distribution
Authors: Li Yuan , Weinberger Daniel M. , Thompson Claudette M. , Trzciński Krzysztof , Lipsitch Marc
Published: October 2013

Streptococcus pneumoniae
(pneumococcus) frequently colonizes the human nasopharynx and is an important cause of pneumonia, meningitis, sinusitis, and otitis media. The outer cell surface of pneumococcus may assume various degrees of negative charge depending on the polysaccharide capsule, of which more than 90 serotypes have been identified. The negative charge of capsular polysaccharides has been proposed to electrostatically repel pneumococci from phagocytic cells, and avoidance of phagocytosis correlates with higher carriage prevalence. We hypothesized that the surface charge of pneumococcus contributes to its success in nasopharyngeal carriage by modulating resistance to phagocyte-mediated killing. Here, we measured the surface charge (zeta potential) of laboratory-constructed strains that share a genetic background but differ in serotype and of clinical strains that differ in serotype and genetic background. A more negative surface charge correlated with higher resistance to nonopsonic killing by human neutrophils
in vitro
. In addition, a more negative zeta potential was associated with higher carriage prevalence in human populations before and after the widespread use of the pneumococcal conjugate vaccine PCV7. We also confirmed that capsule is the major determinant of net surface charge in clinical isolates with diverse backgrounds. We noted that exceptions exist to the idea that a higher magnitude of negative charge predicts higher prevalence. The results indicated that zeta potential is strongly influenced by pneumococcal capsule type but is unlikely to be the only important mechanism by which capsule interacts with host.
Capsular Sialic Acid of Streptococcus suis Serotype 2 Binds to Swine Influenza Virus and Enhances Bacterial Interactions with Virus-Infected Tracheal Epithelial Cells
Authors: Wang Yingchao , Gagnon Carl A. , Savard Christian , Music Nedzad , Srednik Mariela , Segura Mariela , Lachance Claude , Bellehumeur Christian , Gottschalk Marcelo
Published: October 2013

Streptococcus suis
serotype 2 is an important swine bacterial pathogen, and it is also an emerging zoonotic agent. It is unknown how
S. suis
virulent strains, which are usually found in low quantities in pig tonsils, manage to cross the first host defense lines to initiate systemic disease. Influenza virus produces a contagious infection in pigs which is frequently complicated by bacterial coinfections, leading to significant economic impacts. In this study, the effect of a preceding swine influenza H1N1 virus (swH1N1) infection of swine tracheal epithelial cells (NTPr) on the ability of
S. suis
serotype 2 to adhere to, invade, and activate these cells was evaluated. Cells preinfected with swH1N1 showed bacterial adhesion and invasion levels that were increased more than 100-fold compared to those of normal cells. Inhibition studies confirmed that the capsular sialic acid moiety is responsible for the binding to virus-infected cell surfaces. Also, preincubation of
S. suis
with swH1N1 significantly increased bacterial adhesion to/invasion of epithelial cells, suggesting that
S. suis
also uses swH1N1 as a vehicle to invade epithelial cells when the two infections occur simultaneously. Influenza virus infection may facilitate the transient passage of
S. suis
at the respiratory tract to reach the bloodstream and cause bacteremia and septicemia.
S. suis
may also increase the local inflammation at the respiratory tract during influenza infection, as suggested by an exacerbated expression of proinflammatory mediators in coinfected cells. These results give new insight into the complex interactions between influenza virus and
S. suis
in a coinfection model.
Inequalities in avoidable hospitalisation by area income and the role of individual characteristics: a population-based register study in Stockholm County, Sweden
Authors: Löfqvist Therese , Burström Bo , Walander Anders , Ljung Rickard
Published: October 2013

Background

Avoidable hospitalisations are hospital admissions for medical conditions that could potentially have been prevented by outpatient healthcare. They are used as an indicator of access to and quality of primary healthcare.

Aim

To investigate the association between median area income and avoidable hospitalisation and whether potential differences can be explained by contextual or compositional factors.

Method

Median area income was calculated for all 43 city districts and municipalities in Stockholm County during 2005–2007 and grouped into quintiles. The association between median area income and avoidable hospitalisation was studied by calculating age-adjusted rates. To disentangle contextual and compositional effects, ORs with 95% CIs were calculated, controlling for individual age, sex, country of birth, marital status and socioeconomic position.

Results

Rates of avoidable hospitalisation were higher in areas with lower income, 1535 per 100 000 inhabitants in the lowest area income quintile compared with 1179 in the highest area income quintile after age standardisation. For the age group 18–64 years, comparing the lowest quintile with the highest quintile, adjustment for individual characteristics of residents (compositional factors) reduced the crude OR from 1.52 (95% CI 1.44 to 1.60) to 1.12 (95% CI 1.06 to 1.19). For the age group 65–79 years, the ORs were 1.28 (1.21 to 1.36) and 1.06 (1.00 to 1.13), respectively. For those aged 80+ years, no association was found with area median income.

Conclusions

Higher rates of avoidable hospitalisation in low-income areas indicate greater healthcare needs of people living there. This should be addressed by investing in outpatient care for lower socioeconomic groups. The composition of individuals must be considered when studying area characteristics and avoidable hospitalisation.
Reducing unnecessary urinary catheter use and other strategies to prevent catheter-associated urinary tract infection: an integrative review
Authors: Meddings Jennifer , Rogers Mary A M , Krein Sarah L , Fakih Mohamad G , Olmsted Russell N , Saint Sanjay
Published: September 2013

Background

Catheter-associated urinary tract infections (CAUTI) are costly, common and often preventable by reducing unnecessary urinary catheter (UC) use.

Methods

To summarise interventions to reduce UC use and CAUTIs, we updated a prior systematic review (through October 2012), and a meta-analysis regarding interventions prompting UC removal by reminders or stop orders. A narrative review summarises other CAUTI prevention strategies including aseptic insertion, catheter maintenance, antimicrobial UCs, and bladder bundle implementation.

Results

30 studies were identified and summarised with interventions to prompt removal of UCs, with potential for inclusion in the meta-analyses. By meta-analysis (11 studies), the rate of CAUTI (episodes per 1000 catheter-days) was reduced by 53% (rate ratio 0.47; 95% CI 0.30 to 0.64, p<0.001) using a reminder or stop order, with five studies also including interventions to decrease initial UC placement. The pooled (nine studies) standardised mean difference (SMD) in catheterisation duration (days) was −1.06 overall (p=0.065) including a statistically significant decrease in stop-order studies (SMD −0.37; p<0.001) but not in reminder studies (SMD, −1.54; p=0.071). No significant harm from catheter removal strategies is supported. Limited research is available regarding the impact of UC insertion and maintenance technique. A recent randomised controlled trial indicates antimicrobial catheters provide no significant benefit in preventing symptomatic CAUTIs.

Conclusions

UC reminders and stop orders appear to reduce CAUTI rates and should be used to improve patient safety. Several evidence-based guidelines have evaluated CAUTI preventive strategies as well as emerging evidence regarding intervention bundles. Implementation strategies are important because reducing UC use involves changing well-established habits.
Continuing need for and provision of a service for non-standard implant removal
Authors: Pillai Mary , Gazet A Caroline , Griffiths Megan
Published: October 2013

Background and methodology

Information is presented on the management of women referred to a sexual health service during a 1-year period for management of a non-palpable contraceptive implant or of a palpable implant considered unsuitable for routine removal.

Results

Fifty-two women were referred. Thirty-four implants were non-palpable and their depth on ultrasound ranged from 2.7 to 12 mm. Seventeen were fully or partly palpable and their depth ranged from 3 mm or less (16 cases) to 5.6 mm (one case). Nine had had previous failed attempts at removal, including three with two previous failed attempts. Three implants were located at sites other than the medial aspect of the arm, and were associated with long localisation times. Forty-seven implants were removed at a one-stop clinic appointment through a 2–3 mm incision using ring forceps. The mean time for removal from making the incision to complete extraction was 4.8 minutes. Three cases judged to be of higher risk were removed under local anaesthesia in theatre through a 15 mm incision. These included the only case where removal was attempted unsuccessfully in the outpatient clinic. Seven of the implants were Nexplanon®, including four cases seen during the last month of data collection.

Conclusions

Removal with the technique described is rapid, with an average time of 4–5 minutes, and less than 10 minutes in >90% of cases. Preliminary indications suggest that the introduction of Nexplanon has not resolved the problem of deep implant insertion. Based on our experience we suggest criteria for centres providing removal of deep implants.
Nano-rod ZnO as a novel and reusable catalyst for C−P bond formation and hydrophosphonation of isatin derivatives under solvent-free conditions
Authors: Hosseini-Sarvari Mona , Tavakolian Mina
Published: October 2013

A highly efficient method for the synthesis of α1-oxindole-α-hydroxyphosphonates via nano-rod ZnO catalyzed hydrophosphonation of isatin derivatives was developed. The reaction products are in excellent yields using the catalytic system nano-rod ZnO (25 mol%) under solvent-free conditions at room temperature. The catalyst can be reused several times without any significant loss of its activity.
Classical and quantum transport in one-dimensional periodically kicked systems
Authors: Dana Itzhack
Published: October 2013

This paper is a brief review of classical and quantum transport phenomena, as well as related spectral properties, exhibited by one-dimensional periodically kicked systems. Two representative and fundamentally different classes of systems will be considered: those satisfying the classical Kolmogorov−Arnol’d−Moser scenario and those that do not. The experimental realization of some of these systems using atom-optics methods will be mentioned.
The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) as a characteristic component of bacterial endotoxin — a review of its biosynthesis, function, and placement in the lipopolysaccharide core
Authors: Lodowska Jolanta , Wolny Daniel , Węglarz Ludmiła
Published: October 2013

The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) is a characteristic component of bacterial lipopolysaccharide (LPS, endotoxin). It connects the carbohydrate part of LPS with C6 of glucosamine or 2,3-diaminoglucose of lipid A by acid-labile α-ketosidic linkage. The number of Kdo units present in LPS, the way they are connected, and the occurrence of other substituents (P, PEtn, PPEtn, Gal, or β-l-Ara4N) account for structural diversity of the inner core region of endotoxin. In a majority of cases, Kdo is crucial to the viability and growth of bacterial cells. In this paper, the biosynthesis of Kdo and the mechanism of its incorporation into the LPS structure, as well as the location of this unique component in the endotoxin core structures, have been described.
Terrestrial ecosystem monitoring in Canada and the greater role for integrated earth observation
Authors: Pasher Jon , Smith Paul A. , Forbes Mark R. , Duffe Jason
Published: October 2013

Ecosystems are valuable as well as aesthetic. The natural functions of ecosystems can have profound effects on the economy, and human and wildlife health. The aggregate value of these “ecosystem services” may far exceed the economic value derived from resource extraction or industrial development, especially when considering the costs of restoring ecosystems. There is increasing interest, therefore, in monitoring and protecting ecosystems, and accounting for the biodiversity and services they provide. In 2010, Canada undertook a review of ecosystem status and trends that identified the regions and ecosystems where management is most urgently needed. The authors concluded that more large-scale, long-term, standardized, and spatially complete information is needed for effective monitoring and management. Satellite-based earth observation (EO) tools were seen as a means of addressing this information need. In a separate exercise, a list of priority questions for conservation policy and management at a national level was produced: the resolution of three-quarters of those questions appears to depend on EO tools to a significant or critical extent. Canada has a long and successful history in all aspects of earth observation, placing it amongst the leaders in the international remote sensing community. Whereas the need for measuring ecosystem services to humans and wildlife is increasingly important, the challenges for doing so are increasingly significant and the technology required is increasingly complex. Overcoming these challenges is necessary to address emerging conservation priorities including measurement of ecosystem attributes to support habitat conservation for Species at Risk, measuring functional capacity of ecosystems to mitigate effects of climate change, monitoring and mitigating effects of resource extraction, and supporting industrial development in Canada’s north. Addressing emerging priorities requires dialogue among ecologists and decision makers, coordinated at regional and national scales, and requires drawing on the best EO technologies and infrastructure available. This review highlights the urgency of a coordinated approach for innovative applications of EO tools toward conservation and discusses some of the key elements that might be included and opportunities and challenges that might be encountered, by such an approach.
THERMAL MASS SPECTRA OF SCALAR AND PSEUDO-SCALAR MESONS IN IR-IMPROVED SOFT-WALL AdS/QCD MODEL WITH FINITE CHEMICAL POTENTIAL
Authors: CUI LING-XIAO , WU YUE-LIANG
Published: October 2013

The thermal mass spectra of scalar and pseudo-scalar mesons are studied in an IR-improved soft-wall AdS/QCD model. The Reissner–Nordstrom AdS black hole metric is introduced to describe both the finite temperature and density effects. The thermal spectral function is computed, which shows that the position of peak moves toward a smaller value and the width of peak also broadens to a larger value as the temperature increases. The critical temperature at which the peaks are completely dissolved has been found to be around Tc≃160~200 MeV . The effect of chemical potential is shown to be the same as the one caused by the temperature. It is found that when the temperature approaches to zero T≈0, the melting down of mesons occurs at the scaled critical chemical potential μ0/κ≈2.2~2.4 GeV.
DATA ENVELOPMENT ANALYSIS WITH MISSING DATA: A MULTIPLE LINEAR REGRESSION ANALYSIS APPROACH
Authors: CHEN YA , LI YONGJUN , WU HUAQING , LIANG LIANG
Published: October 2013

Data envelopment analysis (DEA) assumes that the data set is precise when performing efficiency evaluation of peer decision making units (DMUs). The current paper proposes a multiple linear regression analysis (MLRA) approach to estimate missing values if some of the entries in the data set are missing. Its algorithm to derive the estimations is also proposed. In order to verify the credibility of the proposed approach, an example of 30 US commercial banks is applied to case analysis. Using the proposed algorithm, the efficiencies of all DMUs are obtained. A Friedman test and a Kendall's Tau rank correlation analysis statistically examine the results. Moreover, the efficiency interval and efficiency distribution for a DMU are obtained considering random errors of the estimations. After that, an example of public secondary schools serves to illustrate the applications in the end.
Measuring neutrophil speed and directionality during chemotaxis, directly from a droplet of whole blood
Authors: Hoang Anh N. , Jones Caroline N. , Dimisko Laurie , Hamza Bashar , Martel Joseph , Kojic Nikola , Irimia Daniel
Published: October 2013

Neutrophil chemotaxis is critical for defense against infections and its alterations could lead to chronic inflammation and tissue injury. The central role that transient alterations of neutrophil chemotaxis could have on patient outcomes calls for its quantification in the clinic. However, current methods for measuring neutrophil chemotaxis require large volumes of blood and are time consuming. To address the need for rapid and robust assays, we designed a microfluidic device that measures neutrophil chemotaxis directly from a single droplet of blood. We validated the assay by comparing neutrophil chemotaxis from finger prick, venous blood and purified neutrophil samples. We found consistent average velocity of (19 ± 6 μm/min) and directionality (91.1%) between the three sources. We quantified the variability in neutrophil chemotaxis between healthy donors and found no significant changes over time. We also validated the device in the clinic and documented temporary chemotaxis deficiencies after burn injuries.