bluuebunny/crossref_metadata_2025 huggingface dataset:
Notification that new names and new combinations have appeared in volume 62, part 3, of the IJSEM
Authors: Euzéby Jean
Published: June 2012

This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol
41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
The Acquisition and Analysis of Polarized Total Internal Reflection Fluorescence Microscopy (polTIRFM) Data: Figure 1.
Authors: Beausang John F. , Sun Yujie , Quinlan Margot E. , Forkey Joseph N. , Goldman Yale E.
Published: June 2012

Polarized total internal reflection fluorescence microscopy (polTIRFM) can be used to detect the spatial orientation and rotational dynamics of single molecules. polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. This protocol describes how to acquire polTIRFM data and then calibrate the setup. Calibration corrects for any systematic variations in beam intensity and unequal detector sensitivities and is performed for each slide after experimental data are recorded. To convert the intensities into angles, one set of (θ, φ, δs, δf, κ) is then determined from one complete cycle of the incident intensities. This process is repeated for every cycle in the trace to measure the time dependence of rotational motions. The collection and analysis of data is similar for the processive motility assay for myosin V and for the twirling filament assay, in which a sparsely labeled actin filament is translocated by a field of unlabeled myosin V.
Embedding Embryos for Episcopic Fluorescence Image Capturing (EFIC)
Authors: Mohun Timothy J. , Weninger Wolfgang J.
Published: June 2012

Episcopic fluorescence image capturing (EFIC) and high-resolution episcopic microscopy (HREM) are related techniques that are used to generate digital volume data and create three-dimensional (3D) images. Both techniques require specimens that are embedded in an appropriate medium, and images are captured from successive sections before removal from the embedded tissue block. EFIC detects autofluorescence emitted from the embedded tissue, whereas HREM requires the tissue to be stained with a fluorescent dye such as eosin. Different procedures are therefore necessary for embedding tissue for EFIC or HREM imaging. This protocol describes the procedure for embedding E11.5 mouse embryos for EFIC imaging. Processing times should be adapted for the size and nature of other specimens.
Embedding Embryos for High-Resolution Episcopic Microscopy (HREM)
Authors: Mohun Timothy J. , Weninger Wolfgang J.
Published: June 2012

Episcopic fluorescence image capturing (EFIC) and high-resolution episcopic microscopy (HREM) are related techniques that are used to generate digital volume data and create three-dimensional (3D) images. Both techniques require specimens that are embedded in an appropriate medium, and images are captured from successive sections before removal from the embedded tissue block. EFIC detects autofluorescence emitted from the embedded tissue, whereas HREM requires the tissue to be stained with a fluorescent dye such as eosin. Different procedures are therefore necessary for embedding tissue for EFIC or HREM imaging. For HREM, the choice of fixative appears to be of little consequence. If gene expression patterns are to be visualized in addition to tissue architecture, whole-mount staining for gene expression patterns using the 4-nitro blue tetrazolium chloride (NBT)/5-bromo-4-chloro-3-indolyl phosphate (BCIP) or LacZ detection system must be performed before embedding of samples. This protocol describes the procedure for embedding E11.5 mouse embryos for HREM imaging. Processing times should be adapted for the size and nature of other specimens.
Power Calculations in Genetic Studies
Authors: Evans David M. , Purcell Shaun
Published: June 2012

The power of a statistical test is the probability that it will yield a statistically significant result given that the null hypothesis is false. In other words, it represents the chance that the study will be successful in detecting a true effect and is dependent on a number of factors, including the magnitude of the effect, the sample size and study design, and the specified false-positive rate. Power calculations are primarily performed during the planning stages of a study, most typically in determining the sample size required. Consideration of statistical power can also sometimes shed light on the results of completed studies, particularly in the interpretation of negative results. In this article, we review the fundamentals of statistical power, discuss how power is calculated (using a genetic case/control study as an example), and consider the most pertinent factors that influence power in genetic studies. Finally, we focus on power in the context of modern whole-genome association studies, in which issues of coverage, multiple testing, and staged designs are paramount.
Episcopic Three-Dimensional Imaging of Embryos
Authors: Mohun Timothy J. , Weninger Wolfgang J.
Published: June 2012

Episcopic fluorescence image capturing (EFIC) and high-resolution episcopic microscopy (HREM) are related techniques that are used to generate digital volume data and create three-dimensional (3D) images. Both techniques require specimens that are embedded in an appropriate medium, and images are captured from successive sections before removal from the embedded tissue block. EFIC detects autofluorescence emitted from the embedded tissue, whereas HREM requires the tissue to be stained with a fluorescent dye such as eosin. Different procedures are therefore necessary for embedding tissue for EFIC or HREM imaging. This article describes episcopic imaging and gives the advantages and disadvantages of the EFIC and HREM techniques. It also describes the imaging setup required to collect volume data and generate 3D images.
Imaging Neuronal Activity with Genetically Encoded Calcium Indicators
Authors: Tian Lin , Hires S. Andrew , Looger Loren L.
Published: June 2012

Genetically encoded calcium indicators (GECIs), which are based on chimeric fluorescent proteins, can be used to monitor calcium transients in living cells and organisms. Because they are encoded by DNA, GECIs can be delivered to the intact brain noninvasively and targeted to defined populations of neurons and specific subcellular compartments for long-term, repeated measurements in vivo. GECIs have improved iteratively and are becoming useful for imaging neural activity in vivo. Here we summarize extrinsic and intrinsic factors that influence a GECI’s performance and provides guidelines for selecting the appropriate GECI for a given application. We also review recent progress in GECI design, optimization, and standardized testing protocols.
Paxillus involutus Strains MAJ and NAU Mediate K+/Na+ Homeostasis in Ectomycorrhizal Populus × canescens under Sodium Chloride Stress
Authors: Li Jing , Bao Siqin , Zhang Yuhong , Ma Xujun , Mishra-Knyrim Manika , Sun Jian , Sa Gang , Shen Xin , Polle Andrea , Chen Shaoliang
Published: June 2012

Salt-induced fluxes of H+, Na+, K+, and Ca2+ were investigated in ectomycorrhizal (EM) associations formed by Paxillus involutus (strains MAJ and NAU) with the salt-sensitive poplar hybrid Populus × canescens. A scanning ion-selective electrode technique was used to measure flux profiles in non-EM roots and axenically grown EM cultures of the two P. involutus isolates to identify whether the major alterations detected in EM roots were promoted by the fungal partner. EM plants exhibited a more pronounced ability to maintain K+/Na+ homeostasis under salt stress. The influx of Na+ was reduced after short-term (50 mm NaCl, 24 h) and long-term (50 mm NaCl, 7 d) exposure to salt stress in mycorrhizal roots, especially in NAU associations. Flux data for P. involutus and susceptibility to Na+-transport inhibitors indicated that fungal colonization contributed to active Na+ extrusion and H+ uptake in the salinized roots of P. × canescens. Moreover, EM plants retained the ability to reduce the salt-induced K+ efflux, especially under long-term salinity. Our study suggests that P. involutus assists in maintaining K+ homeostasis by delivering this nutrient to host plants and slowing the loss of K+ under salt stress. EM  P. × canescens plants exhibited an enhanced Ca2+ uptake ability, whereas short-term and long-term treatments caused a marked Ca2+ efflux from mycorrhizal roots, especially from NAU-colonized roots. We suggest that the release of additional Ca2+ mediated K+/Na+ homeostasis in EM plants under salt stress.
Transcriptional Responses toward Diffusible Signals from Symbiotic Microbes Reveal MtNFP- and MtDMI3-Dependent Reprogramming of Host Gene Expression by Arbuscular Mycorrhizal Fungal Lipochitooligosaccharides
Authors: Czaja Lisa F. , Hogekamp Claudia , Lamm Patrick , Maillet Fabienne , Martinez Eduardo Andres , Samain Eric , Dénarié Jean , Küster Helge , Hohnjec Natalija
Published: June 2012

The formation of root nodules and arbuscular mycorrhizal (AM) roots is controlled by a common signaling pathway including the calcium/calmodulin-dependent kinase Doesn’t Make Infection3 (DMI3). While nodule initiation by lipochitooligosaccharide (LCO) Nod factors is well characterized, diffusible AM fungal signals were only recently identified as sulfated and nonsulfated LCOs. Irrespective of different outcomes, the perception of symbiotic LCOs in Medicago truncatula is mediated by the LysM receptor kinase M. truncatula Nod factor perception (MtNFP). To shed light on transcriptional responses toward symbiotic LCOs and their dependence on MtNFP and Ca2+ signaling, we performed genome-wide expression studies of wild-type, Nod-factor-perception mutant1, and dmi3 mutant roots challenged with Myc- and Nod-LCOs. We show that Myc-LCOs lead to transient, quick responses in the wild type, whereas Nod-LCOs require prolonged incubation for maximal expression activation. While Nod-LCOs are most efficient for an induction of persistent transcriptional changes, sulfated Myc-LCOs are less active, and nonsulfated Myc-LCOs display the lowest capacity to activate and sustain expression. Although all symbiotic LCOs up-regulated a common set of genes, discrete subsets were induced by individual LCOs, suggesting common and specific functions for these in presymbiotic signaling. Surprisingly, even sulfated fungal Myc-LCOs and Sinorhizobium meliloti Nod-LCOs, having very similar structures, each elicited discrete subsets of genes, while a mixture of both Myc-LCOs activated responses deviating from those induced by single treatments. Focusing on the precontact phase, we identified signaling-related and transcription factor genes specifically up-regulated by Myc-LCOs. Comparative gene expression studies in symbiotic mutants demonstrated that transcriptional reprogramming by AM fungal LCOs strictly depends on MtNFP and largely requires MtDMI3.
Identification of a transparent mutant tiger barb Puntius tetrazona and its use for in vivo observation of a Pleistophora sp. (Microsporidia) infection
Authors: Li K. B. , Chang O. Q. , Wang F. , Liu C. , Wang Q. , Liang F. L. , Ma B. Y. , Wu S. Q.
Published: June 2012

A transparent mutant tiger barb Puntius tetrazona was identified and characterized by its transparent body, which allows clear visualization of internal organs. Hybridization of this mutant with the albino variant produces a transparent and albinoid double phenotype, and the transparency of this mutant is controlled by a recessive allele. Light microscopic and ultrastructural examinations show that in contrast to normal individuals, transparent mutants lack iridophores, and light penetrates unimpeded through the body. Pleistophora sp. infection was observed in vivo, allowing live observation of parasite dissemination and the consequent pathological alterations in the fish body as well as the simultaneous acquisition of data on the dynamics and spatial pattern of pathogenic invasion. It is superior to common fish models, as dynamic experimental data can be obtained from individual fish.
Genetic divergence among invasive and native populations ofPlagioscion squamosissimus(Perciformes, Sciaenidae) in Neotropical regions
Authors: Panarari‐Antunes R. S. , Prioli A. J. , Prioli S. M. A. P. , Gomes V. N. , Júlio H. F. , Agostinho C. S. , Silva Filho J. P. , Boni T. A. , Prioli L. M.
Published: June 2012

The genetic divergence among invasive and native populations ofPlagioscion squamosissimusfrom four Neotropical hydrographic basins was assessed using the hypervariable domain of the mitochondrial DNA (mtDNA) control region.Plagioscion squamosissimusis native to the neighbouring hydrographic basins of the Parnaíba and Amazon Rivers, and the latter includes the Araguaia–Tocantins drainage, but it is invasive in other basins due to introductions. The mtDNA nucleotide polymorphism supported the hypothesis that the Amazon and Parnaíba populations constitute the same species and are separated into two independent evolutionary lineages. Absence of nucleotide polymorphism was observed within and amongP. squamosissimuspopulations invasive to the uppper and middle Paraná River basins. Nucleotide divergence was null or low comparing the Paraná invasive populations with the populations native to the Parnaíba River basin, whereas it was significantly high compared to Tocantins populations. These results ascertain thatP. squamosissimuspopulations invasive to the upper Paraná River basin and to the middle Paraná River basin downstream of the Itaipu dam are derived from the Parnaíba River basin. The genetic data presented are potentially useful to assist further studies onP. squamosissimustaxonomic and geographic distribution, development of ecological guidelines for managing populations invasive to the upper Paraná River basin and for preservation of native fish diversity.
Comparison between famciclovir and valacyclovir for acute pain in adult Japanese immunocompetent patients with herpes zoster
Authors: ONO Fumitake , YASUMOTO Shinichiro , FURUMURA Minao , HAMADA Takahiro , ISHII Norito , GYOTOKU Takashi , HIGUCHI Mitsunari , INOKUCHI Kenichiro , JYO Kazuo , KOGA Hideaki , KOMAI Ayako , MARUTA Koji , MASHIKO Tami , MIHARA Tsukasa , MIYAHARA Hiroko , MIYASATO Minoru , MUTO Koichiro , NAGASE Koichi , NAGATA Masakazu , SAKIHAMA Hideki , TANAHASHI Tomoko , UEDA Atsuto , YAMAKAWA Kyoko , OHATA Chika , DAINICHI Teruki , TSURUTA Daisuke , HASHIMOTO Takashi
Published: June 2012

Famciclovir is a guanine analog antiviral drug used commonly for herpes zoster. Efficacy of famciclovir treatment has been reported to be comparable to valacyclovir treatment. Both of these medications reduce the time to complete cessation of zoster‐associated pain including post‐herpetic neuralgia, as compared to acyclovir. We conducted a multicenter, randomized, open clinical trial in order to evaluate the extent of pain relief afforded by these two antiviral drugs during the acute disease phase of herpes zoster. The study group comprised 86 immunocompetent adult patients suffering from herpes zoster, who were treated with either famciclovir or valacyclovir for 7 days. Of these, 55 patients enrolled in this study within 72 h of the onset of the rash and 31 patients after 72 h of the onset. There was a significant reduction in acute herpes zoster pain with famciclovir on day 7 and at 2–3 weeks in both of these patient groups, while with valacyclovir, there was not significant reduction in pain on day 7. Of patients aged 50 years or older, there was a significantly earlier reduction in pain with famciclovir than with valacyclovir. In addition, a significant reduction in the number of patients with pain was observed as early as days 3–4 with famciclovir treatment as compared with valacyclovir treatment. We conclude that famciclovir was superior to valacyclovir in the relief of acute pain of herpes zoster. Accordingly, famciclovir is recommended for herpes zoster patients with moderate symptoms and a visual analog scale score of under 50 mm.
Enhancement of malignant properties of human osteosarcoma cells with disialyl gangliosides GD2/GD3
Authors: Shibuya Hidenobu , Hamamura Kazunori , Hotta Hiroshi , Matsumoto Yasuyuki , Nishida Yoshihiro , Hattori Hisashi , Furukawa Keiko , Ueda Minoru , Furukawa Koichi
Published: May 2012

The expression and implications of gangliosides in human osteosarcomas have not been systematically analyzed. In this study, we showed that gangliosides GD3 and GD2 are highly expressed in the majority of human osteosarcoma cell lines derived from oral cavity regions. Introduction of GD3 synthase cDNA into a GD3/GD2‐negative (GD3/GD2−) human osteosarcoma subline resulted in the establishment of GD3/GD2+ transfectant cells. They showed increased cell migration and invasion activities in wound healing and Boyden chamber invasion assays, respectively, compared to the control cells. When treated with serum, GD3/GD2+ cells showed stronger tyrosine phosphorylation of p130Cas, focal adhesion kinase, and paxillin than GD3/GD2− cells. In particular, paxillin underwent much stronger phosphorylation, suggesting its role in cell motility. Furthermore, we tried to dissect the roles of GD3 and GD2 in the malignant properties of the transfectant cells by establishing single ganglioside‐expressing cells, that is, either GD3 or GD2. Although GD3/GD2+ cells showed the most malignant properties, GD2+ cells showed almost equivalent levels to GD3/GD2+ cells in invasion and migration activities, and in the intensities of tyrosine phosphorylation of paxillin. Among Src family kinases, Lyn was expressed predominantly, and was involved in the invasion and motility of GD3‐ and/or GD2‐expressing transfectants. Furthermore, it was elucidated by gene silencing that Lyn was located in a different pathway from that of FAK to eventually lead paxillin activation. These results suggested that GD2/GD3 are responsible for the enhancement of the malignant features of osteosarcomas, and might be candidate targets in molecular‐targeted therapy.
A new technique for percutaneous dilatational tracheostomy (G‐Trach): preliminary experience in pigs
Authors: Guerra R. , De Monte A. , Girardis M.
Published: June 2012

Tracheostomies are currently used for airway management in patients requiring long‐term respiratory assistance. The dilatational percutaneous technique of forming tracheostomies is a valuable alternative to traditional surgical ‘open’ techniques. In this study, we tested a new dilatational percutaneous tracheostomy device using a balloon dilator with a particular innovative shape (G‐Trach). At the Autonomous University of Barcelona Veterinary Institute, eight pigs (weighing 20–40 kg) were anaesthetised and underwent tracheostomy using the novel G‐Trach technique. The mean (SD) procedure time was 2.63 (0.64) min from tracheal puncture to ventilation through the tracheostomy tube, and the mean (SD) time from positioning the dilator balloon to introducing the cannula was 0.71 (0.38) min. Vital functions and oxygen saturation remained constant throughout the procedures. Postmortem examinations did not reveal any tracheal injury. The G‐Trach seems to be a safe and easy new dilatational percutaneous technique for forming tracheostomies. The minimal subcutaneous tissue dissection could potentially decrease complications when compared with standard dilatational percutaneous tracheostomy methods. To confirm this hypothesis a human trial is ongoing.
A randomised comparison of the self‐pressurised air‐QTM intubating laryngeal airway with the LMA UniqueTM in children*
Authors: Jagannathan N. , Sohn L. E. , Sawardekar A. , Shah R. , Ryan K. , Jagannathan R. , Anderson K.
Published: June 2012

We conducted a randomised trial comparing the self‐pressurised air‐QTM intubating laryngeal airway (air‐Q SP) with the LMA‐Unique in 60 children undergoing surgery. Outcomes measured were airway leak pressure, ease and time for insertion, fibreoptic examination, incidence of gastric insufflation and complications. Median (IQR [range]) time to successful device placement was faster with the air‐Q SP (12 (10–15 [5–18])) s than with the LMA‐Unique (14 (12–17 [6–22]) s; p = 0.05). There were no statistically significant differences between the air‐Q SP and LMA‐Unique in initial airway leak pressures (16 (14–18 [10–29]) compared with 18 (15–20 [10–30]) cmH2O, p = 0.12), an airway leak pressures at 10 min (19 (16–22 [12–30]) compared with 20 (16–22 [10–30]) cmH2O, p = 0.81); fibreoptic position, incidence of gastric insufflation, or complications. Both devices provided effective ventilation without the need for airway manipulation. The air‐Q SP is an alternative to the LMA‐Unique should the clinician prefer a device not requiring cuff monitoring during anaesthesia.
Assessment of potential drug interactions by characterization of human drug metabolism pathways using non‐invasive bile sampling
Authors: Bloomer Jackie C. , Nash Mike , Webb Alison , Miller Bruce E. , Lazaar Aili L. , Beaumont Claire , Guiney William J.
Published: June 2012

Aim

Characterization of the biliary disposition of GSK1325756, using a non‐invasive bile sampling technique and spectrometric analyses, to inform the major routes of metabolic elimination and to enable an assessment of victim drug interaction risk.

Method

Sixteen healthy, elderly subjects underwent non‐invasive bile capture using a peroral string device (Entero‐Test®) prior to and following a single oral dose of GSK1325756 (100 mg). The device was swallowed by each subject and once the weighted string was judged to have reached the duodenum, gallbladder contraction was stimulated in order to release bile. The string was then retrieved via the mouth and bile samples were analyzed for drug‐related material using spectrometric and spectroscopic techniques following solvent extraction.

Results

Nuclear magnetic resonance spectroscopy (NMR) indicated that the O‐glucuronide metabolite was the major metabolite of GSK1325756, representing approximately 80% of drug‐related material in bile. As bile is the major clearance route for GSK1325756 (only 4% of the administered dose was excreted in human urine), this result indicates that uridine 5'‐diphospho‐glucuronosyltransferases (UGTs) are the major drug metabolizing enzymes responsible for drug clearance. The relatively minor contribution made by oxidative routes reduces the concern of CYP‐mediated victim drug interactions.

Conclusion

The results from this study demonstrate the utility of deploying the Entero‐Test® in early human studies to provide information on the biliary disposition of drugs and their metabolites. This technique can be readily applied in early clinical development studies to provide information on the risk of interactions for drugs that are metabolized and eliminated in bile.
Treatment of Philadelphia chromosome‐positive acute lymphoblastic leukaemia with imatinib combined with a paediatric‐based protocol
Authors: Thyagu Santhosh , Minden Mark D. , Gupta Vikas , Yee Karen W.L. , Schimmer Aaron D. , Schuh Andre C. , Lipton Jeffrey H. , Messner Hans A. , Xu Wei , Brandwein Joseph M.
Published: June 2012

Although the combination of tyrosine kinase inhibitors with chemotherapy is widely used for young adults with Philadelphia chromosome positive‐acute lymphoblastic leukaemia (Ph+ ALL), the outcome and safety of this combination using intensive paediatric‐based protocols has not been well described. The clinical course of 32 adults age 18–60 years with Ph+ ALL treated with a paediatric‐based protocol plus imatinib was evaluated. The complete response rate was 94%. Grade 3–4 infections, neuropathy, myopathy and liver function abnormalities were common, resulting in major treatment delays and dose reductions, and declines in performance status (physical deconditioning), particularly in patients aged 41–60 years. Median and 3‐year overall survival (OS) was 40·7 months and 53%, respectively, and median and 3‐year even‐free survival (EFS) was 30·1 months and 50%, respectively. OS and EFS were inferior in deconditioned patients. Of 16 patients who underwent haematopoietic stem cell transplantation (HSCT) in first complete remission, six died of non‐relapse complications. There was no significant difference in OS and EFS between transplanted and non‐transplanted patients, based on an intention‐to‐treat and time‐to‐donor identification analysis. The combination of imatinib with a paediatric‐based regimen in adults produced high response rates, but was associated with considerable toxicity and high non‐relapse mortality post‐HSCT.
Equisetum arvense hydromethanolic extracts in bone tissue regeneration: in vitro osteoblastic modulation and antibacterial activity
Authors: Bessa Pereira C. , Gomes P. S. , Costa‐Rodrigues J. , Almeida Palmas R. , Vieira L. , Ferraz M. P. , Lopes M. A. , Fernandes M. H.
Published: June 2012

Objectives

E
quisetum arvense preparations have long been used to promote bone healing. The aim of this work was to evaluate osteogenic and antibacterial effects of E
. arvense hydromethanolic extracts.

Materials and methods

Dried aerial components of E
. arvense were extracted using a mixture of methanol:water (1:1), for 26 days, yielding three extracts that were tested (10–1000 μg/ml) in human osteoblastic cells: E1, E2 and EM (a mixture of E1 and E2, 1:1). Cell cultures, performed on cell culture plates or over hydroxyapatite (HA) substrates, were assessed for osteoblastic markers. In addition, effects of the extracts on S
taphylococcus aureus were addressed.

Results

Solution E1 caused increased viability/proliferation and ALP activity at 50–500 μg/ml, and deleterious effects at levels ≥1000 μg/ml. E2 inhibited cell proliferation at levels ≥500 μg/ml. EM presented a profile between those observed with E1 and E2. In addition, E1, E2 and EM, 10–1000 μg/ml, inhibited expansion of S
. aureus. Furthermore, E1, tested in HA substrates colonized with osteoblastic cells, causing increase in cell population growth (10–100 μg/ml). E1 also exhibited antibacterial activity against S
. aureus cultured over HA.

Conclusions

Results showed that E
. arvense extracts elicited inductive effects on human osteoblasts while inhibiting activity of S
. aureus, suggesting a potentially interesting profile regarding bone regeneration strategies.
Cord blood Th2‐related chemokine CCL22 levels associate with elevated total‐IgE during preschool age
Authors: Følsgaard N. V. , Chawes B. L. K. , Bønnelykke K. , Jenmalm M. C. , Bisgaard H.
Published: June 2012

Background

Early‐life immune deviation is suspected in the inception of atopic disease.

Objective

To investigate the association between cord blood chemokines and the subsequent development of atopic biomarkers and clinical end‐points during the first 6 years of life.

Methods

The Th1‐associated chemokines CXCL10 and CXCL11 and the Th2‐associated chemokines CCL17 and CCL22 were assessed in cord blood of asymptomatic at‐risk newborn children from the Copenhagen Prospective Study on Asthma in Childhood (COPSAC2000) birth cohort and associated with the longitudinal development of biomarkers and clinical end‐points of asthma, eczema, and allergic rhinitis during the first 6 years of life.

Results

Cord blood CCL22 levels were significantly associated to total‐IgE levels measured at four time‐points during the first 6 years of life; overall odds ratio, 1.54 [CI, 1.25–1.89; P < 0.0001]. CXCL10 and CXCL11 were not associated with development of any atopic disorders or biomarkers.

Conclusion and Clinical Relevance

High cord blood levels of the Th2 related chemokine CCL22 were significantly associated with high total‐ IgE levels during the first 6 years of life, but not with specific sensitization, asthma, eczema or allergic rhinitis. This suggests an inborn skewing of the immune system in healthy newborns developing elevated total‐ IgE later in life.
Persistent molecular microchimerism induces long‐term tolerance towards a clinically relevant respiratory allergen
Authors: Baranyi U. , Pilat N. , Gattringer M. , Linhart B. , Klaus C. , Schwaiger E. , Iacomini J. , Valenta R. , Wekerle T.
Published: June 2012

Background

Development of antigen‐specific preventive strategies is a challenging goal in IgE‐mediated allergy. We have recently shown in proof‐of‐concept experiments that allergy can be successfully prevented by induction of durable tolerance via molecular chimerism. Transplantation of syngeneic hematopoietic stem cells genetically modified to express the clinically relevant grass pollen allergen Phl p 5 into myeloablated recipients led to high levels of chimerism (i.e. macrochimerism) and completely abrogated Phl p 5‐specific immunity despite repeated immunizations with Phl p 5.

Objective

It was unclear, however, whether microchimerism (drastically lower levels of chimerism) would be sufficient as well which would allow development of minimally toxic tolerance protocols.

Methods

Bone marrow cells were transduced with recombinant viruses integrating Phl p 5 to be expressed in a membrane‐anchored fashion. The syngeneic modified cells were transplanted into non‐myeloablated recipients that were subsequently immunized repeatedly with Phl p 5 and Bet v 1 (control). Molecular chimerism was monitored using flow cytometry and PCR. T cell, B‐cell and effector‐cell tolerance were assessed by allergen‐specific proliferation assays, isotype levels in sera and RBL assays.

Results

Here we demonstrate that transplantation of Phl p 5‐expressing bone marrow cells into recipients having received non‐myeloablative irradiation resulted in chimerism persisting for the length of follow‐up. Chimerism levels, however, declined from transient macrochimerism levels to persistent levels of microchimerism (followed for 11 months). Notably, these chimerism levels were sufficient to induce B‐cell tolerance as no Phl p 5‐specific IgE and other high affinity isotypes were detectable in sera of chimeric mice. Furthermore, T‐cell and effector‐cell tolerance were achieved.

Conclusions and Clinical Relevance

Low levels of persistent molecular chimerism are sufficient to induce long‐term tolerance in IgE‐mediated allergy. These results suggest that it will be possible to develop minimally toxic conditioning regimens sufficient for low level engraftment of genetically modified bone marrow.
The combination of FRAX and Ageing Male Symptoms scale better identifies treated HIV males at risk for major fracture
Authors: Pepe Jessica , Isidori Andrea M. , Falciano Mario , Iaiani Giancarlo , Salotti Alessandra , Diacinti Daniele , Del Fiacco Romano , Sbardella Emilia , Cipriani Cristiana , Piemonte Sara , Romagnoli Elisabetta , Lenzi Andrea , Minisola Salvatore
Published: May 2012

Objective

Osteoporosis and hypogonadism are common in men with HIV infection. Ageing Male Symptoms (AMS) scale measures symptoms related to hypogonadism. FRAX provides 10‐year probability of major fractures. We investigated the role of AMS scale combined with FRAX without bone mineral density (BMD), in identifying HIV men with bone fragility.

Design

Cross‐sectional observational study.

Methods

Fifty HIV‐positive men treated with highly active antiretroviral therapy and 27 controls underwent hormonal evaluation, BMD scan and spine X‐ray. The AMS questionnaire was administered.

Results

Osteoporosis was found in 24·0% of HIV patients and in 3·7% of controls (P = 0·05). In HIV patients, 9 radiological vertebral fractures were found (none in controls, P = 0·04). Calculated free testosterone suggested hypogonadism in 26% of HIV patients vs 4% of controls (P = 0·04); an abnormal AMS score (≥27) was found in 62% HIV patients compared with 41% controls (P = 0·04). ROC curves showed that FRAX for major fracture had a 23% sensitivity and a 100% specificity in identifying HIV patients with bone fragility (P = 0·002, with the threshold of 7% at which bisphosphonate therapy is cost‐effective). Considering a value of AMS ≥27, we obtained an 82·6% sensitivity and a 42·9% specificity (P = 0·04). The combination of AMS and FRAX score achieved a 77·3% sensitivity and a 69% specificity (P = 0·02, cut‐off 34).

Conclusion

Combination of FRAX (without BMD) and AMS improved sensitivity of FRAX alone in identifying HIV patients at fracture risk, at the expense of reduced specificity.
Immune regulatory gene polymorphisms as predisposing risk factors for the development of factor VIII inhibitors in Indian severe haemophilia A patients
Authors: Pinto P. , Ghosh K. , Shetty S.
Published: May 2012

Development of inhibitors to factor VIII, a serious complication of replacement therapy in haemophilia A patients, leads to increased bleeding, morbidity and mortality. There is no data on the risk factors for inhibitor development in Indian patients with severe haemophilia A. Our aim was to study the role of immune regulatory gene polymorphisms in the development of inhibitors. Fourteen immune regulatory gene polymorphisms (IL1β, IL4, IL10, TNFA and CTLA4) were analysed in 120 patients with severe haemophilia A, i.e. 50 inhibitor positive patients, and 70 inhibitor negative control patients, by PCR‐RFLP, DNA sequencing and allele‐specific PCRs. The IL10 promoter ‘GCC’ haplotypes overall (P: 0.002, OR: 3.452, 95% CI: 1.607–7.416), and ‘GCC/ATA’ (P: 0.011, OR: 3.492, 95% CI: 1.402–8.696) haplotype, associated with high and intermediate IL10 production, respectively, were significantly higher in inhibitor positive patients, whereas the ‘non‐GCC’ haplotypes overall (P: 0.002,OR: 0.290, 95% CI 0.135–0.622) and ‘ATA/ATA’ haplotype (P: 0.025, OR: 0.278, 95% CI: 0.096–0.802), associated with low IL10 synthesis, were significantly higher among inhibitor negative patients. The TNFA rs1799724 C/T heterozygote prevalence was significantly higher in the inhibitor positive group (P: 0.021, OR: 3.190, 95% CI: 1.273–7.990), whereas the other polymorphisms showed no statistically significant association with the presence of inhibitors. Different immune regulatory gene polymorphisms play a significant role as possible risk factors for the development of inhibitors in severe haemophilia A patients.
Strategy of lipid recognition by invariant natural killer T cells: ‘one for all and all for one’
Authors: Mallevaey Thierry , Selvanantham Thirumahal
Published: June 2012

Invariant natural killer T (iNKT) cells are evolutionarily conserved lipid‐reactive T cells that bridge innate and adaptive immune responses. Despite a relatively restricted T‐cell receptor (TCR) diversity, these cells respond to a variety of structurally distinct foreign (i.e. microbial or synthetic) as well as host‐derived (self‐) lipid antigens presented by the CD1d molecule. These multi‐tasking lymphocytes are among the first responders in immunity, and produce an impressive array of cytokines and chemokines that can tailor the ensuing immune response. Accordingly, iNKT cells play important functions in autoimmune diseases, cancer, infection and inflammation. These properties make iNKT cells appealing targets in immune‐based therapies. Yet, much has to be learned on the mechanisms that allow iNKT cells to produce polarized responses. Responses of iNKT cells are influenced by the direct signals perceived by the cells through their TCRs, as well as by indirect co‐stimulatory (and potentially co‐inhibitory) cues that they receive from antigen‐presenting cells or the local milieu. A decade ago, biochemists and immunologists have started to describe synthetic lipid agonists with cytokine skewing potential, paving a new research avenue in the iNKT cell field. Yet how iNKT cells translate various antigenic signals into distinct functional responses has remained obscure. Recent findings have revealed a unique and innate mode of lipid recognition by iNKT cells, and suggest that both the lipid antigen presented and the diversity of the TCR modulate the strength of CD1d‐iNKT TCR interactions. In this review, we focus on novel discoveries on lipid recognition by iNKT cells, and how these findings may help us to design effective strategies to steer iNKT cell responses for immune intervention.
Personal information privacy and emerging technologies
Authors: Conger Sue , Pratt Joanne H. , Loch Karen D.
Published: June 2012

This research presents a model of personal information privacy (PIP) that includes not only transactional data gathering, but also interorganisational data sharing. Emerging technologies are used as a lens through which the discussion of PIP management is extended. Research directions are developed for aspects of privacy, privacy‐preserving technologies, interorganisational data sharing and policy development.
Tenascin‐C promotes differentiation of rat dental pulp cells in vitro
Authors: Matsuoka K. , Matsuzaka K. , Yoshinari M. , Inoue T.
Published: June 2012

Aim

To investigate the effects of tenascin‐C (TN‐C) on cultured rat dental pulp cells in relation to the expression of Notch signalling.

Methodology

Subcultured dental pulp cells derived from rat incisors were seeded both in wells and on plastic coverslips coated with various concentrations of recombinant human TN‐C. Expression of bone‐related mRNA was then analysed by RT‐PCR and observed by immunohistochemical staining. Encoding of Notch1 and Notch2 (markers of initial differentiation of odontoblast‐like cells), alkaline phosphatase (ALP), osteopontin (OPN) and osteocalcin (OCN) (markers of mineralization) was investigated. Non‐TN‐C‐coated wells were used as controls. Primary antibodies to Notch1, ALP and OCN were used for immunofluorescence staining, and ALP activity was evaluated. Data were compared using Student's t‐test.

Results

Cell proliferation rate in the experimental groups was significantly higher (P < 0.05) than that in the control group at 72 h. Expression of Notch1, Notch2, ALP, OPN and OCN mRNAs was significantly higher (P < 0.05) in the experimental group than that in the control group. Strongly positive staining for Notch1, ALP and OCN was observed in the experimental group. ALP activity was significantly higher (P < 0.01) in the experimental group than in the control group at 24 h.

Conclusion

TN‐C promoted differentiation of rat dental pulp cells by the activation of Notch.
Antimicrobial effectiveness of intracanal medicaments on Enterococcus faecalis: chlorhexidine versus octenidine
Authors: de Lucena J. M. V. M. , Decker E. M. , Walter C. , Boeira L. S. , Löst C. , Weiger R.
Published: June 2012

Aim

To determine the viability of
Enterococcus faecalis in infected human root dentine in vitro after exposure to root canal medicaments based on chlorhexidine and octenidine.

Methodology

Human root segments (n = 40) were infected with
E. faecalis for 8 weeks. Root dentine samples (rd) collected at week 4 served as individual baseline values. At week 8, the root segments were randomly divided into four test groups (n = 10 each) for the placement of one of the following medicaments in the root canals: calcium hydroxide paste (CH), chlorhexidine gel (CHX‐gel) (5.0%), chlorhexidine/gutta‐percha points (CHX‐GP) (active points®; Roeko, Langenau, Germany) and octenidine gel (OCT‐gel) (5.0%) followed by incubation for 4 weeks. The effect on
E. faecalis viability was assessed by two fluorescent dyes (syto 9/propidium iodide) to determine the ‘proportion of viable bacteria’ (PVB%) and number of ‘colony‐forming units’ (CFU). Mean values and 95% confidence intervals (CI) were calculated for PVB% and log CFU, and the difference between groups was established.

Results

Viable and dead bacterial cells were detected in all ‘rd’ samples at weeks 4 and 8. The treatment with CHX‐gel, CHX‐GP and OCT‐gel resulted in significantly lower PVB% values with 15.4%, 3.5% and 0%, respectively. No growth (CFU) was recorded for these samples at week 12. When medicated by CH, the PVB% was increased without a corresponding change in CFUs.

Conclusions

In contrast to calcium hydroxide, both CHX – and octenidine‐based intracanal medicaments were effective in decreasing the viability of
E. faecalis. OCT showed the most favourable results and may have potential as an endodontic medicament.
A novel stop codon mutation within the hepatitis B surface gene is detected in the liver but not in the peripheral blood mononuclear cells of HIV‐infected individuals with occult HBV infection
Authors: Cassini R. , De Mitri M. S. , Gibellini D. , Urbinati L. , Bagaglio S. , Morsica G. , Domenicali M. , Verucchi G. , Bernardi M.
Published: June 2012

Summary.  To characterize occult HBV infection (OHB) in different compartments of HIV+ individuals. This retrospective study involved 38 consecutive HIV+ patients; 24 HBsAg negative (HBV−) and 14 HBsAg positive (HBV+). OHB was assessed in serum samples, liver tissue (LT) and peripheral blood mononuclear cells (PBMC) by genomic amplification of the partial S, X and precore/core regions. HBV genomic analysis was inferred by direct sequencing of PCR products. The intracellular HBV‐DNA was measured by a quantitative real‐time PCR. HBV+ patients were used as a control for HBV replication and genomic profile. In HBV− patients, HBV‐DNA was undetectable in all serum samples, while it was found positive in 7/24 (29%) LT in which genotype D prevailed (57%). HBV‐DNA was found in 6/7 (86%) PBMC of occult‐positive and none of occult‐negative LT. Significantly lower HBV‐DNA load was present in both compartments in OHB+ with respect to the HBV+ group (LT: P = 0.002; PBMC: P = 0.026). In the occult‐positive cases, HBV replication was significantly higher in LT than in PBMC (P = 0.028). A hyper‐mutated S gene in PBMC and a nucleotide mutation at position C695 in LT that produces a translational stop codon at amino acid 181 of the HBs gene characterized OHB. In this group of HIV+ persons, OHB is frequent and exhibits lower replication levels than chronic HBV in the different compartments examined. HBV‐DNA detection in PBMC may offer a useful tool to identify OHB in serum‐negative cases. The novel HBs gene stop codon found in LT could be responsible for reduced production leading to undetectability of HBsAg.
Mechanism of the asymmetric activation of the MinD ATPase by MinE
Authors: Park Kyung‐Tae , Wu Wei , Lovell Scott , Lutkenhaus Joe
Published: June 2012

MinD is a component of the Min system involved in the spatial regulation of cell division. It is an ATPase in the MinD/ParA/Mrp deviant Walker A motif family which is within the P loop GTPase superfamily. Its ATPase activity is stimulated by MinE; however, the mechanism of this activation is unclear. MinD forms a symmetric dimer with two binding sites for MinE; however, a recent model suggested that MinE occupying one site was sufficient for ATP hydrolysis. By generating heterodimers with one binding site for MinE we show that one binding site is sufficient for stimulation of the MinD ATPase. Furthermore, comparison of structures of MinD and related proteins led us to examine the role of N45 in the switch I region. An asparagine at this position is conserved in four of the deviant Walker A motif subfamilies (MinD, chromosomal ParAs, Get3 and FleN) and we find that N45 in MinD is essential for MinE‐stimulated ATPase activity and suggest that it is a key residue affected by MinE binding.
HLA DNA typing: past, present, and future
Authors: Erlich H.
Published: June 2012

The human leukocyte antigen (HLA) class I and class II loci are the most polymorphic genes in the human genome, with a highly clustered and patchwork pattern of sequence motifs. In the three decades since the first HLA gene was isolated by molecular cloning (a cDNA clone of HLA‐B7), thousands of alleles have been identified and the names and sequences of all known alleles have been curated in the IMGT/HLA database. This extensive allelic diversity made and continues to make high‐resolution HLA DNA typing very challenging. The first attempt at HLA DNA typing involved restriction fragment length polymorphism (RFLP) analysis, but this approach had many limitations. The development of PCR in 1985 allowed for the amplification of the polymorphic exons of the HLA class I and class II genes and the analysis of the polymorphic sequence motifs with sequence‐specific oligonucleotide (SSO) hybridization probes. The immobilization of these probes on membranes and later on beads, along with primer sets for sequence‐specific priming (SSP), gave rise to the current set of HLA typing reagents. Sanger sequencing has provided high‐resolution typing but, in many cases, genotyping ‘ambiguity’ remains an issue. In the past few years, the introduction of next‐generation sequencing, with the critical properties of massively parallel and clonal sequencing, has significantly reduced HLA genotyping ambiguity. Here, our lab's efforts to develop high‐resolution and high‐throughput HLA DNA typing using the 454 Sequencing System are reviewed, and the potential future developments and applications of HLA DNA typing are discussed.
Bacterial urinary tract infection after solid organ transplantation in the RESITRA cohort
Authors: Vidal E. , Torre‐Cisneros J. , Blanes M. , Montejo M. , Cervera C. , Aguado J.M. , Len O. , Carratalá J. , Cordero E. , Bou G. , Muñoz P. , Ramos A. , Gurguí M. , Borrell N. , Fortún J. ,   on behalf of the Spanish Network for Research in Infectious Diseases (REIPI)
Published: June 2012

Background

Urinary tract infection (UTI) is the most common infection in renal transplant patients, but it is necessary to determine the risk factors for bacterial UTI in recipients of other solid organ transplants (SOTs), as well as changes in etiology, clinical presentation, and prognosis.

Methods

In total, 4388 SOT recipients were monitored in 16 transplant centers belonging to the Spanish Network for Research on Infection in Transplantation (RESITRA). The frequency and characteristics of bacterial UTI in transplant patients were obtained prospectively from the cohort (September 2003 to February 2005).

Results

A total of 192 patients (4.4%) presented 249 episodes of bacterial UTI (0.23 episodes per 1000 transplantation days); 156 patients were kidney or kidney–pancreas transplant recipients, and 36 patients were liver, heart, and lung transplant recipients. The highest frequency was observed in renal transplants (7.3%). High frequency of cystitis versus pyelonephritis without related mortality was observed in both groups. The most frequent etiology was Escherichia coli (57.8%), with 25.7% producing extended‐spectrum β‐lactamase (ESBL). In all transplants but renal, most cases occurred in the first month after transplantation. Cases were uniformly distributed during the first 6 months after transplantation in renal recipients. Age (odds ratio [OR] per decade 1.1, 95% confidence interval [CI] 1.02–1.17), female gender (OR 1.74, 95% CI 1.42–2.13), and the need for immediate post‐transplant dialysis (OR 1.63, 95% CI 1.29–2.05) were independent variables associated with bacterial UTI in renal and kidney–pancreas recipients. The independent risk factors identified in non‐renal transplants were age (OR per decade 1.79, 95% CI 1.09–3.48), female gender (OR 1.7, 95% CI 1.43–2.49), and diabetes (OR 1.02, 95% CI 1.001–1.040).

Conclusions

UTI was frequent in renal transplants, but also not unusual in non‐renal transplants. Because E. coli continues to be the most frequent etiology, the emergence of ESBL‐producing strains has been identified as a new problem. In both populations, most cases were cystitis without related mortality. Although the first month after transplantation was a risk period in all transplants, cases were uniformly distributed during the first 6 months in renal transplants. Age and female gender were identified as risk factors for UTI in both populations. Other particular risk factors were the need for immediate post‐transplant dialysis in renal transplants and diabetes in non‐renal transplants.