In Silico Assigned Resistance Genes Confer Bifidobacterium with Partial Resistance to Aminoglycosides but Not to Β-Lactams

peer-reviewedBifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.Fiona Fouhy is in receipt of an Irish Research Council for Science, Engineering and Technology EMBARK scholarship and is a Teagasc Walsh fellow. Research in the PDC laboratory is supported by the Irish Government under the National Development Plan through the Science Foundation Ireland Investigator award 11/PI/1137. Research in the RPR, CS, PDC and DvS laboratories is also supported by the Science Foundation of Ireland-funded Centre for Science, Engineering and Technology, the Alimentary Pharmabiotic Centre (grant no.s 02/CE/B124 and 07/CE/B1368) and a HRB postdoctoral fellowship (Grant no. PDTM/20011/9) awarded to MOCM

The effect of posthypnotic suggestion and task difficulty on adherence to health-related requests

The effects of posthypnotic suggestion on health-related behavior, using a behavioral measure of adherence were investigated. Three hundred twenty three students covering the full range of hypnotic suggestibility were prescribed an easy (mood rating) or a difficult (physical activity) task. Participants were randomly assigned to receive either a) hypnosis with posthypnotic suggestions to facilitate performance of the assigned task or b) a social request to perform the assigned task. There were significant effects for type of task and hypnosis, revealing that participants adhered significantly more to the easy task and that hypnosis decreased task adherence. Hypnotic suggestibility did not predict adherence, and its interaction with posthypnotic suggestion was not significant. These results suggest that posthypnotic suggestion may decrease adherence rates regardless of participants’ suggestibility level

Using graded questions to increase timely reading of assigned material

We assigned students in a personality psychology class graded long-answer questions in an attempt to increase their likelihood of reading assigned class material in a timely manner. We evaluated the effectiveness of this technique by examining exam scores and student evaluations. Students performed significantly better on the exam questions that were related to the topics covered by the long-answer questions than they did on exam questions related to other topics. Students also reported having read significantly more of the assigned material when there was a long-answer question as-signed, and they evaluated the method positively and recommended its use in future classes. In an attempt to increase students' comprehension of material presented during lectures, course instructors often as-sign readings to their students before each class. Unfortunately, many students do not read the assigned mate-rial prior to class; in fact, compliance with reading assigned material has decreased in recent years (Burchfield & Sappington, 2000). Students tend to postpone preparation until a few days immediately preceding the tests (Thorne, 2000). Failing to complete readings before class is a strong predictor of nonparticipation (Karp & Yoels, 1976) and negatively affects students' learning and achievement (Bur-roughs, Kearney, & Plax, 1989). Despite the potential and known benefits of reading the assigned material before class, such as enhancing the comprehension of lecture material (Solomon, 1979), motivating students to read may not be an easy task, especially when students are not given an incentive to do so. Carkenord (1994) stated "practical experience … indicates that most students don't read textbooks or journal articles as a result of their intrinsic interest and desire to learn" (p. 164). Accordingly, Burchfield and Sappington (2000) recommended the use of strategies to monitor timely reading compliance and claimed that not doing so would send a message to students that this aspect of learning is optional and of little concern to the instructor. One strategy to monitor and encourage read-ing compliance is the use of quizzes (e.g., Marchant, 2002; Ruscio, 2001); however, quizzes can create undue anxiety in some students. In this study, we tested an alternative strategy to increase the likelihood that students would read the as-signed material prior to class: graded long-answer questions based on the assigned reading material. In particular, we tested whether graded assignments based on assigned readings would increase students' timely reading of the materia

Reflection absorption infrared spectroscopy and temperature programmed desorption investigations of the interaction of methanol with a graphite surface

Reflection absorption infrared spectroscopy (RAIRS) and temperature programmed desorption (TPD) have been used to investigate the adsorption of methanol (CH3OH) on the highly oriented pyrolytic graphite (HOPG) surface. RAIRS shows that CH3OH is physisorbed at all exposures and that crystalline CH3OH can be formed, provided that the surface temperature and coverage are high enough. It is not possible to distinguish CH3OH that is closely associated with the HOPG surface from CH3OH adsorbed in multilayers using RAIRS. In contrast, TPD data show three peaks for the desorption of CH3OH. Initial adsorption leads to the observation of a peak assigned to the desorption of a monolayer. Subsequent adsorption leads to the formation of multilayers on the surface and two TPD peaks are observed which can be assigned to the desorption of multilayer CH3OH. The first of these shows a fractional order desorption, assigned to the presence of hydrogen bonding in the overlayer. The higher temperature multilayer desorption peak is only observed following very high exposures of CH3OH to the surface and can be assigned to the desorption of crystalline CH3OH. (C) 2005 American Institute of Physics

The media equation and team formation: Further evidence for experience as a moderator

This study extends previous media equation research, which showed that interdependence but not identity leads to team affiliation effects with computers. The current study used an identity manipulation that more closely replicated the manipulation used in traditional team and group formation research than the original media equation research in this area. The study also sought further evidence for the relationship between experience with computers and behaviour reflecting a media equation pattern of results. Sixty students from the University of Queensland voluntarily participated in the study. Participants were assigned to one of three conditions: control, human team (a team made of only humans) or human-computer team (a team made of computers and humans). Questionnaire measures assessing participants’ affective experience, attitudes and opinions were taken. Participants of high experience, but not low experience, when assigned to either of the team conditions enjoyed the tasks completed on the computer more than participants who worked on their own. When assigned to a team that involved a computer, participants of high experience, but not low experience, reacted negatively towards the computer (in comparison to high experience participants working on their own or on a team without a computer as a team member) – rating the information provided by the computer lower, rating themselves as less influenced by the computer and changing their own ratings and rankings to be less like those of the computer. These results are interpreted in light of the ‘Black Sheep’ literature and recognized as a media equation pattern of results

Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery

Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.National Institute for Health Researc

Prophylactic use of carvedilol to prevent ventricular dysfunction in patients with cancer treated with doxorubicin

Objective: Deterioration in ventricular function is often observed in patients treated with anthracyclines for cancer. There is a paucity of evidence on interventions that might provide cardio-protection. We investigated whether prophylactic use of carvedilol can prevent doxorubicin-induced cardiotoxicity and whether any observed effect is dose related. Methods: A prospective, randomized, double-blind study in patients treated with doxorubicin, comparing placebo (n = 38) with different doses of carvedilol [6.25 mg/day (n = 41), 12.5 mg/day (n = 38) or 25 mg/day (n = 37)]. The primary endpoint was the measured change in left ventricular ejection fraction (LVEF) from baseline to 6 months. Results: LVEF decreased from 62 ± 5% at baseline to 58 ± 7% at 6-months (p = 0.002) in patients assigned to placebo but no statistically significant changes were observed in any of the 3 carvedilol groups. At 6 months, only one of 116 patients (1%) assigned to carvedilol had an LVEF < 50% compared to four of the 38 assigned to placebo (11%), (p = 0.013). No significant differences were noted between carvedilol and placebo in terms of the development of diastolic dysfunction, clinically overt heart failure or death. Conclusions: Carvedilol might prevent deterioration in LVEF in cancer patients treated with doxorubicin. This effect may not be dose related within the studied range