Expanding the set of rhodococcal Baeyer–Villiger monooxygenases by high-throughput cloning, expression and substrate screening

To expand the available set of Baeyer–Villiger monooxygenases (BVMOs), we have created expression constructs for producing 22 Type I BVMOs that are present in the genome of Rhodococcus jostii RHA1. Each BVMO has been probed with a large panel of potential substrates. Except for testing their substrate acceptance, also the enantioselectivity of some selected BVMOs was studied. The results provide insight into the biocatalytic potential of this collection of BVMOs and expand the biocatalytic repertoire known for BVMOs. This study also sheds light on the catalytic capacity of this large set of BVMOs that is present in this specific actinomycete. Furthermore, a comparative sequence analysis revealed a new BVMO-typifying sequence motif. This motif represents a useful tool for effective future genome mining efforts.

Aspects of holography for theories with hyperscaling violation

We analyze various aspects of the recently proposed holographic theories with general dynamical critical exponent z and hyperscaling violation exponent $\theta$. We first find the basic constraints on $z, \theta$ from the gravity side, and compute the stress-energy tensor expectation values and scalar two-point functions. Massive correlators exhibit a nontrivial exponential behavior at long distances, controlled by $\theta$. At short distance, the two-point functions become power-law, with a universal form for $\theta > 0$. Next, the calculation of the holographic entanglement entropy reveals the existence of novel phases which violate the area law. The entropy in these phases has a behavior that interpolates between that of a Fermi surface and that exhibited by systems with extensive entanglement entropy. Finally, we describe microscopic embeddings of some $\theta \neq 0$ metrics into full string theory models -- these metrics characterize large regions of the parameter space of Dp-brane metrics for $p\neq 3$. For instance, the theory of N D2-branes in IIA supergravity has z=1 and $\theta = -1/3$ over a wide range of scales, at large $g_s N$.Comment: 35 pages; v2: new references added; v3: proper reference [14] added; v4: minor clarification

Network adaptation improves temporal representation of naturalistic stimuli in drosophila eye: II Mechanisms

Retinal networks must adapt constantly to best present the ever changing visual world to the brain. Here we test the hypothesis that adaptation is a result of different mechanisms at several synaptic connections within the network. In a companion paper (Part I), we showed that adaptation in the photoreceptors (R1-R6) and large monopolar cells (LMC) of the Drosophila eye improves sensitivity to under-represented signals in seconds by enhancing both the amplitude and frequency distribution of LMCs' voltage responses to repeated naturalistic contrast series. In this paper, we show that such adaptation needs both the light-mediated conductance and feedback-mediated synaptic conductance. A faulty feedforward pathway in histamine receptor mutant flies speeds up the LMC output, mimicking extreme light adaptation. A faulty feedback pathway from L2 LMCs to photoreceptors slows down the LMC output, mimicking dark adaptation. These results underline the importance of network adaptation for efficient coding, and as a mechanism for selectively regulating the size and speed of signals in neurons. We suggest that concert action of many different mechanisms and neural connections are responsible for adaptation to visual stimuli. Further, our results demonstrate the need for detailed circuit reconstructions like that of the Drosophila lamina, to understand how networks process information

Content and timing of feedback and reflection: A multi-center qualitative study of experienced bedside teachers

Background: Competency-based medical education increasingly recognizes the importance of observation, feedback, and reflection for trainee development. Although bedside rounds provide opportunities for authentic workplace-based implementation of feedback and team-based reflection strategies, this relationship has not been well described. The authors sought to understand the content and timing of feedback and team-based reflection provided by bedside teachers in the context of patient-centered bedside rounds

Cardiovascular magnetic resonance findings in a pediatric population with isolated left ventricular non-compaction

<p>Abstract</p> <p>Background</p> <p>Isolated Left Ventricular Non-compaction (LVNC) is an uncommon disorder characterized by the presence of increased trabeculations and deep intertrabecular recesses. In adults, it has been found that Ejection Fraction (EF) decreases significantly as non-compaction severity increases. In children however, there are a few data describing the relation between anatomical characteristics of LVNC and ventricular function. We aimed to find correlations between morphological features and ventricular performance in children and young adolescents with LVNC using Cardiovascular Magnetic Resonance (CMR).</p> <p>Methods</p> <p>15 children with LVNC (10 males, mean age 9.7 y.o., range 0.6 - 17 y.o.), underwent a CMR scan. Different morphological measures such as the Compacted Myocardial Mass (CMM), Non-Compaction (NC) to the Compaction (C) distance ratio, Compacted Myocardial Area (CMA) and Non-Compacted Myocardial Area (NCMA), distribution of NC, and the assessment of ventricular wall motion abnormalities were performed to investigate correlations with ventricular performance. EF was considered normal over 53%.</p> <p>Results</p> <p>The distribution of non-compaction in children was similar to published adult data with a predilection for apical, mid-inferior and mid-lateral segments. Five patients had systolic dysfunction with decreased EF. The number of affected segments was the strongest predictor of systolic dysfunction, all five patients had greater than 9 affected segments. Basal segments were less commonly affected but they were affected only in these five severe cases.</p> <p>Conclusion</p> <p>The segmental pattern of involvement of non-compaction in children is similar to that seen in adults. Systolic dysfunction in children is closely related to the number of affected segments.</p

Overcoming the barriers of teaching physical examination at the bedside: More than just curriculum design

Background: Physicians in training must achieve a high degree of proficiency in performing physical examinations and must strive to become experts in the field. Concerns are emerging about physicians' abilities to perform these basic skills, essential for clinical decision making. Learning at the bedside has the potential to support skill acquisition through deliberate practice. Previous skills improvement programs, targeted at teaching physical examinations, have been successful at increasing the frequency of performing and teaching physical examinations. It remains unclear what barriers might persist after such program implementation. This study explores residents' and physicians' perceptions of physical examinations teaching at the bedside following the implementation of a new structured bedside curriculum: What are the potentially persisting barriers and proposed solutions for improvement? Methods: The study used a constructivist approach using a qualitative inductive thematic analysis that was oriented to construct an understanding of the barriers and facilitators of physical examination teaching in the context of a new bedside curriculum. Participants took part in individual interviews and subsequently focus groups. Transcripts were coded and themes were identified. Results: Data analyses yielded three main themes: (1) the culture of teaching physical examination at the bedside is shaped and threatened by the lack of hospital support, physicians' motivation and expertise, residents' attitudes and dependence on technology, (2) the hospital environment makes bedside teaching difficult because of its chaotic nature, time constraints and conflicting responsibilities, and finally (3) structured physical examination curricula create missed opportunities in being restrictive and pose difficulties in identifying patients with findings. Conclusions: Despite the implementation of a structured bedside curriculum for physical examination teaching, our study suggests that cultural, environmental and curriculum-related barriers remain important issues to be addressed. Institutions wishing to develop and implement similar bedside curricula should prioritize recruitment of expert clinical teachers, recognizing their time and efforts. Teaching should be delivered in a protected environment, away from clinical duties, and with patients with real findings. Physicians must value teaching and learning of physical examination skills, with multiple hands-on opportunities for direct role modeling, coaching, observation and deliberate practice. Ideally, clinical teachers should master the art of combining both patient care and educational activities

PhoP: A Missing Piece in the Intricate Puzzle of Mycobacterium tuberculosis Virulence

Inactivation of the transcriptional regulator PhoP results in Mycobacterium tuberculosis attenuation. Preclinical testing has shown that attenuated M. tuberculosis phoP mutants hold promise as safe and effective live vaccine candidates. We focused this study to decipher the virulence networks regulated by PhoP. A combined transcriptomic and proteomic analysis revealed that PhoP controls a variety of functions including: hypoxia response through DosR crosstalking, respiratory metabolism, secretion of the major T-cell antigen ESAT-6, stress response, synthesis of pathogenic lipids and the M. tuberculosis persistence through transcriptional regulation of the enzyme isocitrate lyase. We also demonstrate that the M. tuberculosis phoP mutant SO2 exhibits an antigenic capacity similar to that of the BCG vaccine. Finally, we provide evidence that the SO2 mutant persists better in mouse organs than BCG. Altogether, these findings indicate that PhoP orchestrates a variety of functions implicated in M. tuberculosis virulence and persistence, making phoP mutants promising vaccine candidates

The Wiring Economy Principle: Connectivity Determines Anatomy in the Human Brain

Minimization of the wiring cost of white matter fibers in the human brain appears to be an organizational principle. We investigate this aspect in the human brain using whole brain connectivity networks extracted from high resolution diffusion MRI data of 14 normal volunteers. We specifically address the question of whether brain anatomy determines its connectivity or vice versa. Unlike previous studies we use weighted networks, where connections between cortical nodes are real-valued rather than binary off-on connections. In one set of analyses we found that the connectivity structure of the brain has near optimal wiring cost compared to random networks with the same number of edges, degree distribution and edge weight distribution. A specifically designed minimization routine could not find cheaper wiring without significantly degrading network performance. In another set of analyses we kept the observed brain network topology and connectivity but allowed nodes to freely move on a 3D manifold topologically identical to the brain. An efficient minimization routine was written to find the lowest wiring cost configuration. We found that beginning from any random configuration, the nodes invariably arrange themselves in a configuration with a striking resemblance to the brain. This confirms the widely held but poorly tested claim that wiring economy is a driving principle of the brain. Intriguingly, our results also suggest that the brain mainly optimizes for the most desirable network connectivity, and the observed brain anatomy is merely a result of this optimization

Prokayrotic Ubiquitin-Like Protein (Pup) Proteome of Mycobacterium tuberculosis

Prokaryotic ubiquitin-like protein (Pup) in Mycobacterium tuberculosis (Mtb) is the first known post-translational small protein modifier in prokaryotes, and targets several proteins for degradation by a bacterial proteasome in a manner akin to ubiquitin (Ub) mediated proteolysis in eukaryotes. To determine the extent of pupylation in Mtb, we used tandem affinity purification to identify its “pupylome”. Mass spectrometry identified 55 out of 604 purified proteins with confirmed pupylation sites. Forty-four proteins, including those with and without identified pupylation sites, were tested as substrates of proteolysis in Mtb. Under steady state conditions, the majority of the test proteins did not accumulate in degradation mutants, suggesting not all targets of pupylation are necessarily substrates of the proteasome under steady state conditions. Four proteins implicated in Mtb pathogenesis, Icl (isocitrate lyase), Ino1 (inositol-1-phosphate synthase), MtrA (Mtb response regulator A) and PhoP (phosphate response regulator P), showed altered levels in degradation defective Mtb. Icl, Ino1 and MtrA accumulated in Mtb degradation mutants, suggesting these proteins are targeted to the proteasome. Unexpectedly, PhoP was present in wild type Mtb but undetectable in the degradation mutants. Taken together, these data demonstrate that pupylation regulates numerous proteins in Mtb and may not always lead to degradation