Fano resonances in quantum transport with vibrations

Quantum-mechanical scattering involving continuum states coupled to a scatterer with a discrete spectrum gives rise to Fano resonances. Here we consider scatterers that possess internal vibrational degrees of freedom in addition to discrete states. Entanglement between the scattered excitation and vibrational modes complicates analytical and numerical calculations considerably. For the example of one-dimensional scattering we develop a multichannel quantum scattering approach which can determine reflection and transmission probabilities in the presence of vibrations. Application to a linear chain coupled to a control unit containing vibrating sites shows that vibrational degrees of freedom can have a profound effect on quantum transport. For suitable parameters, spectral regions which are opaque in the static case can be rendered transparent when vibrations are included. The formalism is general enough to be applicable to a variety of platforms for quantum transport including molecular aggregates, cold atom chains, quantum-dot arrays and molecular wires based on conjugated polymers

Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences. Availability: http://www.mrc-lmb.cam.ac.uk/genomes/spial/; supplementary information is available at http://www.mrc-lmb.cam.ac.uk/genomes/spial/help.html Contact: [email protected]

Primary treatment of acromegaly with high-dose lanreotide: a case series

<p>Abstract</p> <p>Introduction</p> <p>The first-line treatment for acromegaly is transsphenoidal surgery. In approximately 50% of patients, however, a cure is not possible with surgery and alternatives are needed. Somatostatin analog therapy is the recommended first-line treatment in patients with such cases. Here we provide the first report of a high-dose lanreotide primary therapy in patients with acromegaly.</p> <p>Case presentation</p> <p>Six patients who were not suitable for surgery were given 60 mg of lanreotide (Autogel^®) every four weeks. All patients were German nationals and Caucasian.</p> <p>When the response of our patients was unsatisfactory, the dose was increased sequentially to 90 mg every four weeks, 120 mg every four weeks, 120 mg every three weeks and 180 mg every three weeks. Treatment duration was 12 to 24 months. In all cases, the lanreotide dose was 120 mg every 4 weeks or higher. In five of our patients, growth hormone (GH) levels were successfully reduced (in three patients GH <2.5 ng/ml was achieved). Insulin-like growth factor 1 levels were normalized in three patients and decreased in two patients. One patient failed to show a biochemical response to lanreotide therapy or pegvisomant therapy.</p> <p>Tumor shrinkage or degeneration was observed in the five responding patients. No drug-related adverse events were noted.</p> <p>Conclusions</p> <p>These results suggest that lanreotide at high doses of 120 mg every four weeks or more is an effective first-line therapy for patients with acromegaly that surgery alone cannot treat.</p

Spial: analysis of subtype-specific features in multiple sequence alignments of proteins

Motivation: Spial (Specificity in alignments) is a tool for the comparative analysis of two alignments of evolutionarily related sequences that differ in their function, such as two receptor subtypes. It highlights functionally important residues that are either specific to one of the two alignments or conserved across both alignments. It permits visualization of this information in three complementary ways: by colour-coding alignment positions, by sequence logos and optionally by colour-coding the residues of a protein structure provided by the user. This can aid in the detection of residues that are involved in the subtype-specific interaction with a ligand, other proteins or nucleic acids. Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences

Microbial adaptation to venom is common in snakes and spiders

Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane disrupting activity against multi-drug resistant bacteria. However, bite wound infections are common in developing nations. Investigating the oral and venom microbiome of five snake and two spider species, we evidence viable microorganisms potentially unique to venom for black-necked spitting cobras (Naja nigricollis). Among these are two novel sequence types of Enterococcus faecalis misidentified by commonly used clinical biochemistry procedures as Staphylococcus; the genome sequence data of venom-specific isolates feature an additional 45 genes, at least 11 of which improve membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

Although several studies have provided important insights into the general principles of biological networks, the link between network organization and the genome-scale dynamics of the underlying entities (genes, mRNAs, and proteins) and its role in systems behavior remain unclear. Here we show that transcription factor (TF) dynamics and regulatory network organization are tightly linked. By classifying TFs in the yeast regulatory network into three hierarchical layers (top, core, and bottom) and integrating diverse genome-scale datasets, we find that the TFs have static and dynamic properties that are similar within a layer and different across layers. At the protein level, the top-layer TFs are relatively abundant, long-lived, and noisy compared with the core- and bottom-layer TFs. Although variability in expression of top-layer TFs might confer a selective advantage, as this permits at least some members in a clonal cell population to initiate a response to changing conditions, tight regulation of the core- and bottom-layer TFs may minimize noise propagation and ensure fidelity in regulation. We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population

Theory of Multidimensional Solitons

We review a number of topics germane to higher-dimensional solitons in Bose-Einstein condensates. For dark solitons, we discuss dark band and planar solitons; ring dark solitons and spherical shell solitons; solitary waves in restricted geometries; vortex rings and rarefaction pulses; and multi-component Bose-Einstein condensates. For bright solitons, we discuss instability, stability, and metastability; bright soliton engineering, including pulsed atom lasers; solitons in a thermal bath; soliton-soliton interactions; and bright ring solitons and quantum vortices. A thorough reference list is included.Comment: review paper, to appear as Chapter 5a in "Emergent Nonlinear Phenomena in Bose-Einstein Condensates: Theory and Experiment," edited by P. G. Kevrekidis, D. J. Frantzeskakis, and R. Carretero-Gonzalez (Springer-Verlag

Historic genetic structuring and paraphyly within the Great-tailed Grackle

The Great-tailed Grackle (Quiscalus mexicanus) and Boat-tailed Grackle (Q. major) are sister species that have expanded their ranges during historical times. This expansion has created an area of sympatry between these species in Texas and Louisiana, and between distinctive Great-tailed Grackle subspecies in the southwestern United States and northern Mexico. We investigated the evolutionary histories of both species using mitochondrial DNA sequence data and modern phylogenetic methods. Our results reveal genetic structure within Great-tailed, but not Boat-tailed Grackles. Great-tailed Grackles are separated into two clades, but range expansion in the north has led to secondary contact between them. Boat-tailed Grackles are monophyletic and are embedded within the Great-tailed Grackle assemblage, rendering the latter paraphyletic. These results reveal a complex phylogeographic pattern caused by recent range expansion and secondary contact of once allopatric units

Bacterial Adaptation to Venom in Snakes and Arachnida

Animal venoms are considered sterile sources of antimicrobial compoundswith strong membrane-disrupting activity against multidrug-resistant bacteria. However,venomous bite wound infections are common in developing nations. Investigating theenvenomation organ and venom microbiota offive snake and two spider species, weobserved venom community structures that depend on the host venomous animal spe-cies and evidenced recovery of viable microorganisms from black-necked spitting cobra(Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Amongthe bacterial isolates recovered fromN. nigricollis,weidentified two venom-resistant,novel sequence types ofEnterococcus faecaliswhose genomes feature 16 virulencegenes, indicating infectious potential, and 45 additional genes, nearly half of whichimprove bacterial membrane integrity. Ourfindings challenge the dogma of venom ste-rility and indicate an increased primary infection risk in the clinical management of ven-omous animal bite wounds