Concurrent encoding of frequency and amplitude modulation in human auditory cortex: MEG evidence

September 26, 2007; doi:10.1152/jn.00342.2007. Complex natural sounds (e.g., animal vocalizations or speech) can be characterized by specific spectrotemporal patterns the components of which change in both frequency (FM) and amplitude (AM). The neural coding of AM and FM has been widely studied in humans and animals but typically with either pure AM or pure FM stimuli. The neural mechanisms employed to perceptually unify AM and FM acoustic features remain unclear. Using stimuli with simultaneous sinusoidal AM (at rate f AM � 37 Hz) and FM (with varying rates ƒ FM), magnetoencephalography (MEG) is used to investigate the elicited auditory steady-state response (aSSR) at relevant frequencies (ƒ AM, ƒ FM, ƒ AM � f FM). Previous work demonstrated that for sounds with slower FM dynamics (f FM � 5 Hz), the phase of the aSSR at ƒ AM tracked the FM; in other words, AM and FM features were co-tracked and co-represented by “phase modulation ” encoding. This stud

A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange

<p>Abstract</p> <p>Background</p> <p>Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors.</p> <p>Results</p> <p>The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-<it>Sce</it>I sites in an inverted orientation at positions that flank an identical DNA fragment containing the <it>lac</it>Z selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-<it>Sce</it>I, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-<it>Sce</it>I that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both <it>E. coli </it>and <it>Agrobacterium</it>. The vectors can be accessed through our website <url>http://GResource.hzau.edu.cn</url>.</p> <p>Conclusions</p> <p>The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.</p

Identification of the forensically important flies (Diptera: Muscidae) based on cytochrome oxidase subunit I (COI) gene in China

Accurate species identification is a crucial step in forensic entomology, as the insect collected on a corpse can provide useful information for estimation of postmortem interval (PMI). However, morphological distinction may on occasion be impossible to the adult flies and nymphs of the same genus. DNA-based method can be used as a supplemental means of morphological method. In this study, 31 forensically important Muscidae flies were collected from 15 locations in 11 provinces of China, and a 272 base pair region of the mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced. The monophyletic branches of the phylogenetic tree revealed that this marker is suitable for discrimination between these five species of four genera of Muscidae. The genetic variations found on COI can be applied not only to identify the forensically important species, but also to understand the taxonomic positions of the sarcophagine species. In addition, this research will be instrumental for implementation of the Chinese Muscidae database.Keywords: Forensic science, forensic entomology, Muscidae, cytochrome oxidase subunit I (COI), species identificatio

MeDReaders: a database for transcription factors that bind to methylated DNA

Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development. Hence, we constructed a database, named as MeDReaders, to collect information about methylated DNA binding activities. A total of 731 TFs, which could bind to methylated DNA sequences, were manually curated in human and mouse studies reported in the literature. In silico approaches were applied to predict methylated and unmethylated motifs of 292 TFs by integrating whole genome bisulfite sequencing (WGBS) and ChIP-Seq datasets in six human cell lines and one mouse cell line extracted from ENCODE and GEO database. MeDReaders database will provide a comprehensive resource for further studies and aid related experiment designs. The database implemented unified access for users to most TFs involved in such methylation-associated binding actives. The website is available at http://medreader.org/

West Meets East: New Concepts and Theories

Management scholarship has grown tremendously over the past 60 years. Most of our paradigms originated from North America in the 1950s to the 1980s, inspired by the empirical phenomena and cultural, philosophical, and research traditions of the time. Here following, we highlight the contextual differences between the East and the West in terms of institutions, philosophies, and cultural values and how they are manifest in contemporary management practices. Inspired by theory development in management studies over time, we offer insights into the conditions facilitating new theories, and how these might apply to emergent theories from the East. We discuss the contributions of the six papers included in this special research forum as exemplars of integrating Eastern concepts and contexts to enrich existing management theories. We highlight the difficulty with testing Eastern constructs as distinct from Western ones by discussing the properties of equivalence, salience, and infusion in constructs. We provide directions for future research and encourage an agentic view to creating new theories and paradigms

Preparation and Application of Green Sustainable Solvent Cyrene

The bio-based solvent dihydrolevoglucosenone (Cyrene) is a green and sustainable alternative to petroleum-based dipolar aprotic solvents. Cyrene can be prepared from cellulose in a simple two-step process and can be produced in a variety of yields. Cyrene is compatible with a large number of reactions in the chemical industry and can be applied in organic chemistry, biocatalysis, materials chemistry, graphene and lignin processing, etc. It is also green, non-mutagenic and non-toxic, which makes it very promising for applications. In this paper, we have also screened all articles related to Cyrene on the Web of Science and visualised them through Cite Space

Genome-wide analysis of regulatory proteases sequences identified through bioinformatics data mining in Taenia solium

Background Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of current drugs to prevent re-infection, identification of novel vaccines and chemotherapeutic agents against Taenia solium and related helminth pathogens is a public health priority. The T. solium genome and the predicted proteome were reported recently, providing a wealth of information from which new interventional targets might be identified. In order to characterize and classify the entire repertoire of protease-encoding genes of T. solium, which act fundamental biological roles in all life processes, we analyzed the predicted proteins of this cestode through a combination of bioinformatics tools. Functional annotation was performed to yield insights into the signaling processes relevant to the complex developmental cycle of this tapeworm and to highlight a suite of the proteases as potential intervention targets. Results Within the genome of this helminth parasite, we identified 200 open reading frames encoding proteases from five clans, which correspond to 1.68% of the 11,902 protein-encoding genes predicted to be present in its genome. These proteases include calpains, cytosolic, mitochondrial signal peptidases, ubiquitylation related proteins, and others. Many not only show significant similarity to proteases in the Conserved Domain Database but have conserved active sites and catalytic domains. KEGG Automatic Annotation Server (KAAS) analysis indicated that ~60% of these proteases share strong sequence identities with proteins of the KEGG database, which are involved in human disease, metabolic pathways, genetic information processes, cellular processes, environmental information processes and organismal systems. Also, we identified signal peptides and transmembrane helices through comparative analysis with classes of important regulatory proteases. Phylogenetic analysis using Bayes approach provided support for inferring functional divergence among regulatory cysteine and serine proteases. Conclusion Numerous putative proteases were identified for the first time in T. solium, and important regulatory proteases have been predicted. This comprehensive analysis not only complements the growing knowledge base of proteolytic enzymes, but also provides a platform from which to expand knowledge of cestode proteases and to explore their biochemistry and potential as intervention targets