Diversity of polyketide synthase genes from bacteria associated with the marine sponge Pseudoceratina clavata: culture-dependent and culture-independent approaches

Diverse ketosynthase (KS) genes were retrieved from the microbial community associated with the Great Barrier Reef sponge Pseudoceratina clavata. Bacterial isolation and metagenomic approaches were employed. Phylogenetic analysis of 16S rRNA of culturable sponge-associated bacterial communities comprised eight groups over four phyla. Ten KS domains were amplified from four genera of isolates and phylogenetics demonstrated that these KS domains were located in three clusters (actinobacterial, cyanobacterial and trans-AT type). Metagenomic DNA of the sponge microbial community was extracted to explore community KS genes by two approaches: direct amplification of KS domains and construction of fosmid libraries for KS domain screening. Five KS domains were retrieved from polymerase chain reaction (PCR) amplification using sponge metagenome DNA as template and five fosmid clones containing KS domains found using multiplex PCR screening. Analysis of selected polyketide synthase (PKS) from one fosmid showed that the PKS consists of two modules. Open reading frames located up- and downstream of the PKS displayed similarity with membrane synthesis-related proteins such as cardiolipin synthase. Metagenome approaches did not detect KS domains found in sponge isolates. All KS domains from both metagenome approaches formed a single cluster with KS domains originating from metagenomes derived from other sponge species from other geographical regions.

International Union of Pharmacology. LXVI. Orphan nuclear receptors

Half of the members of the nuclear receptors superfamily are so-called orphan receptors because the identity of their ligand, if any, is unknown. Because of their important biological roles, the study of orphan receptors has attracted much attention recently and has resulted in rapid advances that have helped in the discovery of novel signaling pathways. In this review we present the main features of orphan receptors, discuss the structure of their ligand-binding domains and their biological functions. The paradoxical existence of a pharmacology of orphan receptors, a rapidly growing and innovative field, is highlighted.

RNA: Networks & imaging

The past few years have brought about a fundamental change in our understanding and definition of the RNA world and its role in the functional and regulatory architecture of the cell. The discovery of small RNAs that regulate many aspects of differentiation and development have joined the already known non-coding RNAs that are involved in chromosome dosage compensation, imprinting, and other functions to become key players in regulating the flow of genetic information. It is also evident that there are tens or even hundreds of thousands of other non-coding RNAs that are transcribed from the mammalian genome, as well as many other yet-to-be-discovered small regulatory RNAs. In the recent symposium RNA: Networks & Imaging held in Heidelberg, the dual roles of RNA as a messenger and a regulator in the flow of genetic information were discussed and new molecular genetic and imaging methods to study RNA presented.

Data transmission by pulse compression

Pulse compression techniques originated in radar.The present work is concerned with the utilization of these techniques in general, and the linear FM (LFM) technique in particular, for comnunications. It introduces these techniques from an optimum communications viewpoint and outlines their capabilities.It also considers the candidacy of the class of LFM signals for digital data transmission and the LFM spectrum. Work related to the utilization of LFM signals for digital data transmission has been mostly experimental and mainly concerned with employing two rectangular LFM pulses (or chirps) with reversed slopes to convey the bits 1 and 0 in an incoherent node.No systematic theory for LFM signal design and system performance has been available. Accordingly, the present work establishes such a theory taking into account coherent and noncoherent single-link and multiplex signalling modes. Some new results concerning the slope-reversal chirp pair are obtained. The LFM technique combines the typical capabilities of pulse compression with a relative ease of implementation. However, these merits are often hampered by the difficulty of handling the LFM spectrum which cannot generally be expressed closed-form. The common practice is to obtain a plot of this spectrum with a digital computer for every single set of LFM pulse parameters.Moreover, reported work has been Justly confined to the spectrum of an ideally rectangular chirp pulse with no rise or fall times.Accordingly, the present work comprises a systerratic study of the LFM spectrum which takes the rise and fall time of the chirp pulse into account and can accommodate any LFM pulse with any parameters.It· formulates rather simple and accurate prediction criteria concerning the behaviour of this spectrum in the different frequency regions. These criteria would facilitate the handling of the LFM technique in theory and practice.

1THz-bandwidth polarization-diverse optical phase conjugation of 10x114Gb/s DP-QPSK WDM signals

Polarization diverse optical phase conjugation of a 1THz spectral-band 1.14Tb/s DP-QPSK WDM multiplex is demonstrated for the first time, showing a worst case Q2 penalty of 0.9dB over all conjugate wavelengths, polarizations and OSNR. © 2014 OSA.

Effect of carrier reshaping and narrow MUX-DEMUX filtering in 0.8 bit/s/Hz WDM RZ-DPSK transmission

Effect of the carrier shape in the ultra high dense wavelength division multiplexing (WDM) return to zero differential phase shift keying (RZ-DPSK) transmission has been examined through numerical optimization of the pulse form, duty cycle and narrow multiplex/de-multiplex (MUX/DEMUX) filtering parameters. © 2007 Springer Science+Business Media, LLC.

EDC-mediated oligonucleotide immobilization on a long period grating optical biosensor

We present the development and simplification of label-free fiber optic biosensors based on immobilization of oligonucleotides on dual-peak long period gratings (dLPGs). This improvement is the result of a simplification of biofunctionalization methodology. A one-step 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC)-mediated reaction has been developed for the straightforward immobilization of unmodified oligonucleotides on the glass fiber surface along the grating region, leading to covalent attachment of a 5´-phosphorylated probe oligonucleotide to the amino-derivatized fiber grating surface. Immobilization is achieved via a 5´phosphate-specific linkage, leaving the remainder of the oligonucleotide accessible for binding reactions. The dLPG has been tested in different external media to demonstrate its inherent ultrahigh sensitivity to the surrounding-medium refractive index (RI) achieving 50- fold improvement in RI sensitivity over the previously-published LPG sensor in media with RI’s relevant to biological assays. After functionalization, the dLPG biosensor was used to monitor the hybridization of complementary oligonucleotides showing a detectable oligonucleotide concentration of 4 nM. The proposed one-step EDC reaction approach can be further extended to develop fiber optic biosensors for disease analysis and medical diagnosis with the advances of label-free, real-time, multiplex, high sensitivity and specificity.

Familial adrenal hypoplasia syndromes

The adrenal cortex secretes steroid hormones, including glucocorticoids and mineralocorticoids. Glucocorticoids control body homeostasis, stress, and immune responses, while mineralocorticoids regulate the water and electrolyte balance. A spectrum of genetic defects can disrupt the normal adrenal development, causing adrenal hypoplasia and various forms of adrenal insufficiency, which usually present in infancy or childhood with or without mineralocorticoid deficiency and with or without gonadal dysfunction. The genetic causes of adrenal hypoplasia can be broadly categorized into adrenal hypoplasia due to adrenocorticotropic hormone resistance syndromes (i.e., familial glucocorticoid deficiency and triple A syndrome) and adrenal hypoplasia due to primary defects in the development of the adrenal glands (i.e., X-linked adrenal hypoplasia congenita and primary adrenal hypoplasia caused by steroidogenic factor 1 mutations).

A (kenő)pénz nem boldogít? Gazdaságszociológiai és politikai gazdaságtani elemzések a magyarországi korrupcióról

A tanulmánykötet három részre tagolódik. Az első rész két tanulmánya a korrupció elméleti-fogalmi kereteit tárgyalja. Ebben a fejezetben egyrészt a korrupció általunk használt fogalmának tisztázása mellett a megbízó-megbízott-kliens modell segítségével bemutatjuk a korrupció négy ideáltípusát. Míg a vesztegetést és zsarolást a megbízott és kliens közti, addig a hűtlen kezelést és csalást a megbízó és megbízott közti tranzakcióként definiáljuk. A korrupció ezen alaptípusait irányított gráfok segítségével ábrázoljuk. Másrészt kitekintünk – a többnyire a közgazdaságtan fogalmaiként használatos – információs aszimmetria és morális kockázat jelenségére, oly módon, hogy egyúttal azok politikatudományi alkalmazhatósága mellett is érvelünk. A kötet második részében empirikus elemzések és esettanulmányok segítségével mutatjuk be a korrupció sokszínű jelenségét Magyarországon. Míg médiaelemzésünkben a médiában korábban napvilágot látott korrupciógyanús esetek összegyűjtésével a tranzakciós helyzetek felmérésére és elemzésére teszünk kísérletet, addig a korrupció mélyszerkezetét vizsgálva tipikus magyarországi korrupciós hálózatok társadalmi és intézményi beágyazottságát mutatjuk be, a korrupciós tranzakciókat többszereplős, bonyolult és multiplex gráfokkal ábrázolva. Harmadik tanulmányunk a járadékvadászat és a korrupció kapcsolatát empirikus példák segítségével világítja meg, míg a fejezet utolsó két tanulmánya a villamosenergia-piac működéséről és a szélerőművek telepítésének korrupciós kockázatairól fest részletesebb képet. Végül a kötet harmadik fejezetében különböző antikorrupciós politikák elveire és azok gyakorlati megvalósítási lehetőségeire térünk ki. Ennek keretében egyfelől olyan antikorrupciós reformokat körvonalazunk, amelyek közvetlenül a korrupciós tranzakciók visszaszorítására irányulnak, illetve olyan antikorrupciós kormányzati lépéseket vázolunk, amelyek a szabályozási környezet megváltozására irányulnak. A kötet záró tanulmánya a gyakorlatra helyezi a hangsúlyt. Részint egy korrupciós helyzeteket és azok jogkövetkezményeit is bemutató esettanulmány segítségével megkönnyíti az ide vonatkozó hazai szabályozásban való eligazodást, másfelől – elsősorban vállalkozók számára – javaslatokat fogalmaz meg azzal kapcsolatban, hogy hogyan lehet megelőzni, illetve hatékonyan küzdeni a különböző korrupt tevékenységek ellen.

A korrupció társadalmi és intézményi szerkezete

A tanulmány első részében a megbízó-megbízott-kliens modellt fogalmi keretként alkalmazva a korrupció négy ideáltípusát mutatjuk be: míg a vesztegetést és zsarolást a megbízott és kliens közti, addig a hűtlen kezelést és csalást a megbízó és megbízott közti tranzakcióként definiáljuk. A korrupció ezen alaptípusait irányított gráfok segítségével ábrázoljuk. Ezt követően a korrupciós ügyletek szereplőinek lehetséges (pl. a tranzakciós költségek és a lebukási kockázatok csökkentésére irányuló) motivációit vizsgáljuk, vagyis azt, hogy mely tényezők ösztönzik leginkább a korrupciós helyzetek szereplőit arra, hogy tranzakcióikat különböző típusú személyes, üzleti, politikai és egyéb intézményes kapcsolathálókba ágyazzák. A második részben – támaszkodva korábbi kutatásaink eredményeire – néhány tipikus magyarországi korrupciós tranzakció társadalmi és intézményi beágyazottságát mutatjuk be. Négy esettanulmányt elemzünk részletesen, a bemutatott tipikus (pl. pártfinanszírozáshoz, vagy engedélyek megszerzéséhez kapcsolódó) korrupciós hálózatokat pedig többszereplős, bonyolult és multiplex gráfokkal ábrázoljuk. Végül a komplex hálózatok evolúciós vonatkozásait a szereplők számának, a kapcsolatok komplexitásának, valamint a személyi és/vagy intézményi beágyazottság mértékének tükrében vizsgáljuk. ______ In the first part of the paper four idealtypical corruption transactions are explicated in terms of the principal-agent-client model: bribery and extortion are described as two different types of agent-client relationship, while embezzlement and fraud as two different types of principal-agent relationship. The main idea is to describe these elementary corruption transactions as simple directed graphs. The next section of the paper takes into consideration different kinds of possible motivations (such as the reduction of risks or transaction costs) of the principals, agents and clients, in order to embed their corruption transactions in various kinds of personal, business, political and other institutional networks. In the second part of the paper some typical and stable network configurations are presented, based on a recent empirical corruption research carried out in Hungary. Certain corruption cases (such as party financing or granting of permit) are analyzed in details, and are described as complex and multiple networks. The paper concludes in showing some signs of the evolution of corruption networks in Hungary in terms of the number of actors, of the complexity of network configurations, of the level of personal or institutional embeddedness, and of the multiplexity of relationships.

The development of direct ultra-fast PCR for forensic genotyping using short channel microfluidic systems with enhanced sieving matrices

There are situations in which it is very important to quickly and positively identify an individual. Examples include suspects detained in the neighborhood of a bombing or terrorist incident, individuals detained attempting to enter or leave the country, and victims of mass disasters. Systems utilized for these purposes must be fast, portable, and easy to maintain. The goal of this project was to develop an ultra fast, direct PCR method for forensic genotyping of oral swabs. The procedure developed eliminates the need for cellular digestion and extraction of the sample by performing those steps in the PCR tube itself. Then, special high-speed polymerases are added which are capable of amplifying a newly developed 7 loci multiplex in under 16 minutes. Following the amplification, a postage stamp sized microfluidic device equipped with specially designed entangled polymer separation matrix, yields a complete genotype in 80 seconds. The entire process is rapid and reliable, reducing the time from sample to genotype from 1-2 days to under 20 minutes. Operation requires minimal equipment and can be easily performed with a small high-speed thermal-cycler, reagents, and a microfluidic device with a laptop. The system was optimized and validated using a number of test parameters and a small test population. The overall precision was better than 0.17 bp and provided a power of discrimination greater than 1 in 106. The small footprint, and ease of use will permit this system to be an effective tool to quickly screen and identify individuals detained at ports of entry, police stations and remote locations. The system is robust, portable and demonstrates to the forensic community a simple solution to the problem of rapid determination of genetic identity.

Distribuição da fauna triatomínica e infecção natural pelo Trypanosoma cruzi em diferentes municípios do semiárido do Rio Grande do Norte

The triatomine fauna distribution and the natural infection by Trypanosoma cruzi was evaluated aiming the comprehension of the transmission dynamics of this parasite in the countryside of the State of Rio Grande do Norte. Additionally, the research for Trypanosoma rangeli was also investigated. The captures of triatomines were performed at sylvatic, peridomicile and domicile environments at different municipalities of the central and western mesoregions of this state. The insects were identified and examined by direct method, xenoculture and PCR to detect T. cruzi. The detection of T. rangeli was performed by direct examination of the hemolymph and multiplex PCR of 151 positive specimens for T. cruzi. Of 824 captured insects, the species were distributed in Triatoma brasiliensis (66.4%), Triatoma pseudomaculata (18.2%), Panstrongylus lutzi (12.7%) and Rhodnius nasutus (2.7%), and T. brasiliensis was found in most of the evaluated municipalities. The species were captured at nymph and adult stages, except P. lutzi, exclusively in adult stage. In the sylvatic environment were captured T. brasiliensis (57%), P. lutzi (28%) and T. pseudomaculata (15%) species. At the peridomicile environment were identified T. brasiliensis (74%), T. pseudomaculata (21%) and R. nasutus (5.0%), while in the intradomicile was found only T. brasiliensis. The infection rate of triatomines by T. cruzi was 30.4%, P. lutzi showed highest rate (78%), followed by T. brasiliensis (24.4%), T. pseudomaculata (22.6%) and R. nasutus (4.5%). Infected triatomines indexes at silvatic, peridomicile and domicile environments were of 41.8%, 20.1% and 50.0%, respectively. T. rangeli was only detected by multiplex PCR in 2.6% (4/151) of examined insects, of these 4.4% (3/67) were T. brasiliensis and 1.5% (1/63) P. lutzi species. The data showed that the positivity of P. lutzi allied to its ability to invade domicile attracted by light, suggests a likely participation of this insect between epidemiological transmission cycles of T. cruzi. T. brasiliensis was the only specie present in all environments, what reinforces its importance related to the capacity for adapting to the domestic environment, potential as a vector, and maintenance of sylvatic and domestic transmissions cycles in the semiarid, indicating the necessity of continuous epidemiological surveillance. The presence of T. rangeli in T. brasiliensis and P. lutzi was first recorded in rural zone of this State, broadening the area of occurrence of this protozoan in northeastern Brazil.

Distribuição da fauna triatomínica e infecção natural pelo Trypanosoma cruzi em diferentes municípios do semiárido do Rio Grande do Norte

The triatomine fauna distribution and the natural infection by Trypanosoma cruzi was evaluated aiming the comprehension of the transmission dynamics of this parasite in the countryside of the State of Rio Grande do Norte. Additionally, the research for Trypanosoma rangeli was also investigated. The captures of triatomines were performed at sylvatic, peridomicile and domicile environments at different municipalities of the central and western mesoregions of this state. The insects were identified and examined by direct method, xenoculture and PCR to detect T. cruzi. The detection of T. rangeli was performed by direct examination of the hemolymph and multiplex PCR of 151 positive specimens for T. cruzi. Of 824 captured insects, the species were distributed in Triatoma brasiliensis (66.4%), Triatoma pseudomaculata (18.2%), Panstrongylus lutzi (12.7%) and Rhodnius nasutus (2.7%), and T. brasiliensis was found in most of the evaluated municipalities. The species were captured at nymph and adult stages, except P. lutzi, exclusively in adult stage. In the sylvatic environment were captured T. brasiliensis (57%), P. lutzi (28%) and T. pseudomaculata (15%) species. At the peridomicile environment were identified T. brasiliensis (74%), T. pseudomaculata (21%) and R. nasutus (5.0%), while in the intradomicile was found only T. brasiliensis. The infection rate of triatomines by T. cruzi was 30.4%, P. lutzi showed highest rate (78%), followed by T. brasiliensis (24.4%), T. pseudomaculata (22.6%) and R. nasutus (4.5%). Infected triatomines indexes at silvatic, peridomicile and domicile environments were of 41.8%, 20.1% and 50.0%, respectively. T. rangeli was only detected by multiplex PCR in 2.6% (4/151) of examined insects, of these 4.4% (3/67) were T. brasiliensis and 1.5% (1/63) P. lutzi species. The data showed that the positivity of P. lutzi allied to its ability to invade domicile attracted by light, suggests a likely participation of this insect between epidemiological transmission cycles of T. cruzi. T. brasiliensis was the only specie present in all environments, what reinforces its importance related to the capacity for adapting to the domestic environment, potential as a vector, and maintenance of sylvatic and domestic transmissions cycles in the semiarid, indicating the necessity of continuous epidemiological surveillance. The presence of T. rangeli in T. brasiliensis and P. lutzi was first recorded in rural zone of this State, broadening the area of occurrence of this protozoan in northeastern Brazil.

Coding Strategies and Implementations of Compressive Sensing

This dissertation studies the coding strategies of computational imaging to overcome the limitation of conventional sensing techniques. The information capacity of conventional sensing is limited by the physical properties of optics, such as aperture size, detector pixels, quantum efficiency, and sampling rate. These parameters determine the spatial, depth, spectral, temporal, and polarization sensitivity of each imager. To increase sensitivity in any dimension can significantly compromise the others.

This research implements various coding strategies subject to optical multidimensional imaging and acoustic sensing in order to extend their sensing abilities. The proposed coding strategies combine hardware modification and signal processing to exploiting bandwidth and sensitivity from conventional sensors. We discuss the hardware architecture, compression strategies, sensing process modeling, and reconstruction algorithm of each sensing system.

Optical multidimensional imaging measures three or more dimensional information of the optical signal. Traditional multidimensional imagers acquire extra dimensional information at the cost of degrading temporal or spatial resolution. Compressive multidimensional imaging multiplexes the transverse spatial, spectral, temporal, and polarization information on a two-dimensional (2D) detector. The corresponding spectral, temporal and polarization coding strategies adapt optics, electronic devices, and designed modulation techniques for multiplex measurement. This computational imaging technique provides multispectral, temporal super-resolution, and polarization imaging abilities with minimal loss in spatial resolution and noise level while maintaining or gaining higher temporal resolution. The experimental results prove that the appropriate coding strategies may improve hundreds times more sensing capacity.

Human auditory system has the astonishing ability in localizing, tracking, and filtering the selected sound sources or information from a noisy environment. Using engineering efforts to accomplish the same task usually requires multiple detectors, advanced computational algorithms, or artificial intelligence systems. Compressive acoustic sensing incorporates acoustic metamaterials in compressive sensing theory to emulate the abilities of sound localization and selective attention. This research investigates and optimizes the sensing capacity and the spatial sensitivity of the acoustic sensor. The well-modeled acoustic sensor allows localizing multiple speakers in both stationary and dynamic auditory scene; and distinguishing mixed conversations from independent sources with high audio recognition rate.