On-going generation of multiple forms of HIV-1 intersubtype recombinants in the Yunnan Province of China

Objectives: To investigate the molecular epidemiology of HIV in China's Yunnan Province, where the initial HIV-1 outbreak among injecting drug users (IDU) occurred in 1989, and to analyse the genesis and interrelationship of the epidemic with that in surrounding areas. Design: A molecular epidemiological investigation was conducted among IDU in three prefectures in Yunnan Province, including Wenshan (east), Honghe (southeast) and Dehong (west). Methods: Thirty-nine specimens were collected from consenting IDU in 2000-2001. The nucleotide sequences of 2.6 kb gag-RT and 340 base pair (bp) env (C2/V3) regions were determined. Phylogenetic tree and recombination breakpoint analyses were performed. Results: The circulating recombinant form (CRF), CRF08_BC, predominated in east Yunnan near Guangxi Province (89% in Wenshan and 81% in Honghe), whereas it was not detected in Dehong(0/14) in the west. In contrast, 71% (10/14) of the Dehong isolates were unique recombinant forms (URF), mostly between subtypes B' (Thailand variant of subtype B) and C, with distinct profiles of recombination breakpoints. The subtype B' accounts for the remaining 29% (4/14) of Dehong isolates. Interestingly, two Honghe isolates (2/16) shared some of the precise B'/C recombination breakpoints with CRF07_BC. Conclusion: New recombinant strains are arising continually in west Yunnan near the Myanmar border. Some appeared to be secondary recombinants derived from CRF07_BC that had further recombined with other strains. The uneven distribution of subtypes, CRF and URF, suggests the presence of independent transmission networks and clusters among IDU in Yunnan. (C) 2002 Lippincott Williams Wilkins.

Multiple in-to-Africa dispersals of labeonin fishes (Teleostei: Cyprinidae) revealed by molecular phylogenetic analysis

An out-of-Africa dispersal route has been proposed for many organisms, including modern man. However, counter examples of in-to-Africa dispersal routes are less common. In the present article, the phylogenetic relationships within the Labeoninae, a subfamily of cyprinid fishes distributed in Asia and Africa, were analyzed to investigate the biogeographic processes governing the modern distribution of these Asian and African cyprinids. The mitochondrial DNA cytochrome b gene was used as a molecular marker. The phylogenetic analysis indicated that the subfamily Labeoninae is a monophyletic group, with some Asian labeonins located at the basal position. Two subclades were found that contained both African and Asian species, which highlighted a need for further biogeographic analysis. Based on this analysis, it is proposed that the centre of origin of the Labeoninae was in East Asia. Molecular clock estimation suggests that the Labeoninae arose by the Early Miocene (similar to 23 MYA) during the period of the second Tibetan uplift. Subsequently, two dispersal events of labeonins from Asia into Africa occured in the Early Miocene (similar to 20 MYA) and Late Miocene (similar to 9 MYA) and serve as examples counter to out-of-Africa dispersal.

Zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) mediates multiple intracellular signaling pathways

Insect PGRPs can function as bacterial recognition molecules triggering proteolytic and/or signal transduction pathways, with the resultant production of antimicrobial peptides. To explore if zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) has such effects, RNA interference (siRNA) and high-density oligonucleotide microarray analysis were used to identify differentially expressed genes regulated by zfPGRP-SC. The mRNA levels for a set of genes involved in Toll-like receptor signaling pathway, such as TLRs, SARM, MyD88, TRAF6 and nuclear factor (NF)-kappa B2 (p100/p52), were examined by quantitative RT-PCR (QT-PCR). The results from the arrays and QT-PCR showed that the expression of 133 genes was involved in signal transduction pathways, which included Toll-like receptor signaling, Wnt signaling, BMP signaling, insulin receptor signaling, TGF-beta signaling, GPCR signaling, small GTPase signaling, second-messenger-mediated signaling, MAPK signaling, JAK/STAT signaling, apoptosis and anti-apoptosis signaling and other signaling cascades. These signaling pathways may connect with each other to form a complex network to regulate not just immune responses but also other processes such as development and apoptosis. When transiently over-expressed in HEK293T cells, zfPGRP-SC inhibited NF-kappa B activity with and without lipopolysacharide (LPS) stimulation. (C) 2008 Elsevier Ltd. All rights reserved.

Multiple cohorts of juvenile jack mackerel Trachurus japonicus in waters along the Tsushima Warm Current

The jack mackerel, Trachurus japonicus, has a prolonged spawning season and widely spread spawning grounds. The population in the coastal waters of Japan seems to be composed of several cohorts spawned seasonally from different waters. To understand its population structure along the Tsushima Warm Current, we analysed hatchdates and growth histories of fish from Kunda Bay, the southern, central and northern East China Sea (ECS), the southern Sea of Japan, and Maizuru Bay. Seven cohorts were detected from fish collected between June 2005 and June 2006 in Kunda Bay. Comparing hatchdate distributions and growth trajectories of the seven cohorts with those of the other five regional samples, we did not find that cohorts collected in Kunda Bay originated in the southern ECS. Therefore, these coastal waters of Japan appear to be significant spawning grounds for juvenile jack mackerel. (C) 2008 Elsevier B.V. All rights reserved.

Multiple invasions of europe by east asian cobitid loaches (Teleostei : Cobitidae)

While it has been widely suggested that freshwater fishes from East Asia invaded the western Palaearctic, details about this process are largely unknown. Here, using the cytochrome b gene, we evaluated the phylogenetic relationships of a small group of Eurasian primary freshwater fishes (Cobitidae), which are widely distributed and species rich in East Asia and Europe, with the purpose of inferring their invasion process of Europe from East Asia. Though phylogenetic relationships of cobitids were not well resolved, our analysis could identify three sister groups formed by the European and East Asian cobitids, which brought new insights into the biogeography of the genera Cobitis, Misgurnus, and Sabanejewia. The present results support the view that Asian cobitid fishes may have invaded Europe at least five times independently, and once reverse colonization of European cobitids to East Asia could also be found. Ancestral Sabanejewia might have been the first cobitids to cross Siberia and invade the EMZS (Euro-Mediterranean zoogeographic subregion) about 33.54 million years ago (MYA). One lineage of Cobitis and the ancestor of Misgurnus fossilis (Linnaeus) almost in the same time invaded the Europe, responding to 16.71 MYA and 16.59 MYA, respectively. Three different lineages of Cobitis were found to have invaded the EMZS from East Asia, and once reverse invasion to East Asia occurred to one subclade of European Cobitis. And our data also suggest that the diversity of East Asian cobitid fishes, especially of the genus Cobitis, is greatly underestimated.

Short and long peptidoglycan recognition proteins (PGRPs) in zebrafish, with findings of multiple PGRP homologs in teleost fish

Peptidoglycan recognition protein (PGRP) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect and mammals. Using a database mining approach and RT-PCR, multiple peptidoglycan recognition protein (PGRP) like genes have been discovered in fish including zebrafish Danio rerio, Japanese pufferfish TakiFugu rubripes and spotted green pufferfish Tetraodon nigroviridis. They share the common features of those PGRPs in arthropod and mammals, by containing a conserved PGRP domain. Based on the predicted structures, the identified zebrafish PGRP homologs resemble short and long PGRP members in arthropod and mammals. The identified PGRP genes in T. nigroviridis and TakiFugu rubripes resemble the long PGRPs, and the short PGRP genes have not been found in T. nigroviridis and TakiFugu rubripes databases. Computer modelling of these molecules revealed the presence of three alpha-helices and five or six beta-strands in all fish PGRPs reported in the present study. The long PGRP in teleost fish have multiple alternatively spliced forms, and some of the identified spliced variants, e.g., tnPGRP-L3 and tnPGRP-L4 (in: Tetraodon nigroviridis), exhibited no characters present in the PGRP homologs domain. The coding regions of zfPGRP6 (zf: zebrafish), zfPGRP2-A, zfPGRP2-B and zfPGRP-L contain five exons and four introns; however, the other PGRP-like genes including zfPGRPSC1a, zfPGRPSC2, tnPGRP-L1-, tnPGRP-L2 and frPGRP-L (fr: Takifugu rubripes) contain four exons and three introns. In zebrafish, long and short PGRP genes identified are located in different chromosomes, and an unknown locus containing another long PGRP-like gene has also been found in zebrafish, demonstrating that multiple PGRP loci may be present in fish. In zebrafish, the constitutive expressions of zfPGRP-L, zfPGRP-6 and zfPGRP-SC during ontogeny from unfertilized eggs to larvae, in different organs of adult, and the inductive expression following stimulation by Flavobacterium columnare, were detected by real-time PCR, but the levels and patterns varied for different PGRP genes, implying that different short and long PGRPs may play different roles in innate immune response. (c) 2007 Elsevier Ltd. All rights reserved.

Positive selection on multiple antique allelic lineages of transferrin in the polyploid Carassius auratus

Transferrin polymorphism has been studied in the polyploid Carassius auratus by cloning and sequence analysis of cDNAs from its three subspecies C. auratus gibelio, C. auratus auratus, and C. auratus cuvieri. DNA polymorphism of extremely high extent was shown for the transferrin gene by the 248 segregation sites among coding region sequences of its alleles. The deduced amino acid sequences of the transferrin alleles showed variable theoretical physicochemical parameters, which might constitute molecular basis for their electrophoretic heterogeneity. Positive selection was inferred by the replacement/synonymous ratios larger than 1 in partial allelic lineages which was subsequently confirmed by likelihood simulation under neutral or selection models. Furthermore, the correspondent sites to these selected codons were collectively located at two planes in the crystallographic structure of rabbit transferrin, which suggested that the rapid evolution of C. auratus transferrin might correlate to its adaptation to variable environmental elements such as oxygen pressure. The minimal 26 recombination events were detected among coding sequences of C. auratus transferrin, with partial mosaic sequences and breakpoints identified by identity scanning and information site analyses. Phylogenetic analyses revealed multiple antique allelic lineages of transferrin, which was estimated to diverge fifteen to twenty MYA. All these features strongly suggested the role of balancing selection in long persistence of high transferrin polymorphism in C. auratus. Furthermore, owing to its particular evolutionary backgrounds, the silver crucian carp might possess a distinctive balancing selection mechanism.

Spin injection in the multiple quantum-well LED structure with the Fe/AlO (x) injector

A spin-injection/-detection device has been fabricated based on the multiple quantum well light emitting diode (LED) structure. It is found that only a broad electroluminescence (EL) peak of a full width at half maximum of 8.6 nm appears at the wavelength of 801 nm in EL spectra with a circular luminescence polarization degree of 18%, despite PL spectra always show three well resolved peaks. The kinetic energy gained by injected electrons and holes in their drift along opposite directions broadens the EL peak, and makes three EL peaks converge together. The same process also destroys the injected spin polarization of electrons mainly dominated by the Bir-Aronov-Pikus spin relaxing mechanism.

An experimental study about the influence of well thickness on the electroluminescence of InGaN/GaN multiple quantum wells

The influence of well thickness on the electroluminescence (EL) of InGaN/GaN multiple quantum wells (MQWs) grown by metalorganic chemical vapor deposition is investigated. It is found that the peak wavelength of EL increases with the increase of well thickness when the latter is located in the range of 3.0-5.1 nm. The redshift is mainly attributed to the quantum confined Stark effect (QCSE). As a contrast, it is found that the EL intensity of InGaN/GaN MQWs increases with the increase of well thickness in spite of QCSE. The result of X-ray diffraction demonstrates that the interface become smoother with the increase of well thickness and suggests that the reduced interface roughness can be an important factor leading to the increase of EL intensity of InGaN/GaN MQWs. (C) 2009 Elsevier B.V. All rights reserved.

Ultracompact triplexer by coupling and decoupling of multiple photonic crystal waveguides

We investigate numerically the self-imaging effect in a system of multiple coupled photonic crystal waveguides (M-CPCWs) with asymmetric coupling. Then two couplers of 2-CPCWs and 3-CPCWs are cascaded to form an ultracompact triplexer by employing coupling and decoupling of M-CPCWs. The wavelength of 1310 nm propagates along the input direction because the M-CPCWs are decoupled at the same decoupling frequency. The other two wavelengths (1490 and 1550 nm) are separated by combining multimode interference and the dual mode coupling effect. Only by introducing a single defect near the crossing point between two output photonic crystal waveguides (PCWs) are the high extinction ratios for the three wavelengths achieved simultaneously.

Investigation on multiple-port microcylinder lasers based on coupled modes

Microcylinder resonators with multiple ports connected to waveguides are investigated by 2D finite-difference time-domain (FDTD) simulation for realizing microlasers with multiple outputs. For a 10 mu m radius microcylinder with a refractive index of 3.2 and three 2 mu m wide waveguides, confined mode at the wavelength of 1542.3 nm can have a mode Q factor of 6.7 x 10(4) and an output coupling efficiency of 0.76. AlGaInAs/InP microcylinder lasers with a radius of 10 mu m and a 2 mu m wide output waveguide are fabricated by planar processing techniques. Continuous-wave electrically injected operation is realized with a threshold current of 4 mA at room temperature, and the jumps of output power are observed accompanying a lasing mode transformation.

Effect of Interface Roughness and Dislocation Density on Electroluminescence Intensity of InGaN Multiple Quantum Wells

Effects of interface roughness and dislocation density on the electroluminescence (EL) intensity of InGaN multiple quantum wells (MQWs) are investigated. It is found that the EL intensity increases with the number of satellite peaks in the x-ray diffraction experiments of InGaN MQW samples. It is indicated that the rough interface will lead the reduction of EL intensity of InGaN MQW samples. It is also found that the EL intensity increases with the decrease of dislocation density which is characterized by the x-ray diffraction measurements. It is suggested that the EL intensity of InGaN MQWs can be improved by decreasing the interface roughness and dislocation density.