TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS).

Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.

Quantum dot white light emitting diodes with high scotopic/photopic ratios.

Alloy core/shell CdxZn1-xS/ZnS quantum dots (QDs) are emerging as robust candidates for light-emitting diodes (LEDs), however the emission range of the current CdxZn1-xS/ZnS is quite limited, ranging from 390 to 470 nm. It still remains a challenging task to construct white LEDs based on current CdxZn1-xS/ZnS system. Here, a versatile ZnSe with a moderate band gap is introduced onto the Cd0.1Zn0.9S core. The ZnSe shell, on one hand, can passivate the core surface which leads to bright emissions. On the other hand, it is essential in extending the emission to red region so that the emission wavelengths of Cd0.1Zn0.9S/ZnS and Cd0.1Zn0.9S/ZnSe QDs can cover the whole visible region, which is very important for white LED applications. Two- and four-hump QD-based LEDs are computationally and experimentally investigated. Results show that four-hump quantum dot light-emitting diodes (QLED) have better performances than the two-hump one, in the luminous and the vision properties. The fabricated white LEDs (WLEDs) based on Cd0.1Zn0.9S/ZnS and Cd0.1Zn0.9S/ZnSe QDs exhibits a scotopic/photopic ratio (S/P) ratio as high as 2.52, which exceeds the current limit of 2.50 by common lighting technologies, a color rendering index of 90.3, a luminous efficacy of optical radiation of 460.78 lumen per unit optical power, and a correlated color temperature of 5454 K. These results suggest that CdxZn1-xS/ZnS and CdxZn1-xS/ZnSe quantum dots serving as emitters hold great promise for the next-generation white light source with better S/P ratio.

Enhancing extraction efficiency of quantum dot light-emitting diodes by surface engineering.

Light extraction efficiency significantly affects the final performance of quantum dot light-emitting diodes (QLED) devices. Surface engineering of the substrate has been proved to be an effective method to increase the light extraction efficiency. However, a facile, low cost, and scalable process to modify the QLED substrate's surface remains a perpetual topic, which calls for further study. We herein use the wet chemical etching process to roughen the substrate's surface, and a "multi-pits" like exit surface is formed. These "multi-pits" act as scattering centers that benefits homogeneity of the output light. On the other hand, they also give a rise in output coupling efficiency by inhibiting light propagation of the internally generated photons, owing to the suppressed optical waveguide mode. The external quantum efficiency (EQE) of QLED with a roughened surface shows a 12% increase in maximum value, and over 2.2 fold increase at a high driving voltage than that without surface roughening.

Molecular mechanism of the airborne transmissibility of H9N2 avian influenza A viruses in chickens.

UNLABELLED: H9N2 avian influenza virus has been prevalent in poultry in many parts of the world since the 1990s and occasionally crosses the host barrier, transmitting to mammals, including humans. In recent years, these viruses have contributed genes to H5N1 and H7N9 influenza viruses, threatening public health. To explore the molecular mechanism for the airborne transmission of H9N2 virus, we compared two genetically close strains isolated from chickens in 2001, A/chicken/Shanghai/7/2001(SH7) and A/chicken/Shanghai/14/2001 (SH14). SH7 is airborne transmissible between chickens, whereas SH14 is not. We used reverse genetics and gene swapping to derive recombinant SH7 (rSH7), rSH14, and a panel of reassortant viruses. Among the reassortant viruses, we identified segments HA and PA as governing the airborne transmission among chickens. In addition, the NP and NS genes also contributed to a lesser extent. Furthermore, the mutational analyses showed the transmissibility phenotype predominantly mapped to the HA and PA genes, with HA-K363 and PA-L672 being important for airborne transmissibility among chickens. In addition, the viral infectivity and acid stability are related to the airborne transmissibility. Importantly, airborne transmission studies of 18 arbitrarily chosen H9N2 viruses from our collections confirmed the importance of both 363K in HA and 672L in PA in determining their levels of transmissibility. Our finding elucidates the genetic contributions to H9N2 transmissibility in chickens and highlights the importance of their prevalence in poultry. IMPORTANCE: Our study investigates the airborne transmissibility of H9N2 viruses in chickens and the subsequent epidemic. H9N2 virus is the donor for several prevalent reassortant influenza viruses, such as H7N9/2013 and the H5N1 viruses. Poultry as the reservoir hosts of influenza virus is closely associated with human society. Airborne transmission is an efficient pathway for influenza virus transmission among flocks and individuals. Exploring the mechanism of the airborne transmission of the H9N2 virus in chickens could provide essential data regarding prevention and control of influenza endemics and pandemics.

Prevalence of Cryptosporidium infection in captive lesser panda (Ailurus fulgens) in China.

Cryptosporidium is a global epidemic parasite and one of the most important intestinal pathogens causing diarrhea in animals and humans. Despite extensive research on this parasite group, little is known about rates of Cryptosporidium infection in lesser pandas. In this study, we use molecular diagnostic tools to detect Cryptosporidium infections and identify Cryptosporidium species in the lesser panda. Using a PCR approach, we sequenced the 18S rRNA gene in fecal samples collected from 110 captive lesser pandas held throughout China (approximately one third of the captive population). We determined Cryptosporidium species via a BLAST comparison of our sequences against those of published Cryptosporidium sequences available in GenBank and subsequent phylogenetic analysis. We report that captive lesser pandas were infected with a single Cryptosporidium species, Cryptosporidium andersoni, at a prevalence of 6.36 % (7/110). The present investigation revealed the existence of C. andersoni infection in captive lesser panda and suggested that proper control measures should be taken carefully to protect the welfare of zoo workers and visitors.

Complete genomic sequence of a novel reassortant H11N3 influenza virus isolated from domestic ducks in Jiangsu, China.

For the first time we report the complete genomic sequence of an H11N3 influenza virus from domestic ducks in China. Phylogenetic analysis showed that the H11N3 virus was a novel reassortant with its genes from different subtypes of domestic duck-origin avian influenza viruses, which further underlined that domestic ducks play a key role in the genetic reassortment and evolution of influenza viruses in China.

Prevalence of low pathogenic avian influenza virus in one live bird market in Eastern China from 2002-2011.

The role of live bird markets (LBMs) in the perpetuation of avian influenza virus (AIV) has been well studied worldwide; however, there is a paucity of information on the prevalence of different AIV subtypes in LBMs in Eastern China. In this study, long-term surveillance was conducted to investigate the prevalence of AIV in chickens, ducks, and geese in an LBM in Yangzhou city, Jiangsu province, Eastern China, between July 2002 and May 2011. The study used primary virus isolation and subtype-specific reverse-transcription-PCR. In total, 23 different HA-NA subtype combinations were detected, mainly in domestic ducks. This result suggests that domestic ducks play a more important role in LBMs in Eastern China.

Composition engineering of perovskite absorber assisted efficient textured monolithic perovskite/silicon heterojunction tandem solar cells.

A two-terminal (2T) perovskite/silicon heterojunction tandem solar cell (PVSK/SHJ) is considered one of the most promising candidates for next-generation photovoltaics with the possibility of achieving a power conversion efficiency (PCE) exceeding 30% at low production cost. However, the current mismatch and voltage loss have seriously decreased the performance of 2T PVSK/SHJ tandem solar cells. Here, we report the composition engineering for perovskite top cells to prepare a high performance 2T tandem cell by tuning CsBr co-evaporating rates and increasing concentrations of FAI/FABr solutions. We show that the variation in composition for the perovskite absorber effectively optimized the band gap and diminished the defects of the top cell. Our investigations reveal that the current mismatch of sub-cells was carefully tuned by introducing CsBr at varied co-evaporating rates and the voltage loss was decreased by increasing concentrations of FAI/FABr solutions. Thus, we achieved a PCE of 23.22% in two-terminal monolithic tandems with an area of 1.2 cm2 by tuning the composition of the perovskite absorber.

Characterisation of a highly pathogenic H5N1 clade 2.3.2 influenza virus isolated from swans in Shanghai, China.

In spring 2009, one strain of H5N1 clade 2.3.2 virus was isolated from wild swans in Shanghai, indicating the importance of the wild swan in the ecology of this highly pathogenic avian influenza virus (HPAIV) in Eastern China. Pathogenicity experiments conducted in this study indicated that the virus was highly pathogenic for chickens but lowly pathogenic for mammalian hosts, as evidenced by reduced infection of mice. The analysis of complete genome sequences and genetic evolution showed that A/Swan/Shanghai/10/09 (SW/SH/09) may be derived from the strain A/silky chicken/Shantou/475/2004 (CK/ST/04), which is homologous to the influenza viruses isolated from chicken, duck, pika, little egret, swan, mandarin duck and bar-headed goose in China Hunan, China Qinghai, Mongolia, Russia, Japan, Korea, Laos and Hong Kong during 2007-2011, indicating that the virus has retro-infected diverse wild birds from chicken, and significant spread of the virus is still ongoing through overlapping migratory flyways. On the basis of the molecular analysis, we also found that there was a deletion of the glycosylation site (NSS) in amino acid 156 of the hemagglutinin (HA) protein when compared with that of the other Clade 2.3.2 viruses isolated between 2007 and 2011. More importantly, the sequence analysis of SW/SH/09 virus displayed the drug-resistant mutations on the matrix protein (M2) and neuraminidase (NA) genes.

Isolation and phylogenetic analysis of avian-origin European H1N1 swine influenza viruses in Jiangsu, China.

Isolates of the A(H1N1)pdm2009 virus were first identified in asymptomatic swine in Jiangsu province, China in January 2010, indicating that the virus has retro-infected swine after circulating through humans in mainland China. The purpose of this study was to determine whether the avian-origin European H1N1 swine influenza virus (SIV) and the A(H1N1)pdm2009 virus are cocirculating in swine in Jiangsu province of China. From May 2010 to May 2011, 1,030 nasal swab samples were collected from healthy swine in Jiangsu province of China and were tested for influenza A H1N1 using reverse transcription-PCR. Fragments of the complete genomes of viruses from the samples that were positive for influenza A H1N1 were sequenced and analysed. A total of 32 avian-origin European H1N1 SIVs were isolated, and no A(H1N1)pdm2009 viruses were identified; full-length genomes of 18 strains were sequenced. The eight gene segments of some of the isolated H1N1 viruses have 99.1-99.8% sequence identity with the human A/Jiangsu/ALS1/2011(H1N1) isolates in the same region. Our study indicates that the avian-origin European H1N1 SIVs remain endemic in swine and have retro-infected humans after circulating through swine, which may present a risk factor for public health.

Molecular evolution of the H6 subtype influenza A viruses from poultry in eastern China from 2002 to 2010.

BACKGROUND: Although extensive data demonstrates that the majority of H6 duck isolates belonged to a single H6N2 virus lineage with a single gene constellation in southern China from 2000 to 2005, the prevalence of H6N2 virus in poultry in Eastern China is largely unknown. RESULTS: Epidemiology revealed that H6N2 viruses were the most frequently detected influenza subtypes in live bird markets from 2002 to 2008 in Eastern China, but from 2009 onwards, they were replaced with novel H6N6 viruses. We phylogenetically and antigenically analyzed 42 H6 viruses isolated mainly in domestic ducks from 2002 to 2010 in Eastern China. Surprisingly, none of these isolates grouped with the previously described H6N2 viruses which belonged to a single H6N2 virus lineage with a single gene constellation in domestic ducks in southern China from 2000 to 2005. Two distinct hemagglutinin lineages were identified and they all underwent frequent reassortment with multiple virus subtypes from the natural gene pool, but few reassortants were persistent or prevalent. CONCLUSIONS: Five subtypes of H6 influenza viruses (H6N1, H6N2, H6N5, H6N6 and H6N8) cocirculated in Eastern China, which form a significant part of the natural influenza virus reservoir in domestic ducks, and significant viral reassortment is still ongoing in this species.

Balancing the Electron and Hole Transfer for Efficient Quantum Dot Light-Emitting Diodes by Employing a Versatile Organic Electron-Blocking Layer.

The electron-blocking layer (EBL) is important to balance the charge carrier transfer and achieve highly efficient quantum dot light-emitting diodes (QLEDs). Here, we report the utilization of a soluble tert-butyldimethylsilyl chloride-modified poly( p-phenylene benzobisoxazole) (TBS-PBO) as an EBL for simultaneous good charge carrier transfer balance while maintaining a high current density. We show that the versatile TBS-PBO blocks excess electron injection into the quantum dots (QDs), thus leading to better charge carrier transfer balance. It also restricts the undesired QD-to-EBL electron-transfer process, which preserves the superior emission capabilities of the emitter. As a consequence, the TBS-PBO device delivers an external quantum efficiency (EQE) maximum of 16.7% along with a remarkable current density as high as 139 mA/cm2 with a brightness of 5484 cd/m2. The current density of our device is higher than those of insulator EBL-based devices because of the higher conductivity of the TBS-PBO versus insulator EBL, thus helping achieve high luminance values ranging from 1414 to 20 000 cd/cm2 with current densities ranging from 44 to 648 mA/cm2 and EQE > 14%. We believe that these unconventional features of the present TBS-PBO-based QLEDs will expand the wide use of TBS-PBO as buffer layers in other advanced QLED applications.

Bright alloy type-II quantum dots and their application to light-emitting diodes.

Type-II quantum dots (QDs) are emerging as a promising candidate for full color light sources owing to their advantages in achieving full color light by tuning the heterostructures. Despite the recent developments in type-II QDs, the choices of proper materials are limited for the composition of a high-quality QD and it still remains a big challenge to enhance the photoluminescence (PL) quantum yields (QYs) of type-II QDs for light-emitting diode (LED) applications. Here, we develop CdxZn1-xS/ZnSe/ZnS type-II QDs with a maximum quantum yield as high as 88.5%. Time-resolved PL results show that the ZnS shell suppresses non-radiative pathways by passivating the surface of CdxZn1-xS/ZnSe, thus leading to a high QY. Moreover, our results demonstrate that the outer ZnS also benefits the charge injection and radiative recombinations of the CdxZn1-xS/ZnSe. The LED based on green Cd0.2Zn0.8S/ZnSe/ZnS QDs achieves a current efficiency (CE) of 9.17cdA-1, an external quantum efficiency (EQE) of 8.78% and a low turn-on voltage of ∼2.3V.

Characterization of glutathione S-transferase and its immunodiagnostic potential for detecting Taenia multiceps.

Taenia multiceps is a widespread zoonotic tapeworm parasite which infects cloven-hoofed animals around the world. Animal infection with Coenurus cerebralis, the coenurus larvae of T. multiceps (Tm), is often fatal, which is a major cause of economic losses in stockbreeding. This study amplified the glutathione S-transferase (GST) gene from the total RNA of C. cerebralis. The resulting protein, Tm-GST, consisted of 201 amino acids, and had a predicted molecular mass of 23.1kDa. Its amino acid sequence shares 77.61% similarity with Echinococcus granulosus GST. Recombinant Tm-GST (rTm-GST) was expressed in Escherichia coli. The protein reacted with serum from goats infected with T. multiceps. Immunofluorescence signals indicated that Tm-GST was largely localized in the parenchymatous area of adult T. multiceps; in addition, it was also apparent in the coenurus. An enzyme-linked immunosorbent assay based on rTm-GST showed specificity of 92.8% (13/14) and sensitivity of 90% (18/20) in detecting anti-GST antibodies in serum from naturally infected animals. This study suggests that Tm-GST has the potential to be used as a diagnostic antigen for Coenurosis.

NRP1 Accelerates Odontoblast Differentiation of Dental Pulp Stem Cells Through Classical Wnt/ß-Catenin Signaling.

Neuropilin-1 (NRP1) is one of the members of neuropilin family. It can combine with disparate ligands involved in regulating cell proliferation, apoptosis, and differentiation. The binding of NRP1 to Sema3A stimulates osteoblast differentiation through the classical Wnt/ß-catenin pathway. However, the functions of NRP1 in dental pulp stem cells (DPSCs) are not clear. The aim of our study was to investigate how NRP1 controlled odontoblast differentiation in DPSCs and clarified the underlying mechanisms. NRP1 expression was increased in time-dependent manner along with cell odontoblast differentiation. Overexpression of NRP1 upregulated dentin matrix protein-1, dentin sialophosphoprotein, alkaline phosphatase protein level, and mineralization in DPSCs, while knockdown of NRP1 induced the opposite effects. SiNRP1 similar to DKK1 availably blocked classical Wnt/ß-catenin signaling and odontoblast differentiation. In summary, NRP1, as a promoter of odontoblast differentiation, regulates DPSCs via the classical Wnt/ß-catenin pathway.

Fatty-binding protein and galectin of Baylisascaris schroederi: Prokaryotic expression and preliminary evaluation of serodiagnostic potential.

Baylisascaris schroederi is a common parasite of captive giant pandas. The diagnosis of this ascariasis is normally carried out by a sedimentation-floatation method or PCR to detect eggs in feces, but neither method is suitable for early diagnosis. Fatty acid-binding protein (FABP) and galectin (GAL) exist in various animals and participate in important biology of parasites. Because of their good immunogenicity, they are seen as potential antigens for the diagnosis of parasitic diseases. In this study, we cloned and expressed recombinant FABP and GAL from B. schroederi (rBs-FABP and rBs-GAL) and developed indirect enzyme-linked immunosorbent assays (ELISAs) to evaluate their potential for diagnosing ascariasis in giant pandas. Immunolocalization showed that Bs-FABP and Bs-GAL were widely distributed in adult worms. The ELISA based on rBs-FABP showed sensitivity of 95.8% (23/24) and specificity of 100% (12/12), and that based on rBs-GAL had sensitivity of 91.7% (22/24) and specificity of 100% (12/12).

Prevalence and molecular characterization of Cryptosporidium in giant panda (Ailuropoda melanoleuca) in Sichuan province, China.

BACKGROUND: Cryptosporidium spp. have been extensively reported to cause significant diarrheal disease in humans and domestic animals. On the contrary, little information is available on the prevalence and characterization of Cryptosporidium in wild animals in China, especially in giant pandas. The aim of the present study was to detect Cryptosporidium infections and identify Cryptosporidium species at the molecular level in both captive and wild giant pandas in Sichuan province, China. FINDINGS: Using a PCR approach, we amplified and sequenced the 18S rRNA gene from 322 giant pandas fecal samples (122 from 122 captive individuals and 200 collected from four habitats) in Sichuan province, China. The Cryptosporidium species/genotypes were identified via a BLAST comparison against published Cryptosporidium sequences available in GenBank followed by phylogenetic analysis. The results revealed that both captive and wild giant pandas were infected with a single Cryptosporidium species, C. andersoni, at a prevalence of 15.6% (19/122) and 0.5% (1/200) in captive and wild giant pandas, respectively. CONCLUSIONS: The present study revealed the existence of C. andersoni in both captive and wild giant panda fecal samples for the first time, and also provided useful fundamental data for further research on the molecular epidemiology and control of Cryptosporidium infection in giant pandas.

Enzootic genotype S of H9N2 avian influenza viruses donates internal genes to emerging zoonotic influenza viruses in China.

Avian influenza viruses of subtype H9N2 are widely prevalent in poultry in many Asian countries, and the segmented nature of the viral genome results in multiple distinct genotypes via reassortment. In this study, genetic evolution of H9N2 viruses circulating in eastern China during 2007-2013 was analyzed. The results showed that the diversity of the gene constellations generated six distinct genotypes, in which a novel genotype (S) bearing the backbone of A/chicken/Shanghai/F/98-like viruses by acquiring A/quail/Hong Kong/G1/97-like polymerase basic subunit 2 and matrix genes has gradually established its ecological niche and been consistently prevalent in chicken flocks in eastern China since its first detection in 2007. Furthermore, genotype S possessed the peculiarity to donate most of its gene segments to other emerging influenza A viruses in China, including the novel reassortant highly pathogenic avian influenza H5N2, the 2013 novel H7N7, H7N9 and the latest reassortant H10N8 viruses, with potential threat to poultry industry and human health.

Genome Sequence of a Novel Reassortant H3N2 Avian Influenza Virus from Domestic Mallard Ducks in Eastern China.

The H3 subtype avian influenza virus (AIV) can provide genes for human influenza virus through gene reassortment, which raises great concerns in terms of its potential threat to human health. Here, we report the complete genome sequence of a novel H3N2 AIV isolated from domestic ducks in the Jiangsu province of eastern China in 2004, which is a natural recombinant virus whose genes are derived from H3N8, H5N1, H5N2, H11N2, H4N6, and H1N1 AIVs. This genome will help to understand the epidemiology and molecular characteristics of H3N2 influenza virus in eastern China.

Novel reassortant highly pathogenic H5N2 avian influenza viruses in poultry in China.

There has been multiple evidence that domestic poultry may act as a vessel for the generation of novel influenza A viruses. In this study, we have analyzed the evolution and pathogenicity of 4 H5N2 avian influenza viruses isolated from apparently healthy poultry from H5N1 virus endemic areas in China. Phylogenetic analysis revealed that two of these viruses, A/duck/Eastern China/1111/2011 (DK/EC/1111/11) and A/goose/Eastern China/1112/2011 (GS/EC/1112/11) were derived from reassortment events in which clade 2.3.4 highly pathogenic avian influenza (HPAI) H5N1 viruses acquired novel neuraminidase and nonstructural protein genes. Another two isolates, A/chicken/Hebei/1102/2010 (CK/HB/1102/10) and A/duck/Hebei/0908/2009 (DK/HB/0908/09), possess hemagglutinin (HA) gene belong to clade 7 H5 viruses and other genes from endemic H9N2 viruses, or from viruses of various subtypes of the natural gene pool. All of these H5N2 isolates bear characteristic sequences of HPAI virus at the cleavage site of HA, and animal experiments indicated that all of these viruses but DK/HB/0908/09 is highly pathogenic to chickens. In particular, DK/EC/1111/11 and GS/EC/1112/11 are also highly pathogenic to ducks and moderately pathogenic to mice. All of these 4 viruses were able to replicate in domestic ducks and mice without prior adaptation. The emergence of these novel H5N2 viruses adds more evidence for the active evolution of H5 viruses in Asia. The maintenance of the highly pathogenic phenotype of some of these viruses even after reassortment with a new NA subtypes, their ability to replicate and transmit in domestic poultry, and the pathogenicity in the mammalian mouse model, highlight the potential threat posed by these viruses to both veterinary and public health.