SARS transmission pattern in Singapore reassessed by viral sequence variation analysis

Background

Epidemiological investigations of infectious disease are mainly dependent on indirect contact information and only occasionally assisted by characterization of pathogen sequence variation from clinical isolates. Direct sequence analysis of the pathogen, particularly at a population level, is generally thought to be too cumbersome, technically difficult, and expensive. We present here a novel application of mass spectrometry (MS)–based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore.

Methods and Findings

The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. Analysis of 13 SARS-CoV isolates from the different stages of the Singapore outbreak identified nine sequence variations that could define the molecular relationship between them and pointed to a new, previously unidentified, primary route of introduction of SARS-CoV into the Singapore population. Our direct determination of viral sequence variation from a clinical sample also clarified an unresolved epidemiological link regarding the acquisition of SARS in a German patient. We were also able to detect heterogeneous viral sequences in primary lung tissues, suggesting a possible coevolution of quasispecies of virus within a single host.

Conclusion

This study has further demonstrated the importance of improving clinical and epidemiological studies of pathogen transmission through the use of genetic analysis and has revealed the MS-based analysis to be a sensitive and accurate method for characterizing SARS-CoV genetic variations in clinical samples. We suggest that this approach should be used routinely during outbreaks of a wide variety of agents, in order to allow the most effective control.     

A genome‐wide association study of early‐maturation traits in upland cotton based on the CottonSNP80K array

Genome‐wide association studies (GWASs) efficiently identify genetic loci controlling traits at a relatively high resolution. In this study, variations in major early‐maturation traits, including seedling period (SP), bud period (BP), flower and boll period (FBP), and growth period (GP), of 169 upland cotton accessions were investigated, and a GWAS of early maturation was performed based on a CottonSNP80K array. A total of 49,650 high‐quality single‐nucleotide polymorphisms (SNPs) were screened, and 29 significant SNPs located on chromosomes A6, A7, A8, D1, D2, and D9, were repeatedly identified as associated with early‐maturation traits, in at least two environments or two algorithms. Of these 29 significant SNPs, 1, 12, 11, and 5 were related to SP, BP, FBP, and GP, respectively. Six peak SNPs, TM47967, TM13732, TM20937, TM28428, TM50283, and TM72552, exhibited phenotypic contributions of approximately 10%, which could allow them to be used for marker‐assisted selection. One of these, TM72552, as well as four other SNPs, TM72554, TM72555, TM72558, and TM72559, corresponded to the quantitative trait loci previously reported. In total, 274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations. Finally, our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.     

Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species,as genome progenitors of bread wheat,using SCoT markers

We assessed the molecular genetic diversity and relationships among some Aegilops and Triticum species using 15 start codon-targeted (SCoT) polymorphism markers. A total of 166 bands amplified, of which 164 (98.79%) were polymorphic. Analysis of molecular variance and inter-population differentiation (Gst) indicated high genetic variation within the studied populations. Our analyses revealed high genetic diversity in T. boeoticum, Ae. cylindrica, T. durum and Ae. umbellulata, low diversity in Ae. crassa, Ae. caudata and Ae. speltoides, and a close relationship among Ae. tauschii, T. aestivum, T. durum, T. urartu, and T. boeoticum. Cluster analysis indicated 180 individuals divided into 8 genome homogeneous clades and 11 sub-groups. T. aestivum and T. durum accessions were grouped together, and accessions with the C and U genomes were grouped into the same clade. Our results support the hypothesis that T. urartu and Ae. tauschii are two diploid ancestors of T. aestivum, and also that Ae. caudata and Ae. umbellulata are putative donors of C and U genomes for other Aegilops species that possess these genomes. Our results also revealed that the SCoT technique is informative and can be used to assess genetic relationships among wheat germplasm.     

The inhibitory effect of kokusaginine on the growth of human breast cancer cells and MDR-resistant cells is mediated by the inhibition of tubulin assembly

The emergence of multidrug resistance (MDR) is a significant challenge in breast carcinoma chemotherapy. Kokusaginine isolated from Dictamnus dasycarpus Turcz. has been reported to show cytotoxicity in several human cancer cell lines including breast cancer cells MCF-7. In this study, kokusaginine showed the potent inhibitory effect on MCF-7 multidrug resistant subline MCF-7/ADR and MDA-MB-231 multidrug resistant subline MDA-MB-231/ADR. Kokusaginine markedly induced apoptosis in a concentration-dependent manner in MCF-7/ADR cells. Furthermore, kokusaginine reduced P-gp mRNA and protein levels, and suppressed P-gp function especially in MCF-7/ADR cells. In addition, kokusaginine showed to inhibit tubulin assembly and the binding of colchicine to tubulin by binding directly to tubulin and affects tubulin formation in vitro. Taken together, these results support the potential therapeutic value of kokusaginine as an anti-MDR agent in chemotherapy for breast carcinoma.     

Hollow NiCo2S4 Nanospheres Hybridized with 3D Hierarchical Porous rGO/Fe2O3 Composites toward High‐Performance Energy Storage Device

Hierarchical hollow NiCo₂S₄ microspheres with a tunable interior architecture are synthesized by a facile and cost‐effective hydrothermal method, and used as a cathode material. A three‐dimensional (3D) porous reduced graphene oxide/Fe₂O₃ composite (rGO/Fe₂O₃) with precisely controlled particle size and morphology is successfully prepared through a scalable facile approach, with well‐dispersed Fe₂O₃ nanoparticles decorating the surface of rGO sheets. The fixed Fe₂O₃ nanoparticles in graphene efficiently prevent the intermediates during the redox reaction from dissolving into the electrolyte, resulting in long cycle life. KOH activation of the rGO/Fe₂O₃ composite is conducted for the preparation of an activated carbon material–based hybrid to transform into a 3D porous carbon material–based hybrid. An energy storage device consisting of hollow NiCo₂S₄ microspheres as the positive electrode, the 3D porous rGO/Fe₂O₃ composite as the negative electrode, and KOH solution as the electrolyte with a maximum energy density of 61.7 W h kg^?1 is achieved owing to its wide operating voltage range of 0–1.75 V and the designed 3D structure. Moreover, the device exhibits a high power density of 22 kW kg^?1 and a long cycle life with 90% retention after 1000 cycles at the current density of 1 A g^?1.     

The effects of food and parasitism on reproductive performance of a wild rodent

Food and parasitism can have complex effects on small mammal reproduction. In this study, we tested the effects of sex, food, and parasitism on reproductive performance of the Taiwan field mouse (Apodemus semotus). In a field experiment, we increased food availability for a portion of the mice in the population by providing sorghum seeds to a set of food stations. We reduced parasite intensity of randomly chosen mice through ivermectin treatment. We determined the number and quality of offspring for the mice using paternity analysis. We quantified seed consumption with stable carbon isotope values of mouse plasma and parasite intensity with fecal egg counts of intestinal nematodes and cestodes (FEC). In a laboratory experiment, we reduced parasite intensity of randomly chosen mice through ivermectin treatment. We quantified their immune functions by total white blood cell count, percent granulocyte count, and percent lymphocyte count through hematological analyses. We measured the FEC and energy intake of the mice. From the field experiment, the number of offspring in A. semotus increased with increasing seed consumption. Due to the trade‐off between number and quality of offspring, the offspring quality decreased with increasing seed consumption for the females. The ivermectin treatment did not affect offspring number or quality. However, the FEC was positively correlated with number of offspring. In the laboratory experiment, the percent lymphocyte/granulocyte count changed with parasite intensity at low energy intake, which was relaxed at high energy intake. This study demonstrated positive effects of food availability and neutral effects of parasitism on A. semotus reproduction. However, the benefits of food availability for the females need to take into account the offspring number–quality trade‐off, and at high infection intensity, parasitism might negatively affect offspring quality for the males. We suggest that food availability could mediate the relationships between parasite intensity and immune responses.