Identification of a Novel Picornavirus in Healthy Piglets and Seroepidemiological Evidence of Its Presence in Humans

In this study, we describe a novel porcine parechovirus-like virus (tentatively named PLV-CHN) from healthy piglets in China using 454 high-throughput sequencing. The complete genome of the virus comprises 6832 bp, encoding a predicted polyprotein of 2132 amino acids that is most similar to Ljungan virus (32% identity). A similar virus that belongs to a novel Picornaviridae genus, named swine pasivirus 1 (SPaV-1), was reported during the preparation of this paper. Sequence analysis revealed that PLV-CHN and SPaV1 shared 82% nucleotide identity and 89% amino acid identity. Further genomic and phylogenetic analyses suggested that both SPaV1 and PLV-CHN shared similar genomic characteristics and belong to the same novel Picornaviridae genus. A total of 36 (20.0%) fecal samples from 180 healthy piglets were positive for PLV-CHN by RT-PCR, while no fecal samples from 100 healthy children and 100 children with diarrhea, and no cerebrospinal fluid samples from 196 children with suspected viral encephalitis, was positive for the virus. However, Western blot and enzyme-linked immunosorbent assays using recombinant PLV-CHN VP1 polypeptide as an antigen showed a high seroprevalence of 63.5% in the healthy population. When grouped by age, the antibody-positivity rates showed that the majority of children under 12 years of age have been infected by the virus. It was suggested that PLV-CHN, SPaV1, or an as-yet-uncharacterized virus can infect humans early in life. Thus, investigation of the role of this novel virus is vital.     

水稻二化螟和三化螟基因组ddRADseq文库的构建

本文介绍了构建水稻二化螟和三化螟"双酶切限制性酶切位点关联DNA测序"(Double digest restrictionsite associated DNA sequencing,ddRADseq)文库的方法。利用安捷伦2100生物分析仪对4种单酶切及2种双酶切的酶切产物片段大小及分布范围进行分析,筛选出Mlu C I和Nla III两种限制性内切酶组合对螟虫基因组DNA进行酶切。酶切后的DNA片段两端连接上特定的P1、P2接头后,用Pippin Prep回收大小为285-435 bp的DNA片段。通过PCR扩增进行文库的富集并引入index序列。构建好的ddRADseq文库用琼脂糖凝胶电泳和生物分析仪进行质量检测。本方法所构建的文库DNA片段长度、分布和摩尔浓度能够达到Illumina平台测序的技术要求。本研究证实了利用Mlu C I和Nla III组合酶切构建水稻螟虫基因组ddRADseq文库的可行性,为在水稻螟虫中利用ddRADseq技术开展生物地理学、种群遗传学和系统发育重建等方面的研究奠定基础。     

Epigenetic alteration of imprinted genes during neural differentiation of germline-derived pluripotent stem cells

Spermatogonial stem cells (SSCs), which are unipotent stem cells in the testes that give rise to sperm, can be converted into germline-derived pluripotent stem (gPS) by self-induction. The androgenetic imprinting pattern of SSCs is maintained even after their reprogramming into gPS cells. In this study, we used an in vitro neural differentiation model to investigate whether the imprinting patterns are maintained or altered during differentiation. The androgenetic patterns of H19, Snrpn, and Mest were maintained even after differentiation of gPS cells into NSCs (gPS-NSCs), whereas the fully unmethylated status of Ndn in SSCs was altered to somatic patterns in gPS cells and gPS-NSCs. Thus, our study demonstrates epigenetic alteration of genomic imprinting during the induction of pluripotency in SSCs and neural differentiation, suggesting that gPS-NSCs can be a useful model to study the roles of imprinted genes in brain development and human neurodevelopmental disorders.     

Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways

Background

Cellular responses to extracellular perturbations require signaling pathways to capture and transmit the signals. However, the underlying molecular mechanisms of signal transduction are not yet fully understood, thus detailed and comprehensive models may not be available for all the signaling pathways. In particular, insufficient knowledge of parameters, which is a long-standing hindrance for quantitative kinetic modeling necessitates the use of parameter-free methods for modeling and simulation to capture dynamic properties of signaling pathways.

Results

We present a computational model that is able to simulate the graded responses to degradations, the sigmoidal biological relationships between signaling molecules and the effects of scheduled perturbations to the cells. The simulation results are validated using experimental data of protein phosphorylation, demonstrating that the proposed model is capable of capturing the main trend of protein activities during the process of signal transduction. Compared with existing simulators, our model has better performance on predicting the state transitions of signaling networks.

Conclusion

The proposed simulation tool provides a valuable resource for modeling cellular signaling pathways using a knowledge-based method.

     

Effects of different silvicultural systems on the genetic diversity of <Emphasis Type="Italic">Shorea parvifolia</Emphasis> populations in the tropical rainforest of Southeast Asia

Selective logging systems have been used to prevent the rapid decline of forest resources in Southeast Asia, but little is known about the impacts of selective logging on the genetic diversity of Southeast Asian rainforests. We evaluated the effects of silvicultural systems with differing cutting rotations and enrichment planting regimes on the genetic diversity of Shorea parvifolia, an abundant and ecologically important tree in Southeast Asian rainforests. Our result showed that in most respects the genetic diversity is not significantly different between primary forest and the other silvicultural systems; however, the proportion of private alleles is significantly different between them. Intensive second-rotation (L3) harvesting of individuals >40 cm in diameter at breast height (dbh) resulted in a sizable reduction in the number of reproductive trees and a dramatic decrease in the numbers of rare and private alleles, suggesting a negative impact on the genetic diversity of the remaining tree population. Enrichment planting with S. parvifolia in the logged forest improved some genetic parameters, significantly increasing the number of rare alleles in L3 in particular. We conclude that the genetic diversity of logged tropical forests gradually decreases depending on logging rotation times, especially with respect to sensitive genetic parameters such as the numbers of rare and private alleles, and that enrichment planting with native dipterocarps can maintain or even increase the genetic diversity of logged tropical forests in Southeast Asia.     

Oral Administration of p-Hydroxycinnamic Acid Attenuates Atopic Dermatitis by Downregulating Th1 and Th2 Cytokine Production and Keratinocyte Activation

Atopic dermatitis (AD) is a complex disease that is caused by various factors, including environmental change, genetic defects, and immune imbalance. We previously showed that p-hydroxycinnamic acid (HCA) isolated from the roots of Curcuma longa inhibits T-cell activation without inducing cell death. Here, we demonstrated that oral administration of HCA in a mouse model of ear AD attenuates the following local and systemic AD manifestations: ear thickening, immune-cell infiltration, production of AD-promoting immunoregulatory cytokines in ear tissues, increased spleen and draining lymph node size and weight, increased pro-inflammatory cytokine production by draining lymph nodes, and elevated serum immunoglobulin production. HCA treatment of CD4⁺ T cells in vitro suppressed their proliferation and differentiation into Th1 or Th2 and their Th1 and Th2 cytokine production. HCA treatment of keratinocytes lowered their production of the pro-inflammatory cytokines that drive either Th1 or Th2 responses in AD. Thus, HCA may be of therapeutic potential for AD as it acts by suppressing keratinocyte activation and downregulating T-cell differentiation and cytokine production.     

Effects of Straw Return in Deep Soils with Urea Addition on the Soil Organic Carbon Fractions in a Semi-Arid Temperate Cornfield

Returning straw to deep soil layers by using a deep-ditching-ridge-ploughing method is an innovative management practice that improves soil quality by increasing the soil organic carbon (SOC) content. However, the optimum quantity of straw return has not been determined. To solve this practical production problem, the following treatments with different amounts of corn straw were investigated: no straw return, CK; 400 kg ha^-1 straw, S₄₀₀; 800 kg ha^-1 straw, S₈₀₀; 1200 kg ha^-1 straw, S₁₂₀₀; and 1600 kg ha^-1 straw, S₁₆₀₀. After straw was returned to the soil for two years, the microbial biomass C (MBC), easily oxidized organic C (EOC), dissolved organic C (DOC) and light fraction organic C (LFOC) content were measured at three soil depths (0–10, 10–20, and 20–40 cm). The results showed that the combined application of 800 kg ha^-1 straw significantly increased the EOC, MBC, and LFOC contents and was a suitable agricultural practice for this region. Moreover, our results demonstrated that returning straw to deep soil layers was effective for increasing the SOC content.