Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition

Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of SARS CoV and SARS CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that among the genomes analyzed, two sequence regions in the N-terminal domain “MESEFR” and “SYLTPG” are specific to human SARS CoV-2. In the receptor-binding domain, two sequence regions “VGGNY“ and ”EIYQAGSTPCNGV” and a disulfide bridge connecting 480C and 488C in the extended loop are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, human host sources, and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) as closest to the recent novel human SARS CoV-2 genomes. The bat SARS CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression toward becoming human SARS CoV-2.     

神农架川金丝猴栖息地优势乔木树种遥感识别及其分布特征

针对神农架川金丝猴生境基础研究中乔木树种大范围分布数据难以获取问题,尝试利用多源多时相遥感数据结合专家知识分层次实现树种识别。首先采用冬季Landsat8/OLI数据根据物侯特性分层提取常绿、落叶林的地域范围;进而依据夏季Worldview-2高分遥感影像的实地乔木样本的光谱特征分层次完成常绿树种(巴山冷杉、华山松、青$、刺叶栎)和落叶树种(红桦、日本落叶松、米心水青冈、漆树、锐齿槲栎、椅杨)的识别;并通过实地植被样方及专家知识通过高程数据完成分类结果的修正;最后结合GIS对主要优势树种的地形及地域分布特征进行了空间分析。实验精度表明常绿林中巴山冷杉、华山松、刺叶栎、虫害华山松整体精度较高,落叶林中红桦、漆树等识别精度相对较高,部分树种如椅杨、锐齿槲栎识别精度较低;总体上常绿树种的精度要优于落叶树种。从植物地理学、遥感、GIS三者相结合的角度,将多源、多时相遥感数据与物种物候特性、专家知识进行有效整合,提出了一种乔木树种识别的方法(1)提供了复杂山地环境的主要乔木优势种识别途径,且具有通用性;(2)完成了物种物候特性与遥感数据特性的整合利用,有效降低数据成本费用;(3)配合地面样方及专家知识修正结果,避免了过分依赖光谱特征引起的误判。这将为神农架川金丝猴栖息地保护与恢复提供更精确的数据依据。     

Divergent growth of Norway spruce on Babia Góra Mountain in the western Carpathians

Growth divergence – i.e. the expression of divergent growth trends of neighboring trees – has certain implications for dendrochronological research, for instance in the context of climate reconstructions but also in terms of estimating net ecosystem productivity. Thus, understanding the underlying mechanisms is essential to extend our fundamental dendroecological knowledge. In this context, the Picea genus plays an important role since several of its species were reported to exhibit growth divergence. Here, we investigate a well sampled Norway spruce (Picea abies (L.) Karst) data set for growth divergence comprising ring-width and Blue Intensity measurements from seven sites on Babia Góra Mountain, at the border between Poland and Slovakia. By means of Principal Component Gradient Analysis, inter-series correlations, and climate growth relationships, we are able to show that I) Norway spruce on Babia Góra expressed growth divergence since the 1970s, II) the definition of groups increased the strength of population signals and the stability of climate-growth relationships, and III) Blue Intensity appeared as a more robust proxy for environmental conditions. We discuss soil heterogeneity, genetics, and air pollution as possible underlying mechanisms, thereby indicating further research avenues to obtain a better understanding of growth divergence.     

Nutrients are assimilated efficiently by Lymantria dispar caterpillars from the mature leaves of trees in the Salicaceae

The efficient aquisition of nutrients from leaves by insect herbivores increases their nutrient assimilation rates and overall fitness. Caterpillars of the gypsy moth (Lymantria dispar L.) have high protein assimilation efficiencies (PAE) from the immature leaves of trees such as red oak (Quercus rubra) and sugar maple (Acer saccharum) (71–81%) but significantly lower PAE from their mature leaves (45–52%). By contrast to this pattern, both PAE and carbohydrate assimilation efficiencies (CAE) remain high for L. dispar larvae on the mature leaves of poplar (Populus alba × Populus tremula) grown in greenhouse conditions. The present study tests two alternative hypotheses: (i) outdoor environmental stresses cause decreased nutrient assimilation efficiencies from mature poplar leaves and (ii) nutrients in the mature leaves of trees in the poplar family (Salicaceae) remain readily available for L. dispar larvae. When poplar trees are grown in ambient outdoor conditions, PAE and CAE remain high (approximately 75% and 78%, respectively) in L. dispar larvae, in contrast to the first hypothesis. When larvae feed on the mature leaves of species in the Salicaceae [aspen (Populus tremuloides), cottonwood (Populus deltoides), willow (Salix nigra) and poplar], PAE and CAE also remain high (68–76% and 72–92%, respectively), consistent with the second hypothesis. Larval growth rates are strongly associated with protein assimilation rates, and more strongly associated with protein assimilation rates than with carbohydrate assimilation rates. It is concluded that tree species in the Salicaceae are relatively high‐quality host plants for L. dispar larvae, in part, because nutrients in their mature leaves remain readily available.     

Large‐scale gene expression reveals different adaptations of Hyalopterus persikonus to winter and summer host plants

Host alternation, an obligatory seasonal shifting between host plants of distant genetic relationship, has had significant consequences for the diversification and success of the superfamily of aphids. However, the underlying molecular mechanism remains unclear. In this study, the molecular mechanism of host alternation was explored through a large‐scale gene expression analysis of the mealy aphid Hyalopterus persikonus on winter and summer host plants. More than four times as many unigenes of the mealy aphid were significantly upregulated on summer host Phragmites australis than on winter host Rosaceae plants. In order to identify gene candidates related to host alternation, the differentially expressed unigenes of H. persikonus were compared to salivary gland expressed genes and secretome of Acyrthosiphon pisum. Genes involved in ribosome and oxidative phosphorylation and with molecular functions of heme–copper terminal oxidase activity, hydrolase activity and ribosome binding were potentially upregulated in salivary glands of H. persikonus on the summer host. Putative secretory proteins, such as detoxification enzymes (carboxylesterases and cytochrome P450s), antioxidant enzymes (peroxidase and superoxide dismutase), glutathione peroxidase, glucose dehydrogenase, angiotensin‐converting enzyme, cadherin, and calreticulin, were highly expressed in H. persikonus on the summer host, while a SCP GAPR‐1‐like family protein and a salivary sheath protein were highly expressed in the aphids on winter hosts. These results shed light on phenotypic plasticity in host utilization and seasonal adaptation of aphids.     

Biological control of Myzus persicae (Hemiptera: Aphididae) through banker plant system in protected crops

Banker plants with Aphidius colemani were tested in greenhouse for control of Myzus persicae on arugula and sweet pepper crops and compared to inoculative releases of parasitoids. Banker plants system consisted of pots of oat (non-crop plant) infested with Rhopalosiphum padi (non-pest herbivore). The non-pest herbivore serves as an alternative host for A. colemani (parasitoid of the target crop pest). In the arugula crop significant differences in the pest population between the two strategies of biological control showed the lowest densities of the pest when introducing the banker plant system. In the sweet pepper crop, there was no difference in the pest population between the two strategies of biological control.     

The highly pathogenic H5N1 influenza A virus down‐regulated several cellular MicroRNAs which target viral genome

Higher and prolonged viral replication is critical for the increased pathogenesis of the highly pathogenic avian influenza (HPAI) subtype of H5N1 influenza A virus (IAV) over the lowly pathogenic H1N1 IAV strain. Recent studies highlighted the considerable roles of cellular miRNAs in host defence against viral infection. In this report, using a 3′UTR reporter system, we identified several putative miRNA target sites buried in the H5N1 virus genome. We found two miRNAs, miR‐584‐5p and miR‐1249, that matched with the PB2 binding sequence. Moreover, we showed that these miRNAs dramatically down‐regulated PB2 expression, and inhibited replication of H5N1 and H1N1 IAVs in A549 cells. Intriguingly, these miRNAs expression was differently regulated in A549 cells infected with the H5N1 and H1N1 viruses. Furthermore, transfection of miR‐1249 inhibitor enhanced the PB2 expression and promoted the replication of H5N1 and H1N1 IAVs. These results suggest that H5N1 virus may have evolved a mechanism to escape host‐mediated inhibition of viral replication through down‐regulation of cellular miRNAs, which target its viral genome.     

Reprogramming of Stem Cell Activity to Convert Thorns into Branches

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