2020 Vol. 41, No. 6
Gene regulatory networks play pivotal roles in our understanding of biological processes/mechanisms at the molecular level. Many studies have developed sample-specific or cell-type-specific gene regulatory networks from single-cell transcriptomic data based on a large amount of cell samples. Here, we review the state-of-the-art computational algorithms and describe various applications of gene regulatory networks in biological studies.
Spain has been one of the main global pandemic epicenters for coronavirus disease 2019 (COVID-19). Here, we analyzed >41 000 genomes (including >26 000 high-quality (HQ) genomes) downloaded from the GISAID repository, including 1 245 (922 HQ) sampled in Spain. The aim of this study was to investigate genome variation of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and reconstruct phylogeographic and transmission patterns in Spain. Phylogeographic analysis suggested at least 34 independent introductions of SARS-CoV-2 to Spain at the beginning of the outbreak. Six lineages spread very successfully in the country, probably favored by super-spreaders, namely, A2a4 (7.8%), A2a5 (38.4%), A2a10 (2.8%), B3a (30.1%), and B9 (8.7%), which accounted for 87.9% of all genomes in the Spanish database. One distinct feature of the Spanish SARS-CoV-2 genomes was the higher frequency of B lineages (39.3%, mainly B3a+B9) than found in any other European country. While B3a, B9, (and an important sub-lineage of A2a5, namely, A2a5c) most likely originated in Spain, the other three haplogroups were imported from other European locations. The B3a strain may have originated in the Basque Country from a B3 ancestor of uncertain geographic origin, whereas B9 likely emerged in Madrid. The time of the most recent common ancestor (TMRCA) of SARS-CoV-2 suggested that the first coronavirus entered the country around 11 February 2020, as estimated from the TMRCA of B3a, the first lineage detected in the country. Moreover, earlier claims that the D614G mutation is associated to higher transmissibility is not consistent with the very high prevalence of COVID-19 in Spain when compared to other countries with lower disease incidence but much higher frequency of this mutation (56.4% in Spain vs. 82.4% in rest of Europe). Instead, the data support a major role of genetic drift in modeling the micro-geographic stratification of virus strains across the country as well as the role of SARS-CoV-2 super-spreaders.
Understanding the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and clarifying antiviral immunity in hosts are critical aspects for the development of vaccines and antivirals. Mice are frequently used to generate animal models of infectious diseases due to their convenience and ability to undergo genetic manipulation. However, normal adult mice are not susceptible to SARS-CoV-2. Here, we developed a viral receptor (human angiotensin-converting enzyme 2, hACE2) pulmonary transfection mouse model to establish SARS-CoV-2 infection rapidly in the mouse lung. Based on the model, the virus successfully infected the mouse lung 2 days after transfection. Viral RNA/protein, innate immune cell infiltration, inflammatory cytokine expression, and pathological changes in the infected lungs were observed after infection. Further studies indicated that neutrophils were the first and most abundant leukocytes to infiltrate the infected lungs after viral infection. In addition, using infected CXCL5-knockout mice, chemokine CXCL5 was responsible for neutrophil recruitment. CXCL5 knockout decreased lung inflammation without diminishing viral clearance, suggesting a potential target for controlling pneumonia.
Accumulating studies have been conducted to identify risk genes and relevant biological mechanisms underlying major depressive disorder (MDD). In particular, transcriptomic analyses in brain regions engaged in cognitive and emotional processes, e.g., the dorsolateral prefrontal cortex (DLPFC), have provided essential insights. Based on three independent DLPFC RNA-seq datasets of 79 MDD patients and 75 healthy controls, we performed differential expression analyses using two alternative approaches for cross-validation. We also conducted transcriptomic analyses in mice undergoing chronic variable stress (CVS) and chronic social defeat stress (CSDS). We identified 12 differentially expressed genes (DEGs) through both analytical methods in MDD patients, the majority of which were also dysregulated in stressed mice. Notably, the mRNA level of the immediate early gene FOS (Fos proto-oncogene) was significantly decreased in both MDD patients and CVS-exposed mice, and CSDS-susceptible mice exhibited a greater reduction in Fos expression compared to resilient mice. These findings suggest the potential key roles of this gene in the pathogenesis of MDD related to stress exposure. Altered transcriptomes in the DLPFC of MDD patients might be, at least partially, the result of stress exposure, supporting that stress is a primary risk factor for MDD.
Liver-expressed antimicrobial peptide 2 (LEAP-2) is a cationic peptide that plays an important role in a host’s innate immune system. We previously demonstrated that mudskipper (Boleophthalmus pectinirostris) LEAP-2 (BpLEAP-2) induces chemotaxis and activation of monocytes/ macrophages (MO/MФ). However, the molecular mechanism by which BpLEAP-2 regulates MO/MΦ remains unclear. In this study, we used yeast two-hybrid cDNA library screening to identify mudskipper protein(s) that interacted with BpLEAP-2, and characterized a sequence encoding motile sperm domain-containing protein 2 (BpMOSPD2). The interaction between BpLEAP-2 and BpMOSPD2 was subsequently confirmed by co-immunoprecipitation (Co-IP). Sequence analyses revealed that the predicted BpMOSPD2 contained an N-terminal extracellular portion composed of a CRAL-TRIO domain and a motile sperm domain, a C-terminal transmembrane domain, and a short cytoplasmic tail. Phylogenetic tree analysis indicated that BpMOSPD2 grouped tightly with fish MOSPD2 homologs and was most closely related to that of the Nile tilapia (Oreochromis niloticus). The recombinant BpMOSPD2 was produced by prokaryotic expression and the corresponding antibody was prepared for protein concentration determination. RNA interference was used to knockdown BpMOSPD2 expression in the mudskipper MO/MФ, and the knockdown efficiency was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Knockdown of BpMOSPD2 significantly inhibited BpLEAP-2-induced chemotaxis of mudskipper MO/MФ and BpLEAP-2-induced bacterial killing activity. Furthermore, knockdown of BpMOSPD2 inhibited the effect of BpLEAP-2 on mRNA expression levels of BpIL-10, BpTNFα, BpIL-1β, and BpTGFβ in MO/MФ. In general, BpMOSPD2 directly interacted with BpLEAP-2, and mediated the effects of BpLEAP-2 on chemotaxis and activation of mudskipper MO/MФ. This is the first identification of MOSPD2 as a receptor for LEAP-2.
Trachypithecus, which currently contains 20 species divided into four groups, is the most speciose and geographically dispersed genus among Asian colobines. Despite several morphological and molecular studies, however, its evolutionary history and phylogeography remain poorly understood. Phayre’s langur (Trachypithecus phayrei) is one of the most widespread members of the genus, but details on its actual distribution and intraspecific taxonomy are limited and controversial. Thus, to elucidate the evolutionary history of Trachypithecus and to clarify the intraspecific taxonomy and distribution of T. phayrei, we sequenced 41 mitochondrial genomes from georeferenced fecal samples and museum specimens, including two holotypes. Phylogenetic analyses revealed a robustly supported phylogeny of Trachypithecus, suggesting that the T. pileatus group branched first, followed by the T. francoisi group, and the T. cristatus and T. obscurus groups most recently. The four species groups diverged from each other 4.5–3.1 million years ago (Ma), while speciation events within these groups occurred much more recently (1.6–0.3 Ma). Within T. phayrei, we found three clades that diverged 1.0–0.9 Ma, indicating the existence of three rather than two taxa. Following the phylogenetic species concept and based on genetic, morphological, and ecological differences, we elevate the T. phayrei subspecies to species level, describe a new species from central Myanmar, and refine the distribution of the three taxa. Overall, our study highlights the importance of museum specimens and provides new insights not only into the evolutionary history of T. phayrei but the entire Trachypithecus genus as well.
The interpretation of patterns of biodiversity requires the disentanglement of geographical and environmental variables. Disjunct alpine communities are geographically isolated from one another but experience similar environmental impacts. Isolated homogenous habitats may promote speciation but constrain functional trait variation. In this study, we examined the hypothesis that dispersal limitation promotes taxonomic divergence, whereas habitat similarity in alpine mountains leads to functional convergence. We performed standardized field investigation to sample non-volant small mammals from 18 prominent alpine sites in the Three Parallel Rivers area. We estimated indices quantifying taxonomic and functional alpha- and beta-diversity, as well as beta-diversity components. We then assessed the respective importance of geographical and environmental predictors in explaining taxonomic and functional compositions. No evidence was found to show that species were more functionally similar than expected in local assemblages. However, the taxonomic turnover components were higher than functional ones (0.471±0.230 vs. 0.243±0.215), with nestedness components showing the opposite pattern (0.063±0.054 vs. 0.269±0.225). This indicated that differences in taxonomic compositions between sites occurred from replacement of functionally similar species. Geographical barriers were the key factor influencing both taxonomic total dissimilarity and turnover components, whereas functional beta-diversity was primarily explained by climatic factors such as minimum temperature of the coldest month. Our findings provide empirical evidence that taxonomic and functional diversity patterns can be independently driven by different ecological processes. Our results point to the importance of clarifying different components of beta-diversity to understand the underlying mechanisms of community assembly. These results also shed light on the assembly rules and ecological processes of terrestrial mammal communities in extreme environments.
Species of the spider family Leptonetidae
Simon, 1890 from China are revised based on molecular and morphological data analyses. A new genus, Jingneta Wang & Li gen. nov ., is erected, with Leptoneta cornea Tong & Li, 2008 as the type species. Twenty-two Chinese species previously assigned to the genus Leptoneta Simon, 1872 are revised, with eight transferred to Falcileptoneta Komatsu, 1970, seven transferred to Jingneta gen. nov ., five transferred to Leptonetela Kratochvíl, 1978, and one species each transferred to Longileptoneta Seo, 2015 and Masirana Kishida, 1942. Eight new species are described: i.e., Falcileptoneta shuanglong Wang & Li sp. nov . (♂), Jingneta caoxian Wang & Li sp. nov . (♂♀), J. jingdong Wang & Li sp. nov . (♂♀), Longileptoneta gutan Wang & Li sp. nov . (♂♀), L. huangshan Wang & Li sp. nov . (♂♀), L. shenxian Wang & Li sp. nov . (♂♀), L. yeren Wang & Li sp. nov . (♂), and L. zhuxian Wang & Li sp. nov . (♂♀). In total, 127 leptonetid species from six genera are documented from China: nine species of Falcileptoneta, nine species of Jingneta gen. nov ., 101 species of Leptonetela, six species of Longileptoneta, one species of Masirana, and one species of Rhyssoleptoneta Tong & Li, 2007.