In addition, for BEs, the target bases are limited to an editing window of at least three nucleotides (nt) away from the 5 0 end of the protospacer adjacent motif (PAM), and undesired base substitutions are common, especially when several Cs or As coexist in the editing window (Chen et al., 2019). Although CRISPR/Cas-mediated homologous recombination provides an alternative method for precise targeted gene replacement or gene insertion in plants, it is limited by the low efficiency (Miki et al., 2018). Most recently, a ''search-and-replace'' genome editing technology called prime editing was developed in human cells, which can mediate all 12 possible base-to-base conversions using a reverse transcriptase (RT) paired with CRISPR-Cas9 nickase (Cas9n) (H840A) and a prime editing guide RNA (pegRNA), without DSBs or donor DNA (Anzalone et al., 2019).

Lnk was originally cloned from a rat lymph node cDNA library and shown to participate in T cell signaling. Human Lnk (hLnk) was cloned by screening a Jurkat cell cDNA library. hLnk has a calculated molecular mass of 63 kDa, and its deduced amino acid sequence indicates the presence of an N-terminal proline-rich region, a pleckstrin homology domain, and a Src homology 2 domain. When expressed in COS cells, hLnk migrates with an apparent molecular mass of 75 kDa. Confocal fluorescence microscope analysis indicates that in COS cells transfected with an expression vector encoding a chimeric Lnk-green fluorescent protein, hLnk is found at the juxtanuclear compartment and also appears to be localized at the plasma membrane. Lnk is tyrosine-phosphorylated by p56lck. Following phosphorylation, p56lck binds to tyrosine-phosphorylated hLnk through its Src homology 2 domain. In COS cells cotransfected with hLnk, p56lck, and CD8-ζ, hLnk associated with tyrosine-phosphorylated TCR ζ-chain through its Src homology 2 domain. The overexpression of Lnk in Jurkat cells led to an inhibition of anti-CD3 mediated NF-AT-Luc activation. Our study reveals a potentially new mechanism of T cell-negative regulation.

Cucumber gray mold caused by Botrytis cinerea is considered one of the most serious cucumber diseases. With the advent of Hi-seq technology, it is possible to study the plant–pathogen interaction at the transcriptome level. To the best of our knowledge, this is the first application of RNA-seq to identify cucumber and B. cinerea differentially expressed genes (DEGs) before and after the plant–pathogen interaction. In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. This is the first systematic transcriptome analysis of components related to the B. cinerea–cucumber interaction. Functional genes and putative pathways identified herein will increase our understanding of the mechanism of the pathogen–host interaction.

No abstract

Genes have been thought to affect community ecology and evolution, but their identification at the whole-genome level is challenging. Here, we develop a conceptual framework for the genome-wide mapping of quantitative trait loci (QTLs) that govern interspecific competition and cooperation. This framework integrates the community ecology theory into systems mapping, a statistical model for mapping complex traits as a dynamic system. It can characterize not only how QTLs of one species affect its own phenotype directly, but also how QTLs from this species affect the phenotype of its interacting species indirectly and how QTLs from different species interact epistatically to shape community behavior. We validated the utility of the new mapping framework experimentally by culturing and comparing two bacterial species, Escherichia coli and Staphylococcus aureus, in socialized and socially isolated environments, identifying several QTLs from each species that may act as key drivers of microbial community structure and function.

Abstract-The receptor for advanced glycation end products (RAGE) may play an important role in inflammatory processes and endothelial activation, likely to accelerate the processes of coronary atherosclerotic development, especially in diabetic patients. The factors that regulate arterial expression of RAGE are not completely clear. iabetes-associated cardiovascular complications are one of the major causes of patient mortality. 1 Numerous epidemiological studies suggest that diabetes can accelerate atherosclerosis and increase the incidence of heart attacks and strokes. 2 However, the underlying mechanisms behind this relationship have not been fully elucidated. Recent studies suggest that the receptor of advanced glycation end products (RAGE), a multiligand receptor on vascular cells, may play an important role, especially in diabetic patients, in promoting inflammatory processes and endothelial activation, which accelerate coronary atherosclerotic development. RAGE, a member of the immunoglobulin superfamily of cell surface molecules, was initially isolated from bovine lung; however, subsequent studies from several laboratories demonstrated that RAGE is also expressed on the surface of vascular endothelial and smooth muscle cells. 3 As a multiligand cell surface receptor, the endogenous ligands of RAGE are variable and include advanced glycation end products (AGEs), S100/calgranulins, and high mobility group box 1 protein. 4 Diabetes-associated hyperglycemia and oxidative stress are the main sources of AGEs, which subsequently activate the RAGE pathway and initiate the inflammatory response. 5 Furthermore, RAGE is highly expressed in human atherosclerotic lesions and colocalizes with proinflammatory and pro-oxidative mediators. 6 C-reactive protein (CRP), a key proinflammatory cytokine that is highly elevated in atherosclerotic patients, serves not only as a biomarker for the risk of cardiovascular disease but also functions as an active mediator of atherosclerosis by promoting arterial endothelial activation and macrophage recruitment. 7 Previous studies from our laboratory revealed that CRP potently downregulates endothelial NO synthase protein expression and destabilizes endothelial NO synthase mRNA, resulting in the decreased release of basal and stimulated NO. 8 Furthermore, CRP also induces the expression of macrophage chemoattractant protein 1 (MCP-1), interleukin (IL) 6, IL-8, intercellular adhesion molecule 1, and vascular cell adhesion molecule 1. 9 -11 Therefore, we hypothesized that CRP may upregulate RAGE expression in endothelial cells and, via this pathway, can magnify vascular inflammation, accelerating the process of atherosclerosis.

The gut microbiota may play an important role in affecting human health. To explore the genetic mechanisms underlying microbiota-host relationships, many genome-wide association studies have begun to identify host genes that shape the microbial composition of the gut. It is becoming increasingly clear that the gut microbiota impacts host processes not only through the action of individual microbes but also their interaction networks. However, a systematic characterization of microbial interactions that occur in densely packed aggregates of the gut bacteria has proven to be extremely difficult. We develop a computational rule of thumb for addressing this issue by integrating ecological behavioral theory and genetic mapping theory. We introduce behavioral ecology theory to derive mathematical descriptors of how each microbe interacts with every other microbe through a web of cooperation and competition. We estimate the emergent properties of gut-microbiota networks reconstructed from these descriptors and map host-driven mutualism, antagonism, aggression, and altruism QTLs. We further integrate path analysis and mapping theory to detect and visualize how host genetic variants affect human diseases by perturbing the internal workings of the gut microbiota. As the proof of concept, we apply our model to analyze a published dataset of the gut microbiota, showing its usefulness and potential to gain new insight into how microbes are organized in human guts. The new model provides an analytical tool for revealing the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes.

The most prevalent group A rotavirus found in the diarrheic children was also determined in drinking water sources including raw water, treated water and tap water in Beijing, and then the possible contamination contributions to tap water for human consumption were discussed in this study.