Insights into the rice and Arabidopsis genomes: intron fates, paralogs, and lineage-specific genes

With the availability of near-complete rice genome sequence, high-quality annotation data, and large expression profile datasets, we examined segmental duplication, intron turnover, and paralogous protein family composition in rice. These data suggest a large percentage of the rice genome was involved in segmental duplication creating a large number of paralogous families. We found that singleton and paralogous family genes differed substantially not only in their likelihood of encoding a protein of known or putative function but also in the distribution of specific gene function. We showed that a significant portion of the duplicated genes in rice show divergent expression although a correlation between sequence divergence and correlation of expression could be seen in very young genes. We observed that intron evolution within the rice genome following segmental duplication is dominated by intron loss rather than intron gain. In addition, with the availability of more complete or near-complete plant genomes and transcriptomes across a wide range of species, we identified and characterized conserved Brassicaceae-specific genes and Arabidopsis lineage-specific genes. Lineage specific genes in the Brassicaceae and within Arabidopsis were enriched in genes of no known function and appear to be fast evolving at the protein sequence level

Understanding the Impact of Encrypted DNS on Internet Censorship

DNS traffic is transmitted in plaintext, resulting in privacy leakage. To combat this problem, secure protocols have been used to encrypt DNS messages. Existing studies have investigated the performance overhead and privacy benefits of encrypted DNS communications, yet little has been done from the perspective of censorship. In this paper, we study the impact of the encrypted DNS on Internet censorship in two aspects. On one hand, we explore the severity of DNS manipulation, which could be leveraged for Internet censorship, given the use of encrypted DNS resolvers. In particular, we perform 7.4 million DNS lookup measurements on 3,813 DoT and 75 DoH resolvers and identify that 1.66% of DoT responses and 1.42% of DoH responses undergo DNS manipulation. More importantly, we observe that more than two-thirds of the DoT and DoH resolvers manipulate DNS responses from at least one domain, indicating that the DNS manipulation is prevalent in encrypted DNS, which can be further exploited for enhancing Internet censorship. On the other hand, we evaluate the effectiveness of using encrypted DNS resolvers for censorship circumvention. Specifically, we first discover those vantage points that involve DNS manipulation through on-path devices, and then we apply encrypted DNS resolvers at these vantage points to access the censored domains. We reveal that 37% of the domains are accessible from the vantage points in China, but none of the domains is accessible from the vantage points in Iran, indicating that the censorship circumvention of using encrypted DNS resolvers varies from country to country. Moreover, for a vantage point, using a different encrypted DNS resolver does not lead to a noticeable difference in accessing the censored domains

Leveraging Inlier Correspondences Proportion for Point Cloud Registration

In feature-learning based point cloud registration, the correct correspondence construction is vital for the subsequent transformation estimation. However, it is still a challenge to extract discriminative features from point cloud, especially when the input is partial and composed by indistinguishable surfaces (planes, smooth surfaces, etc.). As a result, the proportion of inlier correspondences that precisely match points between two unaligned point clouds is beyond satisfaction. Motivated by this, we devise several techniques to promote feature-learning based point cloud registration performance by leveraging inlier correspondences proportion: a pyramid hierarchy decoder to characterize point features in multiple scales, a consistent voting strategy to maintain consistent correspondences and a geometry guided encoding module to take geometric characteristics into consideration. Based on the above techniques, We build our Geometry-guided Consistent Network (GCNet), and challenge GCNet by indoor, outdoor and object-centric synthetic datasets. Comprehensive experiments demonstrate that GCNet outperforms the state-of-the-art methods and the techniques used in GCNet is model-agnostic, which could be easily migrated to other feature-based deep learning or traditional registration methods, and dramatically improve the performance. The code is available at https://github.com/zhulf0804/NgeNet

Calnuc plays a role in dynamic distribution of Gαi but not Gβ subunits and modulates ACTH secretion in AtT-20 neuroendocrine secretory cells

In AtT-20 cells ACTH secretion is regulated by both Ca2+ and G proteins. We previously demonstrated that calnuc, an EF-hand Ca2+ binding protein which regulates Alzheimer's β-amyloid precursor protein (APP) biogenesis, binds both Ca2+ as well as Gα subunits. Here we investigate calnuc's role in G protein-mediated regulation of ACTH secretion in AtT-20 neuroendocrine secretory cells stably overexpressing calnuc-GFP. Similar to endogenous calnuc, calnuc-GFP is mainly found in the Golgi, on the plasma membrane (PM), and associated with regulated secretion granules (RSG). By deconvolution immunofluorescence, calnuc-GFP partially colocalizes with Gαi1/2 and Gαi3 at the PM and on RSG. Cytosolic calnuc(ΔSS)-CFP with the signal sequence deleted also partially colocalizes with RSG and partially cosediments with Gαi1/2 in fractions enriched in RSG. Overexpression of calnuc-GFP specifically increases the distribution of Gαi1/2 on the PM whereas the distribution of Gβ subunits and synaptobrevin 2 (Vamp 2) is unchanged. Overexpression of calnuc-GFP or cytosolic calnuc(ΔSS)-CFP enhances ACTH secretion two-fold triggered by mastoparan or GTPγS but does not significantly affect glycosaminoglycan (GAG) chain secretion along the constitutive pathway or basal secretion of ACTH. Calnuc's facilitating effects on ACTH secretion are decreased after introducing anti-Gαi1/2, Gαi3, Gβ or calnuc IgG into permeabilized cells but not when Gα12 or preimmune IgG is introduced. The results suggest that calnuc binds to Gα subunits on the Golgi and on RSG and that overexpression of calnuc causes redistribution of Gαi subunits to the PM and RSG, indicating that calnuc plays a role in dynamic distribution of only Gα but not Gβ subunits. Thus calnuc may connect G protein signaling and calcium signaling during regulated secretion

Intron gain and loss in segmentally duplicated genes in rice

BACKGROUND: Introns are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. In a number of plant species, a large portion of the genome has been segmentally duplicated, giving rise to a large set of duplicated genes. The recent completion of the rice genome in which segmental duplication has been documented has allowed us to investigate intron evolution within rice, a diploid monocotyledonous species. RESULTS: Analysis of segmental duplication in rice revealed that 159 Mb of the 371 Mb genome and 21,570 of the 43,719 non-transposable element-related genes were contained within a duplicated region. In these duplicated regions, 3,101 collinear paired genes were present. Using this set of segmentally duplicated genes, we investigated intron evolution from full-length cDNA-supported non-transposable element-related gene models of rice. Using gene pairs that have an ortholog in the dicotyledonous model species Arabidopsis thaliana, we identified more intron loss (49 introns within 35 gene pairs) than intron gain (5 introns within 5 gene pairs) following segmental duplication. We were unable to demonstrate preferential intron loss at the 3' end of genes as previously reported in mammalian genomes. However, we did find that the four nucleotides of exons that flank lost introns had less frequently used 4-mers. CONCLUSION: We observed that intron evolution within rice following segmental duplication is largely dominated by intron loss. In two of the five cases of intron gain within segmentally duplicated genes, the gained sequences were similar to transposable elements

Dial N for NXDomain: The Scale, Origin, and Security Implications of DNS Queries to Non-Existent Domains

Non-Existent Domain (NXDomain) is one type of the Domain Name System (DNS) error responses, indicating that the queried domain name does not exist and cannot be resolved. Unfortunately, little research has focused on understanding why and how NXDomain responses are generated, utilized, and exploited. In this paper, we conduct the first comprehensive and systematic study on NXDomain by investigating its scale, origin, and security implications. Utilizing a large-scale passive DNS database, we identify 146,363,745,785 NXDomains queried by DNS users between 2014 and 2022. Within these 146 billion NXDomains, 91 million of them hold historic WHOIS records, of which 5.3 million are identified as malicious domains including about 2.4 million blocklisted domains, 2.8 million DGA (Domain Generation Algorithms) based domains, and 90 thousand squatting domains targeting popular domains. To gain more insights into the usage patterns and security risks of NXDomains, we register 19 carefully selected NXDomains in the DNS database, each of which received more than ten thousand DNS queries per month. We then deploy a honeypot for our registered domains and collect 5,925,311 incoming queries for 6 months, from which we discover that 5,186,858 and 505,238 queries are generated from automated processes and web crawlers, respectively. Finally, we perform extensive traffic analysis on our collected data and reveal that NXDomains can be misused for various purposes, including botnet takeover, malicious file injection, and residue trust exploitation

Tumor Suppressor Spred2 Interaction with LC3 Promotes Autophagosome Maturation and Induces Autophagy-Dependent Cell Death

The tumor suppressor Spred2 (Sprouty-related EVH1 domain-2) induces cell death in a variety of cancers. However, the underlying mechanism remains to be elucidated. Here we show that Spred2 induces caspase-independent but autophagy-dependent cell death in human cervical carcinoma HeLa and lung cancer A549 cells. We demonstrate that ectopic Spred2 increased both the conversion of microtubule-associated protein 1 light chain 3 (LC3), GFP-LC3 puncta formation and p62/SQSTM1 degradation in A549 and HeLa cells. Conversely, knockdown of Spred2 in tumor cells inhibited upregulation of autophagosome maturation induced by the autophagy inducer Rapamycin, which could be reversed by the rescue Spred2. These data suggest that Spred2 promotes autophagy in tumor cells. Mechanistically, Spred2 co-localized and interacted with LC3 via the LC3-interacting region (LIR) motifs in its SPR domain. Mutations in the LIR motifs or deletion of the SPR domain impaired Spred2-mediated autophagosome maturation and tumor cell death, indicating that functional LIR is required for Spred2 to trigger tumor cell death. Additionally, Spred2 interacted and co-localized with p62/SQSTM1 through its SPR domain. Furthermore, the co-localization of Spred2, p62 and LAMP2 in HeLa cells indicates that p62 may be involved in Spred2-mediated autophagosome maturation. Inhibition of autophagy using the lysosomal inhibitor chloroquine, reduced Spred2-mediated HeLa cell death. Silencing the expression of autophagy-related genes ATG5, LC3 or p62 in HeLa and A549 cells gave similar results, suggesting that autophagy is required for Spred2-induced tumor cell death. Collectively, these data indicate that Spred2 induces tumor cell death in an autophagy-dependent manner