ALBERT

Description: In this study, a universal protein expression enhancement RNA tool, termed RNAe, was developed by modifying a recently discovered natural long non-coding RNA. At the moment, RNAe is the only technology for gene expression enhancement, as opposed to silencing, at the post-transcriptional level. With this technology, an expression enhancement of 50–1000% is achievable, with more than 200% enhancement achieved in most cases. This work identified the sufficient and necessary element for RNAe function, which was found to be merely 300 nucleotides long and was named minRNAe. It contains a 72-nt 5' pairing sequence which determines the specificity, a 167-nt short non-pairing interspersed nuclear element (SINE) B2 sequence which enhances ribosome recruitment to the target mRNA, and a poly(A) tail, provided together on a plasmid bearing the appropriate sequences. Cellular delivery of RNAe was achieved using routine transfection. The RNAe platform was validated in several widely-used mammalian cell lines. It was proven to be efficient and flexible in specifically enhancing the expression of various endogenous and exogenous proteins of diverse functions in a dose-dependent manner. Compared to the expression-inhibitory tool RNAi, the RNAe tool has a comparable effect size, with an enhancing as opposed to inhibitory effect. One may predict that this brand new technology for enhancing the production of proteins will find wide applications in both research and biopharmaceutical production.

Description: With a rapid growth of data storage in the cloud, data integrity checking in a remote data storage system has become an important issue. A number of protocols, which allow remote integrity checking by a third party, have been proposed. Although those protocols are provably secure, the data privacy issues in those protocols have not been considered. We believe that these issues are equally important since the communication flows of integrity proofs from the cloud server should not reveal any useful information of the stored data. In this paper, we introduce a new definition of data privacy called ‘IND-Privacy’ by an indistinguishability game. It is found that many existing remote integrity proofs are insecure under an IND-Privacy game. It is also found that by adopting witness indistinguishable proofs, the IND-Privacy is achievable. We provide an instantiation that captures data integrity, soundness and IND-privacy.

Description: XRCC4 and XLF are structurally related proteins important for DNA Ligase IV function. XRCC4 forms a tight complex with DNA Ligase IV while XLF interacts directly with XRCC4. Both XRCC4 and XLF form homodimers that can polymerize as heterotypic filaments independently of DNA Ligase IV. Emerging structural and in vitro biochemical data suggest that XRCC4 and XLF together generate a filamentous structure that promotes bridging between DNA molecules. Here, we show that ablating XRCC4's affinity for XLF results in DNA repair deficits including a surprising deficit in VDJ coding, but not signal end joining. These data are consistent with a model whereby XRCC4/XLF complexes hold DNA ends together—stringently required for coding end joining, but dispensable for signal end joining. Finally, DNA-PK phosphorylation of XRCC4/XLF complexes disrupt DNA bridging in vitro , suggesting a regulatory role for DNA-PK's phosphorylation of XRCC4/XLF complexes.

Description: Deleted in Azoospermia Associated Protein 1 (DAZAP1) is a ubiquitous heterogeneous nuclear ribonucleoprotein (hnRNP) that is expressed abundantly in the testis. DAZAP1 deficiency in mice results in growth retardation and spermatogenic arrest. Previous reports on DAZAP1’s binding to several naturally occurring splicing mutations support a role for DAZAP1 in RNA splicing. To elucidate the biological function(s) of DAZAP1 and to search for its natural RNA substrates, we used microarrays to compare the expression profiles and exon usages of wild-type and Dazap1 mutant testes and identified three genes ( Crem , Crisp2 and Pot1a ) with aberrant RNA splicing in the mutant testes. We further demonstrated that DAZAP1, but not DAZAP1 mutant proteins, promoted the inclusion of Crem exon 4, Crisp2 exon 9 and Pot1a exon 4 in splicing reporter transcripts in cultured cells. Additional studies on the binding of DAZAP1 to the exons and their flanking intronic sequences and the effects of minigene deletions on exon inclusion identified regulatory regions in Crem intron 3, Crisp2 intron 9 and Pot1a intron 4 where DAZAP1 bound and regulated splicing. Aberrant splicing of the Pot1a gene, which encodes an essential protein that protects telomere integrity, may partially account for the growth retardation phenotype of DAZAP1-deficient mice.

Description: Brain function and cognitive performance differ between men and women in some measures. The phenotypic variation may be partially due to sex differences in epigenomes and transcriptomes in specific brain regions [e.g. the prefrontal cortex (PFC)]. Genome-wide DNA methylation and gene expression were examined in postmortem PFC of 32 males and 14 females (all were Caucasians) using Illumina's 450K Methylation and HT-12 v4 Gene Expression BeadChips, respectively. Multiple linear regression, Pearson correlation and DAVID functional annotation analyses were applied to investigate sex-biased DNA methylation and gene expression, DNA methylation–gene expression correlation and gene ontology (GO) annotations overrepresented by differentially methylated and expressed genes. A total of 22 124 CpGs showed differential methylation between males and females (2.6 x 10 –38 ≤ P nominal ≤ 0.05), and the P -values of 8357 CpGs withstood multiple-testing correction ( q 〈 0.05). A total of 1489 genes showed differential expression between males and females (4.1 x 10 –36 ≤ P nominal ≤ 0.05), and the P -values of 35 genes survived multiple-testing correction ( q 〈 0.05). A significant correlation ( P correlation 〈 0.05) was observed between methylation levels of 585 differentially methylated CpGs ( P nominal ≤ 0.05) and expression levels of 188 differentially expressed host genes ( P nominal 〈 0.05). The GO terms enriched by these 188 genes (134 on autosomes and 54 on sex chromosomes) were assigned to 24 clusters, and 33 genes involved in the top cluster (enrichment score: 4.7) mainly participate in ribosome structure and function, RNA binding and protein translation. This study demonstrated sex-specific methylomic and transcriptomic profiles in the human PFC. Our findings suggest that sex-biased DNA methylation and gene expression could be either the cause or consequence of differential brain development between males and females.

Description: Small differences in the sensitivity of stomatal conductance to light intensity on leaf surfaces may lead to large differences in total canopy transpiration ( E C ) with increasing canopy leaf area ( L ). Typically, the increase of L would more than compensate for the decrease of transpiration per unit of leaf area ( E L ), resulting in concurrent increase of E C . However, highly shade-intolerant species, such as Larix principis-rupprechtii Mayr., may be so sensitive to increased shading that such compensation is not complete. We hypothesized that in such a stand, windfall-induced spatial variation at a decameter scale would result in greatly reduced E L in patches of high L leading to lower E C than low competition patches of sparse canopy. We further hypothesized that quicker extraction of soil moisture in patches of lower competition will result in earlier onset of drought symptoms in these patches. Thus, patches of low L will transition from light to soil moisture as the factor dominating E L . This process should progressively homogenize E C in the stand even as the variation of soil moisture is increasing. We tested the hypotheses utilizing sap flux of nine trees, and associated environmental and stand variables. The results were consistent with only some of the expectations. Under non-limiting soil moisture, E L was very sensitive to the spatial variation of L , decreasing sharply with increasing L and associated decrease of mean light intensity on leaf surfaces. Thus, under the conditions of ample soil moisture maximum E C decreased with increasing patch-scale L . Annual E C and biomass production also decreased with L , albeit more weakly. Furthermore, variation of E C among patches decreased as average stand soil moisture declined between rain events. However, contrary to expectation, high L plots which transpired less showed a greater E L sensitivity to decreasing stand-scale soil moisture, suggesting a different mechanism than simple control by decreasing soil moisture. We offer potential explanations to the observed phenomenon. Our results demonstrate that spatial variation of L at decameter scale, even within relatively homogeneous, single-species, even-aged stands, can produce large variation of transpiration, soil moisture and biomass production and should be considered in 1-D soil–plant–atmosphere models.

Description: To find efficient spectral classification diagrams to classify emission-line galaxies, especially in large surveys and huge data bases, an artificial neural network (ANN) supervised learning algorithms is applied to a sample of emission-line galaxies from the Sloan Digital Sky Survey data release 9 provided by the Max Planck Institute and the Johns Hopkins University (MPA/JHU) ( http://www.sdss3.org/dr9/spectro/spectroaccess.php ). A two-step approach is adopted. (i) The ANN network must be trained with a subset of objects that are known to be active galactic nuclei (AGNs) hosts, composites or star-forming galaxies, treating the strong emission-line flux measurements as input feature vectors in n -dimensional space, where n is the number of strong emission-line flux ratios. (ii) After the network is trained on a sample of galaxies, the remaining galaxies are classified in the automatic test analysis as AGN hosts, composites or star-forming galaxies. We show that the classification diagrams based on the [N ii ]/Hα versus other emission-line ratio, such as [O iii ]/Hβ, [Ne iii ]/[O ii ], ([O iii ]4959 + [O iii ]5007)/[O iii ]4363, [O ii ]/Hβ, [Ar iii ]/[O iii ], [S ii ]/Hα, and [O i ]/Hα, plus colour, allows us to separate unambiguously AGN hosts, composites or star-forming galaxies. Among them, the diagram of [N ii ]/Hα versus [O iii ]/Hβ achieved an accuracy of 98 per cent for classification of AGN hosts, composites or star-forming galaxies. The other diagrams above except the diagram of [N ii ]/Hα versus [O iii ]/Hβ give an accuracy of ~90 per cent. The code in the paper is available on the web ( http://fshi5388.blog.163.com ).

Description: O -GlcNAcylation is a ubiquitous, dynamic and reversible post-translational protein modification in metazoans, and it is catalysed and removed by O -GlcNAc transferase (OGT) and O -GlcNAcase, respectively. Prokaryotes lack endogenous OGT activity. It has been reported that coexpression of mammalian OGT with its target substrates in Escherichia coli produce O -GlcNAcylated recombinant proteins, but the plasmids used were not compatible, and the expression of both OGT and its target protein were induced by the same inducer. Here, we describe a compatible dual plasmid system for coexpression of OGT and its target substrate for O -GlcNAcylated protein production in E. coli . The approach was validated using the CKII and p53 protein as control. This compatible dual plasmid system contains an arabinose-inducible OGT expression vector with a pUC origin and an isopropyl β - d -thiogalactopyranoside-inducible OGT target substrate expression vector bearing a p15A origin. The dual plasmid system produces recombinant proteins with varying O -GlcNAcylation levels by altering the inducer concentration. More importantly, the O -GlcNAcylation efficiency was much higher than the previously reported system. Altogether, we established an adjustable compatible dual plasmid system that can effectively yield O -GlcNAcylated proteins in E. coli .

Description: Identity-based encryption (IBE) has many appealing applications. However, some traditional IBE schemes may not be secure in the real world due to the side-channel attacks. Leakage-resilient cryptography can capture these attacks by modeling information leakage that adversary can access. In this paper, we apply a hash proof technique in the existing CCA-secure variant of the Gentry's IBE scheme to construct a new leakage-resilient IBE scheme in the bounded-leakage model. The proposed scheme is more computationally efficient than the original Alwen et al. 's leakage-resilient IBE scheme. It enjoys a shorter key (public/secret key) length, and a higher relative key leakage ratio. The new leakage-resilient scheme is proved semantically secure against adaptive chosen ciphertext attack in the standard model under the truncated augmented bilinear Diffie-Hellman exponent ( $q$ -TABDHE) assumption.

Description: The genomes and transcriptomes of hundreds of insects have been sequenced. However, insect community lacks an integrated, up-to-date collection of insect gene data. Here, we introduce the first release of InsectBase, available online at http://www.insect-genome.com . The database encompasses 138 insect genomes, 116 insect transcriptomes, 61 insect gene sets, 36 gene families of 60 insects, 7544 miRNAs of 69 insects, 96 925 piRNAs of Drosophila melanogaster and Chilo suppressalis , 2439 lncRNA of Nilaparvata lugens , 22 536 pathways of 78 insects, 678 881 untranslated regions (UTR) of 84 insects and 160 905 coding sequences (CDS) of 70 insects. This release contains over 12 million sequences and provides search functionality, a BLAST server, GBrowse, insect pathway construction, a Facebook-like network for the insect community (iFacebook), and phylogenetic analysis of selected genes.