QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS (QSAR) FOR BINARY MIXTURES AT NON-EQUITOXIC RATIOS BASED ON TOXIC RATIOS-EFFECTS CURVES

The present study proposed a QSAR model to predict joint effects at non-equitoxic ratios for binary mixtures containing reactive toxicants, cyanogenic compounds and aldehydes. Toxicity of single and binary mixtures was measured by quantifying the decrease in light emission from the Photobacterium phosphoreum for 15 min. The joint effects of binary mixtures (TUsum) can thus be obtained. The results showed that the relationships between toxic ratios of the individual chemicals and their joint effects can be described by normal distribution function. Based on normal distribution equations, the joint effects of binary mixtures at non-equitoxic ratios (TUsumn:m ) can be predicted quantitatively using the joint effects at equitoxic ratios (TUsum1:1). Combined with a QSAR model of TUsum1:1 in our previous work, a novel QSAR model can be proposed to predict the joint effects of mixtures at non-equitoxic ratios (TUsum n:m ). The proposed model has been validated using additional mixtures other than the one used for the development of the model. Predicted and observed results were similar (p\u3e0.05). This study provides an approach to the prediction of joint effects for binary mixtures at non-equitoxic ratios

Searching for bidirectional promoters in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region between two TSSs is commonly designated as a putative "bidirectional promoter". Individual examples of bidirectional gene pairs have been reported for years, as well as a few genome-wide analyses have been studied in mammalian and human genomes. However, no genome-wide analysis of bidirectional genes for plants has been done. Furthermore, the exact mechanism of this gene organization is still less understood.</p> <p>Results</p> <p>We conducted comprehensive analysis of bidirectional gene pairs through the whole <it>Arabidopsis thaliana </it>genome and identified 2471 bidirectional gene pairs. The analysis shows that bidirectional genes are often coexpressed and tend to be involved in the same biological function. Furthermore, bidirectional gene pairs associated with similar functions seem to have stronger expression correlation. We pay more attention to the regulatory analysis on the intergenic regions between bidirectional genes. Using a hierarchical stochastic language model (HSL) (which is developed by ourselves), we can identify intergenic regions enriched of regulatory elements which are essential for the initiation of transcription. Finally, we picked 27 functionally associated bidirectional gene pairs with their intergenic regions enriched of regulatory elements and hypothesized them to be regulated by bidirectional promoters, some of which have the same orthologs in ancient organisms. More than half of these bidirectional gene pairs are further supported by sharing similar functional categories as these of handful experimental verified bidirectional genes.</p> <p>Conclusion</p> <p>Bidirectional gene pairs are concluded also prevalent in plant genome. Promoter analyses of the intergenic regions between bidirectional genes could be a new way to study the bidirectional gene structure, which may provide a important clue for further analysis. Such a method could be applied to other genomes.</p

Direct grafting of tetraaniline via perfluorophenylazide photochemistry to create antifouling, low bio-adhesion surfaces.

Conjugated polyaniline has shown anticorrosive, hydrophilic, antibacterial, pH-responsive, and pseudocapacitive properties making it of interest in many fields. However, in situ grafting of polyaniline without harsh chemical treatments is challenging. In this study, we report a simple, fast, and non-destructive surface modification method for grafting tetraaniline (TANI), the smallest conjugated repeat unit of polyaniline, onto several materials via perfluorophenylazide photochemistry. The new materials are characterized by nuclear magnetic resonance (NMR) and electrospray ionization (ESI) mass spectroscopy. TANI is shown to be covalently bonded to important carbon materials including graphite, carbon nanotubes (CNTs), and reduced graphene oxide (rGO), as confirmed by transmission electron microscopy (TEM). Furthermore, large area modifications on polyethylene terephthalate (PET) films through dip-coating or spray-coating demonstrate the potential applicability in biomedical applications where high transparency, patternability, and low bio-adhesion are needed. Another important application is preventing biofouling in membranes for water purification. Here we report the first oligoaniline grafted water filtration membranes by modifying commercially available polyethersulfone (PES) ultrafiltration (UF) membranes. The modified membranes are hydrophilic as demonstrated by captive bubble experiments and exhibit extraordinarily low bovine serum albumin (BSA) and Escherichia coli adhesions. Superior membrane performance in terms of flux, BSA rejection and flux recovery after biofouling are demonstrated using a cross-flow system and dead-end cells, showing excellent fouling resistance produced by the in situ modification

Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

<p>Abstract</p> <p>Background</p> <p>Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs). Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts.</p> <p>Results</p> <p>We constructed a hierarchical stochastic language (HSL) model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or <it>OsALYL1</it>, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes.</p> <p>Conclusion</p> <p>Our findings indicate that 1) the HSL model can be used to accurately predict core TRRs of transcripts across species and 2) identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.</p

HelixFold-Single: MSA-free Protein Structure Prediction by Using Protein Language Model as an Alternative

AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from the homologous sequences. Nonetheless, searching MSAs from protein databases is time-consuming, usually taking dozens of minutes. Consequently, we attempt to explore the limits of fast protein structure prediction by using only primary sequences of proteins. HelixFold-Single is proposed to combine a large-scale protein language model with the superior geometric learning capability of AlphaFold2. Our proposed method, HelixFold-Single, first pre-trains a large-scale protein language model (PLM) with thousands of millions of primary sequences utilizing the self-supervised learning paradigm, which will be used as an alternative to MSAs for learning the co-evolution information. Then, by combining the pre-trained PLM and the essential components of AlphaFold2, we obtain an end-to-end differentiable model to predict the 3D coordinates of atoms from only the primary sequence. HelixFold-Single is validated in datasets CASP14 and CAMEO, achieving competitive accuracy with the MSA-based methods on the targets with large homologous families. Furthermore, HelixFold-Single consumes much less time than the mainstream pipelines for protein structure prediction, demonstrating its potential in tasks requiring many predictions. The code of HelixFold-Single is available at https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold-single, and we also provide stable web services on https://paddlehelix.baidu.com/app/drug/protein-single/forecast

Should Steroid Therapy Be Necessarily Needed for Autoimmune Pancreatitis Patients with Lesion Resected due to Misdiagnosed or Suspected Malignancy?

To explore whether steroid therapy should be needed for autoimmune pancreatitis patients after operation, eight AIP patients receiving operation were enrolled in this study from January 2007 to July 2013. All patients underwent liver function, CA19-9, and contrast-enhanced CT and/or MRI. Tests of IgG and IgG4 were performed in some patients. Tests of serum TB/DB, γ-GT, and γ-globulin were undergone during the perioperative period. Six cases receiving resection were pathologically confirmed as AIP patients and two were confirmed by intraoperative biopsy. For seven patients, TB/DB level was transiently elevated 1 day or 4 days after operation but dropped below preoperative levels or to normal levels 7 days after operation, and serum γ-GT level presented a downward trend. Serum γ-globulin level exhibited a downward trend among six AIP patients after resection, while an upward trend was found in another two AIP patients receiving internal drainage. Steroid therapy was not given to all six AIP patients until two of them showed new lines of evidence of residual or extrapancreatic AIP lesion after operation, while another two cases without resection received steroid medication. Steroid therapy might not be recommended unless there are new lines of evidence of residual extrapancreatic AIP lesions after resection

FANS: Face annotation by searching large-scale web facial images

Ministry of Education, Singapore under its Academic Research Funding Tier

Protection against SHIV-KB9 Infection by Combining rDNA and rFPV Vaccines Based on HIV Multiepitope and p24 Protein in Chinese Rhesus Macaques

Developing an effective vaccine against HIV infection remains an urgent goal. We used a DNA prime/fowlpox virus boost regimen to immunize Chinese rhesus macaques. The animals were challenged intramuscularly with pathogenic molecularly cloned SHIV-KB9. Immunogenicity and protective efficacy of vaccines were investigated by measuring IFN-γ levels, monitoring HIV-specific binding antibodies, examining viral load, and analyzing CD4/CD8 ratio. Results show that, upon challenge, the vaccine group can induce a strong immune response in the body, represented by increased expression of IFN-γ, slow and steady elevated antibody production, reduced peak value of acute viral load, and increase in the average CD4/CD8 ratio. The current research suggests that rapid reaction speed, appropriate response strength, and long-lasting immune response time may be key protection factors for AIDS vaccine. The present study contributes significantly to AIDS vaccine and preclinical research