Volatile fatty acids distribution during acidogenesis of algal residues with pH control

The anaerobic acidification of protein-rich algal residues with pH control (4, 6, 8, 10) was studied in batch reactors, which was operated at mesophilic(35 °C) condition. The distribution of major volatile fatty acids (VFAs) during acidogenesis was emphasized in this paper. The results showed that the acidification efficiency and VFAs distribution in the acid reactor strongly depended on the pH. The main product for all the runs involved acetic acid except that the proportion of butyric acid acidified at pH 6 was relatively higher. The other organic acids remained at lower levels. The VFAs yield reached the maximum value with about 0.6 g VFAs/g volatile solid (VS) added as pH was 8, and also the content of total ammonia nitrogen (TAN) reached the highest values of 9,629 mg/l. Low acidification degrees were obtained under the conditions at pH 4 and 10, which was not suitable for the metabolism of acidogens. Hydralic retention time (HRT) required for different conditions varied. As a consequence, it was indicated that pH was crucial to the acidification efficiency and products distribution. The investigation of acidogenesis process, which was producing the major substrates, short-chain fatty acids, would play the primary role in the efficient operation of methanogenesis.     

PDK1 is important lipid kinase for RANKL-induced osteoclast formation and function via the regulation of the Akt-GSK3β-NFATc1 signaling cascade

Perturbations in the balanced process of osteoblast-mediated bone formation and osteoclast-mediated bone resorption leading to excessive osteoclast formation and/or activity is the cause of many pathological bone conditions such as osteoporosis. The osteoclast is the only cell in the body capable of resorbing and degrading the mineralized bone matrix. Osteoclast formation from monocytic precursors is governed by the actions of two key cytokines macrophage-colony-stimulating factor and receptor activator of nuclear factor-κB ligand (RANKL). Binding of RANKL binding to receptor RANK initiates a series of downstream signaling responses leading to monocytic cell differentiation and fusion, and subsequent mature osteoclast bone resorption and survival. The phosphoinositide-3-kinase (PI3K)-protein kinase B (Akt) signaling cascade is one such pathway activated in response to RANKL. The 3-phosphoinositide-dependent protein kinase 1 (PDK1), is considered the master upstream lipid kinase of the PI3K-Akt cascade. PDK1 functions to phosphorylate and partially activate Akt, triggering the activation of downstream effectors. However, the role of PDK1 in osteoclasts has yet to be clearly defined. In this study, we specifically deleted the PDK1 gene in osteoclasts using the cathepsin-K promoter driven Cre-LoxP system. We found that the specific genetic ablation of PDK1 in osteoclasts leads to an osteoclast-poor osteopetrotic phenotype in mice. In vitro cellular assays further confirmed the impairment of osteoclast formation in response to RANKL by PDK1-deficient bone marrow macrophage (BMM) precursor cells. PDK1-deficient BMMs exhibited reduced ability to reorganize actin cytoskeleton to form a podosomal actin belt as a result of diminished capacity to fuse into giant multinucleated osteoclasts. Notably, biochemical analyses showed that PDK1 deficiency attenuated the phosphorylation of Akt and downstream effector GSK3β, and reduced induction of NFATc1. GSK3β is a reported negative regulator of NFATc1. GSK3β activity is inhibited by Akt-dependent phosphorylation. Thus, our data provide clear genetic and mechanistic insights into the important role for PDK1 in osteoclasts.     

A Crowned Killer’s Résumé: Genome,Structure, Receptors,and Origin of SARS-CoV-2

Virologica Sinica - The recent emergence and rapid global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose an unprecedented medical and socioeconomic crisis, and the...     

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs

miRDeepFinder is a software package developed to identify and functionally analyze plant microRNAs (miRNAs) and their targets from small RNA datasets obtained from deep sequencing. The functions available in miRDeepFinder include pre-processing of raw data, identifying conserved miRNAs, mining and classifying novel miRNAs, miRNA expression profiling, predicting miRNA targets, and gene pathway and gene network analysis involving miRNAs. The fundamental design of miRDeepFinder is based on miRNA biogenesis, miRNA-mediated gene regulation and target recognition, such as perfect or near perfect hairpin structures, different read abundances of miRNA and miRNA*, and targeting patterns of plant miRNAs. To test the accuracy and robustness of miRDeepFinder, we analyzed a small RNA deep sequencing dataset of Arabidopsis thaliana published in the GEO database of NCBI. Our test retrieved 128 of 131 (97.7%) known miRNAs that have a more than 3 read count in Arabidopsis. Because many known miRNAs are not associated with miRNA*s in small RNA datasets, miRDeepFinder was also designed to recover miRNA candidates without the presence of miRNA*. To mine as many miRNAs as possible, miRDeepFinder allows users to compare mature miRNAs and their miRNA*s with other small RNA datasets from the same species. Cleaveland software package was also incorporated into miRDeepFinder for miRNA target identification using degradome sequencing analysis. Using this new computational tool, we identified 13 novel miRNA candidates with miRNA*s from Arabidopsis and validated 12 of them experimentally. Interestingly, of the 12 verified novel miRNAs, a miRNA named AC1 spans the exons of two genes (UTG71C4 and UGT71C3). Both the mature AC1 miRNA and its miRNA* were also found in four other small RNA datasets. We also developed a tool, ??miRNA primer designer?? to design primers for any type of miRNAs. miRDeepFinder provides a powerful tool for analyzing small RNA datasets from all species, with or without the availability of genome information. miRDeepFinder and miRNA primer designer are freely available at http://www.leonxie.com/DeepFinder.php and at http://www.leonxie.com/miRNAprimerDesigner.php, respectively. A program (called RefFinder: http://www.leonxie.com/referencegene.php) was also developed for assessing the reliable reference genes for gene expression analysis, including miRNAs.     

Willingness to accept HIV pre-exposure prophylaxis among Chinese men who have sex with men

Objective

We investigated the awareness and acceptability of pre-exposure prophylaxis (PrEP) among men who have sex with men (MSM) and potential predicting factors.

Methods

This study was conducted among MSM in Beijing, China. Study participants, randomly selected from an MSM cohort, completed a structured questionnaire, and provided their blood samples to test for HIV infection and syphilis. Univariate logistic regression analyses were performed to evaluate the factors associated with willingness to accept (WTA) PrEP. Factors independently associated with willingness to accept were identified by entering variables into stepwise logistic regression analysis.

Results

A total of 152 MSM completed the survey; 11.2% had ever heard of PrEP and 67.8% were willing to accept it. Univariate analysis showed that age, years of education, consistent condom use in the past 6 months, heterosexual behavior in the past 6 months, having ever heard of PrEP and the side effects of antiretroviral drugs, and worry about antiretroviral drugs cost were significantly associated with willingness to accept PrEP. In the multivariate logistic regression model, only consistent condom use in the past 6 months (odds ratio [OR]: 0.31; 95% confidence interval [CI]: 0.13–0.70) and having ever heard of the side effects of antiretroviral drugs (OR: 0.30; 95% CI: 0.14–0.67) were independently associated with willingness to accept PrEP.

Conclusions

The awareness of PrEP in the MSM population was low. Sexual behavioral characteristics and knowledge about ART drugs may have effects on willingness to accept PrEP. Comprehensive prevention strategies should be recommended in the MSM community.     

Abscisic acid (ABA) inhibition of lateral root formation involves endogenous ABA biosynthesis in Arachis hypogaea L.

ABA has been found to play a significant role in post-embryonic developmental in peanut seedlings. The results from the current study indicate that in the presence of exogenous 10 μmol l⁻¹ ABA, lateral roots (LRs) number decreased and seedling development was delayed. This effect was eliminated by 25 μmol l⁻¹ naproxen, an inhibitor of ABA biosynthesis. The Arabidopsis mutant deficient in ABA biosynthesis, nced3, displays a phenotype with more and longer LRs. We found that ABA decreased root-branching in peanut in a dose-dependent way. ABA-treated seedlings showed higher endogenous ABA levels than the control and naproxen-treated seedlings. RT-PCR results indicated that the expression of AhNCED1, a key gene in the ABA biosynthetic pathway, was significantly up-regulated by exogenous ABA in peanut. The mRNA levels of AhNCED1 began to increase 2 days after ABA treatment. The results from the current study show that ABA inhibits peanut LR development by increasing endogenous ABA contents.     

Synthesis, characterization and photostability of several soluble tetra(quinolin-8-yloxy)metallophthalocyanines

Five tetra(quinolin-8-yloxy)metallophthalocyanines 4a-4e were synthesized from 4-(quinolin-8-yloxy)phthalonitrile in the presence of 1,8-diazabicyclo [5.4.0] undec-7-ene (DBU) as the catalyst, and characterized by MS, ¹H NMR, UV-Vis, IR and elemental analysis, which were consistent with the proposed structures. The Q band wavelength of them is related to the metal species in center of Pc rings and follows an order: Mn > Zn ≈ Cu > Ni ≈ Co. They all possess excellent solubility in several polar organic solvents, such as chloroform and dichloromethane. But the stability of them, especially that with zinc as coordinated center, is very poor in solutions.     

Complete Genome Sequence of Lactobacillus casei Zhang,a New Probiotic Strain Isolated from Traditional Homemade Koumiss in Inner Mongolia,China

Lactobacillus casei Zhang is a new probiotic bacterium isolated from koumiss collected in Inner Mongolia, China. Here, we report the main genome features of L. casei Zhang and the identification of several predicted proteins implicated in interactions with the host.Koumiss, a traditional drink made from mare''s milk by nomadic peoples in China and Mongolia, is believed to be beneficial in the cure of digestive diseases and a wide range of chronic diseases, including tuberculosis, bronchitis, and anemia (3). Lactobacillus casei Zhang is a novel probiotic strain identified by screening of lactic acid bacteria isolated from koumiss samples collected in Inner Mongolia, China, and exhibits high-level resistance to acid and bile stresses, as well as antibacterial, antioxidative, and immunomodulatory properties (6, 7, 11).A whole-genome shotgun strategy was used for sequencing of the genome of L. casei Zhang. pUC18 plasmid libraries with insertions of 1.5 to 2.5 kb and 4 to 6 kb were constructed (8). Gaps were closed by sequencing of PCR products. Base calling and sequence assembly were carried out using the Phred/Phrap/Consed software package (http://www.phrap.org/), and reads giving a total of 6.2-fold coverage were assembled with an error rate of <0.0001. Gene prediction and annotation were performed as described previously (10).The complete genome of L. casei Zhang consists of a 2,861,848-bp circular chromosome and a 36-kb plasmid. The average G+C content of the chromosome is 46.5%, while the plasmid has a lower G+C content (10). The L. casei Zhang genome contains 2,804 predicted coding sequences (CDSs), five rRNA operons, and 59 tRNAs. No functional prophages were identified, except for the previously described prophage remnant (9). Genes for 41 transposases were found in the genome, and this number was much lower than (only about 30%) those of transposase genes in L. casei ATCC 334 and BL23 (1, 4), suggesting that insertion element (IS)-mediated genome diversification was less frequent in L. casei Zhang.Comparative genome analysis revealed that the number of phosphotransferase system (PTS)-related proteins varied significantly in L. casei strains. Almost twice as many PTS components were found in L. casei Zhang and BL23 as in L. casei ATCC 334. In contrast to L. casei ATCC 334, L. casei Zhang was found to have 33 PTS components consisting of 11 complete substrate-specific enzyme II (EII) complexes encoded by six genomic islands. The G+C contents of the six islands ranged from 41 to 47%, similar to the average G+C content of the L. casei Zhang genome. In addition, most of the EII components in L. casei Zhang (81 of 96) were conserved in L. casei BL23, suggesting that a large-scale loss of PTSs occurred in L. casei ATCC 334 during its evolution. Conspicuous redundancy of chromosome-encoded PTSs in L. casei Zhang may offer benefits in the transport and use of a large panel of carbon sources.Genes encoding five putative mucus-binding proteins (LCAZH_0407, LCAZH_2292, LCAZH_2478, LCAZH_2398, and LCAZH_1427) and a cluster of genes encoding bacteriocin biosynthetic proteins (LCAZH_2341 to LCAZH_2348) nearly identical to those in L. casei ATCC 334 and BL23 were identified in L. casei Zhang and may provide this bacterium with some competitive advantages in the gastrointestinal environment (2, 5).In conclusion, the comparative analysis revealed the flexibility of L. casei Zhang in sugar utilization. In addition, some possible hints for its interactions with the host were identified. This genome sequence will be the basis for systematic studies into the mechanism for the probiotic properties of L. casei Zhang.     

Molecular characterization of woodchuck type I interferons and their expression by woodchuck peripheral blood lymphocytes

Interferon (IFN)-alpha and -beta are important antiviral mediators. IFN-alpha is widely used for the treatment of chronic hepatitis B. In our previous studies, a subtype of woodchuck IFN-alpha (wIFN-alpha) was characterized and has been shown to be active in suppressing the replication of woodchuck hepatitis virus (WHV) in vitro and vivo. Here, we refined the analysis of the IFN-alpha/beta system of the woodchuck and studied the expression of wIFN-alpha/beta in peripheral blood lymphocytes (PBLs) from na?ve and WHV-infected woodchucks. A number of wIFN-alpha genes were sequenced and could be classified into 10 subtypes and 3 pseudotypes. The biological activity of different subtypes of wIFN-alpha was demonstrated by their ability to protect woodchuck cells against encephalomyocarditis virus infection and to induce MxA expression in woodchuck cells. Additionally, a partial sequence of wIFN-beta was characterized. A subtyping method for wIFN-alpha based on restriction length polymorphism analysis was developed. Further, the expression of wIFN by woodchuck PBLs after stimulation with polyI/C was investigated. The maximal production of wIFN by woodchuck PBLs occurred within the first 48 h after addition poly I/C. The wIFN-alpha subtypes 1, 4, and 5 were found to be produced by poly I/C-stimulated woodchuck PBLs, indicating a selective expression of wIFN-alpha subtypes. PBLs from chronically WHV-infected woodchucks showed a reduced ability to produce wIFN when stimulated with poly I/C. The results suggest that woodchucks with chronic WHV infection have impaired immunological responses to poly I/C.