Mesostructured zeolites: bridging the gap between zeolites and MCM-41

Surfactant-templating is one of the most versatile and useful techniques to implement mesoporous systems into solid materials. Various strategies based on various interactions between surfactants and solid precursors have been explored to produce new structures. Zeolites are invaluable as size- and shape-selective solid acid catalysts. Nevertheless, their micropores impose limitations on the mass transport of bulky feed and/or product molecules. Many studies have attempted to address this by utilizing surfactant-assisting technology to alleviate the diffusion constraints. However, most efforts have failed due to micro/mesopore phase separation. Recently, a new technique combining the uses of cationic surfactants and mild basic solutions was introduced to synthesise mesostructured zeolites. These materials sustain the unique characteristics of zeolites (i.e., strong acidity, crystallinity, microporosity, and hydrothermal stability), including tunable mesopore sizes and degrees of mesoporosity. The mesostructured zeolites are now commercially available through Rive Technology, and show superior performance in VGO cracking. This feature article provides an overview of recent explorations in the introduction of mesoporosity into zeolites using surfactant-templating techniques. Various porous materials, preparation methods, physical and catalytic properties of mesostructured zeolites will be discussed

Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots.

Peer reviewe

Rapid spread of tomato yellow leaf curl virus in China is aided differentially by two invasive whiteflies

BACKGROUND: Tomato yellow leaf curl virus (TYLCV) was introduced into China in 2006, approximately 10 years after the introduction of an invasive whitefly, Bemisia tabaci (Genn.) B biotype. Even so the distribution and prevalence of TYLCV remained limited, and the economic damage was minimal. Following the introduction of Q biotype into China in 2003, the prevalence and spread of TYLCV started to accelerate. This has lead to the hypothesis that the two biotypes might not be equally competent vectors of TYLCV. METHODOLOGY/PRINCIPAL FINDINGS: The infection frequency of TYLCV in the field-collected B. tabaci populations was investigated, the acquisition and transmission capability of TYLCV by B and Q biotypes were compared under the laboratory conditions. Analysis of B. tabaci populations from 55 field sites revealed the existence of 12 B and 43 Q biotypes across 18 provinces in China. The acquisition and transmission experiments showed that both B and Q biotypes can acquire and transmit the virus, however, Q biotype demonstrated superior acquisition and transmission capability than its B counterparts. Specifically, Q biotype acquired significantly more viral DNA than the B biotype, and reached the maximum viral load in a substantially shorter period of time. Although TYLCV was shown to be transmitted horizontally by both biotypes, Q biotype exhibited significantly higher viral transmission frequency than B biotype. Vertical transmission result, on the other hand, indicated that TYLCV DNA can be detected in eggs and nymphs, but not in pupae and adults of the first generation progeny. CONCLUSIONS/SIGNIFICANCE: These combined results suggested that the epidemiology of TYLCV was aided differentially by the two invasive whiteflies (B and Q biotypes) through horizontal but not vertical transmission of the virus. This is consistent with the concomitant eruption of TYLCV in tomato fields following the recent rapid invasion of Q biotype whitefly in China

Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in eukaryotic genomes and have recently become the marker of choice in a wide variety of ecological and evolutionary studies. The advent of next-generation sequencing (NGS) technologies has made it possible to efficiently genotype a large number of SNPs in the non-model organisms with no or limited genomic resources. Most NGS-based genotyping methods require a reference genome to perform accurate SNP calling. Little effort, however, has yet been devoted to developing or improving algorithms for accurate SNP calling in the absence of a reference genome.</p> <p>Results</p> <p>Here we describe an improved maximum likelihood (ML) algorithm called iML, which can achieve high genotyping accuracy for SNP calling in the non-model organisms without a reference genome. The iML algorithm incorporates the mixed Poisson/normal model to detect composite read clusters and can efficiently prevent incorrect SNP calls resulting from repetitive genomic regions. Through analysis of simulation and real sequencing datasets, we demonstrate that in comparison with ML or a threshold approach, iML can remarkably improve the accuracy of <it>de novo</it> SNP genotyping and is especially powerful for the reference-free genotyping in diploid genomes with high repeat contents.</p> <p>Conclusions</p> <p>The iML algorithm can efficiently prevent incorrect SNP calls resulting from repetitive genomic regions, and thus outperforms the original ML algorithm by achieving much higher genotyping accuracy. Our algorithm is therefore very useful for accurate <it>de novo</it> SNP genotyping in the non-model organisms without a reference genome.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Richard Durbin, Dr. Liliana Florea (nominated by Dr. Steven Salzberg) and Dr. Arcady Mushegian.</p

Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies

Transcriptome-wide targeted genotyping is highly attractive for evolutionary and ecological studies but, until recently, accomplishing this goal presented a major technical barrier for the study of non-model organisms. Our group has recently developed a high-throughput targeted genotyping approach (called HD-Marker) based on the high specificity and accuracy of oligo extension-ligation assays that facilitates the design of assays tailored to meet specific genotyping needs. HD-Marker allows for targeted genotyping of over 10 000 genes in a single tube, with strikingly high capture rate (98%-99%) and genotyping accuracy (97%-99%). With the remarkable advantages of cost-effectiveness and flexibility, we envision that HD-Marker has broad application potential in evolutionary and ecological studies

Decomposition of β-O-4 Linked Lignin Model Compound in Anhydrous Ethanol without any Added Catalyst

The cleavage of a lignin model compound of 2-phenoxyacetophenone (2-PAP) was studied in an anhydrous ethanol solvent. A high conversion of 2-PAP (> 99%) to the desired products (> 80% for phenol) with impressive selectivity was achieved in a stainless steel (T316SS) autoclave without any added catalyst. The stainless steel was analyzed as being effective at catalyzing the decomposition of 2-PAP because of its hydrogen transfer activity and stabilization of reaction intermediates, while anhydrous ethanol served as both a solvent and hydrogen donator. An active hydrogen-promoted reaction network was proposed to explain these results. Further investigation demonstrated that the co-catalyst, Cs2.5H0.5PMo12O40, enhanced the cleavage efficiency, which resulted in high yields of the desired products (> 98% of phenol and > 91% of acetophenone). The proposed method in this study based on the stainless steel-promoted hydrogen transfer reaction, which had the merits of a high conversion efficiency and easy handling, can be expected to develop a promising process for further transformation of lignin to valuable multi-substituted aromatics

Molecular characterization of RXR (Retinoid X Receptor) gene isoforms from the bivalve species Chlamys farreri.

BACKGROUND: Bivalves are among the oldest classes of invertebrates, and they exhibit diverse types of sexual patterning. However, our current understanding of the mechanisms of sex determination and differentiation in bivalves remains very limited. The retinoid X receptors (RXRs), which are members of the nuclear receptor family, are involved in sex differentiation in many organisms. RESULTS: In the present study, four full-length RXR-encoding cDNAs (CfRXRs) named CfRXRa, CfRXRb, CfRXRc and CfRXRd were retrieved from Zhikong scallop (Chlamys farreri). The four RXRs exhibited the conserved five-domain structure of nuclear receptor superfamily members and differed from each other only in the T-box of the C domain. The three variants, designated T (+4), T (+20) and T (+24), contained insertions of 4, 20 and 24 amino acids, respectively. The entire CfRXR gene is composed of eight exons and seven introns, and the four isoforms are generated via alternative mRNA splicing. Expression analysis showed that all four isoforms were expressed in both the testis and the ovary during the differentiation stage, whereas no expression was detected in the growth, mature or resting stages. This result suggests that CfRXRs are involved in germ cell differentiation in both sexes. The expression of the four isoforms was also detected in other tissues examined, including mantle, gill, digestive gland, and adductor muscle of sexually mature male and female Zhikong scallops, implying the multiple biological functions of CfRXRs. CONCLUSION: Our study presents the first report of RXR isoforms in bivalves. Further investigation of the functional roles of different RXR isoforms may provide deep insights into the regulatory mechanism of sex differentiation in C. farreri

Fulvic Acid Promotes Legume–Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis

Addition of nucleoside analogues to peg-IFNα-2a enhances virological response in chronic hepatitis B patients without early response to peg-IFNα-2a: a randomized controlled trial

Abstract Background Current treatments for chronic hepatitis B (CHB) include pegylated interferon alpha (PEG-IFN-α) which is an immune modulator, and nucleos(t)ide analogs (NAs) which directly inhibit HBV DNA polymerase. With the limited efficacy of PEG-IFN-α and prolonged treatment periods associated with NAs, there is an urgent need for novel therapeutic strategies, especially for patients with a poor early response to anti-viral therapy. Methods In this study, 178 patients with chronic hepatitis B (n = 131) and compensated (n = 47) HBV-induced cirrhosis were enrolled, 120 patients with HBeAg (+). All the patients were treated for 12 weeks with PEG-IFN-α. Among them, a total of 138 patients with a poor virological response after 12 weeks were treated for an additional 48 weeks with Peg-IFNα-2a (control) (n = 43), with Peg-IFNα-2a + entecavir (ETV) (n = 49), or Peg-IFNα-2a + adefovir dipivoxil (ADV) (n = 46), and were followed for 48 weeks after therapy. Early virological response was defined as undetectable HBV DNA after anti-viral therapy for 12 weeks. Sustained virological response (SVR) was defined as no change in therapeutic effectiveness after 6 months follow-up, and no recurrence.Therapeutic efficacy was determined by evaluating HBV DNA levels, serum and liver HBsAg levels, liver function tests and liver histology. Results Patients in the Peg-IFNα-2a + ETV and Peg-IFNα-2a + ADV groups showed a significantly greater decrease in HBV DNA levels over time, and a significantly higher SVR compared to patients receiving Peg-INFα-2a monotherapy (both P values <0.05). Although patients receiving combination therapy had a significantly higher change in serum HBsAg levels compared to the monotherapy group, there was no significant difference in liver HBsAg levels between the three treatment groups. Conclusion This study demonstrated that in patients with a poor virological response after 12 weeks of treatment with Peg-IFNα-2a alone, addition of ADV or ETV significantly reduced HBV DNA levels, serum HBsAg levels, and increased SVR. Individualization of anti-viral therapy would ensure that only patients who do not respond to Peg-IFNα-2a would receive combination therapy. Our data have important implications for the treatment of CHB patients who fail to show an early response to Peg-IFNα-2a monotherapy. Trial registration This trial was retrospectively registered on 2012 May 24 at the China Clinical Trials Registry (ChiCTR-OCC-12002196)