Crystal structure of TbAlba1 from Trypanosoma brucei

Alba (Acetylation lowers binding affinity) domain is a small, dimeric nucleic acid-binding domain, which is widely distributed in archaea and numbers of eukaryotes. Alba domain containing proteins have been reported to be involved in many cellular processes, such as regulation of translation, maintaining genome stability, regulation of RNA processing and so on. In Trypanosoma brucei (T. brucei), there are four Alba proteins identified, which are named TbAlba1 to TbAlba4. However, the structure and function of TbAlba proteins are still unknown. Here, we solved the crystal structure of TbAlba1 to a resolution of 2.46 Å. TbAlba1 adopts a similar Alba-fold, which comprises of four β-strands (β1-β4) and three long α-helices (α1-α3). Furthermore, TbAlba1 displays some structural features quite different from other Alba proteins. These differences may imply the diverse biological roles of Alba family members.     

Cytotoxic and α-Glucosidase Inhibitory Xanthones from Garcinia mckeaniana Leaves and Molecular Docking Study

A new racemic xanthone, garmckeanin A ( 1 ), and eight known analogs 2 – 9 were isolated from the ethyl acetate (AcOEt) extract of the Vietnamese Garcinia mckeaniana leaves. Their structures were determined by MS and NMR spectral analyses and compared with the literature. The AcOEt extract showed good cytotoxicity against cancer cell lines KB, Lu, Hep-G2 and MCF7, with IC₅₀ values of 5.40–8.76 μg/mL, and it also possessed α-glucosidase inhibitory activity, with an IC₅₀ value of 9.17 μg/mL. Garmckeanin A ( 1 ) exhibited inhibition of all cancer cell lines, with an IC₅₀ value of 7.3–0.9 μM. Allanxanthone C ( 5 ) successfully controlled KB growth, with an IC₅₀ value of 0.54 μM, higher than that of the positive control, ellipticine (IC₅₀ 1.22 μM). Norathyriol ( 8 ) was a promising α-glucosidase inhibitor, with an IC₅₀ value of 0.07 μM, much higher than that of the positive control, acarbose (IC₅₀ 161.0 μM). The interactions of the potential α-glucosidase inhibitors with the C- and N-terminal domains of human intestinal α-glucosidase were also investigated by molecular docking study. The results indicated that bannaxanthone D ( 2 ), garcinone E ( 4 ), bannaxanthone E ( 6 ), and norathyriol ( 8 ) exhibit higher binding affinity to the C-terminal than to the N-terminal domain through essential residues in the active sites. In particular, compound 8 could be assumed to be the most potent mixed inhibitor.     

The two actin-interacting protein 1 genes have overlapping and essential function for embryonic development in Caenorhabditis elegans

Disassembly of actin filaments by actin-depolymerizing factor (ADF)/cofilin and actin-interacting protein 1 (AIP1) is a conserved mechanism to promote reorganization of the actin cytoskeleton. We previously reported that unc-78, an AIP1 gene in the nematode Caenorhabditis elegans, is required for organized assembly of sarcomeric actin filaments in the body wall muscle. unc-78 functions in larval and adult muscle, and an unc-78-null mutant is homozygous viable and shows only weak phenotypes in embryos. Here we report that a second AIP1 gene, aipl-1 (AIP1-like gene-1), has overlapping function with unc-78, and that depletion of the two AIP1 isoforms causes embryonic lethality. A single aipl-1-null mutation did not cause a detectable phenotype. However, depletion of both unc-78 and aipl-1 arrested development at late embryonic stages due to severe disorganization of sarcomeric actin filaments in body wall muscle. In vitro, both AIPL-1 and UNC-78 preferentially cooperated with UNC-60B, a muscle-specific ADF/cofilin isoform, in actin filament disassembly but not with UNC-60A, a nonmuscle ADF/cofilin. AIPL-1 is expressed in embryonic muscle, and forced expression of AIPL-1 in adult muscle compensated for the function of UNC-78. Thus our results suggest that enhancement of actin filament disassembly by ADF/cofilin and AIP1 proteins is critical for embryogenesis.     

A flow cytometry-based screening system for directed evolution of proteases

Proteases are industrially important enzymes but often have to be improved for their catalytic efficiency and stabilities to suit applications. Flow cytometry screening technology based on in vitro compartmentalization in double emulsion had been developed and applied on directed evolution of paraoxonase and β-galactosidase. Further advancements of flow cytometry-based screening technologies will enable an ultra-high throughput of variants offering novel opportunities in directed enzyme evolution under high mutational loads. For the industrially important enzyme class of proteases, a first flow cytometry-based screening system for directed protease evolution has been developed based on an extracellular protease-deficient Bacillus subtilis strain (WB800N), a model protease (subtilisin Carlsberg), and a water-in-oil-in-water double-emulsion technology. B. subtilis WB800N cells are encapsulated in double emulsion with a fluorogenic substrate (rhodamine 110-containing peptide), allowing the screening of protease variants in femtoliter compartments at high throughput. The protease screening technology was validated by employing an epPCR mutant library with a high mutational load and screened for increased resistance toward the inhibitor antipain dihydrochloride. A variant (K127R, T237P, M239I, I269V, Y310F, I372V) with an improved relative resistance was isolated from a small population of active variants, validating the reported protease flow cytometry screening technology for increased inhibitor resistance.     

Comparison of mRNA expression patterns of class B scavenger receptors in BV2 microglia upon exposure to amyloidogenic fragments of beta-amyloid and prion proteins

The inflammatory responses in Alzheimer's disease and prion diseases are dominated by microglia activation. Scavenger receptors have been recently related to the innate immune activation of microglia initiated by endogenous ligands. In this study, we investigated mRNA expression patterns of B class scavenger receptors CD36 and scavenger receptor B1 (SR-B1) in BV2 microglia upon exposure to amyloid fibril Aβ(1-42) and PrP(106-126), respectively. CD36 and SR-B1 showed similar mRNA expression patterns following each treatment. PrP(106-126) induced a rapid increase of CD36 and SR-B1 mRNA levels in the treated microglia, whereas Aβ(1-42) induced a delayed but persistent increase in the mRNA expression of CD36 and SR-B1. These results suggest a possible involvement of CD36 and SR-B1 in microglial interaction with amyloidogenic fragments of beta-amyloid and prion proteins.     

Identification of two major QTL for yellow seed color in two crosses of resynthesized <Emphasis Type="Italic">Brassica napus</Emphasis> line No. 2127-17

Yellow seed color, which results from a thinner seed coat, is associated with improved feed quality of rapeseed (Brassica napus L.) meal and increased oil and protein content. As this trait follows various genetic models under different genetic backgrounds, a study was performed in two genetic backgrounds to gain a better understanding of the genetic mechanisms underlying yellow seed color. The quantitative trait locus (QTL) analysis was undertaken using two crosses, Quantum ×No. 2127-17 (HZ-1) and No. 2127-17 × 94,570 (HZ-2). In the HZ-1 population, three putative QTL were detected in linkage groups N18, N5, and N3, respectively. For all of them, yellow seed color arose from the No. 2127-17 alleles. Of these QTL, the one in linkage group N18 (Bnsc-18a) explained more than half of the phenotypic variation. In the HZ-2 population, three QTL were found in linkage groups N9, N18, and N8, respectively. Of these QTL, that in linkage group N9 (Bnsc-9a) explained more than half of the phenotypic variation, whereas the QTL Bnsc-18a had a low seed color value and explained only 9.03–11.72% of the phenotypic variation. Bulked segregant analysis (BSA) of the extremes of a BC1 population derived from the cross of No. 2127-17 × 94,570 (HZ-3) identified one major gene that was identical with the QTL Bnsc-9a detected in the HZ-2 population. The QTL Bnsc-18a was common in the HZ-1 and HZ-2 populations, and the others were population-specific. These results suggested that different black-seeded forms had different seed color genes.     

Comparative genomics of the social amoebae <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis> and <Emphasis Type="Italic">Dictyostelium purpureum</Emphasis>

Background

The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.

Results

We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.

Conclusions

The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

     

退化红壤丘陵区森林凋落物初始化学组成与分解速率的关系

通过小盆+凋落袋控制试验,研究了我国南方退化红壤丘陵区8种森林凋落物和4种混合凋落物初始化学组成与分解速率的关系.结果表明:阔叶凋落物中的氮、磷、钾、镁含量显著高于针叶凋落物,木质素、碳含量显著低于针叶凋落物;凋落物分解速率与凋落物初始氮、磷、钾、镁含量呈显著正相关,与凋落物初始碳、木质素含量以及木质素/氮、木质素/磷和碳/磷值呈显著负相关;木质素含量解释了凋落物分解速率变异的54.3%,是影响分解速率的最关键因子,凋落物碳、氮、磷含量也与分解速率密切相关,它们与木质素含量一起可解释分解速率变异的81.4%.在退化红壤丘陵区植被恢复过程中,低木质素含量、高氮磷含量的阔叶物种的引入有利于加速凋落物的分解速率和土壤肥力的恢复进程.     

Liver development and cancer formation in zebrafish

Liver is the largest organ in the human body, and it regulates many physiological processes. Many studies on liver development in different model organisms have demonstrated that the mechanism of hepatogenesis is conserved in vertebrates. The identification of the genes and regulatory pathways involved in liver formation provides a basis for the diagnosis of liver diseases and therapeutic interventions. Hepatocellular carcinoma is the third leading cause of mortality worldwide. In the last decade, genetic alterations, which include the gain and loss of DNA, as well as mutations and epigenomic changes, have been identified as important factors in liver cancer. Many genetic pathways are dysregulated during carcinogenesis. Here, we review the gene regulatory networks that underlie liver organogenesis and the dysregulation of these pathways in liver cancer. The genes and pathways involved in hepatogenesis and liver cancer are largely conserved between zebrafish and humans, making this an ideal model organism for the study of this disease. A better understanding of liver development may aid in the development of new diagnostic and therapeutic approaches to liver cancer.