Genome-Wide Analysis of NAC Transcription Factors and Characterization of the Cold Stress Response in Sweet Osmanthus

Plant Molecular Biology Reporter - Sweet osmanthus (Osmanthus fragrans) is an evergreen aromatic woody tree widely used in landscaping. However, O. fragrans is very sensitive to cold stress, which...     

A mass spectrometry-based high-throughput screening method for engineering fatty acid synthases with improved production of medium-chain fatty acids

Microbial cell factories have been extensively engineered to produce free fatty acids (FFAs) as key components of crucial nutrients, soaps, industrial chemicals, and fuels. However, our ability to control the composition of microbially synthesized FFAs is still limited, particularly, for producing medium-chain fatty acids (MCFAs). This is mainly due to the lack of high-throughput approaches for FFA analysis to engineer enzymes with desirable product specificity. Here we report a mass spectrometry (MS)-based method for rapid profiling of MCFAs in Saccharomyces cerevisiae by using membrane lipids as a proxy. In particular, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) MS was used to detect shorter acyl chain phosphatidylcholines from membrane lipids and a higher m/z peak ratio at 730 and 758 was used as an indication for improved MCFA production. This colony-based method can be performed at a rate of ~2 s per sample, representing a substantial improvement over gas chromatography-MS (typically >30 min per sample) as the gold standard method for FFA detection. To demonstrate the power of this method, we performed site-saturation mutagenesis of the yeast fatty acid synthase and identified nine missense mutations that resulted in improved MCFA production relative to the wild-type strain. Colony-based MALDI-ToF MS screening provides an effective approach for engineering microbial fatty acid compositions in a high-throughput manner.     

The molecular markers of cancer stem cells in head and neck tumors

Head and neck cancer (HNC) is the six most common malignancy worldwide leading to more than 350,000 deaths annually. Despite recent advances in treatment modalities for these patients, there has been only a slight improvement of prognosis. As cancer stem cells (CSCs) have been implicated in tumor cell survival, progression, and response to therapy, the identification of this tumor subpopulation would have important therapeutic and prognostic implications. In this structured appraisal of the literature, Embase, PubMed, and Ovid were searched for publications that investigated CSC markers of HNC in humans. The search was conducted under the PRISMA guidelines with clear inclusion and exclusion criteria for articles published in the last two decades. The review process resulted in the identification of some key CSC-associated molecules such as CD44, ALDH1, CD133, Oct3/4, Nanog, and Sox2, although a single common CSC sorting marker could not be found. These biomarkers were identified in a range of HNCs but the most common one was squamous cell carcinoma (SCC), predominantly oral SCC. Patient cohorts were of variable size (3–195 individuals) and the most common technique used for detection was immunohistochemistry. Some of the molecules were associated with poor prognosis and may be able to inform the choice of appropriate treatment for these patients.     

Aerobryum brevicuspis S.He (Brachytheciaceae), a new species from northern Vietnam

A new species of Aerobryum Dozy & Molk. (Brachytheciaceae), A. brevicuspis S.He from Lao Cai Province, northern Vietnam is described and illustrated. The new species resembles epiphytic A. speciosum Dozy & Molk. in the presence of pendent, sparsely branched stems, similar shape of leaves and areolation, but differs by its apiculate to cuspidate leaf apices, a single, faint or sometimes double costae in branch leaves, rather differentiated alar cells, the presence of a central strand in the stems, and numerous clustered axillary hairs that are often 5-8(-10) cells long.     

Stereoselective Interaction Between Tetrahydropalmatine Enantiomers and CYP Enzymes in Human Liver Microsomes

Tetrahydropalmatine (THP), with one chiral center, is an alkaloid that possesses analgesic and many other pharmacological actives. The aim of the present study is to investigate stereoselective metabolism of THP enantiomers in human liver microsomes (HLM) and elucidate which cytochrome P450 (CYP) isoforms contribute to the stereoselective metabolism in HLM. Additionally, the inhibitions of THP enantiomers on activity of CYP enzymes are also investigated. The results demonstrated that (+)‐THP was preferentially metabolized by HLM. Ketoconazole (inhibitor of CYP3A4/5) inhibited metabolism of (?)‐THP or (+)‐THP at same degree, whereas the inhibition of fluvoxamine (inhibitor of CYP1A2) on metabolism of (+)‐THP was greater than that of (?)‐THP; moreover, the metabolic rate of (+)‐THP was 5.3‐fold of (?)‐THP in recombinant human CYP1A2. Meanwhile, THP enantiomers did not show obvious inhibitory effect on the activity of various CYP isoforms (CYP1A2, 2A6, 2C8, 2C9, 2C19, 2E1, and 3A4/5), whereas (?)‐THP, but not (+)‐THP, significantly inhibited the activity of CYP2D6 with the Ki value of 6.42 ± 0.38 μM. The results suggested that THP enantiomers were predominantly metabolized by CYP3A4/5 and CYP1A2 in HLM, and (+)‐THP was preferentially metabolized by CYP1A2, whereas CYP3A4/5 contributed equally to metabolism of (?)‐THP or (+)‐THP. Besides, the inhibition of CYP2D6 by (?)‐THP may cause drug–drug interaction, which should be considered. Chirality 25:43–47, 2013. © 2012 Wiley Periodicals, Inc.     

On the phylogeny and evolution of Mesozoic and extant lineages of Adephaga (Coleoptera,Insecta)

The relationships of extant and extinct lineages of Adephaga were analysed formally for the first time. Emphasis is placed on the aquatic and semiaquatic groups and their evolution in the Mesozoic. ?Triadogyrus and ?Mesodineutus belong to Gyrinidae, the sister group of the remaining families. ?Triaplidae are the sister group of the following groups (Haliplidae, Geadephaga, Dytiscoidea incl. ?Liadytidae, ?Parahygrobiidae and ?Coptoclavidae [major part]). The lack of a ventral procoxal joint and a very short prosternal process are plesiomorphies of ?Triaplidae. ?Coptoclavidae and ?Timarchopsinae are paraphyletic. ?Timarchopsis is placed in a geadephagan clade. In contrast to other coptoclavids, its metathorax is close to the condition found in Haliplidae, with a complete transverse ridge and coxae with large plates and free mesal walls. ?Coptoclavidae s.str., i.e. excl. ?Timarchopsis, is a dytiscoid subgroup. The mesal metacoxal walls are fused, the coxal plates are reduced, and the transverse ridge is absent. ?Stygeonectes belongs to this dytiscoid coptoclavid unit and is therefore misplaced in ?Timarchopsinae. ?Liadytidae belongs to a dytiscoid subgroup, which also comprises the extant families Aspidytidae, Amphizoidae, Hygrobiidae and Dytiscidae. ?Parahygrobia is the sister group of Hygrobiidae. The larvae are characterized by a broad gula, the absence of the lacinia, retractile maxillary bases and very long urogomphi set with long setae. ?Liadytiscinae is the sister group of extant Dytiscidae. There is no support for a clade ?Eodromeinae and for Trachypachidae incl. ?Eodromeinae. ?Fortiseode is nested within Carabidae. The exclusion of fossil taxa has no effect on the branching pattern. The evolution of Adephaga in the Mesozoic is discussed. Possible reasons for the extinction of ?Coptoclavidae are the rise of teleost fish and the competition of Gyrinidae and Dytiscidae, which possess efficient defensive glands and larval mandibular sucking channels.     

Metabolic engineering of Escherichia coli for enhanced biosynthesis of poly(3-hydroxybutyrate) based on proteome analysis

We have previously analyzed the proteome of recombinant Escherichia coli producing poly(3-hydroxybutyrate) [P(3HB)] and revealed that the expression level of several enzymes in central metabolism are proportional to the amount of P(3HB) accumulated in the cells. Based on these results, the amplification effects of triosephosphate isomerase (TpiA) and fructose-bisphosphate aldolase (FbaA) on P(3HB) synthesis were examined in recombinant E. coli W3110, XL1-Blue, and W lacI mutant strains using glucose, sucrose and xylose as carbon sources. Amplification of TpiA and FbaA significantly increased the P(3HB) contents and concentrations in the three E. coli strains. TpiA amplification in E. coli XL1-Blue lacI increased P(3HB) from 0.4 to 1.6 to g/l from glucose. Thus amplification of glycolytic pathway enzymes is a good strategy for efficient production of P(3HB) by allowing increased glycolytic pathway flux to make more acetyl-CoA available for P(3HB) biosynthesis.     

Expression of a lipase on the cell-surface of Escherichia coli using the OmpW anchoring motif and its application to enantioselective reactions

Microbial-surface display is the expression of proteins or peptides on the surface of cells by fusing an appropriate protein as an anchoring motif. Here, the outer membrane protein W (OmpW) was selected as a fusion partner for functional expression of Pseudomonas fluorescence SIK W1 lipase (TliA) on the cell-surface of Escherichia coli. Localization of the truncated OmpW-TliA fusion protein on the cell-surface was confirmed by immunoblotting and functional assay of lipase activity. Enantioselective hydrolysis of rac-phenylethyl butanoate by the displayed lipase resulted in optically active (R)-phenyl ethanol with 96 % enantiomeric excess and 44 % of conversion in 5 days. Thus, a small outer membrane protein OmpW, is a useful anchoring motif for displaying an active enzyme of ~50 kDa on the cell-surface and the surface-displayed lipase can be employed as an enantioselective biocatalyst in organic synthesis.     

Altitudinal Distribution of Ammonia-Oxidizing Archaea and Bacteria in Alpine Grassland Soils Along the South-Facing Slope of Nyqentangula Mountains,Central Tibetan Plateau

Nitrogen is a major limiting nutrient for the net primary production of terrestrial ecosystems, especially on sentinel alpine ecosystem. Ammonia oxidation is the first and rate-limiting step on nitrification process and is thus crucial to nitrogen cycle. To decipher climatic influence on ammonia oxidizers, their communities were characterized by qPCR and clone sequencing by targeting amoA genes (encoding the alpha subunit of ammonia mono-oxygenase) in soils from 7 sites over an 800 m elevation transect (4400–5200 m a.s.l.), based on “space-to-time substitution” strategy, on a steppe-meadow ecosystem located on the central Tibetan Plateau (TP). Archaeal amoA abundance outnumbered bacterial amoA abundance at lower altitude (<4800 m a.s.l.), but bacterial amoA abundance was greater in surface soils at higher altitude (≥4800 m a.s.l.). Archaeal amoA abundance decreased with altitude in surface soil, while its abundance stayed relatively stable and was mostly greater than bacterial amoA abundance in subsurface soils. Conversely, bacterial amoA abundance gradually increased with altitude at all three soil depths. Statistical analysis indicated that altitude-dependent factors, in particular pH and precipitation, had a profound effect on the abundance and community of ammonia-oxidizing bacteria, but only on the community composition of ammonia-oxidizing archaea along the altitudinal gradient. These findings imply that the shifts in the relative abundance and/or community structure of ammonia-oxidizing bacteria and archaea may result from the precipitation variation along the altitudinal gradient. Thus, we speculate that altitude-related factors (mainly precipitation variation combing changed pH), would play a vital role in affecting nitrification process on this alpine grassland ecosystem located at semi-arid area on TP.     

Three-Dimensional Structure of CAP-Gly Domain of Mammalian Dynactin Determined by Magic Angle Spinning NMR Spectroscopy: Conformational Plasticity and Interactions with End-Binding Protein EB1

Microtubules and their associated proteins play important roles in vesicle and organelle transport, cell motility and cell division. Perturbation of these processes by mutation typically gives rise to severe pathological conditions. In our efforts to obtain atomic information on microtubule-associated protein/microtubule interactions with the goal to understand mechanisms that might potentially assist in the development of treatments for these diseases, we have determined the three-dimensional structure of CAP-Gly (cytoskeleton-associated protein, glycine-rich) domain of mammalian dynactin by magic angle spinning NMR spectroscopy. We observe two conformations in the β2 strand encompassing residues T43-V44-A45, residues that are adjacent to the disease-associated mutation, G59S. Upon binding of CAP-Gly to microtubule plus-end tracking protein EB1, the CAP-Gly shifts to a single conformer. We find extensive chemical shift perturbations in several stretches of residues of CAP-Gly upon binding to EB1, from which we define accurately the CAP-Gly/EB1 binding interface. We also observe that the loop regions may exhibit unique flexibility, especially in the GKNDG motif, which participates in the microtubule binding. This study in conjunction with our previous reports suggests that conformational plasticity is an intrinsic property of CAP-Gly likely due to its unusually high loop content and may be required for its biological functions.