Mechanistic Studies on the 1,2-Spin-Center Shift in Carbohydrate Systems with a Fluorenylcyclopropyl Radical Clock.

The mechanism of the 1,2-spin-center shift in carbohydrate systems was studied with a fluorenylcyclopropyl radical clock. The 1,2-rearrangement of the acyl fluorenylcyclopropane group without opening of the cyclopropane ring provides the strongest evidence that the 1,2-spin-center shift in carbohydrate systems occurs through a concerted transition state without the intermediacy of a 1,3-dioxolanyl radical.

Origin of High Diastereoselectivity in Reactions of Seven-Membered-Ring Enolates.

Unlike many reactions of their six-membered-ring counterparts, the reactions of chiral seven-membered-ring enolates are highly diastereoselective. Diastereoselectivity was observed for a range of substrates, including lactam, lactone, and cyclic ketone derivatives. The stereoselectivity arises from torsional and steric interactions that develop when electrophiles approach the diastereotopic π-faces of the enolates, which are distinguished by subtle differences in the orientation of nearby atoms of the ring.

Dinitrogen Coordination to a High-Spin Diiron(I/II) Species.

Dinitrogen coordination to iron centers underpins industrial and biological fixation in the Haber-Bosch process and by the FeM cofactors in the nitrogenase enzymes. The latter employ local high-spin metal centers; however, iron-dinitrogen coordination chemistry remains dominated by low-valent states, contrasting the enzyme systems. Here, we report a high-spin mixed-valent cis-(µ-1,2-dinitrogen)diiron(I/II) complex [(FeBr)2 (µ-N2 )Lbis ]- (2), where [Lbis ]- is a bis(ß-diketiminate) cyclophane. Field-applied Mössbauer spectra, dc and ac magnetic susceptibility measurements, and computational methods support a delocalized S=7 /2 Fe2 N2 unit with D=-5.23 cm-1 and consequent slow magnetic relaxation.

Functional morphology of the cornea of the Little Penguin Eudyptula minor (Aves).

The cornea is a specialized component of the vertebrate eye that provides protection, refractive power, transparency for optical imaging and mechanical support. However, the corneas of birds have received little attention with no comprehensive study of their functional morphology. Using light microscopy and both scanning and transmission electron microscopy, the first description of the ultrastructure of all of the main components of the cornea in two different-sized individuals of the Little Penguin Eudyptula minor is presented. Two types of microprojections protrude from the surface of the cornea with a predominance of microridges and microvilli found in central (flattened) and peripheral regions, respectively. Epithelial cell density is higher in peripheral cornea, especially in the larger (older) individual, while there is a reduction of epithelial cell density with age. The cornea comprises a thick epithelium uniquely attached to the basement membrane with numerous incursions rather than anchoring fibres and anchoring plaques as is found in other vertebrate corneas. Posterior to Bowman's layer, the orthogonally-arranged collagen fibril lamellae in the stroma form extensive branches and anastomoses. Desçemet's membrane is well-developed with an anterior or foetal portion with long banding. However, the thickness of Desçemet's membrane is larger in the older individual with the inclusion of an additional irregular pale-staining posterior portion. Polygonal endothelial cells extend across the cornea as a monolayer with often tortuous cell junctions. Endothelial cell density increases towards the periphery, but decreases with age. Primary cilia are observed protruding through the central region of some endothelial cells into the anterior segment but subsurface structures resembling cilia suggest that these features may be more common. The ultrastructure of the corneal components reveals a range of functional adaptations that reflect the amphibious lifestyle of this seabird.

A comparison of the ultrastructure of the cornea of the pre- and post-metamorphic axolotl (Ambystoma mexicanum, Amphibia).

The corneal ultrastructure of the pre- and post-metamorphic stages of the neotenic axolotl Ambystoma mexicanum is examined using light microscopy and both scanning and transmission electron microscopy to reveal whether there are any morphological changes associated with a switch in lifestyle. Although the complement of corneal layers remains the same, there are significant quantitative changes in corneal, epithelial and stromal thickness, epithelial and endothelial cell size and density, and the thickness of Bowman's layer and Desçemet's membrane. Microholes in the epithelium and vertical sutures within the stroma are predominant features in the pre-metamorphic stage but are rarely seen in the post-metamorphic stage. There are also significant quantitative centro-peripheral differences in the thickness of the whole cornea, primarily due to differences in the thickness of the stroma in both metamorphic stages. These changes may reflect the physiological demands on the cornea as it switches from a purely aquatic to an amphibious lifestyle, which includes venturing onto land.

Triazine Probes Target Ascorbate Peroxidases in Plants.

Though they are rare in nature, anthropogenic 1,3,5-triazines have been used in herbicides as chemically stable scaffolds. Here, we show that small 1,3,5-triazines selectively target ascorbate peroxidases (APXs) in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays), liverwort (Marchantia polymorpha), and other plant species. The alkyne-tagged 2-chloro-4-methyl-1,3,5-triazine probe KSC-3 selectively binds APX enzymes, both in crude extracts and in living cells. KSC-3 blocks APX activity, thereby reducing photosynthetic activity under moderate light stress, even in apx1 mutant plants. This suggests that APX enzymes in addition to APX1 protect the photosystem against reactive oxygen species. Profiling APX1 with KCS-3 revealed that the catabolic products of atrazine (a 1,3,5-triazine herbicide), which are common soil pollutants, also target APX1. Thus, KSC-3 is a powerful chemical probe to study APX enzymes in the plant kingdom.

Characterization of an A-Site Selective Protein Disulfide Isomerase A1 Inhibitor.

Protein disulfide isomerase A1 (PDIA1) is an endoplasmic reticulum (ER)-localized thiol-disulfide oxidoreductase that is an important folding catalyst for secretory pathway proteins. PDIA1 contains two active-site domains (a and a'), each containing a Cys-Gly-His-Cys (CGHC) active-site motif. The two active-site domains share 37% sequence identity and function independently to perform disulfide-bond reduction, oxidation, and isomerization. Numerous inhibitors for PDIA1 have been reported, yet the selectivity of these inhibitors toward the a and a' sites is poorly characterized. Here, we identify a potent and selective PDIA1 inhibitor, KSC-34, with 30-fold selectivity for the a site over the a' site. KSC-34 displays time-dependent inhibition of PDIA1 reductase activity in vitro with a kinact/ KI of 9.66 × 103 M-1 s-1 and is selective for PDIA1 over other members of the PDI family, and other cellular cysteine-containing proteins. We provide the first cellular characterization of an a-site selective PDIA1 inhibitor and demonstrate that KSC-34 has minimal sustained effects on the cellular unfolded protein response, indicating that a-site inhibition does not induce global protein folding-associated ER stress. KSC-34 treatment significantly decreases the rate of secretion of a destabilized, amyloidogenic antibody light chain, thereby minimizing pathogenic amyloidogenic extracellular proteins that rely on high PDIA1 activity for proper folding and secretion. Given the poor understanding of the contribution of each PDIA1 active site to the (patho)physiological functions of PDIA1, site selective inhibitors like KSC-34 provide useful tools for delineating the pathological role and therapeutic potential of PDIA1.

A Comparison of Bleeding Complications in Patients Undergoing Percutaneous Renal Cryoablation Using Cryoprobes with and without Heat-Based Track Ablation.

PURPOSE: To determine if the use of heat-based track ablation with new-generation cryoprobes is associated with decreased renal cryoablation bleeding complications. MATERIALS AND METHODS: Eighty-nine patients who underwent percutaneous cryoablation for treatment of a solitary renal mass with the use of cryoprobes with track ablation (CwTA) from October 29, 2015, to May 18, 2017, were compared with a propensity score-matched control group of 178 patients who underwent treatment with the use of cryoprobes without track ablation (Cw/oTA) from January 5, 2012, to October 28, 2015. Bleeding complications were assessed with the use of the Clavien-Dindo classification system and compared between the matched patient groups by means of conditional logistic regression, both univariately and in a multivariate model to adjust for imbalanced covariates. Change in patient hemoglobin was evaluated as a secondary measure of periprocedural bleeding. RESULTS: Seven of the 89 patients (7.9%) who underwent percutaneous renal cryoablation with the use of CwTA developed major (grade ≥3) bleeding complications, versus 13 of the 178 patients (7.3%) treated with the use of Cw/oTA. Conditional logistic regression analysis adjusted for potential confounders showed that major, minor, and overall bleeding complications were not associated with the type of cryoprobes used for treatment (P values .727, .370, and .733, respectively). There was also no significant difference in postprocedural change in hemoglobin for patients treated with the use of CwTA compared with Cw/oTA (P = .909). Furthermore, total duration of track ablation in patients with bleeding complications (mean 169 seconds, SD 68, range 60-240) was not significantly different than in patients without bleeding complications (mean 171 seconds, SD 86, range 30-360; P = .940). CONCLUSIONS: The use of cryoprobes with heat-based track ablation did not decrease the incidence of bleeding complications after renal cryoablation compared with procedures performed without track ablation.

Engineering E. coli for the biosynthesis of 3-hydroxy-γ-butyrolactone (3HBL) and 3,4-dihydroxybutyric acid (3,4-DHBA) as value-added chemicals from glucose as a sole carbon source.

3-hydroxy-γ-butyrolactone (3HBL) is a versatile chiral synthon, deemed a top value-added chemical from biomass by the DOE. We recently reported the first biosynthetic pathway towards 3HBL and its hydrolyzed form, 3,4-dihydroxybutyric acid (3,4-DHBA) in recombinant Escherichia coli using glucose and glycolic acid as feedstocks and briefly described their synthesis solely from glucose. Synthesis from glucose requires integration of the endogenous glyoxylate shunt with the 3,4-DHBA/3HBL pathway and co-overexpression of seven genes, posing challenges with respect to expression, repression of the glyoxylate shunt and optimal carbon distribution between the two pathways. Here we discuss engineering this integration. While appropriate media and over-expression of glyoxylate shunt enzymes helped overcome repression, two orthogonal expression systems were employed to address the expression and carbon distribution challenge. Synthesis of up to 0.3g/L of 3HBL and 0.7g/L of 3,4-DHBA solely from glucose was demonstrated, amounting to 24% of the theoretical maximum.

Phenotypic integration plasticity in Daphnia magna: an integral facet of G × E interactions.

Phenotypic integration can be defined as the network of multivariate relationships among behavioural, physiological and morphological traits that describe the organism. Phenotypic integration plasticity refers to the change in patterns of phenotypic integration across environments or ontogeny. Because studies of phenotypic plasticity have predominantly focussed on single traits, a G × E interaction is typically perceived as differences in the magnitude of trait expression across two or more environments. However, many plastic responses involve coordinated responses in multiple traits, raising the possibility that relative differences in trait expression in different environments are an important, but often overlooked, source of G × E interaction. Here, we use phenotypic change vectors to statistically compare the multivariate life-history plasticity of six Daphnia magna clones collected from four disparate European populations. Differences in the magnitude of plastic responses were statistically distinguishable for two of the six clones studied. However, differences in phenotypic integration plasticity were statistically distinguishable for all six of the clones studied, suggesting that phenotypic integration plasticity is an important component of G × E interactions that may be missed unless appropriate multivariate analyses are used.

Diastereoselective Alkylations of Chiral Tetrazolo[1,5-a]azepines via Heterobenzylic Anion Intermediates.

The alkylations of chiral seven-membered rings fused to tetrazoles are highly diastereoselective. The diastereoselectivity depended on the placement and the size of the substituent on the ring and on the electrophile. Subsequent alkylations occurred with high stereoselectivity, allowing for the construction of quaternary stereocenters. Computational studies revealed that torsional effects are responsible for the observed diastereoselectivities. Substituted products can be reduced to the corresponding secondary amines, thus providing an approach for synthesizing diastereomerically enriched azepanes.

Delineating the regions of human transferrin involved in interactions with transferrin binding protein B from Neisseria meningitidis.

Pathogenic bacteria in the Neisseriaceae possess a surface receptor mediating iron acquisition from human transferrin (hTf) that consists of a transmembrane iron transporter (TbpA) and a surface-exposed lipoprotein (TbpB). In this study, we used hydrogen/deuterium exchange coupled to mass spectrometry (H/DX-MS) to elucidate the effects on hTf by interaction with TbpB or derivatives of TbpB. An overall conserved interaction was observed between hTf and full-length or N-lobe TbpB from Neisseria meningitidis strains B16B6 or M982 that represent two distinct subtypes of TbpB. Changes were observed exclusively in the C-lobe of hTf and were caused by the interaction with the N-lobe of TbpB. Regions localized to the 'lip' of the C1 and C2 domains that flank the interdomain cleft represent sites of direct contact with TbpB whereas the peptides within the interdomain cleft that encompass iron binding ligands are inaccessible in the closed (holo) conformation. Although substantial domain separation upon binding TbpB cannot be excluded by the H/DX-MS data, the preferred model of interaction involves binding hTf C-lobe in the closed conformation. Alternate explanations are provided for the substantial protection from deuteration of the peptides encompassing iron binding ligands within the interdomain cleft but cannot be differentiated by the H/DX-MS data.

The Functional Anatomy of the Cornea and Anterior Chamber in Lampreys: Insights From the Pouched Lamprey, Geotria australis (Geotriidae, Agnatha).

Extant lampreys (Petromyzontiformes) are one of two lineages of surviving jawless fishes or agnathans, and are therefore of critical importance to our understanding of vertebrate evolution. Anadromous lampreys undergo a protracted lifecycle, which includes metamorphosis from a larval ammocoete stage to an adult that moves between freshwater and saltwater with exposure to a range of lighting conditions. Previous studies have revealed that photoreception differs radically across the three extant families with the Pouched lamprey Geotria australis possessing a complex retina with the potential for pentachromacy. This study investigates the functional morphology of the cornea and anterior chamber of G. australis, which is specialised compared to its northern hemisphere counterparts. Using light microscopy, scanning and transmission electron microscopy and microcomputed tomography, the cornea is found to be split into a primary spectacle (dermal cornea) and a scleral cornea (continuous with the scleral eyecup), separated by a mucoid layer bounded on each side by a basement membrane. A number of other specialisations are described including mucin-secreting epithelial cells and microholes, four types of stromal sutures for the inhibition of stromal swelling, abundant anastomosing and branching of collagen lamellae, and a scleral endothelium bounded by basement membranes. The structure and function of the cornea including an annular and possibly a pectinate ligament and iris are discussed in the context of the evolution of the eye in vertebrates.

Integrated bioprocessing for the pH-dependent production of 4-valerolactone from levulinate in Pseudomonas putida KT2440.

Enzymes are powerful biocatalysts capable of performing specific chemical transformations under mild conditions, yet as catalysts they remain subject to the laws of thermodynamics, namely, that they cannot catalyze chemical reactions beyond equilibrium. Here we report the phenomenon and application of using extracytosolic enzymes and medium conditions, such as pH, to catalyze metabolic pathways beyond their intracellular catalytic limitations. This methodology, termed "integrated bioprocessing" because it integrates intracellular and extracytosolic catalysis, was applied to a lactonization reaction in Pseudomonas putida for the economical and high-titer biosynthesis of 4-valerolactone from the inexpensive and renewable source levulinic acid. Mutant paraoxonase I (PON1) was expressed in P. putida, shown to export from the cytosol in Escherichia coli and P. putida using an N-terminal sequence, and demonstrated to catalyze the extracytosolic and pH-dependent lactonization of 4-hydroxyvalerate to 4-valerolactone. With this production system, the titer of 4-valerolactone was enhanced substantially in acidic medium using extracytosolically expressed lactonase versus an intracellular lactonase: from <0.2 g liter(-1) to 2.1 +/- 0.4 g liter(-1) at the shake flask scale. Based on these results, the production of 4-hydroxyvalerate and 4-valerolactone was examined in a 2-liter bioreactor, and titers of 27.1 g liter(-1) and 8.2 g liter(-1) for the two respective compounds were achieved. These results illustrate the utility of integrated bioprocessing as a strategy for enabling production from novel metabolic pathways and enhancing product titers.

Biosynthesis of chiral 3-hydroxyvalerate from single propionate-unrelated carbon sources in metabolically engineered E. coli.

BACKGROUND: The ability to synthesize chiral building block molecules with high optical purity is of considerable importance to the fine chemical and pharmaceutical industries. Production of one such compound, 3-hydroxyvalerate (3HV), has previously been studied with respect to the in vivo or in vitro enzymatic depolymerization of biologically-derived co-polymers of poly(3-hydroxybutyrate-co-3-hydroxyvalerate). However, production of this biopolymeric precursor typically necessitates the supplementation of a secondary carbon source (e.g., propionate) into the culture medium. In addition, previous approaches for producing 3HV have not focused on its enantiopure synthesis, and thus suffer from increased costs for product purification. RESULTS: Here, we report the selective biosynthesis of each 3HV stereoisomer from a single, renewable carbon source using synthetic metabolic pathways in recombinant strains of Escherichia coli. The product chirality was controlled by utilizing two reductases of opposing stereoselectivity. Improvement of the biosynthetic pathway activity and host background was carried out to elevate both the 3HV titers and 3HV/3HB ratios. Overall, shake-flask titers as high as 0.31 g/L and 0.50 g/L of (S)-3HV and (R)-3HV, respectively, were achieved in glucose-fed cultures, whereas glycerol-fed cultures yielded up to 0.19 g/L and 0.96 g/L of (S)-3HV and (R)-3HV, respectively. CONCLUSIONS: Our work represents the first report of direct microbial production of enantiomerically pure 3HV from a single carbon source. Continued engineering of host strains and pathway enzymes will ultimately lead to more economical production of chiral 3HV.

The Ultrastructure of the Nictitating Membrane of the Little Penguin (Eudyptula minor, Aves).

The ultrastructure of the nictitating membrane in the little penguin Eudyptula minor was studied using both scanning and transmission electron microscopy to improve our understanding of the function of ocular adnexa in diving birds. Following euthanasia, eyes were enucleated and immersion fixed in Karnovsky's fixative. The nictitating membrane and conjunctiva were embedded in araldite and semi- or ultra-thin sections were stained and photographed using compound and transmission electron microscopes, respectively. Ultrastructural dimensions were measured directly from digital photographs. Surface ultrastructure was examined using scanning electron microscopy. The transparent nictitating membrane consists of a dense stroma surrounded by epithelia on both the external (conjunctival) and internal (bulbar) surfaces. The conjunctival surface of the membrane near the leading edge is covered by microvilli, which transition to microplicae and finally to microridges in the periphery. Beneath the epithelial cells, there is a well-developed basement membrane. Scattered throughout this epithelium are a few goblet cells. The surface of the bulbar epithelium is covered by microvilli near the leading edge, which become denser peripherally. The stroma consists of densely-packed collagen fibrils, which are randomly oriented in bundles near the leading edge but are aligned in the same direction parallel with the epithelial and corneal surfaces and with the leading edge, when the membrane is extended. The ultrastructure of the nictitating membrane in the little penguin differs from other birds and its function is predominantly protective, while preserving clear vision in both water and air.

Metabolic engineering of Escherichia coli for enhanced production of (R)- and (S)-3-hydroxybutyrate.

Synthetic metabolic pathways have been constructed for the production of enantiopure (R)- and (S)-3-hydroxybutyrate (3HB) from glucose in recombinant Escherichia coli strains. To promote maximal activity, we profiled three thiolase homologs (BktB, Thl, and PhaA) and two coenzyme A (CoA) removal mechanisms (Ptb-Buk and TesB). Two enantioselective 3HB-CoA dehydrogenases, PhaB, producing the (R)-enantiomer, and Hbd, producing the (S)-enantiomer, were utilized to control the 3HB chirality across two E. coli backgrounds, BL21Star(DE3) and MG1655(DE3), representing E. coli B- and K-12-derived strains, respectively. MG1655(DE3) was found to be superior for the production of each 3HB stereoisomer, although the recombinant enzymes exhibited lower in vitro specific activities than BL21Star(DE3). Hbd in vitro activity was significantly higher than PhaB activity in both strains. The engineered strains achieved titers of enantiopure (R)-3HB and (S)-3HB as high as 2.92 g liter(-1) and 2.08 g liter(-1), respectively, in shake flask cultures within 2 days. The NADPH/NADP+ ratio was found to be two- to three-fold higher than the NADH/NAD+ ratio under the culture conditions examined, presumably affecting in vivo activities of PhaB and Hbd and resulting in greater production of (R)-3HB than (S)-3HB. To the best of our knowledge, this study reports the highest (S)-3HB titer achieved in shake flask E. coli cultures to date.

High-titer production of monomeric hydroxyvalerates from levulinic acid in Pseudomonas putida.

Hydroxyacids represent an important class of compounds that see application in the production of polyesters, biodegradable plastics and antibiotics, and that serve as useful chiral synthetic building blocks for other fine chemicals and pharmaceuticals. An economical, high-titer method for the production of 4-hydroxyvalerate (4HV) and 3-hydroxyvalerate (3HV) from the inexpensive and renewable carbon source levulinic acid was developed. These hydroxyvalerates were produced by periodically feeding levulinate to Pseudomonas putida KT2440 expressing a recombinant thioesterase II (tesB) gene from Escherichia coli K12. The titer of 4HV in shake flask culture reached 13.9+/-1.2 g L(-1) from P. putida tesB(+) cultured at 32 degrees C in LB medium periodically supplemented with glucose and levulinate. The highest 3HV titer obtained was 5.3+/-0.1 g L(-1) in M9 minimal medium supplemented with glucose and levulinate.

De novo biosynthetic pathways: rational design of microbial chemical factories.

Increasing interest in the production of organic compounds from non-petroleum-derived feedstocks, especially biomass, is a significant driver for the construction of new recombinant microorganisms for this purpose. As a discipline, Metabolic Engineering has provided a framework for the development of such systems. Efforts have traditionally been focused, first, on the optimization of natural producers, later progressing towards re-construction of natural pathways in heterologous hosts. To maximize the potential of microbes for biosynthetic purposes, new tools and methodologies within Metabolic Engineering are needed for the proposition and construction of de novo designed pathways. This review will focus on recent advances towards the design and assembly of biosynthetic pathways, and provide a Synthetic Biology perspective for the construction of microbial chemical factories.

Are cysteine-rich and COOH-terminal domains of dystrophin critical for sarcolemmal localization?

It has been hypothesized that the tight localization of dystrophin at the muscle membrane is carried out by its cysteine-rich and/or carboxyl domains. We report the results of biochemical and immunocytochemical investigations of dystrophin in muscle from a 1-yr-old patient with a large deletion that removes the distal part of the dystrophin gene, thus spanning the exons coding for the cysteine-rich and the carboxy-terminal domains, and extends beyond the glycerol kinase and congenital adrenal hypoplasia genes. Immunological analysis of muscle dystrophin shows that the deletion results in the production of a truncated, but stable, polypeptide correctly localized at the sarcolemma. These data indicate that neither the cysteine-rich domain, nor the carboxyl domain, are necessary for the appearance of normal dystrophin sarcolemmal localization.