Machine learning model of the catalytic efficiency and substrate specificity of acyl-ACP thioesterase variants generated from natural and in vitro directed evolution.

Modulating the catalytic activity of acyl-ACP thioesterase (TE) is an important biotechnological target for effectively increasing flux and diversifying products of the fatty acid biosynthesis pathway. In this study, a directed evolution approach was developed to improve the fatty acid titer and fatty acid diversity produced by E. coli strains expressing variant acyl-ACP TEs. A single round of in vitro directed evolution, coupled with a high-throughput colorimetric screen, identified 26 novel acyl-ACP TE variants that convey up to a 10-fold increase in fatty acid titer, and generate altered fatty acid profiles when expressed in a bacterial host strain. These in vitro-generated variant acyl-ACP TEs, in combination with 31 previously characterized natural variants isolated from diverse phylogenetic origins, were analyzed with a random forest classifier machine learning tool. The resulting quantitative model identified 22 amino acid residues, which define important structural features that determine the catalytic efficiency and substrate specificity of acyl-ACP TE.

Dynamic relationships among pathways producing hydrocarbons and fatty acids of maize silk cuticular waxes.

The hydrophobic cuticle is the first line of defense between aerial portions of plants and the external environment. On maize (Zea mays L.) silks, the cuticular cutin matrix is infused with cuticular waxes, consisting of a homologous series of very long-chain fatty acids (VLCFAs), aldehydes, and hydrocarbons. Together with VLC fatty-acyl-CoAs (VLCFA-CoAs), these metabolites serve as precursors, intermediates and end-products of the cuticular wax biosynthetic pathway. To deconvolute the potentially confounding impacts of the change in silk microenvironment and silk development on this pathway, we profiled cuticular waxes on the silks of the inbreds B73 and Mo17, and their reciprocal hybrids. Multivariate interrogation of these metabolite abundance data demonstrates that VLCFA-CoAs and total free VLCFAs are positively correlated with the cuticular wax metabolome, and this metabolome is primarily affected by changes in the silk microenvironment and plant genotype. Moreover, the genotype effect on the pathway explains the increased accumulation of cuticular hydrocarbons with a concomitant reduction in cuticular VLCFA accumulation on B73 silks, suggesting that the conversion of VLCFA-CoAs to hydrocarbons is more effective in B73 than Mo17. Statistical modeling of the ratios between cuticular hydrocarbons and cuticular VLCFAs reveals a significant role of precursor chain length in determining this ratio. This study establishes the complexity of the product-precursor relationships within the silk cuticular wax-producing network by dissecting both the impact of genotype and the allocation of VLCFA-CoA precursors to different biological processes, and demonstrates that longer chain VLCFA-CoAs are preferentially utilized for hydrocarbon biosynthesis.

Bimetallic Co/Zn zeolitic imidazolate framework ZIF-67 supported Cu nanoparticles: An excellent catalyst for reduction of synthetic dyes and nitroarenes.

In this study, a sub-class of microporous crystalline metal organic frameworks (MOFs) with zeolite-like configurations, i.e., zeolitic imidazolate frameworks of single node ZIF-67 and binary nodes ZIF-Co/Zn are used as the supports to develop Cu nanoparticles based nanocatalysts. Their catalytic activities are comparatively evaluated where Cu(x)@ZIF-Co/Zn exhibits better performances than Cu(x)@ZIF-67 in the reduction of synthetic dyes and nitroarenes. For instance, the Cu(0.25)@ZIF-Co/Zn catalyst shows an excellent reaction rate of 2.088 × 10-2 s-1 and an outstanding activity of 104.4 s-1gcat-1 for the reduction of methyl orange. The same catalyst also performs an exceptional catalytic activity in the hydrogenation of p-nitrophenol to p-aminophenol with the activity of 216.5 s-1gcat-1. A synergistic role of unique electronic properties rising from the direct contact of Cu NPs with the bimetallic nodes ZIF-Co/Zn, higher surface area of support, appropriate Cu loading and maintainable microporous frameworks with higher thermal and hydrolytic stability collectively enhances the catalytic activity of Cu(x)@ZIF-Co/Zn. Moreover, this catalyst shows excellent stability and recyclability, which can retain high conversion after reuse for 10 cycles.

A multigenotype maize silk expression atlas reveals how exposure-related stresses are mitigated following emergence from husk leaves.

The extraordinarily long stigmatic silks of corn (Zea mays L.) are critical for grain production but the biology of their growth and emergence from husk leaves has remained underexplored. Accordingly, gene expression was assayed for inbreds 'B73' and 'Mo17' across five contiguous silk sections. Half of the maize genes (∼20,000) are expressed in silks, mostly in spatiotemporally dynamic patterns. In particular, emergence triggers strong differential expression of ∼1,500 genes collectively enriched for gene ontology terms associated with abiotic and biotic stress responses, hormone signaling, cell-cell communication, and defense metabolism. Further, a meta-analysis of published maize transcriptomic studies on seedling stress showed that silk emergence elicits an upregulated transcriptomic response that overlaps strongly with both abiotic and biotic stress responses. Although the two inbreds revealed similar silk transcriptomic programs overall, genotypic expression differences were observed for 5,643 B73-Mo17 syntenic gene pairs and collectively account for >50% of genome-wide expression variance. Coexpression clusters, including many based on genotypic divergence, were identified and interrogated via ontology-term enrichment analyses to generate biological hypotheses for future research. Ultimately, dissecting how gene expression changes along the length of silks and between husk-encased and emerged states offers testable models for silk development and plant response to environmental stresses.

A metabolomics study of ascorbic acid-induced in situ freezing tolerance in spinach (Spinacia oleracea L.).

Freeze-thaw stress is one of the major environmental constraints that limit plant growth and reduce productivity and quality. Plants exhibit a variety of cellular dysfunctions following freeze-thaw stress, including accumulation of reactive oxygen species (ROS). This means that enhancement of antioxidant capacity by exogenous application of antioxidants could potentially be one of the strategies for improving freezing tolerance (FT) of plants. Exogenous application of ascorbic acid (AsA), as an antioxidant, has been shown to improve plant tolerance against abiotic stresses but its effect on FT has not been investigated. We evaluated the effect of AsA-feeding on FT of spinach (Spinacia oleracea L.) at whole plant and excised-leaf level, and conducted metabolite profiling of leaves before and after AsA treatment to explore metabolic explanation for change in FT. AsA application did not impede leaf growth, instead slightly promoted it. Temperature-controlled freeze-thaw tests revealed AsA-fed plants were more freezing tolerant as indicated by: (a) less visual damage/mortality; (b) lower ion leakage; and (c) less oxidative injury, lower abundance of free radicals ( O 2 · - and H2O2). Comparative leaf metabolite profiling revealed clear separation of metabolic phenotypes for control versus AsA-fed leaves. Specifically, AsA-fed leaves had greater abundance of antioxidants (AsA, glutathione, alpha- & gamma-tocopherol) and compatible solutes (proline, galactinol, and myo-inositol). AsA-fed leaves also had higher activity of antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, and catalase). These changes, together, may improve FT via alleviating freeze-induced oxidative stress as well as protecting membranes from freeze desiccation. Additionally, improved FT by AsA-feeding may potentially include enhanced cell wall/lignin augmentation and bolstered secondary metabolism as indicated by diminished level of phenylalanine and increased abundance of branched amino acids, respectively.

Short versus prolonged freezing differentially impacts freeze - thaw injury in spinach leaves: mechanistic insights through metabolite profiling.

Plant tissues subjected to short or prolonged freezing to a fixed sub-freezing temperature are expected to undergo similar freeze-desiccation but the former causes substantially less injury than the latter. To gain metabolic insight into this differential response, metabolome changes in spinach (Spinacia oleracea L.) leaves were determined following short-term (0.5 and 3.0 h) vs. prolonged freezing (5.5 and 10.5 h) at -4.5°C resulting in reversible or irreversible injury, respectively. LD50 , the freezing duration causing 50% injury, was estimated to be ∼3.1 h and defined as the threshold beyond which tissues were irreversibly injured. From 39 identified metabolites, 19 were selected and clustered into 3 groups: (1) signaling-related (salicylic acid, aliphatic and aromatic amino acids), (2) injury-related (GABA, lactic acid, maltose, fatty acids, policosanols, TCA intermediates) and (3) recovery-related (ascorbic acid, α-tocopherol). Initial accumulation of salicylic acid during short-term freezing followed by a decline may be involved in triggering tolerance mechanisms in moderately injured tissues, while its resurgence during prolonged freezing may signal programmed cell death. GABA accumulated with increasing freezing duration, possibly to serve as a 'pH-stat' against cytoplasmic acidification resulting from lactic acid accumulation. Mitochondria seem to be more sensitive to prolonged freezing than chloroplasts since TCA intermediates decreased after LD50 while salicylic acid and maltose, produced in chloroplasts, accumulate even at 10.5-h freezing. Fatty acids and policosanols accumulation with increasing freezing duration indicates greater injury to membrane lipids and epicuticular waxes. Ascorbic acid and α-tocopherol accumulated after short-term freezing, supposedly facilitating recovery while their levels decreased in irreversibly injured tissues.

Clinical Significance of "Double-hit" and "Double-protein" expression in Primary Gastric B-cell Lymphomas.

BACKGROUND AND AIMS: Primary gastric B-cell lymphoma is the second most common malignancy of the stomach. There are many controversial issues about its diagnosis, treatment and clinical management. "Double-hit" and "double-protein" involving gene rearrangement and protein expression of c-Myc and bcl2/bcl6 are the most used terms to describe DLBCL poor prognostic factors in recent years. However, very little is known about the role of these prognostic factors in primary gastric B-cell lymphomas. This study aims to obtain a molecular pathology prognostic model of gastric B-cell lymphoma for clinical stratified management by evaluating how the "double-hit" and "double-protein" in tumor cells as well as microenvironmental reaction of tumor stromal tissue affect clinical outcome in primary gastric B-cell lymphomas. METHODS: Data and tissues of 188 cases diagnosed with gastric B-cell lymphomas were used in this study. Tumor tissue microarray (TMA) of formalin fixed and paraffin embedded (FFPE) tissues was constructed for fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) analysis with a serial of biomarkers containing MYC, BCL2, BCL6, CD31, SPARC, CD10, MUM1 and Ki-67. Modeled period analysis was used to estimate 3-year and 5-year overall survival (OS) and disease-free survival (DFS) distributions. RESULTS: There was no definite "double-hit" case though the gene rearrangement of c-Myc (5.9%), bcl2 (0.1%) and bcl6 (7.4%) was found in gastric B-cell lymphomas. The gene amplification or copy gains of c-Myc (10.1%), bcl-2 (17.0%) and bcl-6 (0.9%) were present in these lymphomas. There were 12 cases of the lymphomas with the "double-protein" expression of MYC and BCL2/BCL6. All patients with "double-protein" gastric B-cell lymphomas had poor outcome compared with those without. More importantly, "MYC-BCL2-BCL6" negative group of gastric B-cell lymphoma patients had favorable clinical outcome regardless clinical stage, pathological types and therapeutic modalities. And the similar better prognosis was found in the cases with low microvessel density (MVD) in tumor tissue and high expression of SPARC (SPARC≥5%) in stromal cells. CONCLUSIONS: "Double-hit" lymphoma was rare among primary gastric lymphoma, while patients with multiple gene amplification and/or copy gains of c-Myc, bcl2 and bcl6, and "double-protein" gastric B-cell lymphomas had a poor clinical outcome. In addition, patients with MYC, BCL2 and BCL6 expression negative or low MVD in tumor tissue with high expression of SPARC in stromal cells could have better prognosis than other gastric B-cell lymphomas regardless of their clinical stage and pathological types. These results would be of very importance for clinical stratified management and precision medicine of gastric B-cell lymphomas.

A quick guide to CRISPR sgRNA design tools.

Targeted genome editing is now possible in nearly any organism and is widely acknowledged as a biotech game-changer. Among available gene editing techniques, the CRISPR-Cas9 system is the current favorite because it has been shown to work in many species, does not necessarily result in the addition of foreign DNA at the target site, and follows a set of simple design rules for target selection. Use of the CRISPR-Cas9 system is facilitated by the availability of an array of CRISPR design tools that vary in design specifications and parameter choices, available genomes, graphical visualization, and downstream analysis functionality. To help researchers choose a tool that best suits their specific research needs, we review the functionality of various CRISPR design tools including our own, the CRISPR Genome Analysis Tool (CGAT; http://cropbioengineering.iastate.edu/cgat ).

Understanding the cellular mechanism of recovery from freeze-thaw injury in spinach: possible role of aquaporins, heat shock proteins, dehydrin and antioxidant system.

Recovery from reversible freeze-thaw injury in plants is a critical component of ultimate frost survival. However, little is known about this aspect at the cellular level. To explore possible cellular mechanism(s) for post-thaw recovery (REC), we used Spinacia oleracea L. cv. Bloomsdale leaves to first determine the reversible freeze-thaw injury point. Freeze (-4.5°C)-thaw-injured tissues (32% injury vs <3% in unfrozen control) fully recovered during post-thaw, as assessed by an ion leakage-based method. Our data indicate that photosystem II efficiency (Fv/Fm) was compromised in injured tissues but recovered during post-thaw. Similarly, the reactive oxygen species (O2 (•-) and H2 O2 ) accumulated in injured tissues but dissipated during recovery, paralleled by the repression and restoration, respectively, of activities of antioxidant enzymes, superoxide dismutase (SOD) (EC. 1.14.1.1), and catalase (CAT) (EC.1.11.1.6) and ascorbate peroxidase (APX) (EC.1.11.1.11). Restoration of CAT and APX activities during recovery was slower than SOD, concomitant with a slower depletion of H2 O2 compared to O2 (•-) . A hypothesis was also tested that the REC is accompanied by changes in the expression of water channels [aquaporines (AQPs)] likely needed for re-absorption of thawed extracellular water. Indeed, the expression of two spinach AQPs, SoPIP2;1 and SoδTIP, was downregulated in injured tissues and restored during recovery. Additionally, a notion that molecular chaperones [heat shock protein of 70 kDa (HSP70s)] and putative membrane stabilizers [dehydrins (DHNs)] are recruited during recovery to restore cellular homeostasis was also tested. We noted that, after an initial repression in injured tissues, the expression of three HSP70s (cytosolic, endoplasmic reticulum and mitochondrial) and a spinach DHN (CAP85) was significantly restored during the REC.

Is expression of aquaporins (plasma membrane intrinsic protein 2s, PIP2s) associated with thermonasty (leaf-curling) in Rhododendron?

It is postulated that leaf thermonasty (leaf curling) in rhododendrons under sub-freezing temperatures is caused by water redistribution due to extracellular freezing. We hypothesize that aquaporins (AQPs), the transmembrane water-channels, may be involved in regulating water redistribution and thus leaf curling. Our experimental system includes two Rhododendron species with contrasting leaf curling behavior whereby it was observed in R. catawbiense but not in R. ponticum. We compared leaf movements and the expression of two AQPs, i.e. R. catawbiense/ponticum plasma-membrane intrinsic protein 2 (Rc/RpPIP2;1 and Rc/RpPIP2;2), in the two species under freezing-rewarming and dehydration-rehydration cycles. To determine the relationship between extracellular freezing and leaf-curling, we monitored leaf-curling in R. catawbiense with or without controlled ice-nucleation. Our data indicate that extracellular freezing may be required for leaf curling. Moreover, in both species, PIP2s were up-regulated at temperatures that fell in ice-nucleation temperature range. Such up-regulation could be associated with the bulk-water efflux caused by extracellular freezing. When leaves were frozen beyond the ice-nucleation temperature range, PIP2s were continuously down-regulated in R. catawbiense along with the progressive leaf curling, as also observed for RcPIP2;2 in dehydrated leaves; as leaves uncurled during re-warming/rehydration, RcPIP2 expression was restored. On the other hand, R. ponticum, a non-curling species, exhibited substantial up-regulation of RpPIP2s during freezing/dehydration. Taken together, our data suggest that RcPIP2 down-regulation was associated with leaf curling. Moreover, the contrasting PIP2 expression patterns combined with leaf behavior of R. catawbiense and R. ponticum under these two cycles may reflect different strategies employed by these two species to tolerate/resist cellular dehydration.

Proteomic changes associated with freeze-thaw injury and post-thaw recovery in onion (Allium cepa L.) scales.

The ability of plants to recover from freeze-thaw injury is a critical component of freeze-thaw stress tolerance. To investigate the molecular basis of freeze-thaw recovery, here we compared the proteomes of onion scales from unfrozen control (UFC), freeze-thaw injured (INJ), and post-thaw recovered (REC) treatments. Injury-related proteins (IRPs) and recovery-related proteins (RRPs) were differentiated according to their accumulation patterns. Many IRPs decreased right after thaw without any significant re-accumulation during post-thaw recovery, while others were exclusively induced in INJ tissues. Most IRPs are antioxidants, stress proteins, molecular chaperones, those induced by physical injury or proteins involved in energy metabolism. Taken together, these observations suggest that while freeze-thaw compromises the constitutive stress protection and energy supply in onion scales, it might also recruit 'first-responders' (IRPs that were induced) to mitigate such injury. RRPs, on the other hand, are involved in the injury-repair program during post-thaw environment conducive for recovery. Some RRPs were restored in REC tissues after their first reduction right after thaw, while others exhibit higher abundance than their 'constitutive' levels. RRPs might facilitate new cellular homeostasis, potentially by re-establishing ion homeostasis and proteostasis, cell-wall remodelling, reactive oxygen species (ROS) scavenging, defence against possible post-thaw infection, and regulating the energy budget to sustain these processes.

Dehydrin metabolism is altered during seed osmopriming and subsequent germination under chilling and desiccation in Spinacia oleracea L. cv. Bloomsdale: possible role in stress tolerance.

Osmopriming improves seed germination performance as well as stress tolerance. To understand the biochemistry of osmopriming-induced seed stress tolerance, we investigated dehydrin (DHN) accumulation patterns at protein and transcript level (determined by immunoblotting and qPCR) during priming, and subsequent germination under optimal and stress conditions (i.e. chilling and desiccation) in spinach (Spinacia oleracea L. cv. Bloomsdale) seeds. Our data indicate enhanced germination performance of primed seeds is accompanied by increased accumulation of three dehydrin-like proteins (DLPs): 30, 26, and 19-kD. Moreover, 30, 26 and 19-kD DLPs that first only transiently accumulated during priming re-accumulated in response to stresses, suggesting an evidence for 'cross-tolerance', which is initially induced by priming and later recruited during post-priming germination under stresses. Study with CAP85, a spinach DHN, corroborates above observations at the gene-expression and protein accumulation level. Additionally, our results suggest that during seed germination and seedling establishment, CAP85 expression may be regulated by the interplay of two factors: seedling development and stress responses. In conclusion, our data suggest that 30, 26, and 19-kD dehydrin-like proteins and CAP85 may be used as potential biochemical/molecular markers for priming-induced stress tolerance in 'Bloomsdale' spinach.

Dynamics of the antioxidant system during seed osmopriming, post-priming germination, and seedling establishment in Spinach (Spinacia oleracea).

Osmopriming is a pre-sowing treatment that improves seed germination performance and stress tolerance. To understand osmopriming physiology, and its association with post-priming stress tolerance, we investigated the antioxidant system dynamics during three stages: during osmopriming, post-priming germination, and seedling establishment. Spinach seeds (Spinacia oleracea L. cv. Bloomsdale) were primed with -0.6 MPa PEG at 15°C for 8 d, and dried at room temperature for 2 d. Unprimed and primed germinating seeds/seedlings were subjected to a chilling and desiccation stresses. Seed/seedling samples were collected for antioxidant assays and germination performance and stress tolerance were evaluated. Our data indicate that: (1) during osmopriming the transition of seeds from dry to germinating state represses the antioxidant pathways (residing in dry seeds) that involve CAT and SOD enzymes but stimulates another pathway (only detectable in imbibed seeds) involving APX; (2) a renewal of antioxidant system, possibly required by seedling establishment, occurs after roughly 5 d of germination; (3) osmopriming strengthens the antioxidant system and increases seed germination potential, resulting in an increased stress tolerance in germinating seeds. Osmopriming-mediated promotive effect on stress tolerance, however, may diminish in relatively older (e.g. ~5-week) seedlings.

The effect of sesamol on systemic oxidative stress and hepatic dysfunction in acutely iron-intoxicated mice.

This study investigated the effect of sesamol (3,4-methylenedioxyphenol) on systemic oxidative stress and hepatic function in acutely iron-intoxicated mice. Sesamol reduced the levels of lipid peroxidation, hydroxyl radical, iron production and superoxide anion generation, and xanthine oxidase activity in iron-intoxicated mice. In addition, sesamol decreased the serum levels of aspartate aminotransferase and alanine aminotransferase, and ameliorated iron-intoxication-induced histological changes in the liver. In summary, sesamol might attenuate systemic oxidative stress by reducing xanthine oxidase and improving hepatic function in iron-intoxicated mice.

Sesame oil protects against lead-plus-lipopolysaccharide-induced acute hepatic injury.

Lead (Pb) increases lipopolysaccharide (LPS)-induced tumor necrosis factor alpha, which causes liver damage. In this study, we investigated the effect of sesame oil on Pb-plus-LPS (Pb + LPS)-induced acute liver damage in mice. Mice were given sesame oil (8 mL/kg orally) just after Pb acetate (10 mmol/kg i.p.) plus LPS (5 mg/kg i.p.). Aspartate aminotransferase, alanine aminotransferase, tumor necrosis factor-alpha, interleukin-1beta, nitric oxide, and inducible nitric oxide synthase levels were examined. Sesame oil significantly decreased serum aspartate aminotransferase and alanine aminotransferase levels in Pb + LPS-stimulated mice. Sesame oil reduced Pb + LPS-induced tumor necrosis factor-alpha, interleukin-1beta, and nitric oxide production in serum and liver tissue. Furthermore, sesame oil decreased inducible nitric oxide synthase expression in leukocytes and liver tissue in Pb + LPS-treated mice. We hypothesize that the inhibition of proinflammatory cytokines and nitric oxide might be involved in sesame oil-associated protection against Pb + LPS-induced acute hepatic injury in mice.

Sesame oil attenuates Cisplatin-induced hepatic and renal injuries by inhibiting nitric oxide-associated lipid peroxidation in mice.

Although cisplatin (cis-diamminedichloroplatinum) is an effective drug for the treatment of several solid tumors and has been used therapeutically for decades, several cisplatin-induced side effects have limited its therapeutic dosage in clinical studies. Our aim was to examine the effect of sesame oil on cisplatin-induced hepatic and renal injuries in mice (8-week-old female SPF C57BL/6) given subcutaneous cisplatin (0, 5, 10, or 20 mg/kg). Hepatic and renal functions, lipid peroxidation (LPO) levels, and reactive oxygen free radicals were evaluated 3 days after cisplatin administration, and tumor volumes were recorded 0, 3, 6, and 9 days after cisplatin administration. Sesame oil (i) potently attenuated cisplatin-associated hepatic and renal injuries; (ii) decreased cisplatin-initiated LPO as well as the production of hydroxyl radical, peroxynitrite, and nitrite in blood and tissue; and (iii) did not affect the antitumor capacity exerted by cisplatin in mice with melanoma. We suggest that sesame oil attenuates cisplatin-induced hepatic and renal damage by at least partially inhibiting nitric oxide-associated LPO in mice. Sesame oil might be a new approach for preventing cisplatin-induced multiple organ injury during the treatment of tumors.

Sesame oil attenuates acute iron-induced lipid peroxidation-associated hepatic damage in mice.

Acute iron intoxication from the accidental ingestion of iron-containing preparations is one important cause of death in children. The aim of this study was to investigate the protective effect of sesame oil on acute iron-induced lipid peroxidation (LPO) and hepatic injury in mice. Acute iron intoxication was induced by giving ferric nitrilotriacetate to mice. Hepatic function was assessed using blood biochemistry. Free radicals were determined using a high-performance chemiluminescence analyzer. Ferric nitrilotriacetate increased serum ferrous (Fe) and LPO levels, and induced acute hepatic injury. Sesame oil (a) dose-dependently decreased acute iron-induced LPO and hepatic injury, (b) reduced acute iron-associated hydroxyl radical and superoxide anion generation, and (c) inhibited the activity of xanthine oxidase in acute iron intoxication. Thus, sesame oil might ameliorate LPO and acute hepatic injury by inhibiting xanthine oxidase-initiated superoxide anion generation, thereby reducing hydroxyl radical production, at least partially, in acutely iron-intoxicated mice.