• Economic losses of carbon emissions from circum-Arctic permafrost regions under RCP-SSP scenarios

      Chen, Yating; Liu, Aobo; Zhang, Zhihua; Hope, Chris; Crabbe, M. James C.; Beijing Normal University; Shandong University; Cambridge University; University of Oxford; University of Bedfordshire (Elsevier, 2018-12-20)
      Under rapid Arctic warming, the vast amount of labile organic carbon stored in Arctic permafrost soils poses a potentially huge threat. Thawing permafrost will release hundreds of billion tons of soil carbon into the atmosphere in the form of CO2 and CH4 that would further intensify global warming and bring more challenges to human society. In this study, we use the PInc-PanTher model to estimate carbon emissions from thawing permafrost in the circum-Arctic during 2010-2100 followed by the PAGE09 integrated assessment model to evaluate the net economic losses caused by these permafrost carbon emissions. Our results show that in terms of net present value (NPV), the release of CO2 and CH4 from circum-Arctic permafrost will generate estimated net economic losses of US$2.5 trillion (5-95% range: 0.3-11.2 US$ trillion) under the RCP4.5-SPP1 scenario and US$12.7 trillion (5-95% range: 1.6-41.8 US$ trillion) under the RCP8.5-SPP3 scenario between 2010-2100, which contribute ~4.9% and ~6.4% respectively of net economic losses of global carbon emissions.
    • Effect and mechanism of Ganoderma lucidum spores on alleviation diabetic cardiomyopathy in a pilot in vivo study

      Shaher, Fahmi; Wang, Shuqiu; Qiu, Hong-Bin; Hu, Yu; Zhang, Yu; Wang, Weiqun; AL-ward, Hisham; Abdulghani, Mahfoudh A. M.; Baldi, Salem; Zhou, Shaobo; et al. (Dove Press, 2020-12-07)
      Background: Ganoderma lucidum spores (GLS) exhibit disease prevention properties, but no study has been carried out on the anti-diabetic cardiomyopathy property of GLS. The aim of this study is to evaluate the hyperglycemia-mediated cardiomyopathy protection and mechanisms of GLS in diabetic rats induced by streptozotocin (STZ). Methods: Male SD rats were randomly divided into three groups. Two groups were given STZ (50 mg/kg, i.p.) treatment and when their fasting plasma glucose was above 16.7 mmol/L, one group was given placebo, as diabetic group; and another group was given GLS (300 mg/kg) treatment. The group without STZ treatment was given placebo as a control group. The experiment lasted 70 days. The histology of myocardium and biomarkers of antioxidant, myocardial injury, pro-inflammatory cytokines, pro-apoptotic proteins and phosphorylation of key proteins in PI3K/AKT pathway were assessed. Results: Biochemical analysis showed that GLS treatment significantly reduced the blood glucose (-20.3%) and triglyceride (-20.4%) levels compared to diabetic group without treatment. GLS treatment decreased the content of MDA (-25.6%) and activity of lactate dehydrogenase (-18.9%) but increased the activity of GSH-Px (65.4%). Western blot analysis showed that GLS treatment reduced the expression of both alpha-smooth muscle actin and brain natriuretic peptide. Histological analysis on the cardiac tissue micrographs showed that GLS treatment reduced the collagen fibroses and glycogen reactivity in myocardium. Both western blot and immunohistochemistry analyses showed that GLS treatment decreased the expression levels of pro-inflammatory factors (cytokines IL-1β, and TNF-α) as well as apoptosis regulatory proteins (Bax, caspase-3 and -9), but increased the Bcl-2. Moreover, GLS treatment significantly increased the phosphorylation of key proteins involved in PI3K/AKT pathway, e.g. p-AKT p-PI3K and mTOR. Conclusion: The results indicated that GLS treatment alleviates diabetic cardiomyopathy by reducing hyperglycemia, oxidative stress, inflammation, apoptosis and further attenuating the fibrosis and myocardial dysfunction induced by STZ through the stimulation of the PI3K/Akt/mTOR signaling pathway.
    • Effect of culture medium on morphogenic processes in vitro in Cinchona officinalis L.

      Moreno Serrano, José Antonio; Pérez Ruíz, César; Moreno Fierro, Ivonne; Moreno Fierro, Jorge (Facultad de Ciencias Agrarias. Universidad Nacional de Cuyo, 2019-06-30)
      This paper describes the effect of the various plant growth regulators of the culture medium on morphogenic processes in vitro in Cinchona officinalis L, a highly vulnerable species from southern Ecuador. To do this, different concentrations of NaOCl were used in combination with different immersion times for seed disinfection; for seed germination in vitro GA3 was added to the MS basal culture medium in different concentrations, and for morphogenic processes in vitro, different concentrations of auxins and cytokinins were combined. The decrease in the contamination rate was with high concentrations of NaOCl and an increase in the germination rate in 45 days with the addition of 1.0 mg L-1 GA3 to the culture medium the hormonal combination of 0.5 mg L-1 NAA + 2.5 mg L-1 BAP showed a high rate of shoot proliferation and with 1.0 mg L-1 NAA a high number of roots was obtained. In the callogenesis phase, the best results were obtained with 1.0 mg L-1 2,4-D + 0.5 mg L-1 BAP for callus proliferation. In vitro propagation protocols were generated in Cinchona officinalis L, for the preservation and conservation of the species.
    • Effect of dietary fatty acids on tumorigenesis of colon cancer induced by methyl nitrosourea in rats

      Zhou, Shaobo; Wang, G.; Chen, B.; Wang, P.; ; Chinese Academy of Preventive Medicine (Begell House, 2000-01-01)
      We studied the effect of dietary fatty acid composition on the tumorigenesis of colon cancer induced by methyl nitrosourea (MNU) in rats. Five groups of Sprague-Dawley male rats were fed with semi-synthetic diets that contained different proportions of beef tallow, soybean oil, alkana oil, corn oil, and fish oil for 180 days. Each group was matched with a control group fed with the same diet. The experimental groups were given MNU in PBS i.p. 6 times at weekly intervals. The control groups were given PBS only. The incidence of colon cancer, the average volume of the tumors, PCNA, cell kinetics, membrane lipid fluidity, ALP activity, and the content of PGE2 in colonic mucous and the fatty acid distribution in the testis pad fat were measured at the end of the experiment. The results showed that the incidence of colon cancer and the average volume of the tumors in animals fed with diets that contained mainly beef tallow, soybean oil, or alkana oil were significantly higher than that in animals fed with diets that contained mainly fish oil. The diet containing 13.9% of SFA, 16.4% of MUFA, and 68.8% of PUFA showed the strongest inhibition effect. This may be due to the mechanism of protecting the membrane lipid fluidity, decreasing the amount of PCNA in colon cells, the number of propidium iodine-labeled cells in S phase, the activity of ALP and inhibiting the production of AA and thus decreasing the amount of PGE2.
    • The effect of polyploidy and hybridization on the evolution of floral colour in Nicotiana (Solanaceae)

      Le Comber, Steven C.; Chittka, Lars; Dodsworth, Steven; Verity, Robert; Kelly, Laura J.; Knapp, Sandra; Baldwin, Ian T.; Chase, Mark W.; Mhiri, Corinne; Kovařík, Aleš; et al. (Oxford University Press, 2015-05-15)
      Background and Aims. Speciation in angiosperms can be accompanied by changes in floral colour that may influence pollinator preference and reproductive isolation. This study investigates whether changes in floral colour can accompany polyploid and homoploid hybridization, important processes in angiosperm evolution. Methods. Spectral reflectance of corolla tissue was examined for 60 Nicotiana (Solanaceae) accessions (41 taxa) based on spectral shape (corresponding to pigmentation) as well as bee and hummingbird colour perception in order to assess patterns of floral colour evolution. Polyploid and homoploid hybrid spectra were compared with those of their progenitors to evaluate whether hybridization has resulted in floral colour shifts. Key Results. Floral colour categories in Nicotiana seem to have arisen multiple times independently during the evolution of the genus. Most younger polyploids displayed an unexpected floral colour, considering those of their progenitors, in the colour perception of at least one pollinator type, whereas older polyploids tended to resemble one or both of their progenitors. Conclusions. Floral colour evolution in Nicotiana is weakly constrained by phylogeny, and colour shifts do occur in association with both polyploid and homoploid hybrid divergence. Transgressive floral colour in N. tabacum has arisen by inheritance of anthocyanin pigmentation from its paternal progenitor while having a plastid phenotype like its maternal progenitor. Potentially, floral colour evolution has been driven by, or resulted in, pollinator shifts. However, those polyploids that are not sympatric (on a regional scale) with their progenitor lineages are typically not divergent in floral colour from them, perhaps because of a lack of competition for pollinators.
    • Effects of Jitai tablet, a traditional Chinese medicine, on plasma adrenocorticotropic hormone and cortisol levels in Heroin addicts during abstinence

      Fan, Hua-Ying; Sun, Li; Li, Xiao-xiao; Zhou, Shaobo; Liang, Jun-cheng; Yan, Ben-yong; Li, Yu; Deng, Yan-ping; Peking University; University of Bedfordshire; et al. (Mary Ann Liebert, 2014-07-10)
      Objectives: To investigate the changes in adrenocorticotropic hormone (ACTH) and cortisol in heroin addicts given Jitai tablet treatment during abstinence. Design: Double-blind, randomized, placebo-controlled clinical trial. Settings/Location: Drug Rehabilitation Bureau of Shanghai Police, China. Participants: 99 volunteers, including 69 heroin addicts and 30 healthy volunteers. Interventions: 69 heroin addicts randomly divided into two groups: the Jitai tablet group, which comprised 34 heroin addicts given Jitai tablet treatment during abstinence, and the placebo group, which comprised 35 heroin addicts given placebo. A control group consisted of 30 sex- and age-matched healthy volunteers. Outcome Measures: ACTH and cortisol in plasma were measured in all groups at baseline and in the Jitai tablet and placebo groups on the third, seventh, and 14th days of abstinence. Results: Levels of both ACTH ( p < .01) and cortisol ( p < .001) were significantly higher in heroin addicts at baseline than in the healthy volunteers. Jitai tablet treatment restored plasma cortisol levels to normal more rapidly than did placebo treatment ( p < .05), but not ACTH levels. A positive correlation between ACTH and cortisol values at baseline ( p < .01) was also found with withdrawal symptom scores and daily dosages of heroin. Conclusions: Heroin addicts could respond to Jitai tablets through changes in the hypothalamus-pituitaryadrenal axis.
    • Effects of stimulation of mu opioid and nociceptin/orphanin FQ peptide (NOP) receptors on alcohol drinking in rhesus monkeys

      Flynn, Shawn M.; Epperly, Phillip M.; Davenport, April T.; Cami-Kobeci, Gerta; Husbands, Stephen M.; Ko, Mei-Chuan; Czoty, Paul W. (Nature Publishing Group, 2019-04-10)
      Alcohol use disorder (AUD) persists as a devastating public health problem; widely effective pharmacological treatments are needed. Evidence from rodent models suggests that stimulating brain receptors for the neuropeptide nociceptin/orphanin FQ (NOP) can decrease ethanol drinking. We characterized the effects of the mu opioid peptide (MOP) receptor agonist buprenorphine and the buprenorphine analog (2S)-2-[(5R,6R,7R,14S)-N-cyclopropylmethyl-4,5-epoxy-6,14-ethano-3-hydroxy-6 methoxymorphinan-7-yl]-3,3-dimethylpentan-2-ol (BU08028), which stimulates MOP and NOP receptors, in a translational nonhuman primate model of AUD. Rhesus monkeys drank a 4% ethanol solution 6 h per day, 5 days per week via an operant behavioral panel in their home cages. To assess behavioral selectivity, monkeys responded via a photo-optic switch to earn food pellets. After characterizing the acute effects of BU08028 (0.001–0.01 mg/kg, i.m.) and buprenorphine (0.003–0.056 mg/kg, i.m.), the drugs were administered chronically using a model of pharmacotherapy assessment that incorporates clinical aspects of AUD and treatment. Acutely, both drugs decreased ethanol drinking at doses that did not affect food-maintained responding. During chronic treatment, effects of BU08028 and buprenorphine were maintained for several weeks without development of tolerance or emergence of adverse effects. BU08028 was ~0.5 and 1.0 log units more potent in acute and chronic studies, respectively. The selective NOP receptor agonist SCH 221510 also selectively decreased ethanol intakes when given acutely (0.03–1.0 mg/kg, i.m.), whereas the MOP antagonist naltrexone (1.7–5.6 mg/kg, i.m.) decreased both ethanol intake and food pellets delivered. These data demonstrate that bifunctional MOP/NOP agonists, which may have therapeutic advantages to MOP-selective drugs, can decrease alcohol drinking in nonhuman primates.
    • Electrochemical detection of non-esterified fatty acid by layer-by-layer assembled enzyme electrodes

      Kang, Jing; Hussain, Anisah T.; Catt, Michael; Trenell, Michael I.; Haggett, Barry G.D.; Yu, Eileen Hao; Newcastle University; University of Bedfordshire (Elsevier, 2013-09-12)
      In this study, detection and measurement of non-esterified fatty acids (NEFA) concentration has been achieved by electrochemical method in one operation step. Multilayer films of poly(dimethyldiallyammonium chloride) (PDA) wrapped multi-wall carbon nanotubes (MWCNTs) and two enzymes acyl-CoA synthetase (ACS) and acyl-CoA oxidase (ACOD) were assembled on a carbon screen printed electrode by the layer-by-layer (LbL) immobilization. The fine polymer-enzyme layers produced by the LbL method, allowed mass transport from the reactant cascading down the layers to accomplish the two-step enzyme reactions. The polymer-CNTs and enzyme modified electrode exhibited good electrocatalytical property retaining enzyme activity. Linear increase of anodic current from H2O2 produced from NEFA oxidation was observed with the increasing concentrations of oleic acid. These results indicate a promising technique for a simple, rapid one-step determination of NEFA for diabetes management.
    • Encapsulation of α-tocopherol in whey protein isolate/chitosan particles using oil-in-water emulsion with optimal stability and bioaccessibility

      Xu, Weili; Lv, Kangxing; Mu, Wei; Zhou, Shaobo; Yang, Yang; University of Bedfordshire; Harbin Institute of Technology (Elsevier, 2021-05-23)
      The aim of this study was to develop an oil-in-water (O/W) emulsion using whey protein isolate (WPI)-chitosan (CN) complex to encapsulate α-tocopherol and to characterize their stability and bioaccessibility in vitro. The O/W emulsions prepared under the optimal conditions (mass ratio of WPI:CN = 1: 1, corn oil containing 5 g/100 g of α-tocopherol) exhibited a monomodal distribution (d = 803.3 ± 6.9 nm) with encapsulation rate of 86.3 ± 2.3%. The emulsions were stable under NaCl (0–150 mmol/L), sugar (0–5 g/100 g), 55 °C for 30 min, pH 5–6.5, even storage for 20 d at 4 °C and 25 °C. During gastric digestion, WPI situated at the surface of emulsion particles can be digested into small molecular peptides by pepsin, but the structure of the core-shell particles remained due to the cross-linking with CN. During intestinal digestion, the structure of the particles disintegrated over the digestion time, and the inner-oil phase was released. Release profiles of the α-tocopherol and free fatty acids showed a burst effect followed by slow release. These results suggest that the WPI-CN complex could be used to achieve a controlled and sustainable release of liposoluble bioactive compounds from O/W emulsions.
    • Engineering nucleotide specificity of succinyl-CoA synthetase in blastocystis: the emerging role of gatekeeper residues

      Vashisht, Kapil; Verma, Sonia; Gupta, Sunita; Lynn, Andrew M.; Dixit, Rajnikant; Mishra, Neelima; Valecha, Neena; Hamblin, Karleigh; Maytum, Robin; Pandey, Kailash C.; et al. (American Chemical Society, 2017-01-24)
      Charged, solvent-exposed residues at the entrance to the substrate binding site (gatekeeper residues) produce electrostatic dipole interactions with approaching substrates, and control their access by a novel mechanism called "electrostatic gatekeeper effect". This proof-of-concept study demonstrates that the nucleotide specificity can be engineered by altering the electrostatic properties of the gatekeeper residues outside the binding site. Using Blastocystis succinyl-CoA synthetase (SCS, EC 6.2.1.5), we demonstrated that the gatekeeper mutant (ED) resulted in ATP-specific SCS to show high GTP specificity. Moreover, nucleotide binding site mutant (LF) had no effect on GTP specificity and remained ATP-specific. However, via combination of the gatekeeper mutant with the nucleotide binding site mutant (ED+LF), a complete reversal of nucleotide specificity was obtained with GTP, but no detectable activity was obtained with ATP. This striking result of the combined mutant (ED+LF) was due to two changes; negatively charged gatekeeper residues (ED) favored GTP access, and nucleotide binding site residues (LF) altered ATP binding, which was consistent with the hypothesis of the "electrostatic gatekeeper effect". These results were further supported by molecular modeling and simulation studies. Hence, it is imperative to extend the strategy of the gatekeeper effect in a different range of crucial enzymes (synthetases, kinases, and transferases) to engineer substrate specificity for various industrial applications and substrate-based drug design.
    • Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

      Gu, Zhuoya; Jin, Ke; Crabbe, M. James C.; Zhang, Yang; Nan, Peng; Zhang, Zhaolei; Zhong, Yang; Liu, Xiaolin; Huang, Yanyan; Hua, Mengyi (Springer, 2016-04-08)
      Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.
    • Establishment of a stable complex formed from whey protein isolate and chitosan and its stability under environmental stresses

      Xu, Weili; Tang, Yinzhao; Yang, Yang; Wang, Guijie; Zhou, Shaobo; Harbin Institute of Technology; University of Bedfordshire (Elsevier, 2020-10-22)
      This study aimed to investigate the stability of a complex formed with whey protein isolate (WPI) and chitosan under environmental stress. The optical density, particle size, zeta potential, chemical characteristics, electrostatic interactions, and surface morphology were evaluated for the stable complexes; the optimum conditions for the generation of the stable complex were 0.2% (wt/wt) whey protein with 0.05% (wt/wt) chitosan at pH 5.7. Under these conditions, the complex particle size was 217.8 ± 11.3 nm and the zeta potential was 16.7 ± 0.92 mV. The complex was formed through electrostatic interactions between the amine groups of chitosan (-NH3+) and carboxyl groups of whey protein (-COO−), and contained a porous network interspaced by heterogeneously sized vacuoles. The complex displayed stable physiochemical characteristics under environmental stresses including NaCl (0–75 mM) or sugar (0–5%) at ambient temperature and upon heating for 15 min at 25–65 °C, up to 65 °C for 30 min. Moreover, the complex could be stably stored for 30 d at 4 °C and for 20 d at 25 °C. The present results provide theoretical insights into the industrial production of chitosan-protein complexes and for microencapsulation of sensitive food or medicinal ingredients to increase their intestinal absorption.
    • Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers

      Liu, Jie; Zhang, Yichen; Diao, Xia; Yu, Kun; Dai, Xiongwei; Qu, Peng; Crabbe, M. James C.; Zhang, Ti-Cao; Qiao, Qin; Yunnan University; et al. (Elsevier, 2021-06-25)
      Fragaria nilgerrensis is a diploid wild strawberry widely distributed in Southwest China. Its white color and “peach-like” fragrance of fruits are valuable characters for the genetic improvement of cultivated strawberry plants. Its strong biotic and abiotic resistance and tolerance also enable it to survive in different habitats in the field. In this study, we evaluated the level of genetic variation within and between 16 populations with 169 individuals of F. nilgerrensis using 16 newly developed EST-SSR (expressed sequence tag-simple sequence repeats) markers. The results show that the genetic diversity of this species was high, based on Nei’s genetic diversity (0.26) and polymorphic loci (0.41), although it is self-compatible and has clonal propagation. Significant genetic differentiation among populations was also detected by AMOVA analysis (Fst = 0.34), which could be indicative of little gene flow (Nm = 0.43) in F. nilgerrensis. The phylogenetic tree indicates that most of individuals from the same population have clustered together. These populations were not grouped based on the geographical distance, consistent with the Mantel test result (R2 = 0.0063, P > 0.05). All the populations were assigned into two ancestral groups, with some individuals admixed, suggesting ancestral gene flow had occurred between these two groups. Our developed EST-SSR markers as well as the genetic diversity and population structure analysis of F. nilgerrensis are important for genetic improvement in the breeding process. Moreover, the populations that contain high genetic diversity would be a priority for collection and conservation.
    • Evidence for the assembly of a bacterial tripartite multidrug pump with a stoichiometry of 3:6:3.

      Janganan, Thamarai K.; Bavro, Vassiliy N; Zhang, Li; Matak-Vinkovic, Dijana; Barrera, Nelson P.; Venien-Bryan, Catherine; Robinson, Carol V.; Borges-Walmsley, Maria Ines; Walmsley, Adrian R.; University of Durham; et al. (American Society for Biochemistry and Molecular Biology, 2011-07-29)
      The multiple transferable resistance (mTR) pump from Neisseria gonorrhoeae MtrCDE multidrug pump is assembled from the inner and outer membrane proteins MtrD and MtrE and the periplasmic membrane fusion protein MtrC. Previously we established that while there is a weak interaction of MtrD and MtrE, MtrC binds with relatively high affinity to both MtrD and MtrE. MtrD conferred antibiotic resistance only when it was expressed with MtrE and MtrC, suggesting that these proteins form a functional tripartite complex in which MtrC bridges MtrD and MtrE. Furthermore, we demonstrated that MtrC interacts with an intraprotomer groove on the surface of MtrE, inducing channel opening. However, a second groove is apparent at the interface of the MtrE subunits, which might also be capable of engaging MtrC. We have now established that MtrC can be cross-linked to cysteines placed in this interprotomer groove and that mutation of residues in the groove impair the ability of the pump to confer antibiotic resistance by locking MtrE in the closed channel conformation. Moreover, MtrE K390C forms an intermolecular disulfide bond with MtrC E149C locking MtrE in the open channel conformation, suggesting that a functional salt bridge forms between these residues during the transition from closed to open channel conformations. MtrC forms dimers that assemble into hexamers, and electron microscopy studies of single particles revealed that these hexamers are arranged into ring-like structures with an internal aperture sufficiently large to accommodate the MtrE trimer. Cross-linking of single cysteine mutants of MtrC to stabilize the dimer interface in the presence of MtrE, trapped an MtrC-MtrE complex with a molecular mass consistent with a stoichiometry of 3:6 (MtrE(3)MtrC(6)), suggesting that dimers of MtrC interact with MtrE, presumably by binding to the two grooves. As both MtrE and MtrD are trimeric, our studies suggest that the functional pump is assembled with a stoichiometry of 3:6:3.
    • Exploring Angiosperms353: an open, community toolkit for collaborative phylogenomic research on flowering plants

      Baker, William J.; Dodsworth, Steven; Forest, Felix; Graham, Sean W.; Johnson, Matthew G.; McDonnell, Angela J.; Pokorny, Lisa; Tate, Jennifer; Wicke, Susann; Wickett, Norman J.; et al. (Wiley, 2021-07-22)
      The unveiling of the angiosperm (flowering plant) tree of life over the past three decades has been one of the great success stories of modern plant biology. Flowering plants underpin most terrestrial biomes: they fix vast amounts of terrestrial carbon, in turn producing a substantial fraction of planetary oxygen, and drive major biogeochemical cycles. The bulk of human calories are derived either directly (crops) or indirectly (fodder) from angiosperms, as are many medicines, fuel, dyes, beverages, timber, fibers, and other materials. Countless indispensable and mundane items that impact human existence find their origins in flowering plants, and without them, life would be decidedly drearier—imagine a world without herbs, spices, or garden flowers, for example. In this context, the importance of a comprehensive understanding of the angiosperm tree of life cannot be overstated. The tree of life is the fundamental, biological roadmap to the evolution and properties of plants (e.g., Wong et al., 2020). For evolutionary biologists, phylogenies allow us to better understand the spectacular rise of the flowering plants to dominance over the past 140 million or so years (e.g., Lutzoni et al., 2018; Ramírez-Barahona et al., 2020). Information about angiosperm phylogenetic relationships also underpins modern angiosperm classification (e.g., APG IV, 2016), and helps us to better understand species origins and boundaries (e.g., Fazekas et al., 2009). Today, tree of life research is undergoing a renaissance due to the development of powerful, new phylogenomic methods (Dodsworth et al., 2019). In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set (Johnson et al., 2019), and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.
    • Exploring Angiosperms353: developing and applying a universal toolkit for flowering plant phylogenomics

      McDonnell, Angela J.; Baker, William J.; Dodsworth, Steven; Forest, Felix; Graham, Sean W.; Johnson, Matthew G.; Pokorny, Lisa; Tate, Jennifer; Wickett, Norman J.; Wicke, Susann; et al. (Wiley, 2021-07-26)
      Special Issue Introduction. Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale et al., 2020). The ability to sequence a customizable predefined genomic subset for several dozens or even hundreds of taxa allows in-depth analyses and the testing of phylogenetic hypotheses in ways that were not previously possible (reviewed in McKain et al., 2018). The most popular methods for targeted sequencing of genomic loci in phylogenomics include (long-)amplicon sequencing (Rothfels et al., 2017) and hybridization capture (Mandel et al., 2014; Weitemier et al., 2014). Targeted amplicon sequencing is based on single-fragment PCR amplification or by using multiplexing methods such as a microfluidic PCR-based amplification of multiple pre-selected genomic regions (e.g., Zhang and Ozdemir, 2009; Ho et al., 2014), which can then be pooled and sequenced. Massively parallel amplicon sequencing was first used in medical diagnostics (Turner et al., 2009) and was later applied to metazoan phylogenetics (Bybee et al., 2011; O’Neill et al., 2013). Microfluidic PCR and long-amplicon sequencing were subsequently applied in plant systematics (Uribe-Convers et al., 2014, 2016; Gostel et al., 2015). Amplicon-based methods can be time consuming as they require careful optimization and validation of primers. These methods are also susceptible to many of the common problems in PCR (such as nonspecific products, inability to amplify large loci in their entirety, or simply no products). Recently, amplicon approaches have been largely supplanted by hybridization-based targeted enrichment, which allows for relatively rapid probe design with reference to a few related transcriptomes or genomes, and allows simultaneous and efficient recovery of many hundreds of genes.
    • Extensive plastid-nuclear discordance in a recent radiation of Nicotiana section Suaveolentes (Solanaceae)

      Dodsworth, Steven; Christenhusz, Maarten J.M.; Conran, John G.; Guignard, Maite S.; Knapp, Sandra; Struebig, Monika; Leitch, Andrew R.; Chase, Mark W. (Oxford University Press, 2020-05-24)
      Nicotiana section Suaveolentes is the largest section of Nicotiana and is a monophyletic group of allotetraploid species. Most of the species are endemic to Australia, but three species occur on islands in the South Pacific as far east as French Polynesia and one species is native to Namibia. Here, we present phylogenetic results based on genome skimming, with near-complete taxon sampling and multiple accessions sampled for several species. These represent the first phylogenetic results for the section that include most recognized taxa, using wild-sourced material wherever possible. Despite known chromosome number and genome size changes in the section, there is little divergence in the ribosomal DNA operon (26S, 18.S and 5.8S plus associated spacers) and plastid genomes, with little to no taxonomic signal in plastome phylogenetic results and clear plastid-nuclear discordance. These results contrast with strong morphological differentiation (both floral and vegetative) between most of the core Australian taxa and obvious differences in ecological preferences. Together, these initial results portray Nicotiana section Suaveolentes as experiencing recent and ongoing radiation in the arid zone of Australia.
    • Extreme climate response to marine cloud brightening in the arid Sahara-Sahel-Arabian Peninsula zone

      Zhu, Yuanzhuo; Zhang, Zhihua; Crabbe, M. James C.; Shandong University; Beijing Normal University; Oxford University; University of Bedfordshire; Shanxi University (Emerald, 2021-02-08)
      Purpose Climatic extreme events are predicted to occur more frequently and intensely and will significantly threat the living of residents in arid and semi-arid regions. Therefore, this study aims to assess climatic extremes’ response to the emerging climate change mitigation strategy using a marine cloud brightening (MCB) scheme. Design/methodology/approach Based on Hadley Centre Global Environmental Model version 2-Earth System model simulations of a MCB scheme, this study used six climatic extreme indices [i.e. the hottest days (TXx), the coolest nights (TNn), the warm spell duration (WSDI), the cold spell duration (CSDI), the consecutive dry days (CDD) and wettest consecutive five days (RX5day)] to analyze spatiotemporal evolution of climate extreme events in the arid Sahara-Sahel-Arabian Peninsula Zone with and without MCB implementation. Findings Compared with a Representative Concentration Pathways 4.5 scenario, from 2030 to 2059, implementation of MCB is predicted to decrease the mean annual TXx and TNn indices by 0.4–1.7 and 0.3–2.1°C, respectively, for most of the Sahara-Sahel-Arabian Peninsula zone. It would also shorten the mean annual WSDI index by 118–183 days and the mean annual CSDI index by only 1–3 days, especially in the southern Sahara-Sahel-Arabian Peninsula zone. In terms of extreme precipitation, MCB could also decrease the mean annual CDD index by 5–25 days in the whole Sahara and Sahel belt and increase the mean annual RX5day index by approximately 10 mm in the east part of the Sahel belt during 2030–2059. Originality/value The results provide the first insights into the impacts of MCB on extreme climate in the arid Sahara-Sahel-Arabian Peninsula zone.
    • Factors affecting targeted sequencing of 353 nuclear genes from herbarium specimens spanning the diversity of angiosperms

      Brewer, Grace E.; Clarkson, James J.; Maurin, Olivier; Zuntini, Alexandre R.; Barber, Vanessa; Bellot, Sidonie; Biggs, Nicola; Cowan, Robyn S.; Davies, Nina M.; Dodsworth, Steven; et al. (Frontiers, 2019-09-12)
      The world’s herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high molecular weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that 1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially, 2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used, 3) taxon specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens, 4) all herbarium sheets should, in future, be annotated with details of the preservation method used, 5) long-term storage of herbarium specimens should be in stable low humidity and low temperature environments, and 6) targeted sequencing with universal probes, such as Angiosperms353 should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
    • Family-level sampling of mitochondrial genomes in Coleoptera: compositional heterogeneity and phylogenetics

      Timmermans, Martijn J.T.N.; Barton, Christopher; Haran, Julien; Ahrens, Dirk; Culverwell, C. Lorna; Ollikainen, Alison; Dodsworth, Steven; Foster, Peter G.; Bocak, Ladislav; Vogler, Alfried P. (Oxford University Press, 2015-12-08)
      Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be sampled more densely. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5 and nad6 genes. Credible tree topologies were obtained with the nhPhyML (‘non-homogeneous’) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher-level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia (Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia)))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, whilst compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.