Phylogenetic analysis is sometimes regarded as being an intimidating, complex process that requires expertise and years of experience. In fact, it is a fairly straightforward process that can be ...learned quickly and applied effectively. This Protocol describes the several steps required to produce a phylogenetic tree from molecular data for novices. In the example illustrated here, the program MEGA is used to implement all those steps, thereby eliminating the need to learn several programs, and to deal with multiple file formats from one step to another (Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739). The first step, identification of a set of homologous sequences and downloading those sequences, is implemented by MEGA's own browser built on top of the Google Chrome toolkit. For the second step, alignment of those sequences, MEGA offers two different algorithms: ClustalW and MUSCLE. For the third step, construction of a phylogenetic tree from the aligned sequences, MEGA offers many different methods. Here we illustrate the maximum likelihood method, beginning with MEGA's Models feature, which permits selecting the most suitable substitution model. Finally, MEGA provides a powerful and flexible interface for the final step, actually drawing the tree for publication. Here a step-by-step protocol is presented in sufficient detail to allow a novice to start with a sequence of interest and to build a publication-quality tree illustrating the evolution of an appropriate set of homologs of that sequence. MEGA is available for use on PCs and Macs from www.megasoftware.net.
Over the past two decades, bioorthogonal chemistry has become a preferred tool to achieve site‐selective modifications of proteins. However, there are only a handful of commonly applied bioorthogonal ...reactions and they display some limitations, such as slow rates, use of unstable or cytotoxic reagents, and side reactions. Hence, there is significant interest in expanding the bioorthogonal chemistry toolbox. In this regard, boronic acids have recently been introduced in bioorthogonal chemistry and are exploited in three different strategies: 1) boronic ester formation between a boronic acid and a 1,2‐cis diol; 2) iminoboronate formation between 2‐acetyl/formyl‐arylboronic acids and hydrazine/hydroxylamine/semicarbazide derivatives; 3) use of boronic acids as transient groups in a Suzuki–Miyaura cross‐coupling or other reactions that leave the boronyl group off the conjugation product. In this Review, we summarize progress made in the use of boronic acids in bioorthogonal chemistry to enable site‐selective labeling of proteins and compare these methods with the most commonly utilized bioorthogonal reactions.
Truth B told: This Review describes recent advances in the use of boronic acids in bioorthogonal chemistry to enable site‐selective labeling of proteins. Strategies include boronic ester condensation and iminoboronate formation, as well as their application as labeling reagents in Suzuki–Miyaura cross‐coupling and other covalent bond‐forming reactions.
We announce the release of kSNP3.0, a program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. kSNP3.0 is a significantly improved ...version of kSNP v2.
kSNP3.0 is implemented as a package of stand-alone executables for Linux and Mac OS X under the open-source BSD license. The executable packages, source code and a full User Guide are freely available at https://sourceforge.net/projects/ksnp/files/
barryghall@gmail.com.
Policymakers worldwide are considering requiring warnings for sugary drinks. A growing number of experimental studies have examined sugary drink warnings' impacts, but no research to our knowledge ...has synthesized this literature. To inform ongoing policy debates, this study aimed to identify the effects of sugary drink warnings compared with control conditions.
We systematically searched 7 databases on June 21, 2019, and October 25, 2019. We also searched reference lists of relevant articles. Two investigators independently screened titles, abstracts, and full texts to identify peer-reviewed articles that used an experimental protocol to examine the effects of sugary drink warnings compared to a control condition. Two investigators independently extracted study characteristics and effect sizes from all relevant full-text articles. We meta-analyzed any outcome assessed in at least 2 studies, combining effect sizes using random effects meta-analytic procedures. Twenty-three experiments with data on 16,241 individuals (mean proportion female, 58%) were included in the meta-analysis. Most studies took place in Latin America (35%) or the US or Canada (46%); 32% included children. Relative to control conditions, sugary drink warnings caused stronger negative emotional reactions (d = 0.69; 95% CI: 0.25, 1.13; p = 0.002) and elicited more thinking about the health effects of sugary drinks (d = 0.65; 95% CI: 0.29, 1.01; p < 0.001). Sugary drink warnings also led to lower healthfulness perceptions (d = -0.22; 95% CI: -0.27, -0.17; p < 0.001) and stronger disease likelihood perceptions (d = 0.15; 95% CI: 0.06, 0.24; p = 0.001). Moreover, sugary drink warnings reduced both hypothetical (d = -0.32; 95% CI: -0.44, -0.21; p < 0.001) and actual consumption and purchasing behavior (d = -0.17; 95% CI: -0.30, -0.04; p = 0.012). Statistically significant effects were not observed for perceptions of added sugar or positive sugary drink attitudes (p's > 0.10). Moderation analyses revealed that health warnings (e.g., "Beverages with added sugar contribute to obesity") led to greater reductions in hypothetical sugary drink purchases than did nutrient warnings (e.g., "High in sugar"; d = -0.35 versus -0.18; Qb = 4.04; p = 0.04). Limitations of this study include that we did not review grey literature and that we were unable to conduct moderation analyses for several prespecified moderators due to an insufficient number of studies.
This international body of experimental literature supports sugary drink warnings as a population-level strategy for changing behavior, as well as emotions, perceptions, and intentions.
PROSPERO ID 146405.
•Whole crickets were enzymatically hydrolyzed using alcalase with varying parameters.•Solubility improved over a wide pH range, compared with the unhydrolyzed cricket.•Some trials showed better ...emulsion capacity while all trials were more stable.•Hydrolysates showed higher foamability but inferior foam stability to the control.
Recently, the benefits of entomophagy have been widely discussed. Due to western cultures’ reluctance, entomophagy practices are leaning more towards incorporating insects into food products. In this study, whole crickets (Gryllodes sigillatus) were hydrolyzed with alcalase at 0.5, 1.5, and 3.0% (w/w) for 30, 60, and 90min. Degree of hydrolysis (DH), amino acid composition, solubility, emulsion and foaming properties were evaluated. Hydrolysis produced peptides with 26–52% DH compared to the control containing no enzyme (5% DH). Protein solubility of hydrolysates improved (p<0.05) over a range of pH’s, exhibiting >30% soluble protein at pH 3 and 7 and 50–90% at alkaline pH, compared with the control. Emulsion activity index ranged from 7 to 32m2/g, while foamability ranged from 100 to 155% for all hydrolysates. These improved functional properties demonstrate the potential to develop cricket protein hydrolysates as a source of functional alternative protein in food ingredient formulations.
The civil rights and black power movements expanded popular awareness of the history and culture of African Americans. But, as Stephen Hall observes, African American authors, intellectuals, ...ministers, and abolitionists had been writing the history of the black experience since the 1800s. With this book, Hall recaptures and reconstructs a rich but largely overlooked tradition of historical writing by African Americans.Hall charts the origins, meanings, methods, evolution, and maturation of African American historical writing from the period of the Early Republic to the twentieth-century professionalization of the larger field of historical study. He demonstrates how these works borrowed from and engaged with ideological and intellectual constructs from mainstream intellectual movements including the Enlightenment, Romanticism, Realism, and Modernism. Hall also explores the creation of discursive spaces that simultaneously reinforced and offered counternarratives to more mainstream historical discourse. He sheds fresh light on the influence of the African diaspora on the development of historical study. In so doing, he provides a holistic portrait of African American history informed by developments within and outside the African American community.
Multicomponent reactions (MCR), transformations employing three or more simple substrates in a single and highly atom-economical operation, are very attractive in both natural product synthesis and ...diversity-oriented synthesis of druglike molecules. Several popular multicomponent reactions were designed by combining two well-established individual reactions that utilize mutually compatible substrates. In this regard, it is not surprising that the merging of two reactions deemed as workhorses of stereoselective synthesis, the Diels–Alder cycloaddition and carbonyl allylboration, would produce a powerful and highly versatile tandem MCR process. The idea of using 1,3-dienylboronates in 4 + 2 cycloadditions as a means to produce cyclic allylic boronates was first reported by Vaultier and Hoffmann in 1987. In their seminal study, a 1-boronodiene was reacted with electron-poor alkenes, and the intermediate cycloadducts were isolated and added to aldehydes in a separate step leading to α-hydroxyalkylated carbocycles via a highly diastereoselective allylboration reaction. The one-pot three-component variant was realized in 1999 by Lallemand and co-workers, and soon after groups led by Hall and Carboni reported heterocyclic variants of the tandem 4 + 2 cycloaddition/allylboration to prepare α-hydroxyalkylated piperidine and pyran containing compounds, respectively. These classes of heterocycles are ubiquitous in Nature and are important components of pharmaceuticals. This Account summarizes the development and evolution of this powerful multicomponent reaction for accessing nonaromatic heterocycles and its many applications in natural products synthesis and drug discovery. The aza4 + 2cycloaddition/allylboration MCR was first optimized in our laboratory using 4-boronylhydrazonobutadienes and N-substituted maleimides, and it was exploited in the preparation of combinatorial libraries of polysubstituted imidopiperidines that feature as many as four elements of chemical diversity. Biological screening of these druglike imidopiperidine libraries unveiled promising bioactive agents such as A12B4C3, the first reported inhibitor of the human DNA repair enzyme, polynucleotide kinase-phosphatase (hPNKP). Related applications of this MCR in target-oriented synthesis also led to total syntheses of palustrine alkaloids. The inverse electron-demand oxa4 + 2 cycloaddition/allyboration variant can take advantage of Jacobsen’s chiral Cr(III)salen catalyst, affording a rare example of catalytic enantioselective MCR, one that provides a rapid access to α-hydroxyalkyl dihydropyrans in high enantio- and diastereoselectivity. This process exploits 3-boronoacrolein pinacolate as the heterodiene with ethyl vinyl ether or various 2-substituted enol ethers, along with a wide variety of aldehydes in the allylation stage. This versatile methodology was deployed in total syntheses of thiomarinol antibiotics, goniodiol and its derivatives, and the complex anticancer macrolide palmerolide A. More recent work from our laboratory centered on the regio- and stereoselective Suzuki–Miyaura cross-coupling of the dihydropyranyl boronates, thus providing a glimpse of the potential for new multicomponent variants that merge hetero4 + 2 cycloadditions of 1-borylated heterodienes with transition metal-catalyzed transformations. This stereoselective MCR strategy holds great promise for provoking continuing applications in complex molecule synthesis and drug discovery, and is likely to inspire new and innovative MCR-based approaches to nonaromatic heterocycles.
Combined results from different independent studies suggest that acclimatization to high altitude induces a slowly developing sympathetic activation, even at levels of hypoxia that cause no acute ...chemoreflex‐mediated sympathoexcitation. We here provide direct neurophysiological evidence for this phenomenon. In eight Danish lowlanders, we quantified mean arterial blood pressure (MAP), heart rate (HR), and muscle sympathetic nerve activity (MSNA), twice at sea level (normoxia and with acute hypoxic exposure to 12.6% O2) and twice at high altitude (after 10 and 50 days of exposure to 4100 m). Measurements were also obtained in eight Bolivian highlanders on one occasion at high altitude. Acute hypoxic exposure caused no increase in MSNA (15 ± 2 vs 16 ± 2 bursts per min, respectively, and also MAP and HR remained stable). In contrast, from sea level to 10 and 50 days in high‐altitude increases were observed in MAP: 72 ± 2 vs 78 ± 2 and 75 ± 2 mm Hg; HR: 54 ± 3 vs 67 ± 3 and 65 ± 3 beats per min; MSNA: 15 ± 2 vs 42 ± 5 and 42 ± 5 bursts per min, all P < .05. Bolivian subjects had high levels of MSNA: 34 ± 4 bursts per min. The simultaneous increase in MAP, HR, and MSNA suggests high altitude‐induced sympathetic activity, which is sustained in well‐acclimatized lowlanders. The high MSNA levels in the Bolivian highlanders suggest lifelong sympathetic activation at high altitude.
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