Publications

Abstract The expected change in fitness under inbreeding due to deleterious recessive alleles depends on the amount of inbreeding load harbored by a population, that is, the load of deleterious recessive mutations concealed in the heterozygous state, and the opposing effect of genetic purging to remove such a load. This change in fitness can be thus predicted if an estimate of the inbreeding load and the purging coefficient (the parameter that quantifies the amount of purging) are available. These two parameters can be estimated in pedigreed populations, as has been shown for populations under random mating. A question arises whether these parameters can also be estimated under other breeding systems as well as whether they allow accurate prediction of the corresponding expected change in fitness. In conservation programs, it is usually recommended to preserve genetic diversity by equalizing contributions from parents to progeny and avoiding inbred matings. Regular systems of inbreeding have also been proposed as breeding conservation strategies to purge the inbreeding load. Using computer simulations, we first test a method to jointly estimate the initial inbreeding load and the purging coefficient in populations subjected to equalization of parental contributions, circular mating, and partial full‐sib mating. Then, using the expected values of the inbreeding coefficient and the variance of family size, as well as the estimates of the inbreeding load and the purging coefficient, we make simple predictions of the change in fitness over generations under these breeding systems and compare them with simulation results. We discuss how these fitness predictions can help undertaking conservation designs under different breeding scenarios.

Core-shell CdSe/ZnS quantum dots (QDs) dispersed in a droplet of organic solvent have been applied for the first time as luminescent probes for the selective detection of volatile species. Luminescence quenching caused by volatile species was examined after their trapping onto a drop using the headspace single-drop microextraction (HS-SDME) approach along with microvolume fluorospectrometry. The novel method is characterized by low reagent and sample consumption, especially regarding QDs, a reduction about 500-fold for each analysis being attained in comparison with luminescent probing in aqueous phase using conventional luminescence spectrometers with 1 cm quartz cells for measurement. To assess QDs as luminescent probes along with HS-SDME, 14 volatile species were tried. Strong luminescence quenching (i.e., I(0)/I > 2.5) was observed for species such as CH(3)Hg(+) and Se(IV) after hydridation with NaBH(4). Moderate luminescent quenching (I(0)/I ≈ 2) was observed for species such as Hg(II) after its conversion into Hg(0), H(2)S, and methylcyclopentadienyl-manganese tricarbonyl (MMT). Small luminescence quenching effects (i.e., 1< I(0)/I <2) were caused by other hydride forming species such as As(III), Sb(III), Te(IV), and Bi(III), as well as SnBu(4), volatile amines, and endosulfan. Detection limits of 6.3 × 10(-9) and 1.6 × 10(-7) M were obtained for Se(IV) and CH(3)Hg(+), respectively. Repeatability expressed as relative standard deviation (N = 7) was about 5%. QD-HS-SDME-μvolume-fluorospectrometry allows one to carry out matrix separation, preconcentration, and confinement of QDs, hence achieving a selective, sensitive, fast, environmentally friendly, and miniaturized luminescence assay.

AbstractThe Peltigera canina species complex consists of foliose lichenized bitunicate ascohymenial discomycetes forming section Peltigera within the genus Peltigera (Lecanoromycetes, lichen-forming Ascomycetes). To test the circumscription of highly polymorphic species and to resolve relationships among putative members of the P. canina complex, part of the nuclear ribosomal DNA large subunit (LSU rDNA) and the entire internal-transcribed spacer (ITS rDNA) were sequenced for 84 individuals representing 33 putative Peltigera taxa. Seventeen of the 25 taxa from the P. canina complex are well established and widely accepted. The remaining eight taxa have been proposed recently but are undescribed. A hypervariable region in ITS1 (ITS1-HR, sites 111–237 in our alignment) showed remarkable variation in length, especially in the P. canina complex, ranging from 8 to 126 bp, and contained several microsatellites. We describe here an alignment-free method to code such large gap-rich hypervariable regions for phylogenetic analyses. Variation among ITS1-HR sequences greatly contributed to species delimitation and species identification and can be a major asset to future population studies for specific species within section Peltigera. Sequences of ITS1-HR alone were sufficient to identify all existing species of Peltigera from the P. canina species complex and related sections Retifoveatae and Horizontales included in this study. However, only when INAASE (for short ambiguously aligned regions) and ITS1-HR coded characters were added to the combined analysis of nonambiguous LSU and ITS sites was it possible to reach the level of phylogenetic resolution and support necessary to disentangle the P. canina complex. We report here complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. canina complex (P. canina, P. cinnamomea, P. degenii, P. evansiana, P. frigida, P. kristinssonii, P. laciniata, P. lambinonii, P. lepidophora, P. membranacea, P. monticola, P. ponojensis, P. praetextata, P. rufescens and P. ulcerata). Four of the eight newly proposed but undescribed taxa most likely represent new species (P. “fuscopraetextata”, P. “neocanina”, P. “neorufescens” and P. “scotteri”) within the P. canina complex. We found that morphologically and chemically distinct P. didactyla s. str. and P. didactyla var. extenuata form two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level (P. extenuata). The North American and European populations of the morphologically uniform P. degenii might represent two sibling species because they were found to be genetically distinct and monophyletic. Two major monophyletic groups within the P. canina complex (CICADE = CInnamomea + CAnina + DEgenii group and PORUDI = POnojensis + RUfescens + DIdactyla group) seem to be correlated with different humidity preferences. Although some authors previously have suggested interspecies recombination within the P. canina complex, we did not find statistically significant evidence for this phenomenon based on LSU and ITS sequences.KeywordsBayesian inferencegap-rich alignmentsINAASE charactersinternal transcribed spacer (ITS1, 5.8S, ITS2)lichenized Ascomycotamaximum likelihoodmaximum parsimonymicrosatellitesmorphospeciesnuclear large-subunit ribosomal DNA (LSU rDNA)Peltigera canina species complexPeltigeralesphylogeneticssection Peltigera We are very grateful to Orvo Vitikainen, Pak Yau Wong, Claude Roy, Philippe Clerc, Emmanuël Sérusiaux, Bruce McCune, Molly McMullen, Stanislaw Cieslinski, Urszula Bielczyk and Valérie Reeb, who generously forwarded material for this study, as well as Peter Wagner for performing a compatibility analysis. J.M. thanks Bruce McCune for his helpful comments and corrections and Molly McMullen for her careful reading of the manuscript. This research was financially supported by NSF grants (DEB-9615542 and DEB-0133891) to F.L. and the Kosciuszko Foundation scholarship (1999/2000) to J.M. Sequences were generated in the Pritzker Laboratory for Molecular Systematics and Evolution at the Field Museum, Chicago.

Appraised for being one of the oldest staple nutritive foods mainly in the Arabian Peninsula, the date palm tree (<i>Phoenix dactylifera</i> L.), is a crop native to the subtropical and tropical regions of Southern Asia and Africa. Different parts of the date tree have been extensively studied for their nutritional and therapeutic properties. Despite an array of publications on the date tree, there has been no attempt to compile in a single study the traditional uses, nutritive value, phytochemical profile, the medicinal properties as well as the potential of the different plant parts as a functional food. Therefore, this review endeavors to systematically review the scientific literature to highlight the traditional uses of date fruit and parts around the world, the nutritional profile of several parts and the medicinal properties. A total of 215 studies was retrieved (traditional uses (n = 26), nutritional (n = 52), and medicinal (n = 84)). Scientific articles were further categorized as in vitro (n = 33), in vivo (n = 35), and clinical (n = 16) evidences. Date seeds were found to be effective against <i>E. coli</i> and <i>Staphylococcus aureus</i>. Aqueous date pollen was used to manage hormonal problems and boost fertility. Palm leaves showed anti-hyperglycemic effects <i>via</i> inhibition of α-amylase and α-glucosidase. Unlike previous studies, this study highlighted the functional roles of all the plant parts of the palm tree and provided insights into the various mechanism of action of their bioactive compounds. Although scientific shreds of evidence have been growing over the years, there is still a dearth of studies concerning the clinical validation of the date fruit and other plant parts to provide strong evidence on their medicinal uses. In conclusion, <i>P. dactylifera</i> can be regarded as a potent medicinal plant with prophylactic potential and should be further explored to alleviate the burden of both communicable and non-communicable diseases.

Abstract Dietary flavonoids can be detected in plasma as protein‐bound conjugates. Flavonoids–protein interaction is expected to modulate the bioavailability of flavonoids. In this work, the binding flavonoid isomers (galangin, baicalein, apigenin, and genistein; MW=270.25) and B‐ring hydroxylation flavonols (galangin, kaempferol, quercetin, and myricetin, which share the same structure on the A and C rings but have 0, 1, 2, and 3 moieties of ‐OH on the B‐ring, respectively) to protein were investigated by fluorescence quenching method. The apparent binding constants (K a ) of were flavonoid isomers determined as: flavones (106–107 L mol−1)>isoflavone≈flavonol (105 L mol−1). For B‐ring hydroxylation flavonols, the binding affinity increased with increasing number of hydroxyl groups on the B‐ring. The binding constants (K a ) were determined as follows: myricetin>quercetin>kaempferol>galangin.

Energy (ATP) is essentially required to keep activity of our body, for example, the brain consumes a lot of ATP required for the Na+,K+-ATPase (pump) to maintain the low intracellular Na+ concentration essentially important for generation of the action potential for keeping neuronal activity. Under the normal condition, protons (H+) are produced as by-products of ATP generation. Various types of proton-excluding transporters exclude the produced protons to the interstitial fluid to keep the normal intracellular pH (Figure 1). The excluded protons move into the blood vessel via the interstitial space (Figure 1). Under the normal condition, the pH of arterial blood and interstitial fluid is not changed mainly via excretion of the produced protons into urine and partly via the lung as CO2 (Figure 1). Even if protons are transported into blood vessels, the pH of arterial blood is strictly controlled within the range of 7.35–7.45 by strong pH buffering factors such as hemoglobin (Hb) and albumin (Figure 2) (Aoi, Zou, Xiao, & Marunaka, 2020; Marunaka, 2018). In contrast, the interstitial fluid has only relatively weak pH buffers such bicarbonate and phosphate (Figure 2), therefore the interstitial fluid pH is variable depending on the metabolic condition (i.e., the amounts of produced protons) (Figure 2). Compared with normal conditions, much more protons are produced via glycolysis in cancer (Warburg effect) and diabetes (Figure 3A) (Bhattacharya, Omar, Feroz, & Soong, 2016; Chen, Liu, Li, & Chen, 2018; Gillies, Pilot, Marunaka, & Fais, 2019; Liberti & Locasale, 2016; Lu, 2019; Pillai et al., 2019; Potter, Newport, & Morten, 2016). The large amount of produced protons are excluded to the interstitial fluid to keep the normal intracellular pH by highly expressed acid transporters such as monocarboxylate transporter, H+-ATPase (pump), and Na+/H+ exchanger (Figure 1): most parts of the protons move into blood vessels, but some parts of the protons remain in the interstitial fluid (Figure 3A). Even in the case that a large amount of protons move into blood vessels, the pH of arterial blood is strictly controlled within the range of 7.35–7.45 by strong pH buffering factors such as hemoglobin (Hb) and albumin (Figure 2) (Aoi et al., 2020; Marunaka, 2018). In contrast, the local acidity around cells (interstitial fluids) less than pH of 7.0 (in some case, pH becomes ∼6.2; Puppulin et al., 2018) occurs in cases of cancers and diabetes. The difference of pH control in body fluids depends on the presence of pH buffer factors, since the interstitial fluid has no strong pH buffers such as Hb and albumin (Figure 2) (Aoi et al., 2020; Marunaka, 2018). The absence of strong pH buffers such as Hb and albumin in the interstitial fluid different from blood is a weak point regarding pH control. However, if the interstitial fluid would have strong pH buffers such as Hb and albumin, the collection of the metabolites produced in metabolic tissues into the capillary blood vessels driven by oncotic osmotic pressures does not function, resulting in death. This means that the absence of strong pH buffers in the interstitial fluid are essential events for maintenance of our life. Thus, occurrence of the local acidity around cells in diabetes and cancer is not avoided in usual cases. As mentioned above, cancer cells with no mitochondrial function express highly acid-excluding transporters, causing extremely high acidity in the interstitial fluid (Figure 3) (Gillies et al., 2019; Pillai et al., 2019; Puppulin et al., 2018). In contrast, normal cells express much less acid-excluding transporters compared with cancer cells (Gillies et al., 2019; Pillai et al., 2019): this means that normal cells has much weak ability defensing acidic environments, resulting in being easily destroyed by acidic environments. Thus, cancer cells destroy normal cells by acidifying the extracellular environments around normal cells, then produce the growing-up space for cancer cells themselves. The acidity would also diminish the activity and expression of cell adhesion factor, enabling for cancer cells to detach themselves from the primary lesion and cause metastases (Gillies et al., 2019; Pillai et al., 2019; Sumarokova et al., 2018). Some foods, so-called "alkalizing foods," have strong ability to elevate the lowered pH of body fluids observed in cancer and diabetes. The word of "alkalizing foods" is very popularly disseminated; however, the alkalizing mechanism is not so well understood. Representative "alkalizing foods" are weak organic acids containing carboxyl groups (the lower part of Figure 3B) (Aoi et al., 2020; Marunaka, 2018). Weak organic acids containing carboxyl groups are really acids at the oral intake (the lower part of Figure 3B), however only the carboxyl group but not the proton (H+) is absorbed via the intestine and the colon (the lower part of Figure 3B). The absorbed part of carboxyl group is an important factor chelating protons (H+) produced inside of the body (the upper part of Figure 3B). Acidity of the interstitial fluid around cells observed in diabetes (Aoi et al., 2013; Hosogi et al., 2018; Marunaka, Yoshimoto, Aoi, Hosogi, & Ikegaya, 2014) produces insulin resistance (Hayata, Miyazaki, Niisato, Yokoyama, & Marunaka, 2014). The improvement of acidity of the interstitial fluid (elevation of pH) increases insulin sensitivity (improvement of insulin resistance) (Aoi et al., 2013; Hosogi et al., 2018). Thus, the intake of alkalizing foods would elevate the lowed interstitial fluid pH in diabetes and cancer, resulting in improvement of insulin resistance and prevention of cancer cell growth and metastasis (Aoi et al., 2020; Marunaka, 2018). This work was supported by a grant-in-aid from Japan Society of the Promotion of Science (18H03182 to Y.M.).