An extensive analysis of the African rice genetic diversity through a global genotyping

Key message

We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species.

Abstract

Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.     

Acute Effect of Ammonia on Branched-Chain Amino Acid Oxidation and Incorporation into Proteins in Astrocytes and in Neurons in Primary Cultures

14CO2 production and incorporation of label into proteins from the labeled branched-chain amino acids, leucine, valine, and isoleucine, were determined in primary cultures of neurons and of undifferentiated and differentiated astrocytes from mouse cerebral cortex in the absence and presence of 3 mM ammonium chloride. Production of 14CO2 from [1-14C]leucine and [1-14C]valine was larger than 14CO2 production from [U-14C]leucine and [U-14C]valine in both astrocytes and neurons. In most cases more 14CO2 was produced in astrocytes than in neurons. Incorporation of labeled branched-chain amino acids into proteins varied with the cell type and with the amino acid. Addition of 3 mM ammonium chloride greatly suppressed 14CO2 production from [1-14C]-labeled branched chain amino acids but had little effect on 14CO2 production from [U-14C]-labeled branched-chain amino acids in astrocytes. Ammonium ion, at this concentration, suppressed the incorporation of label from all three branched-chain amino acids into proteins of astrocytes. In contrast, ammonium ion had very little effect on the metabolism (oxidation and incorporation into proteins) of these amino acids in neurons. The possible implications of these findings are discussed, especially regarding whether they signify variations in metabolic fluxes and/or in magnitudes of precursor pools.     

Untersuchungen zum GPT-System unter besonderer Berücksichtigung des stummen Allels GPT0

Zusammenfassung Von 4208 nichtverwandten freiwilligen Blutspendern aus Hessen wurden die GPT-Phänotypen bestimmt und folgende Genfrequenzen errechnet: GPT¹=0,5228; GPT²=0,4737; GPT³=0,0035.Bei der Untersuchung von 108 Familien mit 159 Kindern ergab sich keine Abweichung von der Erbregel.Eine im Rahmen der Familienuntersuchungen zunächst als entgegengesetzte Homozygotie von Mutter und Kind imponierende Diskrepanz konnte durch den Nachweis eines stummen Gens (GPT⁰) abgeklärt werden.Die derzeit vorliegenden Ergebnisse über den GPT-Polymorphismus werden im Hinblick auf dessen Einführung in die forensische Vaterschaftsbegutachtung diskutiert.

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Studies on the GPT system, with special reference to the silent gene GPT⁰

Summary The GPT phenotypes were determined in 4208 non-related voluntary blood donors in Hessen. The following gene frequencies were calculated: GPT¹=0.5228; GPT²=0.4737; GPT³=0.0035.In a study of 108 families with 159 children no exceptions to the laws of inheritance were observed.In this family study one discrepancy, at first assumed to be a mother/child incompatibility (opposite homozygosity) proved to be due to a silent gene (amorph), GPT⁰.The results published on GPT polymorphism hitherto are discussed, with special reference to its implications for the assessment of paternity in forensic medicine.

     

A new inhibitor of adenine nucleotide translocase in mitochondria: agaric acid.

The effect of agaric acid (α cetyl citric acid) on the transport of ADP and ATP has been examined in rat liver mitochondria. Respiration stimulated by ADP is progresively inhibited by agaric acid; maximal inhibition is attained at 40 μM agaric acid. ATPase activity is inhibited 30% by 20 μM agaric acid. The exchange of adenine nucleotides is competitively inhibited by agaric acid.     

Association of MT-ND5 gene variation with mitochondrial respiratory control ratio and NADH dehydrogenase activity in Tibet chicken embryos

NADH dehydrogenase (complex I) couples the oxidation of NADH for the reduction of ubiquinone with the generation of a proton gradient that can be used for the synthesis of ATP. We have found a missense mutation in the MT-ND5 subunit of NADH dehydrogenase in the Tibet chicken breed. In the present study, the mitochondrial respiratory control ratio (RCR) and NADH dehydrogenase activity in Tibet chicken embryonic brain with different genotypes were measured. Significant differences between animals carrying mitochondria with the EF493865.1:m.1627A vs. EF493865.1:m.1627C alleles were observed for RCR and enzyme activity.     

Amphiphilic block copolymers enhance the cellular uptake of DNA molecules through a facilitated plasma membrane transport

Amphiphilic block copolymers have been developed recently for their efficient, in vivo transfection activities in various tissues. Surprisingly, we observed that amphiphilic block copolymers such as Lutrol® do not allow the transfection of cultured cells in vitro, suggesting that the cell environment is strongly involved in their mechanism of action. In an in vitro model mimicking the in vivo situation we showed that pre-treatment of cells with Lutrol®, prior to their incubation with DNA molecules in the presence of cationic lipid, resulted in higher levels of reporter gene expression. We also showed that this improvement in transfection efficiency associated with the presence of Lutrol® was observed irrespective of the plasmid promoter. Considering the various steps that could be improved by Lutrol®, we concluded that the nucleic acids molecule internalization step is the most important barrier affected by Lutrol®. Microscopic examination of transfected cells pre-treated with Lutrol® confirmed that more plasmid DNA copies were internalized. Absence of cationic lipid did not impair Lutrol®-mediated DNA internalization, but critically impaired endosomal escape. Our results strongly suggest that in vivo, Lutrol® improves transfection by a physicochemical mechanism, leading to cellular uptake enhancement through a direct delivery into the cytoplasm, and not via endosomal pathways.     

Bioactive Molecules Derived from Snake Venoms with Therapeutic Potential for the Treatment of Thrombo-Cardiovascular Disorders Associated with COVID-19

The Protein Journal - As expected, several new variants of Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) emerged and have been detected around the world throughout this Coronavirus...     

Effect of Trichodesma indicum extract on cough reflex induced by sulphur dioxide in mice.

The effect of methanol extract of whole plants of Trichodesma indicum R. Br. has been investigated on sulphur dioxide (SO2) induced cough reflex in Swiss albino mice. The extract has demonstrated significant (p < 0.001) inhibition in frequency of cough in all the tested doses when compared with untreated control group. The effect persisted up to 90 min of its oral administration and also comparable to that of the effect exhibited by the standard drug (Codeine phosphate). This study confirmed the traditional use of this plant in the treatment of cough. Determination of underlying mechanism of beneficial effect is major topic requiring further comprehensive investigation.     

Functional significance of Micraspis discolor (F.) (Coccinellidae: Coleoptera) in rice ecosystem

Coccinellids are key predators that are conserved and augmented in agricultural ecosystems, to achieve biological control of pests. Actual quantification of field predation has not been attempted for many of the beneficial coccinellids. Numerous reports show coccinellids as opportunistic, feeding on a variety of food material in addition to their preferred prey. Micraspis discolor is the most abundant species of coccinellid in rice ecosystems and touted as a biocontrol option for brown planthopper (BPH), Nilaparvata lugens (Stal), a key pest of rice. However, it has been reported as both entomophagous and phytophagous. Native polyacrylamide gel electrophoresis (PAGE) was used to separate esterases from whole‐body homogenates of Micraspis and its prey viz., green leafhopper (GLH) Nephotettix virescens (Distant), BPH N. lugens, whitebacked planthopper (WBPH) Sogatella furcifera (Horvath), aphid Rhopalosiphum padi L., thrips, Haplothrips sp., and pollen. Field‐collected beetles showed a range of bands, some corresponding with pollen and GLH, while others were different from prey offered, indicating a wider range of prey spectrum than envisaged. Feeding preference studies confirmed a preference for pollen and GLH in no‐choice (H = 20.724; P = 0.001) and multiple‐choice tests (H = 20.52; P < 0.001) and a significant preference for pollen over all insects offered in the paired‐choice test (t = 5.099; P = 0.007). The abundance of adult M. discolor in rice at flowering phase does not correspond to prey abundance in the field but rather reflects an inclination to pollen feeding more than entomophagy.     

A negative influence of manure on calcareous soils

Summary On a soil rich in CaCO₃ in a semiaride climate in Algeria a hard soil layer, impermeable for plant roots, was formed in a depth of 20–40 cm after farmyard manure application and irrigation. To find the reason soil samples of this field were taken and leaching experiments were carried out in the laboratory, with the result that much more Caions and HCO₃-ions were leached out of the soils with farmyard manure application than from the soils without manure. Probably the high amount of CO₂, being liberated by the organic matter, and the irrigation water dissolved the CaCO₃ in the soil, and the formed Ca- and HCO₃-ions followed the movement of water in the soil. Where the Ca(HCO₃)₂ reached soil layers with a less amount of CO₂, CaCO₃ precipitated and formed the hard soil layer. In order to avoid the formation of such calcareous crusts on irrigated, limy soils in a dry climate it is recommended to fertilize rather often small quantities instead of rarely big quantities of farmyard manure.