Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria

The iron(II)- and 2-oxoglutarate (2OG)-dependent dioxygenase AlkB from Escherichia coli (EcAlkB) repairs alkylation damage in DNA by direct reversal. EcAlkB substrates include methylated bases, such as 1-methyladenine (m¹A) and 3-methylcytosine (m³C), as well as certain bulkier lesions, for example the exocyclic adduct 1,N⁶-ethenoadenine (εA). EcAlkB is the only bacterial AlkB protein characterized to date, and we here present an extensive bioinformatics and functional analysis of bacterial AlkB proteins. Based on sequence phylogeny, we show that these proteins can be subdivided into four groups: denoted 1A, 1B, 2A and 2B; each characterized by the presence of specific conserved amino acid residues in the putative nucleotide-recognizing domain. A scattered distribution of AlkB proteins from the four different groups across the bacterial kingdom indicates a substantial degree of horizontal transfer of AlkB genes. DNA repair activity was associated with all tested recombinant AlkB proteins. Notably, both a group 2B protein from Xanthomonas campestris and a group 2A protein from Rhizobium etli repaired etheno adducts, but had negligible activity on methylated bases. Our data indicate that the majority, if not all, of the bacterial AlkB proteins are DNA repair enzymes, and that some of these proteins do not primarily target methylated bases.     

Genetic diversity, compatibility patterns and seed quality in isolated populations of Cypripedium calceolus (Orchidaceae)

Cypripedium calceolus has suffered an alarming decline, and today mainly occurs in small and isolated populations. In Denmark there are only two populations, close to each other and situated far from other European stands. One population is stagnant or in slow decline, whereas the other is in rapid increase. We examined the levels of genetic diversity and compatibility and seed quality following experimental crosses. No genetic variation could be detected in plastid and nuclear markers within or between the two populations—in contrast to results previously reported from other European populations of C. calceolus. This may indicate a founder effect in both populations, but it could also be the outcome of prolonged inbreeding or reflect a genetic bottleneck after the populations were established. According to fruit dimensions and frequency of fully developed seeds there was full self-compatibility in the stagnant population, and partial late-acting self-incompatibility in the proliferating population. In combination with previous reports from other countries, this suggests that several self-incompatibility systems may occur in C. calceolus. Seeds from the older and stagnant population performed more poorly in germination tests in vitro than seeds from the thriving population. The difference needs not be genetically based, but could be due to environmental differences during seed maturation, producing different seed quality or dormancy characteristics. However, low level of genetic diversity within the populations may affect their ability to adapt and the possibility of inbreeding depression should be investigated.     

Human METTL20 Is a Mitochondrial Lysine Methyltransferase That Targets the β Subunit of Electron Transfer Flavoprotein (ETFβ) and Modulates Its Activity

Proteins are frequently modified by post-translational methylation of lysine residues, catalyzed by S-adenosylmethionine-dependent lysine methyltransferases (KMTs). Lysine methylation of histone proteins has been extensively studied, but it has recently become evident that methylation of non-histone proteins is also abundant and important. The human methyltransferase METTL20 belongs to a group of 10 established and putative human KMTs. We here found METTL20 to be associated with mitochondria and determined that recombinant METTL20 methylated a single protein in extracts from human cells. Using an methyltransferase activity-based purification scheme, we identified the β-subunit of the mitochondrially localized electron transfer flavoprotein (ETFβ) as the substrate of METTL20. Furthermore, METTL20 was found to specifically methylate two adjacent lysine residues, Lys²⁰⁰ and Lys²⁰³, in ETFβ both in vitro and in cells. Interestingly, the residues methylated by METTL20 partially overlap with the so-called “recognition loop” in ETFβ, which has been shown to mediate its interaction with various dehydrogenases. Accordingly, we found that METTL20-mediated methylation of ETFβ in vitro reduced its ability to receive electrons from the medium chain acyl-CoA dehydrogenase and the glutaryl-CoA dehydrogenase. In conclusion, the present study establishes METTL20 as the first human KMT localized to mitochondria and suggests that it may regulate cellular metabolism through modulating the interaction between its substrate ETFβ and dehydrogenases. Based on the previous naming of similar enzymes, we suggest the renaming of human METTL20 to ETFβ-KMT.     

Boron removal and recovery from water and wastewater

Boron is an important element for plants, humans, and animals in limited amounts. However, excess amounts can cause adverse effects in both humans and plants, necessitating its removal from certain systems. Boron compounds are used in many industrial applications, including in developing sectors like alternative energy technology; as a result, the need for this element is increasing and industries are looking towards boron recovery for the sustained use of this element in their products. While the literature on boron removal strategies is abundant, there is a relative lack of studies on boron recovery, with no review papers having yet addressed this topic. In this review, both boron removal and recovery techniques involving conventional approaches and membrane processes are examined to juxtapose the states of the science in these two related—and increasingly important—processes.

Graphical abstract

     

Evidence that gestation duration and lactation duration are coupled traits in primates

Gestation duration and lactation duration are usually treated as independently evolving traits in primates, but the metabolic theory of ecology (MTE) suggests both durations should be determined by metabolic rate. We used phylogenetic generalized least-squares linear regression to test these different perspectives. We found that the allometries of the durations are divergent from each other and different from the scaling exponent predicted by the MTE (0.25). Gestation duration increases much more slowly (0.06 < m < 0.12), and lactation duration much more quickly (0.36 < m < 0.52) with body mass than the MTE predicts. By contrast, we found that the combined duration of gestation and lactation is consistent with the MTE''s predictions (0.22 < m < 0.35). These results suggest that gestation duration and lactation duration might best be viewed as distinct but coupled adaptations. When transferring energy to their offspring, primate mothers must meet metabolically dictated physiological requirements while optimizing the timing of the switch from gestation to lactation in relation to some as-yet-unidentified body-size-related factor.     

Qualitative Identification of Carboxylic Acids,Boronic Acids,and Amines Using Cruciform Fluorophores

Molecular cruciforms are X-shaped systems in which two conjugation axes intersect at a central core. If one axis of these molecules is substituted with electron-donors, and the other with electron-acceptors, cruciforms'' HOMO will localize along the electron-rich and LUMO along the electron-poor axis. This spatial isolation of cruciforms'' frontier molecular orbitals (FMOs) is essential to their use as sensors, since analyte binding to the cruciform invariably changes its HOMO-LUMO gap and the associated optical properties. Using this principle, Bunz and Miljanić groups developed 1,4-distyryl-2,5-bis(arylethynyl)benzene and benzobisoxazole cruciforms, respectively, which act as fluorescent sensors for metal ions, carboxylic acids, boronic acids, phenols, amines, and anions. The emission colors observed when these cruciform are mixed with analytes are highly sensitive to the details of analyte''s structure and - because of cruciforms'' charge-separated excited states - to the solvent in which emission is observed. Structurally closely related species can be qualitatively distinguished within several analyte classes: (a) carboxylic acids; (b) boronic acids, and (c) metals. Using a hybrid sensing system composed from benzobisoxazole cruciforms and boronic acid additives, we were also able to discern among structurally similar: (d) small organic and inorganic anions, (e) amines, and (f) phenols. The method used for this qualitative distinction is exceedingly simple. Dilute solutions (typically 10^-6 M) of cruciforms in several off-the-shelf solvents are placed in UV/Vis vials. Then, analytes of interest are added, either directly as solids or in concentrated solution. Fluorescence changes occur virtually instantaneously and can be recorded through standard digital photography using a semi-professional digital camera in a dark room. With minimal graphic manipulation, representative cut-outs of emission color photographs can be arranged into panels which permit quick naked-eye distinction among analytes. For quantification purposes, Red/Green/Blue values can be extracted from these photographs and the obtained numeric data can be statistically processed.     

Total phenolic content, flavonoid concentration, antioxidant and antimicrobial activity of methanol extracts from three Seseli L. taxa

The present study describes the total phenolic content, concentrations of flavonoids and in vitro antioxidant and antimicrobial activity of methanol extracts from Seseli pallasii Besser, S. libanotis (L.) Koch ssp. libanotis and S. libanotis (L.) Koch ssp. intermedium (Rupr.) P. W. Ball, growing wild in Serbia. The total phenolic content in the extracts was determined using Folin-Ciocalteu reagent and their amounts ranged between 84.04 to 87.52 mg GA (gallic acid)/g. The concentrations of flavonoids in the extracts varied from 4.75 to 19.37 mg Qu (quercetin)/g. Antioxidant activity was analyzed using DPPH reagent. Antioxidant activity ranged from 0.46 to 4.63 IC₅₀ (mg/ml) and from 1.98 to 2.19 mg VitC (vitamin C)/g when tested with the DPPH and ABTS reagents, respectively, using BHA and VitC as controls. The antimicrobial activity of the extracts was investigated using a micro-well dilution assay for the most common human gastrointestinal pathogenic bacterial strains: Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 9027, Salmonella enteritidis ATCC 13076, Bacillus cereus ATCC 10876, Listeria monocytogenes ATCC15313, Staphylococcus aureus ATCC 25923 and Candida albicans ATCC 10231. This finding suggests that Seseli species may be considered as a natural source of antioxidants and antimicrobial agents.     

Zinc,copper, and magnesium concentrations in hair of children from Southeastern Turkey

Zinc, copper, and magnesium concentrations in hair were measured in groups of children varying in one condition—protein-energy malnutrition, ricketts, thalassemia, malignancy, cardiac failure, or after prolonged infection and in healthy controls. As compared with controls, copper and magnesium concentrations were low in all groups, whereas higher values were obtained for hair zinc. These results showed that a generalized copper and magnesium deficiency were observed in the southeastern part of Turkey. However, zinc deficiency couldn’t be detected as far as the hair zinc values were concerned, although all of the subjects fell within the 50 percentile limits for their age-appropriate weights and heights.