NOR Activity Research Articles

Bacillus subtilis, a promising bacterial candidate for trapping nanoplastics during water treatment

As a probiotic, Bacillus subtilis (B. subtilis) has a wide range of application values. In this study, the trap by B. subtilis and the effect of NPs on its growth physiology were studied. Confocal laser scanning microscopy (LCSM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) confirmed that PS-NPs were trapped by B. subtilis when they were exposed to PS-NPs. At this point, most of the PS-NPs are clustered around B. subtilis. Flow cytometry showed that at 10 mg/L, 73.7 % of PS-NPs' environmental state changed. The complexity of 9.73 %, 23.77 %, 43.27 %, and 65.13 % of B. subtilis increased at PS-NP concentrations of 10, 20, 50, and 200 mg/L, respectively. The increase in overall EPS secretion ranged from 0.51 ∼ 7.13 μg/mL after adding different concentrations of PS-NPs. The effect of different concentrations of PS-NPs on NAR activity ranged from −11.38 ∼ 16.2 %, on NIR activity from −17.90 ∼ 7.22 %, on NOR activity from −15.10 ∼ 7.69 % and on NO2R activity from −14.01 ∼ 17.03 %. These results indicated that B. subtilis can process nitrogen compounds in water while capturing NPs in the environment. They have the potential to be candidate bacteria in the water treatment process, and specific applications are needed to research further.

Regulating the Ni-O bond length by constructing Ni(OH)2/CNTs heterostructure for enhanced nucleophile electrocatalytic oxidation

The electro-driven generation of the active Ni(OH)O species is crucial for the Ni(OH)2 to efficiently drive the nucleophilic oxidation reaction. However, the strategy to facilitate the generation of the Ni(OH)O species is only limited to the construction of the Pt/Ni(OH)2 heterostructures. In this study, carbon nanotubes (CNTs) are employed to reduce the dehydrogenation energy of the Ni(OH)2 by constructing Ni(OH)2/60CNTs heterostructures. The CNTs shorten the Ni-O bond length and increase the valence state of Ni atoms in Ni(OH)2, thus highly promoting the generation of Ni(OH)O. When the Ni(OH)2/60CNTs heterostructure is used for urea oxidation reaction, it displays highly enhanced catalytic activity relative to pure Ni(OH)2, attaining a current density of 10 mA cm−2 at 1.36 V versus reversible hydrogen electrode. This work provides a new strategy for reducing the dehydrogenation energy of the Ni(OH)2 and will inspire more research work on the recognition of the impact of metal–oxygen bond length on NOR activity.

Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in Arabidopsis

Arabidopsis thaliana has two ribosomal RNA (rRNA) gene loci, nucleolus organizer regions NOR2 and NOR4 , whose complete sequences are missing in current genome assemblies. Ultralong DNA sequences assembled using an unconventional approach yielded ~5.5- and 3.9-Mbp sequences for NOR2 and NOR4 in the reference strain, Col-0. The distinct rRNA gene subtype compositions of the NORs enabled the positional mapping of their active and inactive regions, using RNA sequencing to identify subtype-specific transcripts and DNA sequencing to identify subtypes associated with flow-sorted nucleoli. Comparisons of wild-type and silencing-defective plants revealed that most rRNA gene activity occurs in the central region of NOR4 , whereas most, but not all, genes of NOR2 are epigenetically silenced. Intervals of low CG and CHG methylation overlap regions where gene activity and gene subtype homogenization are high. Collectively, the data reveal the genetic and epigenetic landscapes underlying nucleolar dominance (differential NOR activity) and implicate transcription as a driver of rRNA gene concerted evolution.

Effects of nitrogen input on N2O production and enzyme activity in Luoshijiang Wetland sediments, China

We examined the effects of nitrate (NO3--N) and ammonium (NH4+-N) input at different concentrations (0, 1, 5 and 25 mg·kg-1) on N2O production rate from the surface sediment (0-5 cm) of Luoshijiang Wetland, located upstream from Lake Erhai. The contribution of nitrification, denitrification, nitrifier denitrification, and other factors to the N2O production rate in sediments was studied by the inhibitor method. The relationships between N2O production and the activities of hydroxylamine (HyR), nitrate (NAR), nitric oxide (NOR), and nitrous oxide (NOS) reductases in sediments were analyzed. We found that NO3--N input significantly increased total N2O production rate (1.51-11.35 nmol·kg-1·h-1), which led to N2O release, whereas NH4+-N input decreased that (-0.80 to -0.54 nmol·kg-1·h-1), causing N2O absorption. NO3--N input did not change the dominant roles of nitrification and nitrifier denitrification in N2O production in sediments, but increased the contributions of these two factors to 69.5% and 56.5%, respectively. The NH4+-N input significantly changed N2O gene-ration process, and the nitrification and nitrifier denitrification changed from N2O release to uptake. There was a positive correlation between total N2O production rate and NO3--N input. NO3--N input significantly increased NOR activity and decreased NOS activity, thereby promoting N2O production. The total N2O production rate in sediments was negatively correlated with NH4+-N input. NH4+-N input significantly increased the activities of HyR and NOR, decreased NAR activity, and inhibited N2O production. Nitrogen inputs with different forms and concentrations changed the degree of contribution and mode of N2O production by affecting enzyme activities in sediments. NO3--N input significantly promoted N2O production, acting as a source of N2O, while NH4+-N input inhibited N2O production, resulting in an N2O sink.

First cytogenetic characterization of the Amazon Catfish Leiarius marmoratus (Gill, 1870) and its hybrid with Pseudoplatystoma reticulatum (Eigenmann & Eigenmann, 1889)

This study reports the first cytogenetic characterization of the Amazonian catfish Leiarius marmoratus (“jandiá”) and its F1 (first generation) hybrid “cachandiá” with Pseudoplatystoma reticulatum (“cachara”). A diploid number of 56 chromosomes and a single argyrophilic nucleolus organizer region (Ag-NOR) in the short arm of two sub-telocentric chromosomes were observed for both L. marmoratus and P. reticulatum, but with differences in the karyotype formula and the size of the chromosome pair with NORs. The hybrid showed 2n = 56 chromosomes with an intermediate karyotype when compared to the parental species. A single Ag-NOR was maintained in the hybrid but located in two chromosomes with marked differences in size and presenting intraindividual variation in NOR activity (nucleolar dominance). For L. marmoratus and the hybrid, heterochromatic bands were predominately distributed in the terminal, centromeric, and sub-centromeric regions of some chromosomes and 5S rDNA sites located in two distinct sub-telocentric chromosomes, similar to the previously described for P. reticulatum. The data suggested that the hybrid karyotype might be insufficient for a precise discrimination of hybrids, however, Ag-NOR can be used as a chromosome marker to differentiate “cachandiá” from L. marmoratus and P. reticulatum. The current study also provides insights into the chromosomal features of L. marmoratus and contributes with novel cytogenetic information of this native Amazonian catfish included in the Pimelodidae family.

NO and N2 O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains.

Fungal denitrification is claimed to produce non-negligible amounts of N2 O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with . Enzymatic reduction of (NIR) and NO (NOR) was assessed by correcting measured NO- and N2 O-kinetics for abiotic NO- and N2 O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2 O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2 O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2 O as a response to an abiotic NO production from the medium.

How dynamic could be the 45S rDNA cistron? An intriguing variability in a grasshopper species revealed by integration of chromosomal and genomic data.

To better understand the structure and variability of the 45S rDNA cistron and its evolutionary dynamics in grasshoppers, we performed a detailed analysis combining classical and molecular cytogenetic data with whole-genome sequencing in Abracris flavolienata, which shows extraordinary variability in the chromosomal distribution for this element. We found astonishing variability in the number and size of rDNA clusters at intra- and inter-population levels. Interestingly, FISH using distinct parts of 45S rDNA cistron (18S rDNA, 28S rDNA, and ITS1) as probes revealed a distinct number of clusters, suggesting independent mobility and amplification of the 45S rDNA components. This hypothesis is consistent with the higher genomic coverage of almost the entire cistron of 45S rDNA observed in A. flavolineata compared to other grasshoppers, besides coverage variability along the 45S rDNA cistron in the species. In addition, these differences in coverage for distinct components of the 45S rDNA cistron indicate emergence of pseudogenes evidenced by existence of truncated sequences, demonstrating the rDNA dynamics in the species. Although the chromosomal distribution of 18S rDNA was highly variable, the chromosomes 1, 3, 6, and 9 harbored rDNA clusters in all individuals with the occurrence of NOR activity in pair 9, suggesting ancestry or selective pressures to prevent pseudogenization of rDNA sequences in this chromosome pair. Additionally, small NORs and cryptic rDNA loci were observed. Finally, there was no evidence of enrichment and association of transposable elements, at least, inside or nearby rDNA cistron. These findings broaden our knowledge of rDNA dynamics, revealing an independent movement and amplification of segments of 45S rDNA cistron, which in A. flavolineata could be attributed to ectopic recombination.

HP1 knockdown is associated with abnormal condensation of almost all chromatin types in a grasshopper (Eyprepocnemis plorans)

Heterochromatin protein 1 (HP1) is a highly conserved family of eukaryotic proteins required for heterochromatic gene silencing and euchromatic gene transcription regulation. In addition, HP1 is involved in chromatin organization and protection of chromosome integrity during cell division. Here, we present a cytological and molecular analysis of the effects of HP1 knockdown in Eyprepocnemis plorans, a grasshopper species polymorphic for supernumerary heterochromatic chromosomes. Our results revealed contrasting effects of HP1 knockdown on gene activity. While the Bub1 gene decreased in expression level in HP1 knockdown animals, NOR activity, rRNA and, contrarily to previous reports in Drosophila, Hsp70 gene expression remained unchanged. Furthermore, HP1 knockdown resulted in abnormal chromatin condensation, chromosomal bridges, higher frequency of macrospermatids, loss of muscle mass and hemolymph amount as well as a low number of dividing cells and survival reduction. All these phenotypes are very likely due to the chromatin condensation disruption observed for almost all kinds of chromatin.

Argyrophilic nucleolar organizing region associated protein synthesis in hair root cells of humans at different developmental stages and sex

Argyrophilic nucleolar organizing region (AgNORs) associated proteins are important for cell proliferation and various diseases. We investigated AgNOR protein synthesis in hair root cells of males and females at different ages using two-dimensional image analysis. Experiments were performed on 58 healthy male and 24 healthy female volunteers in three groups according to age and sex. Hair root cells obtained from hair follicles were stained with silver. Total AgNOR number/total nuclear number (TAN/TNN) and total AgNOR area/nuclear area (TAA/NA) for each nucleus were analyzed. The only significant difference was observed in TAA/NA values for males and females from 6 to 12 years old. We suggest that the difference is due to high NOR activity caused by increased growth hormone production in hair root cells.

Investigation of genome polymorphism and seed coat anatomy of species of section Adenolinum from the genus Linum

Twelve species of section Adenolinum from genus Linum have been studied using cytogenetic methods (DAPI/C-banding, Ag-NOR staining, FISH with 5S and 26S rDNA probes), RAPD analysis, and seed surface ultrastructure and seed coat anatomy investigation. Karyotype analysis revealed that these species have a chromosome number of 2n = 18 or 2n = 36. The DAPI/C-banding patterns enabled the identification of all chromosomes and revealed the similarities in chromosome patterns in all of the studied species. It was found that 18-chromosome plants are diploids, whereas 36-chromosome forms are tetraploids. In diploid species, 5S and 26S rRNA genes are located in similar positions on a single pair of chromosomes or on two chromosome pairs in tetraploids. Ag-NOR staining showed NOR activity in both genomes of tetraploids. RAPD analysis and seed coat anatomy investigation revealed some interspecies differences. Species from nearby areas have more similar RAPD characteristics compared with more geographically distant species. The results of this study may serve as an additional argument in favour of a monophyletic origination of the Adenolinum species and its strong isolation from other Linum species.

Chromosome banding and essential oils composition of Brazilian accessions of Lippia alba (Verbenaceae)

The essential oil components and a karyotypic analysis of five Lippia alba (Verbenaceae) accessions from Brazil were performed with the objective of investigating the variation among different populations. The chemistry analysis allowed the grouping of the accessions in two main chemotypes: neral chemotype (LaCat, LaJF and LaRJ) and linalool chemotype (LaGua and LaVC). However, large karyotypic differences, verified by different chromosome banding techniques, were not detected. The results presented the same chromosome number for all accessions (2n = 30) with 10 metacentric chromosomes and 5 submetacentric. The chromosome banding showed great blocks of constitutive heterochromatin (C-bands) around the centromeric region, which was rich in AT bases (DAPI+), while the CMA bands were observed only in terminal regions of six chromosomes. Through Ag-NOR techniques, only two active pairs of NORs were detected on the three pairs of secondary constrictions (the NOR activity is discussed). This work relates the pattern of heterochromatin for Lippia alba for the first time.

Additional nucleoli and NOR activity during meiotic prophase I in larch (Larix decidua Mill.)

Transcriptional activity was investigated in successive stages of prophase I (male meiosis) of larch meiocytes. Br-UTP incorporated into RNA was detected by light and electron microscopy. Two peaks of RNA synthesis were identified in the nucleolus. The first occurred during the zygotene-pachytene stage and the second (not previously described in plant meiocytes) in the diplotene. These processes correlated with a considerable increase in nucleolus volume during these periods. At the end of the zygotene, several perinucleolar structures lying close to each other and containing rRNA, argyrophilic proteins, U3 small nucleolar RNA, and fibrillarin were observed. The occurrence of newly formed RNA was also observed in these structures. This suggests that the observed perinucleolar structures correspond to the additional nucleoli known from animals.

Nucleolus size variation during meiosis and NOR activity of a B chromosome in the grasshopper Eyprepocnemis plorans

The number of nucleoli and nucleolar area were measured in meiotic cells from males of the grasshopper Eyprepocnemis plorans collected in three natural populations. Number of nucleoli per cell showed no significant correlation among cells in different meiotic stages, but there was strong positive correlation for nucleolar area between leptotene and interkinesis cells in individuals from distant populations (Salobreña in Spain, and Smir in Morocco). No correlation was, however, observed for both parameters between the meiotic stages analysed in individuals from the population of Torrox (Spain). The number of nucleoli at leptotene was about double the number at interkinesis, as expected from the double ploidy level at leptotene and the corresponding double number of rDNA clusters. Leptotene nucleolar area, however, was about fourfold that in interkinesis, presumably due to higher requirements for ribosome biogenesis in meiosis I than meiosis II. In Torrox, diplotene cells showed a lower number of nucleoli but larger nucleolar area than in leptotene cells, suggesting an increase in nucleolus size during prophase I. Significant differences were found among populations for nucleolar area but not for number of nucleoli, the smallest nucleolar area being observed in Torrox, which is the population harbouring the most parasitic B chromosome variant. No clear effects on nucleolar area or number of nucleoli were associated with the B-chromosome number. However, B-chromosome effects on the nucleolar area were apparent in the Torrox population when data were analysed with respect to a B-chromosome odd-even pattern in leptotene and interkinesis cells. However, in diplotene cells no odd-even pattern was observed for both nucleolar parameters, suggesting that the increase in nucleolar size from leptotene to diplotene dilutes the leptotene odd-even pattern. The rDNA distally located in the B chromosome was associated with a nucleolus in 6.5% out of the 247 diplotene cells analysed. The implications of these findings are discussed in the context of B chromosomes as stress-causing genome parasites and the nucleolus as a sensor of stress.

A new assay for nitric oxide reductase reveals two conserved glutamate residues form the entrance to a proton-conducting channel in the bacterial enzyme

A specific amperometric assay was developed for the membrane-bound NOR [NO (nitric oxide) reductase] from the model denitrifying bacterium Paracoccus denitrificans using its natural electron donor, pseudoazurin, as a co-substrate. The method allows the rapid and specific assay of NO reduction catalysed by recombinant NOR expressed in the cytoplasmic membranes of Escherichia coli. The effect on enzyme activity of substituting alanine, aspartate or glutamine for two highly conserved glutamate residues, which lie in a periplasmic facing loop between transmembrane helices III and IV in the catalytic subunit of NOR, was determined using this method. Three of the substitutions (E122A, E125A and E125D) lead to an almost complete loss of NOR activity. Some activity is retained when either Glu122 or Glu125 is substituted with a glutamine residue, but only replacement of Glu122 with an aspartate residue retains a high level of activity. These results are interpreted in terms of these residues forming the mouth of a channel that conducts substrate protons to the active site of NOR during turnover. This channel is also likely to be that responsible in the coupling of proton movement to electron transfer during the oxidation of fully reduced NOR with oxygen [U. Flock, N. J. Watmough and P. Adelroth (2005) Biochemistry 44, 10711-10719].

NOR activity and repeat sequences of the paternal sex ratio chromosome of the parasitoid wasp Trichogramma kaykai

Part of the male population of the wasp Trichogramma kaykai carries a B chromosome that manipulates its host sex ratio in favour of males. The only known repeat on this paternal sex ratio (PSR) chromosome is the 45S rDNA, which includes here five different internal transcribed spacer 2 (ITS2) sequences. In this report, we describe that only part of these ITS2 sequences is transcribed. The absence of transcription of some ITS2 sequences might explain the presence of multiple ITS2 sequences on the PSR chromosome since homogenization of rDNA spacers is thought to occur only in transcribed regions. Analysis of the only other known tandem repeat in Trichogramma, the EcoRI repeat, showed that it is absent from the PSR chromosome, and that the T. kaykai EcoRI repeat has 98 and 77% DNA sequence homology with the T. deion and T. brassicae EcoRI repeats, respectively. The size of the PSR chromosome measures 9 Mbp and is equal to 3.9% of the haploid T. kaykai genome. Finally, fluorescent in situ hybridization with a pool of high and moderate repetitive T. kaykai DNA (C0t-50) revealed only a very few major tandem repeats on the Trichogramma genome and only 45S rDNA on the PSR chromosome.

FISH detection of ribosomal cistrons and assortment-distortion for X and B chromosomes in Dichroplus pratensis (Acrididae)

Assortment-distortion with respect to the X and NOR activity of a rare mitotically stable B chromosome (B_N), was examined in 16 males of Dichroplus pratensis (Acrididae: Melanoplinae) from Argentine populations. In 1B individuals, the X and B associate preferentially during prophase I reaching a maximum level of association at zygotene. Frequency of X/B association remains relatively high up to diplotene-diakinesis and decreases steeply towards metaphase I. The percent X/B association at each stage is positively influenced by association at the previous stage, and interindividual variability in X/B association decreases as the frequency of association increases. Both chromosomes tended to preferentially orientate toward the same pole at MI (mean ratio of 16 individuals, 1.50:1) which determined an excess of XB and 00 second spermatocytes over X0 and 0B ones (1.39:1). No significant differences occurred between the MI, AI and MII assortment ratios. Fluorescent in situ hybridisation (FISH) confirmed that the B chromosome carries ribosomal genes and helped to establish that, during spermiogenesis, both the B and the normal NOR-bearing chromosome (S₈) are clustered near the centriole adjunct region of spermatids. However, FISH failed to reveal the existence of inactive ribosomal cistrons in the X chromosome, as previously suggested, thus providing no support to a simple origin of the B from the X.

Transcriptional activity of an inversion split NOR in barley (Hordeum vulgare L.).

The transcriptional activity of NORs in a new structural mutant of barley (PK-88-4) was studied based on the positive reaction of NORs of metaphase chromosomes with AgNO3 and the number and size of silver-stained nucleoli in somatic interphase cells and meiocytes. PK-88-4 proved to contain a pericentric inversion that split NOR 7 into two unequal parts residing in the opposite arms of the reconstructed chromosome 7(5). This chromosomal rearrangement enables testing of intrachromosomal suppression of NORs and provides insight into the mechanisms of intraspecific nucleolar dominance. Both parts of the split NOR proved to be transcriptionally active, and are not subject to intrachromosomal nucleolar dominance. Thus, translocation-induced intraspecific nucleolar dominance is probably the result of interaction of NOR6 and NOR7 or other genetic factors located on the NOR-bearing chromosomes 6(6H) and 7(5H).

Pinealectomy-associated decrease in ribosomal gene activity in rats.

A decrease in ribosomal gene activity is an essential feature of the aging process as it was observed in Alzheimer's disease, in elderly Down's patients and in elderly healthy people. It is well known that aging is also associated with a reduction in melatonin synthesis. We studied 24 male Wistar rats cytogenetically, by using Ag-stained NOR (6 three-month-old rats underwent pinealectomy and were studied after 20 days; 6 control rats of the same age; 6 three-month-old rats underwent pinealectomy and were studied after 8 months; 6 control rats of the same age). Our results indicate that the absence of the pineal gland leads to a decrease in NOR activity. Further studies are necessary to determine if pinealectomy in rats could provide an animal model for aging.

Modification of wheat rDNA loci by rye B chromosomes: a chromatin organization model.

The rDNA loci, and their associated NORs, on chromosomes 1B and 6B of the hexaploid wheat cv. Lindström have been used as a chromatin marker to investigate the functional basis of the phenotype effects of introgressed supernumerary B chromosomes (Bs) of rye. The rye Bs themselves lack genes, other than those which determine their mitotic drive mechanism, and the way in which they can modulate characters determined by the A chromosome background has always been a puzzle. An isogenic line of Lindström plants carrying different numbers of Bs was used as the experimental system to see how different doses of Bs (from 0 to 6) affected the activity of the wheat NORs and the organization of their rDNA loci at interphase. Silver staining on metaphase chromosomes was used to evaluate the previous activity of the NORs, and to reveal variations in their size; and the pTa71 FISH probe from wheat was used to visualize structural modifications to the interphase rDNA loci. A single B had no measurable effect, but, as the B-number increased, there were significant changes in the physical dimensions of the metaphase NORs, reflecting reduced levels of their activity earlier in the cell cycle, and also in the condensation patterns of the interphase rDNA loci. In addition, the higher B-numbers caused a size heteromorphism between the homologous NORs. A model is discussed which interprets the phenotypic effects of Bs generically, in nucleotypic terms, based of their being 'genetically inert' but 'chromosomally active'.

Physical mapping, expression patterns and interphase organisation of rDNA loci in Portuguese endemic Silene cintrana and Silene rothmaleri.

Double target in situ hybridization to root tip metaphase and interphase cells of Silene cintrana and Silene rothmaleri was used to allocate the position of 18S-5.8S-25S and 5S rRNA genes. In both species, the 18S-5.8S-25S rDNA probe labelled four sites located on the short arms of two submetacentric chromosomes. Only one locus for 5S rDNA was mapped adjacent to 18S-5.8S-25S genes in a subterminal position on the centromere side: in S. rothmaleri the 5S rDNA locus was adjacent to the small 18S-5.8S-25S locus while in S. cintrana it was near the large one. The NOR activity analysed by Ag-staining in metaphase cells revealed proportionality between in situ labelling dimensions and Ag-NORs. In both species all rDNA loci were potentially active, although in S. rothmaleri a tendency for the expression of only one locus was observed. Interphase organisation analysis of rDNA showed some differences between both species that were correlated with NOR activity.