Inflammation in the avian spleen: timing is everything

Background

Human cells depend critically on the signal recognition particle (SRP) for the sorting and delivery of their proteins. The SRP is a ribonucleoprotein complex which binds to signal sequences of secretory polypeptides as they emerge from the ribosome. Among the six proteins of the eukaryotic SRP, the largest protein, SRP72, is essential for protein targeting and possesses a poorly characterized RNA binding domain.

Results

We delineated the minimal region of SRP72 capable of forming a stable complex with an SRP RNA fragment. The region encompassed residues 545 to 585 of the full-length human SRP72 and contained a lysine-rich cluster (KKKKKKKKGK) at postions 552 to 561 as well as a conserved Pfam motif with the sequence PDPXRWLPXXER at positions 572 to 583. We demonstrated by site-directed mutagenesis that both regions participated in the formation of a complex with the RNA. In agreement with biochemical data and results from chymotryptic digestion experiments, molecular modeling of SRP72 implied that the invariant W577 was located inside the predicted structure of an RNA binding domain. The 11-nucleotide 5e motif contained within the SRP RNA fragment was shown by comparative electrophoresis on native polyacrylamide gels to conform to an RNA kink-turn. The model of the complex suggested that the conserved A240 of the K-turn, previously identified as being essential for the binding to SRP72, could protrude into a groove of the SRP72 RNA binding domain, similar but not identical to how other K-turn recognizing proteins interact with RNA.

Conclusions

The results from the presented experiments provided insights into the molecular details of a functionally important and structurally interesting RNA-protein interaction. A model for how a ligand binding pocket of SRP72 can accommodate a new RNA K-turn in the 5e region of the eukaryotic SRP RNA is proposed.     

Forest carbon balance under elevated CO2

Free-air CO₂ enrichment (FACE) technology was used to expose a loblolly pine (Pinus taeda L.) forest to elevated atmospheric CO₂ (ambient + 200 µl l^-1). After 4 years, basal area of pine trees was 9.2% larger in elevated than in ambient CO₂ plots. During the first 3 years the growth rate of pine was stimulated by ~26%. In the fourth year this stimulation declined to 23%. The average net ecosystem production (NEP) in the ambient plots was 428 gC m^-2 year^-1, indicating that the forest was a net sink for atmospheric CO₂. Elevated atmospheric CO₂ stimulated NEP by 41%. This increase was primarily an increase in plant biomass increment (57%), and secondarily increased accumulation of carbon in the forest floor (35%) and fine root increment (8%). Net primary production (NPP) was stimulated by 27%, driven primarily by increases in the growth rate of the pines. Total heterotrophic respiration (R_h) increased by 165%, but total autotrophic respiration (R_a) was unaffected. Gross primary production was increased by 18%. The largest uncertainties in the carbon budget remain in separating belowground heterotrophic (soil microbes) and autotrophic (root) respiration. If applied to temperate forests globally, the increase in NEP that we measured would fix less than 10% of the anthropogenic CO₂ projected to be released into the atmosphere in the year 2050. This may represent an upper limit because rising global temperatures, land disturbance, and heterotrophic decomposition of woody tissues will ultimately cause an increased flux of carbon back to the atmosphere.     

Activity of some Nile River aquatic macrophyte extracts against the cyanobacterium Microcystis aeruginosa

The anti-algal activity of five macrophyte extracts on the cyanobacterium Microcystis aeruginosa in Egypt was investigated in 2013. Extract activity varied according to plant type, extracting solvent and its concentration. The highest inhibitory activity was achieved with ethanol extract at a concentration of 80 mg l^?1, followed by chloroformic extracts, at 60 mg l^?1. Methanolic extracts of Eichhornia crassipes and Polygonum tomentosum inhibited growth of Microcystis aeruginosa at all concentrations. Acetonic extracts inhibited algal growth at 60 mg l^?1, except for the extract of Ceratophyllum subdemersum, which showed stimulation of M. aeruginosa growth. Eichhornia crassipes ethanolic extract exerted the most powerful inhibition by more than five-fold, 570.17%, followed by those of P. tomentosum, Saccharum spontaneum, Ceratophyllum demersum and C. subdemersum, 559.48, 553.99, 544.11 and 366.51%, respectively. Phytochemical screening for the tested plant extracts revealed the presence of biologically active substances of different concentrations, with P. tomentosum having the highest polyphenols, 1.95% of dry weight.     

The gene for leukoencephalopathy with vanishing white matter is located on chromosome 3q27.

Leukoencephalopathy with vanishing white matter (VWM) is an autosomal recessive disorder with normal early development and, usually, childhood-onset neurological deterioration. At present, diagnosis of VWM is based on clinical examination and the results of repeat magnetic resonance imaging and magnetic resonance spectroscopy, which show that, with time, increasing amounts of the cerebral white matter vanish and are replaced by cerebrospinal fluid. We have performed a genome linkage screening of a panel of 19 families of different ethnic origins. Significant linkage to chromosome 3q27 was observed in a 7-cM interval between markers D3S3730 and D3S3592, with a maximum multipoint LOD score of 5.1 calculated from the entire data set. The results of genealogical studies have suggested that seven parents in four Dutch families with VWM may have inherited an allele for the disease from a common ancestor who lived at least eight generations ago. Analysis of these families provided further evidence for the localization of the gene for VWM to 3q27. The patients shared a haplotype spanning 5 cM between markers D3S1618 and D3S3592. In one family of a different ethnic background, the patient had, in the same region, homozygosity for 13 consecutive markers spanning at least 12 cM, suggesting consanguinity between the parents. A healthy sibling of this patient had the same homozygous haplotype, which suggests that the healthy sibling is presymptomatic for the disease.     

Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis

BackgroundThe incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries of the former Soviet Union, where >20% of new cases and >50% of previously treated cases have resistance to rifampin and isoniazid. Transmission of resistant strains, as opposed to resistance selected through inadequate treatment of drug-susceptible tuberculosis (TB), is the main driver of incident MDR-TB in these countries.Methods and findingsWe conducted a prospective, genomic analysis of all culture-positive TB cases diagnosed in 2018 and 2019 in the Republic of Moldova. We used phylogenetic methods to identify putative transmission clusters; spatial and demographic data were analyzed to further describe local transmission of Mycobacterium tuberculosis. Of 2,236 participants, 779 (36%) had MDR-TB, of whom 386 (50%) had never been treated previously for TB. Moreover, 92% of multidrug-resistant M. tuberculosis strains belonged to putative transmission clusters. Phylogenetic reconstruction identified 3 large clades that were comprised nearly uniformly of MDR-TB: 2 of these clades were of Beijing lineage, and 1 of Ural lineage, and each had additional distinct clade-specific second-line drug resistance mutations and geographic distributions. Spatial and temporal proximity between pairs of cases within a cluster was associated with greater genomic similarity. Our study lasted for only 2 years, a relatively short duration compared with the natural history of TB, and, thus, the ability to infer the full extent of transmission is limited.ConclusionsThe MDR-TB epidemic in Moldova is associated with the local transmission of multiple M. tuberculosis strains, including distinct clades of highly drug-resistant M. tuberculosis with varying geographic distributions and drug resistance profiles. This study demonstrates the role of comprehensive genomic surveillance for understanding the transmission of M. tuberculosis and highlights the urgency of interventions to interrupt transmission of highly drug-resistant M. tuberculosis.

In a prospective genome surveillance study, Chongguang Yang and colleagues investigate the dynamics of multidrug-resistant tuberculosis transmission in Moldova.     

Association between living environment and human oral viral ecology

The human oral cavity has an indigenous microbiota known to include a robust community of viruses. Very little is known about how oral viruses are spread throughout the environment or to which viruses individuals are exposed. We sought to determine whether shared living environment is associated with the composition of human oral viral communities by examining the saliva of 21 human subjects; 11 subjects from different households and 10 unrelated subjects comprising 4 separate households. Although there were many viral homologues shared among all subjects studied, there were significant patterns of shared homologues in three of the four households that suggest shared living environment affects viral community composition. We also examined CRISPR (clustered regularly interspaced short palindromic repeat) loci, which are involved in acquired bacterial and archaeal resistance against invading viruses by acquiring short viral sequences. We analyzed 2 065 246 CRISPR spacers from 5 separate repeat motifs found in oral bacterial species of Gemella, Veillonella, Leptotrichia and Streptococcus to determine whether individuals from shared living environments may have been exposed to similar viruses. A significant proportion of CRISPR spacers were shared within subjects from the same households, suggesting either shared ancestry of their oral microbiota or similar viral exposures. Many CRISPR spacers matched virome sequences from different subjects, but no pattern specific to any household was found. Our data on viromes and CRISPR content indicate that shared living environment may have a significant role in determining the ecology of human oral viruses.     

AMP-deaminase activity in denervation atrophy of the amphibian skeletal muscle

The substrate (AMP) and co-factor (ATP)-dependent kinetic parameters of AMP-deaminase have been studied in the contralateral and denervated gastrocnemius muscles of frog, Rana hexadactyla. An increasing in apparent affinity (Km) and maximal velocity (V) were found with denervated muscle enzyme as compared to the contralateral muscle enzyme. The activation energy (delta E) values were found to be decreased on denervation suggesting increased catalytic efficiency of denervated muscle enzyme.     

Collagen binding by lactobacilli

¹²⁵I-labeled type I collagen (Cn-I) binding of 92 fresh isolates and 18 type culture collection strains of lactobacilli was tested. More than 75% of the strains bound Cn-I. The binding was inhibited by excess of unlabeled Cn-I, gelatin, and was sensitive to proteinase K. Other proteins such as fibronectin and albumin and various carbohydrates such asD-galactose,D-fucose, andD-mannose did not inhibit the binding. Therefore, we propose binding of Cn-I to lactobacilli involving specific surface protein(s).     

Microsomal enzymes in malnutrition as determined by plasma half life of antipyrine.

Nutritional-pharmacological interactions were studied in a group of malnourished subjects. Antipyrine was used to evaluate mixed-function oxidase in man. The results indicated that the rate of disappearance of antipyrine from plasma was strongly influenced by the nutritional status of the individual. The half life of antipyrine was modified in undernourished subjects and those with nutritional oedema. This finding indicates that drug regimens may have to be adjusted in patients who have antipyrine half lives that are shorter or longer than normal. Otherwise drug treatment may be inadequate or, in patients with impaired microsomal enzyme activity, potentially dangerous.