Prevalence of a Novel Division-Level Bacterial Lineage in Lake Dhanmondi, Dhaka, Bangladesh, as Revealed by Deep Sequencing of 16S rRNA Gene Amplicons

A culture-independent study of the bacterial diversity in Lake Dhanmondi, located in the central region of Dhaka city, Bangladesh, was carried out using deep sequence analysis of 16S rRNA gene PCR amplicons. The results revealed the presence of a group of bacteria, termed LD11, phylogenetically unrelated to any previously cultivated bacteria at the phylum level. LD11 sequences comprised about 1.7?% of the total sequence reads after quality assessment. LD11 appears to constitute a novel division with a deep evolutionary lineage apparently branching between the Chloroflexi and Thermi-Deinococci phyla. Sequence similarity with molecular data from freshwater environments indicates that LD11 represents a widespread and novel clade of freshwater bacteria for which no cultivated representatives are yet available.     

Pre-hydrolysis improves utilisation of dietary protein in the larval teleost Atlantic halibut (Hippoglossus hippoglossus L.)

A protein preparation labelled by incorporation of [U]¹⁴C-AA was hydrolysed to various degrees and administered to a teleost fish larva (Atlantic halibut, Hippoglossus hippoglossus L.) by tube-feeding, and its post-administration utilisation was studied. Three treatments were prepared: IntP—intact protein, PHP—pepsin-hydrolysed protein, and HHP—highly hydrolysed protein (using pepsin, trypsin, endoproteinase Glu-C, Asp-N, and Pro-C). At small doses (11.4±1.5 μg larvae⁻¹), the intact protein (IntP) was digested and absorbed to 36±5.5%. However, the relative absorption efficiency of the intact protein was reduced as the dose increased. Absorption efficiency was higher when the protein was hydrolysed prior to feeding the larvae and was constant at 63% (R²=98) independent of degree of proteolysis and dose (ranging from 3.5 to 35 μg larvae⁻¹). The initial absorption rate increased with the degree of hydrolysis. Calculations based on data collected during the first 30-120 min show that the absorption of PHP and HHP into extra-intestinal body tissues was 2.2 and 3 times as fast, respectively, as that of intact protein. However, the rates of absorption did not influence the distribution of absorbed AA into either catabolism or anabolism, as all larvae, independent of which protein solution they were given, catabolised 42±7% of the absorbed AA, and accumulated 49±6% into the body tissue, during the 20 h post-feeding incubation period.Larval age and size did not influence the absorption and utilisation of the hydrolysed protein preparations. This was different from the intact protein, as significantly higher fractions of the intact protein were absorbed by the larvae at 31 days past first feeding (dpff) than by larvae at 25 dpff. Analysis of the faecal evacuation suggested that the poor protein utilisation in the younger larvae was due to enhanced faecal evacuation, which in some larvae was more than 50% only 4 h post diet administration, at a time when the process of digestion and absorption was far from complete. This indicated that faecal evacuation is a critical factor in the utilisation of slowly digested and absorbed feed components, such as intact proteins, by fish larvae.     

Sustained release of corticosterone in rats affects reactivity, but does not affect habituation to immobilization and acoustic stimuli

Depression is often preceded by stressful life events and accompanied with elevated cortisol levels and glucocorticoid resistance. It has been suggested that a major depressive disorder may result from impaired coping with and adaptation to stress. The question is whether or not hypothalamus-pituitary-adrenal (HPA)-axis dysfunction influences the process of adaptation. We examined the effect of a dysregulated HPA-axis on the adaptation to acoustic stimuli in rats with or without preceding restraint stress. HPA-axis function was altered via slow release of corticosterone (CORT, 90 mg) from subcutaneously implanted pellets for 7 or 14 days. The rate of body temperature increases during restraint (10 min) and the response to acoustic stimuli (of 80+120 dB) were used to quantify daily stress reactivity. Rats habituated to either stress regardless of CORT treatment. CORT treatment combined with restraint decreased the initial reactivity and the variability in response, but the rate of habituation was not influenced. These results show that suppressing normal HPA-axis function by chronic exposure to CORT does affect the course of habituation, but not habituation per se. This implies that altered HPA-axis function in depressed patients may not be causally related to stress coping, but instead may influence the course of the disorder.     

Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA

Human UNG2 is a multifunctional glycosylase that removes uracil near replication forks and in non-replicating DNA, and is important for affinity maturation of antibodies in B cells. How these diverse functions are regulated remains obscure. Here, we report three new phosphoforms of the non-catalytic domain that confer distinct functional properties to UNG2. These are apparently generated by cyclin-dependent kinases through stepwise phosphorylation of S23, T60 and S64 in the cell cycle. Phosphorylation of S23 in late G1/early S confers increased association with replication protein A (RPA) and replicating chromatin and markedly increases the catalytic turnover of UNG2. Conversely, progressive phosphorylation of T60 and S64 throughout S phase mediates reduced binding to RPA and flag UNG2 for breakdown in G2 by forming a cyclin E/c-myc-like phosphodegron. The enhanced catalytic turnover of UNG2 p-S23 likely optimises the protein to excise uracil along with rapidly moving replication forks. Our findings may aid further studies of how UNG2 initiates mutagenic rather than repair processing of activation-induced deaminase-generated uracil at Ig loci in B cells.     

Human AlkB homolog 1 is a mitochondrial protein that demethylates 3-methylcytosine in DNA and RNA

The Escherichia coli AlkB protein and human homologs hABH2 and hABH3 are 2-oxoglutarate (2OG)/Fe(II)-dependent DNA/RNA demethylases that repair 1-methyladenine and 3-methylcytosine residues. Surprisingly, hABH1, which displays the strongest homology to AlkB, failed to show repair activity in two independent studies. Here, we show that hABH1 is a mitochondrial protein, as demonstrated using fluorescent fusion protein expression, immunocytochemistry, and Western blot analysis. A fraction is apparently nuclear and this fraction increases strongly if the fluorescent tag is placed at the N-terminal end of the protein, thus interfering with mitochondrial targeting. Molecular modeling of hABH1 based upon the sequence and known structures of AlkB and hABH3 suggested an active site almost identical to these enzymes. hABH1 decarboxylates 2OG in the absence of a prime substrate, and the activity is stimulated by methylated nucleotides. Employing three different methods we demonstrate that hABH1 demethylates 3-methylcytosine in single-stranded DNA and RNA in vitro. Site-specific mutagenesis confirmed that the putative Fe(II) and 2OG binding residues are essential for activity. In conclusion, hABH1 is a functional mitochondrial AlkB homolog that repairs 3-methylcytosine in single-stranded DNA and RNA.     

Growth and ecophysiological acclimation of the foliose lichen Lobaria pulmonaria in forests with contrasting light climates

This study aims to assess biomass and area growth of 600 thalli of the old forest lichen, Lobaria pulmonaria, transplanted to three successional boreal forest stands with (1) natural rainfall regime, (2) additional moistening during dry days, and (3) additional moistening with added nutrients. Mean biomass growth during 100 days varied from 8.3% in the dark young spruce forest to 23.1% in the clear-cut area, with the old forest in between (16.0%). Additional moistening did not enhance lichen growth, probably because the transplantation period was wet. Nutrient additions slightly increased area growth compared to artificial water additions only. Growth was determined by a combination of external (forest stand, site factors) and internal factors (chlorophyll content, biomass per area). Transplants acclimated to high light by increasing thickness and chlorophyll a/b-ratio. Some visible bleaching and a strong positive correlation between chlorophyll content per area and lichen growth in clear-cuts suggest some high light-induced chlorophyll degradation. We believe that biomass growth and natural occurrence of L. pulmonaria is controlled by a delicate balance between light availability and desiccation risk, and that the species is confined to old forests due to a physiological trade-off between growth potential and fatal desiccation damage, both of which increase with increasing light. The discrepancy between potential and realized ecological niches is probably caused by a long-term risk to be killed in open habitats by high light during long periods with no rain.     

Occurrence of Vibrio parahaemolyticus, V. cholerae, and V. vulnificus in Norwegian Blue Mussels (Mytilus edulis)

Vibrio parahaemolyticus, V. cholerae, and V. vulnificus were isolated from 10.3%, 1.0%, and 0.1% of 885 blue mussel samples, respectively. Four of the samples contained trh(+) V. parahaemolyticus, while no tdh-positive isolates were detected. The V. cholerae isolates were non-O:1/non-O:139 serotypes and were ctxA negative.     

Pectic polysaccharides from Biophytum petersianum Klotzsch, and their activation of macrophages and dendritic cells

The Malian medicinal plant Biophytum petersianum Klotzsch (Oxalidaceae) is used as a treatment against various types of illnesses related to the immune system, such as joint pains, inflammations, fever, malaria, and wounds. A pectic polysaccharide obtained from a hot water extract of the aerial parts of B. petersianum has previously been reported to consist of arabinogalactans types I and II (AG-I and AG-II), probably linked to a rhamnogalacturonan backbone. We describe here further structural characteristics of the main polysaccharide fraction (BP1002) and fractions obtained by enzymatic degradations using endo-alpha-d-(1-->4)-polygalacturonase (BP1002-I to IV). The results indicate that in addition to previously reported structures, rhamnogalacturan type II and xylogalacturonan areas appear to be present in the pectic polymer isolated from the plant. Atomic force microscopy confirmed the presence of branched structures, as well as a polydisperse nature. We further tested whether the BP1002 main fraction or the enzymatically degraded products could induce immunomodulating activity through stimulation of subsets of leukocytes. We found that macrophages and dendritic cells were activated by BP1002 fractions, while there was little response of T cells, B cells, and NK cells. The enzymatic treatment of the BP1002 main fraction gave important information on the structure-activity relations. It seems that the presence of rhamnogalacturonan type I is important for the bioactivity, as the bioactivity decreases with the decreased amounts of rhamnose, galactose, and arabinose. The demonstration of bioactivity by the plant extracts might indicate the mechanisms behind the traditional medical use of the plant.