Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.

Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed

The upflow anaerobic sludge blanket (UASB) reactor is a microcosm for the methanogenic degradation of organic matter in anaerobic environments, and depends on the auto-formation of dense 3D biofilms of 1–3 mm in diameter, referred to as granular sludge (biogranules). Past research has shown that UASB and other methanogenic reactors are extremely stable functionally, but the underlying basis of the functional stability is not well understood. In this study, microbial dynamics in the communities residing in UASB biogranules were analysed to determine responses to short-term perturbations (change in reactor feed). The reactor was fed with simulated brewery wastewater (SBWW) for 1.5 months (phase 1), acetate/sulfate for 2 months (phase 2), acetate alone for 3 months (phase 3) and then a return to SBWW for 2 months (phase 4). Analysis of 16S rRNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB gene-based-clone libraries showed a relatively simple community composed mainly of the methanogenic archaea (Methanobacterium and Methanosaeta), members of the green non-sulfur (Chloroflexi) group of bacteria and Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related bacterial sequences. The mcrA clone libraries were dominated throughout by Methanobacterium- and Methanospirillum-related sequences. Although the reactor performance remained relatively stable throughout the experiment, community diversity levels generally decreased for all libraries in response to a change from SBWW to acetate alone feed. There was a large transitory increase noted in 16S diversity at the 2 month sampling on acetate alone, entirely related to an increase in bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels. Our results demonstrated that microbial communities, even highly structured ones such as in UASB biogranules, are very capable of responding to rapid and major changes in their environment.

Altered subjective appetite parameters in Crohn's disease patients

BACKGROUND AND AIM

Altered appetite and early satiety may promote anorexia associated with Crohn's disease. The aim of this study was to assess the impact of disease activity on subjective appetite parameters in Crohn's disease patients.

METHODS

Seventeen patients with Crohn's disease and 15 healthy controls (8 M: 7 F, 34 (20-35) years) were studied. Subjects rated their hunger, desire to eat, fullness and level of satiety using visual analogue scales after an overnight fast. Subjects were reassessed after ingestion of 500 and 1000 ml water. Anthropometry was used to determine percentage body fat. Serum leptin & TNF- alpha levels were assessed using immunoassay. Disease activity was determined using the Harvey-Bradshaw index.

RESULTS

Hunger ratings for active Crohn's disease patients were significantly lower than controls at baseline (P<0.05). Desire to eat was lower in patients with active Crohn's disease than controls both at baseline (95% CI, 0.3 mm, 40.7 mm) and after ingestion of 500 ml water (95% CI, 1.25 mm, 51.9 mm) (P<0.05). Serum leptin concentrations were significantly associated with percent body fat (r=0.57;P<0.001) and, after correcting for body fat status, tended to be higher in patients with active Crohn's disease (mean 0.9 ng/ml/% body fat; SD 0.8 ng/ml/% body fat) compared with either patients with inactive disease (mean 0.4 ng/ml/% body fat; SD 0.3 ng/ml/% body fat) or healthy controls (mean 0.3 ng/ml/% body fat; SD 0.2 ng/ml/% body fat) (P=0.15, ns). Appetite parameters and serum leptin concentrations showed no significant correlation.

CONCLUSIONS

Subjective appetite parameters were altered in patients with active Crohn's disease. At baseline, patients with active Crohn's disease were less hungry than healthy controls and had less desire to eat. After ingestion of 500 ml of water, desire to eat was significantly less in patients with active disease as compared with healthy controls. Serum leptin concentration corrected for percent body fat tended to be higher in patients with active Crohn's disease compared with inactive Crohn's disease and healthy controls, but the differences did not reach statistical significance.

Serum interleukin-6 levels in metastatic renal cell carcinoma before treatment with interleukin-2 correlates with paraneoplastic syndromes but not patient survival

PURPOSE

We sought to determine the frequency of interleukin-6 (IL-6) expression in renal cancer cell lines, the frequency of the detection of IL-6 in the serum of patients with metastatic renal cell carcinoma, whether serum IL-6 level correlates with the development of paraneoplastic syndromes and whether serum IL-6 level in patients with metastatic renal cancer correlates with response to treatment with interleukin-2 (IL-2) or patient survival.

MATERIALS AND METHODS

Conditioned media from 21 cell lines from 20 patients were examined for IL-6. We identified 2 matched groups of patients with metastatic renal cancer (30 responders and 29 nonresponders) to IL-2 based immunotherapy. Stored pretreatment serum specimens were evaluated for IL-6. Medical records were reviewed to determine the presence of paraneoplastic syndromes.

RESULTS

IL-6 was detected in 19 of 21 renal cancer cell lines (90%) obtained from 20 patients with metastatic renal cancer as well as in the serum of 33 of 59 patients (56%) with metastatic renal cell carcinoma. A significant association between serum IL-6 level and anemia (p = 0.0032), elevated platelet count (p = 0.01), decreased albumin (p = 0.034) and elevated alkaline phosphatase (p = 0.04) was found. A trend was noted of the association of increased serum IL-6 level and fever (p = 0.051). No correlation was found between pretreatment serum IL-6 level and survival or response to IL-2.

CONCLUSIONS

IL-6 was frequently secreted by renal cancer cell lines but it was only present in the serum of approximately half of the patients with metastatic renal cancer. Elevations of serum IL-6 were associated with paraneoplastic manifestations frequently seen in patients with renal cancer, including anemia, thrombocytosis, decreased albumin and elevations of alkaline phosphatase (Stauffer's syndrome). A weak relationship was noted between serum IL-6 level and fever but none was noted between that and survival or response to IL-2.

Molecular cloning and characterization of a pea chitinase gene expressed in response to wounding, fungal infection and the elicitor chitosan

The fungicidal class I endochitinases (E.C.3.3.1.14, chitinase) are associated with the biochemical defense of plants against potential pathogens. We isolated and sequenced a genomic clone, DAH53, corresponding to a class I basic endochitinase gene in pea, Chi1. The predicted amino acid sequence of this chitinase contains a hydrophobic C-terminal domain similar to the vacuole targeting sequences of class I chitinases isolated from other plants. The pea genome contains one gene corresponding to the chitinase DAH53 probe. Chitinase RNA accumulation was observed in pea pods within 2 to 4 h after inoculation with the incompatible fungal strain Fusarium solani f. sp. phaseoli, the compatible strain F. solani f.sp. pisi, or the elicitor chitosan. The RNA accumulation was high in the basal region (lower stem and root) of both fungus challenged and wounded pea seedlings. The sustained high levels of chitinase mRNA expression may contribute to later stages of pea's non-host resistance.

Clones of T cells discriminate between native and deglycosylated forms of MHC class II antigen in allostimulation

The aim of this study was to clarify the role of the oligosaccharide side chains of MHC Class II antigens in allostimulation. The approach was to cleave the oligosaccharides from protein by subjecting plasma membranes (PM) of the Daudi cell line to chemical deglycosylation yielding deglycosylated (dgl) proteins and a supernatant fraction containing plasma membrane oligosaccharides (dgl sup). MHC Class II antigens affinity purified from the native and the dgl PM were inserted into the plasma membrane of peripheral blood leukocytes (PBL) used as stimulators in a mixed leukocyte reaction (MLR). Cells used as stimulators and as responders were from the same donor. Both native and to a lesser extent the dgl antigen could elicit a proliferative as well as a cytolytic (CML) response. A comparable reduction in the CML reaction was also obtained when native antigen was used to elicit effector cells, but the target was stripped of N-linked oligosaccharides by pretreatment with tunicamycin (TM). Five clones of responding cells raised against the native antigen were studied. Two gave proliferative reactions of equal magnitude to native and to dgl antigen alike, while three responded only to the native form. These three clones did not lyse TM-treated target cells. Inhibition experiments of CML were performed with either the dgl sup containing Daudi PM oligosaccharides or with an anti MHC-Class II MoAb. CML reactivity of the three clones which responded to native antigen was blocked by the dgl sup but not by the anti-MHC antibody. Conversely, the reaction of the two clones reactive to both forms of antigen was only inhibited by the anti-MHC antibody using intact or TM-treated targets. Accordingly, in terms of the latter set of clones oligosaccharide side chains of MHC may not be required for allostimulation. Data obtained with the set of three clones suggest that oligosaccharides could act as target of cytotoxic T cells.

Analysis of barley nitrate reductase cDNA and genomic clones

Barley nitrate reductase cDNA and genomic clones were isolated by homology with the barley nitrate reductase cDNA clone bNRp10 and sequenced. This is the first reported analysis of a full-length nitrate reductase gene and its corresponding cDNA in the same species. The longest cDNA clone extends to within 9 bp of the ATG start codon and the sequence is similar to that reported for the higher plant NR sequences. As expected, the amino acid sequence of barley nitrate reductase is more related closely to the rice (84% homology) than to the Arabidopsis (62%) sequence. Four different polyA addition sites were identified from sequence analysis of nine barley NR cDNA clones. A 7.3 kb region of a genomic recombinant lambda clone was subcloned as two contiguous BamHI fragments into p Bluescript, designated pMJ7 and pMJ8, and sequenced. These clones include the entire nitrate reductase coding region, one large intron, 2.7 kb of untranslated sequence 5' to the translation start codon and 0.25 kb 3' to the translation termination codon. The mRNA cap site was identified as a cytosine, 111 bases upstream of the ATG translation start codon. The putative CAAT and TATA boxes were identified at -115 and -33 bp, respectively, with the mRNA cap site designated as +1. The barley nitrate reductase gene coding region strongly favors G or C in the third codon position.

The organization and expression of a maize ribosomal protein gene family

We have isolated several Zea mays cDNAs encoding the 40S subunit ribosomal protein S14. In maize, this ribosomal protein is encoded by a small multigene family, at least three members of which are expressed. S14 transcript levels are highest in mitotically active tissues, such as seedling shoot, developing endosperm, and tassel primordia, and lowest in tissues with little cell division, such as mature leaf and root. Very little S14 RNA is present in pollen, suggesting that translation of pollen mRNAs during pollen germination uses preformed ribosomes. During kernel development, the highest levels of S14 transcripts in endosperm tissue are found at 10-12 days postpollination; S14 RNA levels decline continuously from this point onward. The period of maximal expression of the S14 ribosomal protein gene appears to precede the onset of storage protein synthesis and does not correlate with the reported times of increased nucleolar volume or genome amplification.

Time-varying effects in mice and rats of several synthetic ACTH preparations

Circadian stage-dependent effects characterize synthetic ACTH 1-17 preparation (HOE 433 = Synchrodyn 1-17), tested in mice and rats, with reference notably to corticosterone and aldosterone production in vitro and to the behavior of rhythms in these two corticoids as an aspect of the adrenal cortical pacemaker of the circadian system. The possibility to advance or delay the rhythm in serum corticosterone by ACTH 1-17 also is demonstrated, as is a differential behavior of the circadian rhythm in serum aldosterone. Differences in timing of circadian corticosterone and aldosterone responses also are described and await further scrutiny for ultradian and infradian (notably circannual) modulation.