Improvement in enzyme productivities from mold cultivations using the liquid-phase oxygen supply strategy

Cultivations of Aspergillus niger cells in which oxygen was provided through the liquid-phase oxygen supply strategy (which involves the need-based decomposition of H2O2 pulses to yield the necessary oxygen) were studied. Concentrations of H2O2 in the range of 1 to 5 mM were found to be suitable for use in cultivations. The growth rate constant of 0.17 h(-1) obtained in the H2O2-based cultivation, was comparable to that obtained in the cultivation with aeration; however, the maximum cell concentration in the H2O2-based cultivation was 124% of that obtained in cultivation with aeration. Maximum concentrations of catalase, protease and glucose oxidase obtained in the H2O2-based cultivation, were 240%, 172%, and 124% respectively, of those obtained in the cultivation with aeration. Further, the specific enzyme levels (units per gram cell) of catalase and protease obtained in the H2O2-based cultivation were 172% and 156% of those obtained in the cultivation with aeration, whereas, the specific glucose oxidase levels were comparable. In addition, the oxygen profiles inside the pellets ofA. niger during both the modes of oxygen supply were described using mathematical models. Studies to elucidate the mechanism of oxygen availability showed that the decomposition of the H2O2 supplied in the extracellular space occurred intracellularly, as well as extracellularly, to yield oxygen. Also, the proton motive force (PMF) was found to be involved in the process of oxygen availability from H2O2 to A. niger cells.     

An Analysis of the Role of the Indigenous Microbiota in Cholesterol Gallstone Pathogenesis

Background and Aims

Cholesterol gallstone disease is a complex process involving both genetic and environmental variables. No information exists regarding what role if any the indigenous gastrointestinal microbiota may play in cholesterol gallstone pathogenesis and whether variations in the microbiota can alter cholesterol gallstone prevalence rates.

Methods

Genetically related substrains (BALB/cJ and BALB/cJBomTac) and (BALB/AnNTac and BALB/cByJ) of mice obtained from different vendors were compared for cholesterol gallstone prevalence after being fed a lithogenic diet for 8 weeks. The indigenous microbiome was altered in these substrains by oral gavage of fecal slurries as adults, by cross-fostering to mice with divergent flora at <1day of age or by rederiving into a germ-free state.

Results

Alterations in the indigenous microbiome altered significantly the accumulation of mucin gel and normalized gallbladder weight but did not alter cholesterol gallstone susceptibility in conventionally housed SPF mice. Germ-free rederivation rendered mice more susceptible to cholesterol gallstone formation. This susceptibility appeared to be largely due to alterations in gallbladder size and gallbladder wall inflammation. Colonization of germ-free mice with members of altered Schaedler flora normalized the gallstone phenotype to a level similar to conventionally housed mice.

Conclusions

These data demonstrate that alterations in the gastrointestinal microbiome may alter aspects of cholesterol gallstone pathogenesis and that in the appropriate circumstances these changes may impact cholesterol cholelithogenesis.     

Isolation of Helicobacter spp. from Mice with Rectal Prolapses

Enterohepatic Helicobacter species (EHS) often are associated with typhlocolitis and rectal prolapse in mice. We sought to describe rectal prolapses histologically, relate lesions to mouse genotype and EHS infection status, and characterize EHS pathogens on our campus. Our mouse population was housed among 6 facilities on our main campus and a seventh, nearby facility. We investigated cases of rectal prolapse over 1 y and included 76 mice, which were broadly categorized according to genotype. Microscopically, lesions ranged from mild to severe typhlocolitis, often with hyperplastic and dysplastic foci. Neoplastic foci tended to occur at the ileocecal–colic junction. Lesions were most severe in strains that had lower-bowel inflammatory disease, notably IL10, Rag1, and Rag2 knockout strains; prolapses occurred in these strains when housed both in areas with endemic EHS and in our Helicobacter-free barrier facility. Most mice with rectal prolapses were immunocompromised genetically modified mice; however, the most frequently sampled strain, the lamellipodin knockout, was noteworthy for its high incidence of rectal prolapse, localized distal colonic and rectal lesions, and lack of known immunodeficiency. This strain is being explored as a model of rectal carcinoma. Most of the colons examined tested PCR-positive for EHS, often with coinfections. Although H. bilis is prevalent on our campus, we did not find this organism in any mice exhibiting clinical signs of rectal prolapse. Identification of H. apodemus in 22% of cases has fueled increased surveillance on our campus to characterize this organism and differentiate it from the closely related H. rodentium.Abbreviations: EHS, enterohepatic Helicobacter species; IBD, inflammatory bowel disease; RFLP, restriction-fragment–length polymorphism; RP, rectal prolapseRectal prolapse (RP) occurs commonly in laboratory mice and is often associated with lower-bowel inflammation. Mice have a relatively short and poorly supported distal colon, which lacks a serosal covering.³⁰ This anatomic weakness, coupled with a microbial insult, toxic injury, or space-occupying neoplastic masses within the gastrointestinal tract, are the predisposing factors for tenesmus and RP (Figure 1). In the context of microbial insults, the pathogenesis involves diffuse or multifocal inflammation in the more proximal segments of colon or distal colon, which can result in thickened edematous tissue and tenesmus, triggering a prolapse.^6,30,40 Bacteria most often associated with this condition are the enterohepatic Helicobacter species (EHS) and Citrobacter rodentium; although in theory any pathogenic bacteria causing colitis may predispose mice to RP.^1,11,13,38Open in a separate windowFigure 1.Mouse rectal prolapse. An example of the clinical presentation of rectal prolapse in laboratory mice. Note the attachment of bedding and nesting material in the film of mucous that frequently is seen covering the exposed rectal tissue. Generally the tissue becomes severely erythematous, as can be appreciated in this photograph.Although the clinical presentation of RP may occur in immunocompetent mice, it is most often associated with mice that have a spontaneous or transgenic mutation causing immunodeficiency.^11,13,38 Indeed, these naturally occurring murine pathogens are used to model inflammatory bowel disease in strains that are highly susceptible to typhlocolitis with EHS infection; examples include Il10^−/− and Rag-deficient mice.^{3,5,8,9,13,16,19,20,22,40} In addition, H. hepaticus and other EHS including H. typhlonius, H. rodentium, and H. bilis, which are known to persistently colonize the intestinal crypt of the lower bowel, have been shown to induce colitis-associated cancer in susceptible immunodeficient strains of mice.^{4,7,9,23,24,27,29,31}In 1999, our institution introduced a rodent importation policy to reduce the introduction of murine pathogens. As part of this program, all approved commercial vendors were screened to ensure animals were SPF for EHS. Any random-source mice (typically imported from other academic institutions for collaborative projects) were required to be rederived by embryo transfer. In comparing PCR data between 1999 (prior to implementing the ET policy) and 2009, we found that after more than a decade of strict rederivation and husbandry practices that reduce fecal–oral transmission, EHS prevalence was markedly reduced.²¹ Despite this success, these practices did not completely eradicate rodent EHS. Of particular note, 2 facilities on campus house well-established long-term breeding colonies, many of which are unique transgenic lines with various immunodeficiencies, that are used primarily for immunology and cancer research. Rederivation of each of these strains was considered to be cost-prohibitive; thus EHS has remained endemic in these breeding colonies for more than a decade, as evident by our recent surveillance for EHS prevalence.²¹ The species known to be prevalent on our campus prior to the current study included H. hepaticus, H. rodentium, H. typhlonius, and H. bilis; in a few isolated areas, H. mastomyrinus was identified also.²¹Although EHS infections often are subclinical, we sought to correlate the presence of EHS-endemic areas with clinical lower-bowel inflammation (evident by rectal prolapse). In this survey of laboratory mice at our institution, we identified patterns in mouse strain susceptibility to RP, RP association with EHS, and histopathologic findings and correlated specific EHS species with clinical disease. Because we sought to study spontaneous infections, we excluded any mice on study with experimentally induced inflammatory bowel disease (IBD), including Helicobacter-induced IBD and chemically induced colitis models.From July 2011 to July 2012, a total of 63 mice with RP from these 6 facilities at our institution were necropsied as part of this investigation. In addition, 13 mice with RP were identified at a nearby research institute housing mice known to have endemic EHS.     

Inferring short tandem repeat variation from paired-end short reads

The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method’s ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.     

A novel chromosomal abnormality t (9;14)(p24;q13) in B-acute lymphoblastic leukemia

Acute lymphoblastic leukemia is a malignant disease of the bone marrow in which early lymphoid precursors proliferate and replace the normal hematopoietic cells of the marrow. We describe the clinical, morphologic, immunophenotypic and cytogenetic findings in the case of a 26-year-old man with B-lymphoblastic leukemia. Surface marker analysis revealed that they are positive for CD markers CD10, CD19, CD13, CD34, CD45 and HLA-DR, but negative for CD20, CD33, CD117 and CD11C markers. Cytogenetic analysis established a novel translocation, t (9;14)(p24;q13). Apart from this, spectral karyotyping revealed an additional translocation, t (6p; 14q). This is the first documented case of B-lymphoblastic leukemia with concurrent occurrence of both abnormalities. Further studies are needed to understand the role of this abnormality in carcinogenesis.     

Genomic and functional characterization of coleopteran insect-specific α-amylase inhibitor gene from Amaranthus species

The smallest 32 amino acid α-amylase inhibitor from Amaranthus hypochondriacus (AAI) is reported. The complete gene of pre-protein (AhAI) encoding a 26 amino acid (aa) signal peptide followed by the 43 aa region and the previously identified 32 aa peptide was cloned successfully. Three cysteine residues and one disulfide bond conserved within known α-amylase inhibitors were present in AhAI. Identical genomic and open reading frame was found to be present in close relatives of A. hypochondriacus namely Amaranthus paniculatus, Achyranthes aspera and Celosia argentea. Interestingly, the 3′UTR of AhAI varied in these species. The highest expression of AhAI was observed in A. hypochondriacus inflorescence; however, it was not detected in the seed. We hypothesized that the inhibitor expressed in leaves and inflorescence might be transported to the seeds. Sub-cellular localization studies clearly indicated the involvement of AhAI signal peptide in extracellular secretion. Full length rAhAI showed differential inhibition against α-amylases from human, insects, fungi and bacteria. Particularly, α-amylases from Helicoverpa armigera (Lepidoptera) were not inhibited by AhAI while Tribolium castaneum and Callosobruchus chinensis (Coleoptera) α-amylases were completely inhibited. Molecular docking of AhAI revealed tighter interactions with active site residues of T. castaneum α-amylase compared to C. chinensis α-amylase, which could be the rationale behind the disparity in their IC₅₀. Normal growth, development and adult emergence of C. chinensis were hampered after feeding on rAhAI. Altogether, the ability of AhAI to affect the growth of C. chinensis demonstrated its potential as an efficient bio-control agent, especially against stored grain pests.     

Biosequestration of carbon dioxide using a silicified carbonic anhydrase catalyst

Using recombinant DNA technology, we constructed a dual fusion gene expression plasmid, pRCAH-30, encoding carbonic anhydrase (CA) from the cyanobacterium Synechocystis sp. PCC6803, an R5 peptide sequence, and an affinity (His)₆ tag, to allow the simultaneous purification and immobilization of the encoded fusion enzyme, termed RCAH. The expressed fusion protein was approximately 30 kDa, and could be rapidly purified using affinity resins. To enhance enzyme activity, the R5 peptide facilitated immobilization by means of silicification with tetramethoxysilane; the aggregated particles were approximately 300 nm in diameter. Activity tests revealed that the enzyme functioned optimally between pH 7.0 and 7.5; maximum stability was achieved between 25 and 45°C, at pH 6.0 ～ 8.0. Activity of the fusion enzyme persisted, even after encapsulation by biomimetic silicification. In fact, silicone embedding stabilized the enzyme structure, thereby increasing its stability and reusability rate under different environmental conditions. In addition, the silicified enzyme reduced waste CO₂ gas from 800 to 42 ppm, resulting in a gas capture rate of 94.7% after conversion. Thus, the construct developed in this study can be effectively utilized for the sequestration of industrial waste CO₂ gas.