A de novo designed N-terminal disulphide bridge stabilizes the Trichoderma reesei endo-1,4-beta-xylanase II

We have successfully engineered a disulphide bridge into the N-terminal region of Trichoderma reesei endo-1,4-beta-xylanase II (XYNII) by substituting Thr-2 and Thr-28 with cysteine. The T2C:T28C mutational changes increased the half-life in thermal inactivation of this mesophilic enzyme from approximately 40 s to approximately 20 min at 65 degrees C, and from less than 10 s to approximately 6 min at 70 degrees C. Therefore, the N-terminal disulphide bridge enables the use of XYNII at substantially higher temperatures than permitted by its native mesophilic counterpart. Altogether, thermostability increased by about 15 degrees C. The kinetic properties of the mutant XYNII were maintained at the level of the wild type enzyme. Our findings demonstrated that a properly designed disulphide bridge, here within the N-terminal region of XYNII, can be very effective in resisting thermal inactivation.     

Apoptosis in gallbladder carcinomas and dysplasias, its relation to the expression of caspases 3, 6 and 8 and apoptosis regulating proteins bcl-2, mcl-1 and bax

In this study we investigated apoptosis and the expression of caspases 3, 6 and 8 and bcl-2, mcl-1 and bax in 39 gallbladder carcinomas and 7 epithelial dysplasias. The average apoptotic index was 0.68 +/- 0.91%. The extent of apoptosis was higher in grade II-III than grade I tumours or epithelial dysplasias (p = 0.003). Also, tumours invading beyond serosa or into other organs (T3-T4) had a higher apoptotic index than other tumours (p = 0.05). Caspase 3 expression was found in 37 (95%) and caspase 6 and 8 expression each in 30 (77%) carcinomas. Their expression associated with each other and tended to increase along with the progression of the lesions. Bcl-2 expression was found in only 4 (10%) tumours. In contrast, mcl-1 positivity was found in 34 (87%) and bax positivity in all cases. The results show that apoptosis is increased along with progression of the neoplastic lesions of the gallbladder epithelium. Caspases 3, 6 and 8 are strongly expressed in gallbladder carcinomas suggesting that they contribute to the increased apoptosis observed in them. Of the bcl-2 family proteins, bcl-2 was expressed infrequently suggesting that it does not play any significant role in apoptosis inhibition in gallbladder tumours.     

Xylanase production by Trichoderma reesei Rut C-30 grown on L-arabinose-rich plant hydrolysates

The suitability of L-arabinose-rich plant hydrolysates as carbon sources and inducers of xylanase production in Trichoderma reesei Rut C-30 was tested. Significantly higher xylanase activities were obtained in cultures on oat husk and sugar beet pulp hydrolysates than on lactose. In batch culture with oat husk hydrolysate and lactose, the xylanase activity was about 9 times higher ( approximately 510 IU/ml) than in lactose ( approximately 60 IU/ml). Even higher xylanase activity ( approximately 630 IU/ml) was obtained when the batch cultivations were done on sugar beet pulp hydrolysate and lactose. In a fed-batch culture using oat husk hydrolysate-lactose the xylanase activity was as high as 1350 IU/ml in 4 days. The cellulase production clearly decreased when T. reesei was cultured on both hydrolysates compared to the cultivation on lactose. Moreover, the relative amounts of the xylanases I-III were similar regardless the used carbon source.     

Three MADS-box genes similar to APETALA1 and FRUITFULL from silver birch (Betula pendula)

Despite intensive research on genetic regulation of flower development there are still only a few studies on the early phases of this process in perennial plants like trees. The aim of this study has been to identify genes that regulate early stages of inflorescence development in silver birch ( Betula pendula Roth) and to follow the expression of these genes during development of the unisexual birch inflorescences. Here we describe the cloning and characterization of 3 cDNAs representing MADS-box genes designated BpMADS3, BpMADS4 and BpMADS5, all belonging to the AP1/SQUA group of plant MADS-box genes. According to RNA blot analysis, all 3 genes are active during the development of both male and female inflorescences. However, differences in patterns of expression suggest that they play different roles. BpMADS3 is most similar in sequence to AP1 and SQUA, but it seems to have the highest expression at late developmental stages. BpMADS4 is most similar in sequence to the Arabidopsis gene FRUITFULL , but is expressed, in addition to developing inflorescences, in shoots and roots. BpMADS5 is also similar to FRUITFULL; its expression seems to be inflorescence-specific and continues during fruit development. Ectopic expression of either BpMADS3, BpMADS4 or BpMADS5 with the CaMV 35S promoter in tobacco results in extremely early flowering. All of these birch genes seem to act early during the transition to reproductive phase and might be involved in the determination of the identity of the inflorescence or flower meristem. They could apparently be used to accelerate flowering in various plant species.     

Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site

We have determined the crystal structure of Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal) at a 1.2? resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4? resolutions, respectively. Tr-β-gal is a potential enzyme for lactose hydrolysis in the dairy industry and belongs to family 35 of the glycoside hydrolases (GH-35). The high resolution crystal structures of this six-domain enzyme revealed interesting features about the structure of Tr-β-gal. We discovered conformational changes in the two loop regions in the active site, implicating a conformational selection-mechanism for the enzyme. In addition, the Glu200, an acid/base catalyst showed two different conformations which undoubtedly affect the pK(a) value of this residue and the catalytic mechanism. The electron density showed extensive glycosylation, suggesting a structure stabilizing role for glycans. The longest glycan showed an electron density that extends to the eighth monosaccharide unit in the extended chain. The Tr-β-gal structure also showed a well-ordered structure for a unique octaserine motif on the surface loop of the fifth domain.     

Impact of beta-glucan on the faecal microbiota of polypectomized patients: a pilot study

Beta-glucans are polysaccharides present in the cell walls of higher plants, in the seeds of some cereals, and certain yeasts and fungi also produce them. It is suggested that they exhibit, among many other health benefits, protective effects against carcinogenesis in the colon, but there is not enough human data to support this. The aim of the study was to determine the effect of barley-derived beta-glucan in the gut microbiota of polypectomized patients. Subjects were randomly assigned to consume 125 g of bread per day with beta-glucan (3 g/d), or without (placebo group), for 3 months. Thirty-three polypectomized men and women (mean age 57.6 years) were recruited into the study, but only 20 completed. Subjects did not consume any probiotics, prebiotics or antibiotics 2 months prior the intervention, or during the study. Stool samples were collected at baseline, on days 30 and 90 of intervention, as well as 2 weeks after the intervention, for enumeration of total aerobes and anaerobes, coliforms, E. coli, enterococci, Bacteroides spp., Clostridium perfringens, bifidobacteria, lactobacilli and Candida spp. Faecal bacterial enzyme activity (beta-glucuronidase and beta-glucosidase), pH, faecal moisture and the concentration of volatile fatty acids in the faeces were measured. Gastrointestinal symptoms were also recorded. Overall, no significant differences were observed in bacterial viable counts between the two feeding groups. Group specific analysis for β-glucan group revealed significantly decreased total coliform counts on the 30th day of the trial compared to the baseline (p = 0.041). Clostridium perfringens concentration increased without reaching statistical significance, on the 30th day, while it decreased significantly on the 90th day of the intervention compared to the 30th day (p = 0.016). An increase was noted in the molar ratio of acetate on the 90th day of the trial compared to placebo (p = 0.018). The molar ratio of butyrate presented a trend to increase on the 30th day, which decreased (p = 0.013) on the 90th day and then increase 2 weeks after the intervention (p = 0.017) compared to placebo. A decrease was recorded in the β-glucan group in the bloating and abdominal pain score after the 30th day of the intervention (Day 30–37) compared to placebo. During β-glucan administration we did not observe any changes on beta-glucuronidase or beta-glucosidase activity, faecal pH, or on faecal moisture.     

Life-cycle climate impacts of peat fuel: calculation methods and methodological challenges

Purpose

There has been lively debate, especially in Finland and Sweden, on the climate impacts of peat fuel. Previous studies of peat fuel's life-cycle climate impacts were controversial in their interpretation. The aim of this paper is conclusive examination of the issues of LCA methodology, derived from critical review of previous studies and recalculation based on the latest knowledge of greenhouse gas balances related to peat fuel’s utilisation and the radiative forcing impacts of greenhouse gases.

Methods

The most recent findings on emissions and the gas fluxes between soil, vegetation and atmosphere were used in calculation of the life-cycle climate impacts of the various peat fuel utilisation chains by means of LCA methodology. In the main, the calculation methods and rules were the same as in the previous studies, with the aim being to distinguish the impact of peat fuel’s utilisation from that of the natural or semi-natural situation. A dynamic method was employed for assessing changes in radiative forcing. The results of alternative peat fuel utilisation chains were compared to the corresponding result for coal.

Results

There are many steps in peat fuel LCA, where different assumptions lead to different outcomes. Determining the functional unit, reference situations and system boundaries, as well as the emission calculation methods, is important from this point of view. Determination of the initial reference situation emerged as one of the critical points in the calculations. Time scale can strongly affect the final outcomes in a study where effects of long-term land-use change are considered.

Conclusions

Each peatland area is unique. The higher the greenhouse gas emissions in the initial reference situation, the greater is the climate impact of the area and the more suitable the area is for peat extraction. The study showed that more greenhouse gas flux measurements are needed, for better assessment of the climate impacts of different potential peat extraction sites. Climate change mitigation requires quick actions, and uncertainties related to emissions are higher for longer time spans. Therefore, it can be concluded that a perspective spanning more than 100 years is inappropriate in peat fuel's life-cycle climate impact assessments.     

Carbon storage change and δ13C transitions of peat columns in a partially forestry-drained boreal bog

Background and aims

In forestry-drained peatlands, drying leads to changes in C cycling which could affect peat δ¹³C. Furthermore, the δ¹³C profile of the entire peat column may reveal effects of earlier climatic periods.

Methods

We measured peat δ¹³C and C inventories in adjacent peat profiles, two collected from undrained and two from the drained side of a bog that was partially ditch-drained 37 years earlier. The cores were sliced into 10-cm subsamples for analyses; matching of the profiles based on surface levelling, peat stratigraphic correlation and a horizontal ash layer found in both profiles.

Results

Surface subsidence of 30 cm was observed in the dried site and the uppermost 160 cm in the undrained site contained an excess of 5.9 kg m⁻² of C compared with the corresponding strata of the ditch-drained site. The δ¹³C values increased but markedly only in the thin surface layer of the drained site, indicating low δ¹³C of the missing C (ca. –30‰). In the deeper strata, dating to Mid-Holocene, high dry bulk density, C%, N%, humification index and low C/N ratio were connected to low δ¹³C of peat.

Conclusions

Drainage of 37 years increased δ¹³C values in the upper peat profile of the drained bog and led to the selective loss of ¹³C depleted C. Results indicate that C balance studies can be aided by C isotope analyses. Low δ¹³C values in the peat profile indicate the existence of a wet fen stage during the moist and warm period during Mid-Holocene.

     

Germline loss‐of‐function variants in MBD4 are rare in Finnish patients with uveal melanoma

Uveal melanoma (UM) is a rare intraocular cancer with the highest incidence in northern latitudes. Metastases develop in approximately 50% of patients, whereafter the median survival is 13 months. Generally, the mutation burden of these tumors is low. Germline variants predisposing to UM have been previously described in BRCA1‐associated protein 1 (BAP1). Recently, germline and somatic loss‐of‐function (LOF) variants in the methyl‐CpG‐binding domain 4 (MBD4) gene have been found to cause a hypermutated UM, and MBD4 also has been put forward as a gene predisposing to UM. We sequenced for MBD4 germline variants in 440 Finnish patients with UM and identified seven rare exonic missense variants in 16 (3.6%) patients, of which one likely alters MBD4 function. The frequency of likely pathogenic variants in our cohort is 0.23% (1/432; 95% CI, 0.01–1.28). We identified no LOF variants though their frequency in the Finnish population is 0.052%. Thus, our data do not support the suggestion that MBD4 germline variants predispose to UM. Somatic loss of MBD4 might modify the mutational burden in UM and change its response to immune checkpoint inhibitors.