Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development

The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.     

Benthic communities on a sandy Ligurian beach (NW Mediterranean)

The different components of the benthic community of a sandy microtidal beach (Arenzano) in Liguria (NW Mediterranean) were investigated during late spring (May) 2002 and 2003. Sampling was carried out in two transects, chosen in order to represent the characteristics of the entire beach and their eventual spatial variations. Each transect included two stations: one placed in the swash zone (SW) and one in the surf zone (SF). Although no significant differences were found in the sediment texture over the 2 years (t-tests p > 0.1 for all the granulometric fractions), notwithstanding an increase in the mean grain size (from 0.8 to 1.1 mm) between the sampling periods, 2002 was characterised by a higher quantity of organic matter (on average 14.4 vs. 3.6 gC m⁻² for the sum of proteins, carbohydrates and lipids) and higher bacterial biomass (on average 1.9 vs. 0.9 gC m⁻²). The metazoan assemblages (meiofauna and macrofauna) were also richer (density = 2.9 × 10⁵ vs. 1.0 × 10⁵ ind. m⁻², biomass = 0.09 vs. 0.03 gC m⁻² for meiofauna; density = 1988 vs. 739 ind. m⁻², biomass = 0.14 vs. 0.03 gC m⁻² for macrofauna) in 2002. A significant quantitative reduction (t-test for proteins, carbohydrates and lipids, at least p = 0.004) in the food supply in 2003 affected the abundance of the metazoans, as confirmed by a multivariate analysis that clearly differentiated the 2 years, and seemed to inhibit their relationships within the benthic food web. The bacterial biomass was always dominant, even under the least favourable trophic conditions, due to the ability of bacteria to adapt to a very harsh environment. Our results suggest that the food supply played an important role in the benthic community structures of the beach during late spring, bacteria being the key organisms within the benthic system. The communities seemed to be bottom-up controlled, while predation seemed to be irrelevant.     

NMR characterization of the polysaccharidic fraction from Lentinula edodes grown on olive mill waste waters

A high-field NMR study of the polysaccharidic fraction extracted from Lentinula edodes mycelium grown on olive mill waste waters is reported. Diffusion-ordered NMR spectroscopy (DOSY) was applied to the polysaccharidic fraction. The results showed the presence of two polysaccharides of different sizes, whose structures were revealed using one- and two-dimensional NMR techniques. These two polysaccharides were identified as xylan and lentinan.     

Cytostatic properties of a novel compound derived from Penicillium pinophilum: an in vitro study

3-O-Methylfunicone (OMF), a secondary metabolite produced by Penicillium pinophilum, inhibits the in vitro growth of plant pathogenic fungi. This specific property suggested that the compound could be used against other fungal pathogenic activities, including dermatological ones. However, for such applications, toxicological side-effects should be taken into account, in order to prevent other types of risk to mammalian cells. Therefore, investigations were made of the basic toxicity of OMF toward a human tumour cell line. The compound was found to have a cytostatic effect, which represents a counter-indication to its use as a therapeutic agent in dermatology, but suggests that it may have potential as an anti-tumour agent. This study confirmed the validity of in vitro systems for preliminary assays on new compounds, in order to avoid the use of animals in toxicological studies.     

Comparative structural analysis of low-molecular mass fragments of Rapana venosa hemocyanin obtained using two different procedures

Different fragments of the hemocyanin (Hc) isolated from the gastropod Rapana venosa containing a single functional unit (50 kDa), two functional units (100 kDa) and three functional units (150 kDa) were obtained in a dissociating buffer in the presence of Zn2+ and purified to homogeneity. Their conformations in solution were studied by means of small angle X-ray scattering (SAXS) and compared with those of the corresponding fragments previously obtained by limited proteolysis [Arch. Biochem. Biophys., 2000, 373, 154]. The overall shape of each fragment was determined using an ab initio approach. The crystal structures of the functional unit e from the same Hc and from another molluscan Hc (Octopus dofleini) were used to model 100 and 150 kDa fragments using rigid body movements to fit the corresponding SAXS patterns. Interesting differences were observed between the functional unit organization in the low-molecular mass fragments according to the two preparation methods, suggesting different localizations within the 11S functional subunit.     

Vitamin D Supplementation and Breast Cancer Prevention: A Systematic Review and Meta-Analysis of Randomized Clinical Trials

In recent years, the scientific evidence linking vitamin D status or supplementation to breast cancer has grown notably. To investigate the role of vitamin D supplementation on breast cancer incidence, we conducted a systematic review and meta-analysis of randomized controlled trials comparing vitamin D with placebo or no treatment. We used OVID to search MEDLINE (R), EMBASE and CENTRAL until April 2012. We screened the reference lists of included studies and used the “Related Article” feature in PubMed to identify additional articles. No language restrictions were applied. Two reviewers independently extracted data on methodological quality, participants, intervention, comparison and outcomes. Risk Ratios and 95% Confident Intervals for breast cancer were pooled using a random-effects model. Heterogeneity was assessed using the I² test. In sensitivity analysis, we assessed the impact of vitamin D dosage and mode of administration on treatment effects. Only two randomized controlled trials fulfilled the pre-set inclusion criteria. The pooled analysis included 5372 postmenopausal women. Overall, Risk Ratios and 95% Confident Intervals were 1.11 and 0.74–1.68. We found no evidence of heterogeneity. Neither vitamin D dosage nor mode of administration significantly affected breast cancer risk. However, treatment efficacy was somewhat greater when vitamin D was administered at the highest dosage and in combination with calcium (Risk Ratio 0.58, 95% Confident Interval 0.23–1.47 and Risk Ratio 0.93, 95% Confident Interval 0.54–1.60, respectively). In conclusions, vitamin D use seems not to be associated with a reduced risk of breast cancer development in postmenopausal women. However, the available evidence is still limited and inadequate to draw firm conclusions. Study protocol code: FARM8L2B5L.     

Lesion Load May Predict Long-Term Cognitive Dysfunction in Multiple Sclerosis Patients

Background

Magnetic Resonance Imaging (MRI) techniques provided evidences into the understanding of cognitive impairment (CIm) in Multiple Sclerosis (MS).

Objectives

To investigate the role of white matter (WM) and gray matter (GM) in predicting long-term CIm in a cohort of MS patients.

Methods

303 out of 597 patients participating in a previous multicenter clinical-MRI study were enrolled (49.4% were lost at follow-up). The following MRI parameters, expressed as fraction (f) of intracranial volume, were evaluated: cerebrospinal fluid (CSF-f), WM-f, GM-f and abnormal WM (AWM-f), a measure of lesion load. Nine years later, cognitive status was assessed in 241 patients using the Symbol Digit Modalities Test (SDMT), the Semantically Related Word List Test (SRWL), the Modified Card Sorting Test (MCST), and the Paced Auditory Serial Addition Test (PASAT). In particular, being SRWL a memory test, both immediate recall and delayed recall were evaluated. MCST scoring was calculated based on the number of categories, number of perseverative and non-perseverative errors.

Results

AWM-f was predictive of an impaired performance 9 years ahead in SDMT (OR 1.49, CI 1.12–1.97 p = 0.006), PASAT (OR 1.43, CI 1.14–1.80 p = 0.002), SRWL-immediate recall (OR 1.72 CI 1.35–2.20 p<0.001), SRWL-delayed recall (OR 1.61 CI 1.28–2.03 p<0.001), MCST-category (OR 1.52, CI 1.2–1.9 p<0.001), MCST-perseverative error(OR 1.51 CI 1.2–1.9 p = 0.001), MCST-non perseverative error (OR 1.26 CI 1.02–1.55 p = 0.032).

Conclusion

In our large MS cohort, focal WM damage appeared to be the most relevant predictor of the long-term cognitive outcome.     

Altered Metabolic and Stemness Capacity of Adipose Tissue-Derived Stem Cells from Obese Mouse and Human

Adipose stem cells (ASCs) are an appealing source of cells for therapeutic intervention; however, the environment from which ASCs are isolated may impact their usefulness. Using a range of functional assays, we have evaluated whether ASCs isolated from an obese environment are comparable to cells from non-obese adipose tissue. Results showed that ASCs isolated from obese tissue have a reduced proliferative ability and a loss of viability together with changes in telomerase activity and DNA telomere length, suggesting a decreased self-renewal capacity. Metabolic analysis demonstrated that mitochondrial content and function was impaired in obese-derived ASCs resulting in changes in favored oxidative substrates. These findings highlight the impact of obesity on adult stem properties. Hence, caution should be exercised when considering the source of ASCs for cellular therapies since their therapeutic potential may be impaired.