Towards an ecological basis for the conservation of subalpine heath-grassland on the upper ridges of the Vosges

Abstract. The subalpine oligotrophic heath-grasslands, assigned to the Pulsatillo-Vaccinietum and Violo-Nardetum, occurring at the upper ridges in the Vosges at 1100 - 1300 m a.s.l. are of conservational interest because they form natural, mature and stable ecosystems. The Pulsatillo-Vaccinietum is particularly rich in endemic plant species and subspecies due to a local oceanic-subarctic climate and the continuous occurrence of the community throughout the Holocene period, when the association was not affected by changes in the prevailing environmental conditions. After a period of abandonment during and after World War II, agriculture was intensified through mineral fertilization and liming, sometimes mowing, and even ploughing and sowing. Seven pastures were selected to estimate the present plant biodiversity. Losses of biodiversity were assessed on the Kastelberg ridge by diachronic analysis of the vegetation composition and structure over the last 30 years. Species diversity changed in both associations through a decrease in the abundance of oligotrophic, acidophilic species, typical of the mountains of western Europe, and an extension of grassland types of the Violo-Nardetum trifolietosum. Strategies for a return to more natural conditions include the abandonment of fertilization and liming, except locally around farms. Regular mowing is needed in order to decrease the nutrient level of the sites.     

Assessing the utility of whole genome amplified DNA for next‐generation molecular ecology

DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low‐quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next‐generation sequencing of nonmodel taxa. To address this knowledge deficit, we use multiple displacement amplification (MDA) and double‐digest RAD sequencing on the grey mouse lemur (Microcebus murinus) to quantify bias in genome coverage and SNP calls when compared to raw genomic DNA (gDNA). We focus our efforts in providing baseline estimates of potential bias by following manufacturer's recommendations for starting DNA quantities (>100 ng). Our results are strongly suggestive that MDA enrichment does not introduce systematic bias to genome characterization. SNP calling between samples when genotyping both de‐novo and with a reference genome are highly congruent (>98%) when specifying a minimum threshold of 20X stack depth to call genotypes. Relative genome coverage is also similar between MDA and gDNA, and allelic dropout is not observed. SNP concordance varies based on coverage threshold, with 95% concordance reached at ~12X coverage genotyping de‐novo and ~7X coverage genotyping with the reference genome. These results suggest that MDA may be a suitable solution for next‐generation molecular ecological studies when DNA quantity would otherwise be a limiting factor.     

后基因组时代的工业生物技术

简述了工业生物技术的发展背景和意义,分析了基因组学和功能基因组学发展对工业生物技术的推动作用,重点介绍了本期专刊发表的代谢工程、发酵工程以及工业酶与生物催化领域的17篇论文。     

A decade of <Emphasis Type="Italic">Bt</Emphasis> cotton in Chinese fields: Assessing the direct effects and indirect externalities of Bt cotton adoption in China

The objective of this study is to examine whether or not the gains from reduced spraying for bollworms are being sustained more than one decade after the initial adoption in 2007. Based on farm-level data collected by the authors in 1999–2007 in 16 villages from 4 provinces, this study shows that insecticides applied for controlling bollworms have declined. This analysis supports Chinese policy makers’ decision to not require refuges of non-Bt cotton fields. It also suggests that past studies may have underestimated the benefits from adopting Bt technology.     

β-Galactosidase from Lactobacillus pentosus: Purification,characterization and formation of galacto-oligosaccharides

A novel heterodimeric β-galactosidase with a molecular mass of 105 kDa was purified from crude cell extracts of the soil isolate Lactobacillus pentosus KUB-ST10-1 using ammonium sulphate fractionation followed by hydrophobic interaction and affinity chromatography. The electrophoretically homogenous enzyme has a specific activity of 97 U_oNPG/mg protein. The K_m, k_cat and k_cat/K_m values for lactose and o-nitrophenyl-β-D-galactopyranoside (oNPG) were 38 mM, 20 s^-1, 530 M^-1·s^-1 and 1.67 mM, 540 s^-1, 325 000 M^-1·s^-1, respectively. The temperature optimum of β-galactosidase activity was 60–65°C for a 10-min assay, which is considerably higher than the values reported for other lactobacillal β-galactosidases. Mg²⁺ ions enhanced both activity and stability significantly. L. pentosus β-galactosidase was used for the production of prebiotic galacto-oligosaccharides (GOS) from lactose. A maximum yield of 31% GOS of total sugars was obtained at 78% lactose conversion. The enzyme showed a strong preference for the formation of β-(1→3) and β-(1→6) linkages, and the main transgalactosylation products identified were the disaccharides β-D-Galp-(1→6)-D -Glc, β-D-Galp-(1→3)-D -Glc, β-D -Galp-(1→6)-D -Gal, β-D -Galp-(1→3)-D -Gal, and the trisaccharides β-D -Galp-(1→3)-D -Lac, β-D -Galp-(1→6)-D -Lac.     

Daunomycin interaction with DNA: Microcalorimetric studies of the thermodynamics and binding mechanism

Nucleic acids are an important target for many therapeutics. Small molecules that bind to nucleic acids are important in many aspects of medicines, particularly in cancer chemotherapy. In recent years, many studies have utilized polynucleic acids with various sequences to demonstrate the binding mechanism of daunomycin, a potent anticancer drug. This study describes that isothermal titration calorimetry is a useful tool for studying the fundamental binding mechanism systemically. The results suggest that the binding free energy is more favorable when the temperature is increased. The binding entropy contributes to this effect. Furthermore, the amine group on daunomycin contributes electrostatic interaction that induces the binding process. In addition, enthalpy-entropy compensation is also exhibited in the daunomycin-DNA binding mechanism. This study used an easy, convenient method of performing a systemic study in a recognition system. The results from this study provide additional information about microscopic mechanisms for molecular design and molecular recognition.     

Cofactor regeneration for sustainable enzymatic biosynthesis

Oxidoreductases are attractive catalysts for biosynthesis of chiral compounds and polymers, construction of biosensors, and degradation of environmental pollutants. Their practical applications, however, can be quite challenging since they often require cofactors such as nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP). These cofactors are generally expensive. Efficient regeneration of cofactors is therefore critical to the economic viability of industrial-scale biotransformations using oxidoreductases. The chemistry of cofactor regeneration is well known nowadays. The challenge is mostly regarding how to achieve the regeneration with immobilized enzyme systems which are preferred for industrial processes to facilitate the recovery and continuous use of the catalysts. This has become a great hurdle for the industrialization of many promising enzymatic processes, and as a result, most of the biotransformations involving cofactors have been traditionally performed with living cells in industry. Accompanying the rapidly growing interest in industrial biotechnology, immobilized enzyme biocatalyst systems with cofactor regeneration have been the focus for many studies reported since the late 1990s. The current paper reviews the methods of cofactor retention for development of sustainable and regenerative biocatalysts as revealed in these recent studies, with the intent to complement other reviewing articles that are mostly regeneration chemistry-oriented. We classify in this paper the methods of sustainable cofactor regeneration into two categories, namely membrane entrapment and solid-attachment of cofactors.     

Microbial community succession and lignocellulose degradation during agricultural waste composting

The changes of microbial community during agricultural waste composting were successfully studied by quinone profiles. Mesophilic bacteria indicated by MK-7 and mesophilic fungi containing Q-9 as major quinone were predominant and seemed to be important during the initial stage of composting. Actinobacteria indicated by a series of partially saturated and long-chain menaquinones were preponderant during the thermophilic period. While Actinobacteria, fungi and some bacteria, especially those microbes containing MK-7(H4) found in Gram-positive bacteria with a low G+C content or Actinobacteria were found cooperate during the latter maturating period. Since lignocellulsoe is abundant in the agricultural wastes and its degradation is essential for the operation of composting, it’s important to establish the correlation between the quinone profiles changes and lignocellulose degradation. The microbes containing Q-9 or Q-10(H2) as major quinone were found to be the most important hemicellulose and cellulose degrading microorganisms during composting. While the microorganisms containing Q-9(H2) as major quinone and many thermophilic Actinobacteria were believed to be responsible for lignin degradation during agricultural waste composting.