Smaug destroys a huge treasure

Smaug, a protein repressing translation and inducing mRNA decay, directly controls an unexpectedly large number of maternal mRNAs driving early Drosophila development.See related research, http://genomebiology.com/2014/15/1/R4Regulation of translation and mRNA stability is a key aspect of early metazoan development. One of the best studied factors involved in these processes is the Drosophila protein Smaug. In this issue of Genome Biology, Chen et al. [1] report that a large number of maternal mRNAs in the fly embryo are probably regulated directly by Smaug.     

Oligonucleotide recombination: a hidden treasure

In Swingle et al. we demonstrate that it is possible to use recombineering to direct a variety of changes in wild-type bacterial cells without the addition of phage-encoded proteins. This discovery is potentially applicable to biological engineering in a wide variety of bacterial species. Here we describe key features of oligo recombination as it is currently understood, and propose strategies for expanding the utility of oligo recombination for bioengineering.     

Basidiomycetes harbour a hidden treasure of proteolytic diversity

This survey is the first to investigate the proteolytic potential of a large number of basidiomycetes. Aqueous extracts of 43 basidiomycetes were investigated for their content of proteolytic activities, using gelatin zymography. The activities were characterised qualitatively using class specific inhibitors. All four catalytic classes of proteases were present, with 4% of all activities classified as aspartic, 5% as cysteine, 6% as metallo and 22% as serine proteases, while the remaining activities could not be assigned unambiguously. The majority of the latter were not inhibited by any of the inhibitors used and were termed insensitive. Different proteolytic activities are evenly distributed among members of all orders of basidiomycetes, although some taxa are a richer source of proteases than others. A significant number of the cysteine protease activities shown here have not previously been reported in basidiomycetes. The fungal cysteine and serine protease inhibitors, clitocypin and CNSPI (Clitocybe nebularis serine protease inhibitor), both inhibited a number of activities and even a few activities that were otherwise insensitive to all other inhibitors used, hence indicating their potential for a regulatory role. The number and diversity of proteases in basidiomycetes are seen to be remarkable and encourage further investigation.     

Mollusc shells as metagenomic archives: The true treasure is the chest itself

Mollusc shells, beyond the treasure of information inherently conveyed through their morphology and chemical composition also have the capacity to preserve DNA sequences over the long term in their inner structure. This has been clearly demonstrated for the first time in the study published in this issue of Molecular Ecology Resources by Der Sarkissian et al. ( 2017 ). With a methodology specifically dedicated to ancient DNA and solid matrices, the authors were able to successfully extract and amplify DNA from marine shells spanning the last 7,000 years. Furthermore, using metagenomic analyses, they could identify important factors affecting DNA recovery. Using reference genomes and sequences in a targeted approach to assign high‐throughput sequencing reads, the authors revealed both the presence of endogenous mollusc DNA and a potent pathogen of Manilla clam. Collectively, the results presented in this study open extremely promising research avenues, from palaeogenomics and evolutionary biology to ecological genomics at population and community levels, as well as the opportunity to fine‐tune diagnostic tools for conservation and aquaculture purposes. Last but not least, this study also offers exciting perspectives in epigenomics and the evolution of regulatory processes in the context of adaptation to global change. It can be easily expected that the approach developed by Der Sarkissian et al. ( 2017 ) will be pursued and extensively investigated in the near future by the scientific community interested in these issues.     

A treasure house of comparative embryology

The Embryo Collection of the Hubrecht Laboratory is a treasure house of comparative embryology. It is the largest and most important collection of its kind in the world, and consists of thousands of vertebrate embryos stored in alcohol, or prepared as histological sections. Many elusive species are included in the collection, some represented by complete developmental series. The accompanying archives offer a remarkable insight into the methods used to collect embryos form wild animals, as well as the motives behind the founders of the collection. Carefully maintained, documented and catalogued, the collection is available for study by all interested scientists. We argue that this collection is one of the greatest biodiversity resources in existence.     

Spread of hepatitis virus as a threat to national security

Information on viral hepatitis A, B and C morbidity in Russia is presented. A distinct trend to decreased viral hepatitis B and C morbidity in 2001-2002 in comparison with the 1990-ies is noted. Nevertheless, there is still unfavorable prognosis regarding high hepatitis B morbidity among the population of reproductive age, as well as among adolescents, which increases the risk for children at an early age. In addition, a new specific feature of hepatitis A spread is observed: morbidity in this infection is shifted to older age groups. The role of vaccinal prophylaxis in the decrease of hepatitis A and B morbidity, virus safety of blood and its components, the quality of the diagnostics of chronic hepatitis, especially hepatitis C, are discussed. The complex of measures for the prophylaxis of viral hepatitis is proposed.     

Decline in the Primary Productivity of Northwestern European Forests as a Consequence of Climate Aridization

Average annual age-dependent changes of carbon accumulation in the stemwood of major forest species (pine, spruce, and birch) of the taiga zone of the northwestern European Russia (Karelia) were analyzed. The changes in carbon accumulation were assessed by comparing carbon reserves in tree stands of various ages. Net primary productivity of photosynthesis (NPP) and the proportionality coefficient between respiratory decarboxylation and carbon reserves in wood were calculated. NPP clearly decreased with increasing climate aridization (aridity index). However, the time of the attainment of climax state by a stand did not depend on the latitudinal climate gradient. Hence, only the size of heterotrophic part of phytomass determines annual carbon losses in northern-taiga stands. It is concluded that the climate dependency of the long-term carbon storage in the phytomass of boreal forests is mainly determined by the climate effect on photosynthetic carbon sequestration.__________Translated from Fiziologiya Rastenii, Vol. 52, No. 4, 2005, pp. 513–517.Original Russian Text Copyright © 2005 by Voronin, Konovalov, Bolondinskii, Kaipiainen, Mao.     

A biological treasure metagenome: pave a way for big science

The trend of recent researches, in which synthetic biology and white technology through system approaches based on “Omics technology” are recognized as the ground of biotechnology, indicates the coming of the ‘metagenome era’ that accesses the genomes of all microbes aiming at the understanding and industrial application of the whole microbial resources. The remarkable advance of technologies for digging out and analyzing metagenome is enabling not only practical applications of metagenome but also system approaches on a mixed-genome level based on accumulated information. In this situation, the present review is purposed to introduce the trends and methods of research on metagenome and to examine big science led by related resources in the future.     

日本演习林制度对中国生物多样性保护与国家公园建设的启示

演习林是日本通过农林院校管辖和运行的自然林地与人工林, 兼具科教、生物多样性保护、生态旅游与林木生产等功能。演习林的责、权、利明确, 能够实现长期、稳定的保护与利用, 与自然保护区、国家公园既有区别又相辅相成, 是日本经济协调发展与快速实现生态恢复的一个重要保障。目前, 日本约有30所高等院校拥有演习林, 演习林面积约占日本森林总面积的5‰, 其中东京大学的演习林建立最早、运行与管理机制最为完善。演习林主要有三大功能: 教学实践、科学研究、社会服务。演习林主要负责人是大学教师, 教师既参与科教也参与管理, 实现了教授治校、科教与社会服务的协调发展。当前, 我国正处于生物多样性保护的转型期和国家公园试点建设的关键阶段, 农林类高校或研究所可借鉴日本演习林制度, 主动参与到国家“绿水青山就是金山银山”的绿色发展理念和实践中; 涉及生物学与农林学科的科学工作者应积极承担当地自然保护区、森林公园、国家公园等的建设与管护。政府可以引导和吸纳有着充足研究经费、学术水平较高的农林与生物学类高校(特别是相关学科被列入“世界一流学科”建设行列的高校)在有条件的自然保护区或城市周边开辟高校直辖林地, 实现教学实践、研究与保护、社会服务等共建共存模式, 提升我国高校农林与生物学科研究水平, 促进我国生物多样性的可持续保护和国家公园的高标准建设。     

Application of a Coupled Photosynthesis–Stomatal Conductance Model to Analysis of Carbon Assimilation by Spruce and Larch Trees in the Forests of Russia

Photosynthetic activities of common spruce (Picea abies (L.) Karst.) and Dahurian larch (Larix gmelinii (Rupr) Rupr ex Kuzen) were analyzed on the basis of datasets obtained for 110- to 130-year-old forest stands in Middle Russia and East Siberia. Using a Li-Cor 6200 gas analyzer, photosynthesis was measured in parallel with transpiration, stomatal conductance, CO₂ concentrations in ambient air and intercellular spaces, the photosynthetically active radiation, air temperature, and air humidity. The data were examined within the framework of a biochemical model of photosynthesis of Farquhar et al. [1] in combination with the stomatal conductance model proposed by Jarvis [2]. The species-specific differences in carbon assimilation rates were discovered, and dependences of photosynthesis on the needle age, light regime, and growth conditions were revealed. The model parameters obtained were used to simulate the photosynthetic rates in spruce and larch trees at various weather conditions.     

Green algae as a structural element of phytoperiphyton communities in streams of NW Russia

Observations were made on the development and distribution of phytoperiphyton communities in 66 lake-river systems in NW Russia from Lake Ladoga to the Barents Sea. In total, 130 genera and 648 species were identified from different substrates, belonging to Cyanophyta (19.1%), Bacillariophyta (59.6%), Chlorophyta (18.7%), and algae from other orders (2.6%). In all streams diatoms dominated by species richness, but they were surpassed by green algae in terms of biomass. The green algae ranged from small planktonic forms to large filamentous species and produced easily visible algal communities. Among the planktonic forms the desmids were the most diverse group. They occurred in attached communities of all rivers and, while never abundant, were widespread. The attached community’s biomass was dominated by green algae. Among these, the filamentous algae Mougeotia sp., Oedogonium sp., Zygnema sp., Spirogyra sp. and Ulothrix zonata exhibited mass development in streams. Their distribution was patchy in the basin, with a total cover varying from less than 1% to 90% of the stream bottom. In some river stretches the diversity and predominance of green algae could be due, in part, to poorly developed riparian canopies. The term periphyton adopted here follows the definition of Odum (1971): “Assemblages which include both plant and animal organisms growing attached to submerged objects”. The prefix phyto- is added to indicate that of the whole biocoenoses only phototrophs are considered in this study. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.