Pattern analysis in landscape ecology: progress, challenges and outlook

Landscape pattern indices or landscape metrics, an important means in landscape pattern analysis, has resulted in the prosperity of landscape ecology. However, landscape pattern analysis was criticized recently for its poor correlation with ecological processes. In this paper, the current situation and challenges in landscape pattern analysis was elaborated, and the future of landscape pattern analysis was discussed. We believe that the landscape metrics is still the main method in spatial pattern analysis, and is important for landscape ecology. However, there are 3 challenges in landscape pattern analysis: (1) how to develop new methods by integrating explicit ecological sense in landscape pattern analysis? (2) How to link landscape pattern and ecological processes? (3) How to apply the theory of “matrix-patch-corridor” to practice? In future, 5 issues are to be addressed: (1) to develop a methodology to describe landscape pattern in a dynamic manner; (2) to explore the ecological sense of landscape pattern using a series of landscape metrics; (3) to develop new methods for landscape pattern analysis related to ecological processes; (4) to conduct landscape pattern analysis at multi-dimensions; (5) to explain the relationship between landscape pattern and ecological processes by multi-scale pattern analysis.     

生物能源的几点新思考

对目前粮食生物能源和非粮原料生物能源发展过程中遇到的若干问题进行综述和探讨。生物能源的健康发展需要有多元化的观点、多元化的选择和多元化的目标。     

景观生态学中的格局分析：现状、困境与未来

作为景观格局分析的重要手段,景观格局指数的提出与发展极大地推动了景观生态学的发展,但是由于众多景观格局指数在指示生态学过程方面的不足,近年来景观格局分析已经走入困境。在总结近年来国内外相关研究的基础上,对景观格局分析的现状、困境及未来发展方向进行了综述。景观格局分析仍然是景观生态学的重要方面,景观格局指数仍然是景观格局分析的主要手段。但是如何建立具有生态学意义的景观格局指数和分析方法,如何将景观格局与生态过程联系起来,以及如何将＂基质—斑块—廊道＂的景观生态学理论应用到实际中是目前景观格局分析面临的主要困境。基于对景观格局分析现状及困境的认识,提出了景观格局分析未来的5个发展方向：（1）景观格局分析应该从目前的静态格局描述发展到对动态格局的刻画,只有找到刻画动态格局的方法,才能将格局和过程有机地联系在一起;（2）通过对多种景观格局指数的联合应用,发掘景观格局指数集合体对生态过程的解释能力;（3）发展基于生态过程的景观格局指数和分析方法;（4）通过多维景观格局分析,定量研究景观格局演变与生态过程之间的关系;（5）多尺度景观格局分析,将为解决格局与过程的关系提出有效手段。     

海洋微生物学：新机遇，新挑战

海洋占地球表面积的71%,海洋微生物对海洋及人类的生活有重大影响。由于特殊的生存环境,海洋微生物能产生陆栖微生物所不能产生的结构新颖、作用特殊的生物活性物质,有潜力应用于医疗、食品、环境保护等各个领域。海洋微生物研究充满了新的机遇,同时也面临着新的挑战。《微生物学通报》本期推出了"海洋微生物学主题刊",旨在展现我国海洋微生物学研究的最新进展和成果,促进我国海洋微生物学的交流和发展。     

Toward novel vaccines against tuberculosis: current hopes and obstacles

Approximately 2 million people die of tuberculosis (TB) each year. The current vaccine, Bacille Calmette-Guérin (BCG), albeit widely employed, does not protect against adult pulmonary disease, and new vaccines are urgently needed to reduce the incidence of TB worldwide. New insights into the cellular and molecular mechanisms that underlie the interactions between Mycobacterium tuberculosis and its host have been exploited to develop novel vaccine candidates that recently have entered clinical trials. This review provides a brief overview of different approaches toward a new vaccination strategy and summarizes major challenges for the next decade.     

Plant coevolution: evidences and new challenges

Abstract

Coevolution has been defined as the reciprocal genetic change in interacting species owing to natural selection imposed by each on the other. The process of coevolution between plants and the surrounding biota – including viruses, fungi, bacteria, nematodes, insects, and mammals – is considered by many biologists to have generated much of the earth's biological diversity. While much of the discussion on plant coevolution focuses on single plant–enemy interactions, a wide array of other micro and macro coevolutive processes co-occur in the same individual plant, posing the question whether we should talk about plant coevolutions. In this review article, I begin by briefly discussing the framework of coevolution theory and explore the complexities of studying coevolution in natural conditions. Then I analyze the difference between plants, microbes and animal coevolution, by exploring the above- and below-ground behaviors.     

Amphibian diversity in Polish cities: Taxonomic diversity,functional diversity and evolutionary distinctiveness

As a process affecting animal communities, urbanization has been the subject of numerous studies. However, amphibians are still among the least studied vertebrate groups in urbanized landscapes. Generally, it has been found that the process of loss of amphibian diversity is nonrandom, with species from older evolutionary lines at greater risk. Regional data on amphibian assemblages in urban areas is a very useful tool for assessing how these assemblages react to changes.The aim of the present paper is to assess the diversity of amphibians in Polish cities based on data in the relevant literature, exploring different metrics (e.g., taxonomic, functional, and evolutionary diversity) calculated in amphibian species assemblages. We used data from 18 articles (including grey literature), characterized by comparable research methods and published between 1999 and 2017.Overall, amphibian species richness (ASR) amounted to an average of 9 species, ranging from 5 to 11 species per city. The higher species richness occurred in Białystok in North-west of Poland. Functional evenness (FEve), evolutionary distinctiveness (ED sum), and functional richness (FRic) were strongly positively correlated with ASR. However, ED mean was not significantly correlated with the total number of species in the community. Three taxa, the hybridogenetic water frogs Pelophylax esculentus complex, the common toad Bufo bufo, and the common frog Rana temporaria, occurred in all analyzed amphibian assemblages. Our study is one of the first attempts to compare urban amphibian assemblages, using different and complementary diversity metrics on a large spatial scale. In conclusion, we highlight that urban areas play an important role for conservation of amphibians, because they support amphibian assemblages characterized by a high level of overall diversity.     

Recombinase-mediated cassette exchange (RMCE): traditional concepts and current challenges

Traditional DNA transduction routes used for the modification of cellular genomes are subject to unpredictable alterations, as the cell-intrinsic repair machinery may affect both the integrity of the transgene and the recipient locus. These problems are overcome by recombinase-mediated cassette exchange (RMCE) approaches enabling predictable expression patterns by the nondisruptive insertion of a gene cassette at a pre-characterized genomic locus. The destination is marked by a “tag” consisting of two heterospecific recombination target sites (RTs) at the flanks of a selection marker. Provided on a circular donor vector, an analogous cassette encoding the gene of interest can cleanly replace the resident cassette under the influence of a site-specific recombinase. RMCE was first based on the yeast integrase Flp but had to give way to the originally more active phage-derived Cre enzyme. To be effective, both Tyr-recombinases have to be applied at a considerable concentration, which, in the case of Cre, triggers endonucleolytic activities and therefore cellular toxicity. This review addresses the particularities of both recombination routes depending on the structure of the synaptic complex and on improved integrase and RT variants. While the performance of Flp-RMCE can now firmly rely on optimized Flp variants and multiple sets of functional target sites (FRTs), the Cre system suffers from the promiscuity of its RT mutants, which is explained in molecular terms. At present, RMCE enters applications in the stem cell field. Remarkable efforts are noted in the framework of various mouse mutagenesis programs, which, in their first phase, have targeted virtually all genes and now start to shift their emphasis from gene trapping to gene modification.     

互惠共生微生物：新资源，新技术，新机遇，新挑战

2020年9月联合国环境规划署发布《全球生物多样性展望-5》(GBO-5)报告,助力世界实现协商一致的愿景——到2050年“与自然和谐相处”。其实,原本地球上的所有生物都是相互依存、互惠共生于地球村的,尽管存在少数“坏分子”。但由于人类的贪婪,过度扩张才导致地球“千疮百孔”的面貌,严重威胁到人类文明可持续发展。通过最近20年的研究,互惠共生微生物(mutualistic symbiotic microbes,MSM)从其丰富的群落多样性到种质新资源、从多种多样的生理生态功能到作用机制、从基础探究到新技术研发,为实现人与自然和谐相处的愿景提供了新机遇,同时也面临新挑战。令人可喜的是,中国在MSM研究领域取得了令世人瞩目的成果。《微生物学通报》于2020年11期特别推出了“互惠共生微生物专栏”,旨在展现中国MSM研究的最新进展和成果,促进生物共生学的发展壮大。     

Gas exchange across avian eggshells oscillates in phase with heartbeat

Rahn et al. (J. Appl. Physiol. 69: 1546-1548, 1990) showed that the gas pressure in a plethysmograph containing an intact egg oscillates in phase with electrocardiogram (ECG) and that this pressure variation could be used as a noninvasive way to determine the heart rate of an avian embryo. One possible mechanism to account for the pressure oscillation is the mechanical movement of the embryonic heart, which leads to volume shifts of gas within the plethysmograph. Another possibility is that the oscillation of gas pressure with heartbeat is pulsatile gas exchange resulting from pulsatile blood flow. If gas exchange were transiently stopped, a pressure signal dependent on gas exchange should disappear, while a pressure signal dependent on cardiovascular motion should persist. Using a number of late-age hen eggs (at days 15-20 of incubation), we tested these hypotheses by suddenly changing the gas composition surrounding an egg and measuring the effect of the pressure oscillation. We found that 1) after 5% CO2-95% N2 was flushed into the plethysmograph (presumably halting gas exchange), pressure oscillations went almost to zero and the ECG signal remained; after air was flushed back to the plethysmograph, the pressure signal returned to control level; 2) after 20% CO2-20% O2-60% N2 was flushed into the plethysmograph (presumably increasing net gas exchange), the pressure signal increased 2.5-fold compared with that in air; and 3) after 1% CO2-99% N2 was flushed into the plethysmograph (presumably reversing gas exchange), the oscillation pressure decreased to one-fourth of that in air and the phase of pressure relative to ECG reversed compared with the phase in air.(ABSTRACT TRUNCATED AT 250 WORDS)     

The new understanding of Arabidopsis thaliana proteins associated with salinity

Abstract

Salt stress is a major abiotic stress limiting the productivity and the geographical distribution of many plant species. Arabidopsis thaliana is an excellent model with rich genetic resources for modern plant biology research. To comprehensively and representatively understand salt-response mechanisms in A. thaliana, we applied the first attempt to use the most data (252 of 10,469 reviewed A. thaliana protein) from public protein database for displaying the enriched protein domains, Kyoto Encyclopedia of Genes and Genomes pathways, molecular functions, and cell localizations involved in salt-response. The data were analyzed by Database for Annotation Visualization and Integrated Discovery. Our results indicated salt-response proteins cross-talked not only with drought and temperature stress as previously reported but also with further stresses such as bacterium, light, metal ion, radiation, and wounding stress. Multiple cellular localizations under salt stress indicated proteins were versatile. In addition, 27 proteins have the characteristics with response to multiple stresses and localization in multiple places. We called it the ‘space-stress’ double cross-talk effects, which indicated that A. thaliana proteins dealt with salt stress and other stresses in a reciprocal economical way. An enriched bioinformatics analysis of the large data could provide clues and basis for the development of salt-response potential biomarkers for plant growth and crop productivity.     

The plant sHSP superfamily: five new members in Arabidopsis thaliana with unexpected properties

The small heat shock proteins (sHsps), which are ubiquitous stress proteins proposed to act as chaperones, are encoded by an unusually complex gene family in plants. Plant sHsps are classified into different subfamilies according to amino acid sequence similarity and localization to distinct subcellular compartments. In the whole Arabidopsis thaliana genome, 19 genes were annotated to encode sHsps, of which 14 belong to previously defined plant sHsp families. In this paper, we report studies of the five additional sHsp genes in A. thaliana, which can now be shown to represent evolutionarily distinct sHsp subfamilies also found in other plant species. While two of these five sHsps show expression patterns typical of the other 14 genes, three have unusual tissue specific and developmental profiles and do not respond to heat induction. Analysis of intracellular targeting indicates that one sHsp represents a new class of mitochondrion-targeted sHsps, while the others are cytosolic/nuclear, some of which may cooperate with other sHsps in formation of heat stress granules. Three of the five new proteins were purified and tested for chaperone activity in vitro. Altogether, these studies complete our basic understanding of the sHsp chaperone family in plants. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

PRMT11: a new Arabidopsis MBD7 protein partner with arginine methyltransferase activity

Plant methyl-DNA-binding proteins (MBDs), discovered by sequence homology to their animal counterparts, have not been well characterized at the physiological and functional levels. In order better to characterize the Arabidopsis AtMBD7 protein, unique in bearing three MBD domains, we used a yeast two-hybrid system to identify its partners. One of the interacting proteins we cloned is the Arabidopsis arginine methyltransferase 11 (AtPRMT11). Glutathione S-transferase pull-down and co-immunoprecipitation assays confirmed that the two proteins interact with each other and can be co-isolated. Using GFP fluorescence, we show that both AtMBD7 and AtPRMT11 are present in the nucleus. Further analyses revealed that AtPRMT11 acts as an arginine methyltransferase active on both histones and proteins of cellular extracts. The analysis of a T-DNA mutant line lacking AtPRMT11 mRNA revealed reduced levels of proteins with asymmetrically dimethylated arginines, suggesting that AtPRMT11, which is highly similar to mammalian PRMT1, is indeed a type I arginine methyltransferase. Further, AtMBD7 is a substrate for AtPRMT11, which post-translationally modifies the portion of the protein-containing C-terminal methylated DNA-binding domain. These results suggest the existence of a link between DNA methylation and arginine methylation.     

Gas exchange strategy in the Nile crocodile: a morphometric study

Summary The respiratory surface area (S_AR) per kilogram body mass (M_B), the harmonic mean thickness of the air-blood barrier (_htR) in the gas exchange tissue, and the anatomical diffusion factor (ADF=S_AR/_htR per M_B) were calculated for four juvenile Nile crocodiles. The ADF of three small specimens (mean M_B=3.59 kg) was 625 cm²·m^–1·kg^–1. The values varied considerably among individuals and were similar to that of a 5.68-kg specimen (593 cm²·m^–1·kg^–1). Only 9% of the ADF is located in the anterior third of the lung, which because of its conical shape makes up only 14 percent of the total lung volume. Particularly in the middle third of the lung, the proximal region near the intrapulmonary bronchus displays a greater ratio of respiratory/non-respiratory surface areas than do more distally located sampling sites. The _htR is also significantly smaller proximally than distally. The cumulative ADF per unit M_B is greater than that previously reported for this species on the basis of overall estimates of S_AR and _htR, but is still less than that of lizards and testudinids. The disposition of ADF between distal air storage region and the intrapulmonary bronchus is consistent with a bidirectional cross-current gas exchange model.Abbreviations ADF anatomical diffusion factor - %AR percent of S_A included in the effective respiratory zone - M _B body mass - NVP non-ventilatory period - %P percent of total lung volume containing parenchyma - S _A total surface area of intrapulmonary septa - S _ANR that portion ofS _A lying out the effective respiratory zone - S _V surface-to-volume ratio in the parenchyma - _htR harmonic mean thickness of the air-blood tissue barrier within the respiratory zone - V _P parenchymal volume - VP ventilatory period