Nitrogen and phosphorus content in plant species of Mediterranean ecosystems in Greece

The values of nitrogen phosphorus ratios measured in green parts of evergreen sclerophylls, seasonal dimorphic, deciduous and herbaceous plants found in Mediterranean-type ecosystems of Greece, form a homogeneous group, which is comparable only with those of analogous ecosystems of California but not with Mediterranean systems of the southern hemisphere.Nomenclature follows: Tutin et al., 1964. Flora Europaea.Support of National Research Foundation (Greece) and NATO (SRG-12) is gratefully acknowledged.     

Temperature stress and survival ability of Mediterranean sclerophyllous plants

ABSTRACT

The Mediterranean climate with hot and dry summer periods, and low winter temperatures and episodic frosts in northern, altitudinal and continental districts, demands from evergreen broadleaved woody plants an adequate and flexible acclimation to the climatic constraints.

In this brief survey on some responses of Mediterranean sclerophylls to temperature stress, the following is presented and discussed: criteria for cold and heat limits of photosynthetic function; winter depression and summer photoinactivation of photosynthesis; peculiar patterns of tissue freezing of scleromorphous leaves and limits of frost resistance of various plant parts and ontogenetic stages; heat impairment of chloroplasts and thermotolerance of sclerophyllous species; survival capacity and recovery after damage. Risks of damage to plants in relation to stressful temperatures in Mediterranean regions are estimated. Cold stress and drought stress indices, according to Mitrakos (1980), have been applied to characterise different localities in Italy. Additionally, a heat stress index for the Mediterranean region is proposed. Future research topics are suggested.     

Are Sclerophylls and Malacophylls Hydraulically Different?

This work tests the hypothesis that sclerophylls (i.e. hard-leaved species) would be less efficient than malacophylls (i.e. soft-leaved species) in terms of water transport through the stem as well as within the leaf blade. Mean leaf surface area (A_L), leaf specific mass (LSM) as well as shoot (K_WL), stem (K_SL) and leaf (K_LL) hydraulic conductances were measured in eight Mediterranean evergreen sclerophylls and eight temperate deciduous malacophylls. No difference was observed between the two groups in terms of K_LL and of the contribution of leaves to the overall shoot hydraulic resistance. Leaves represented in all cases 48 to 90 % of the shoot hydraulic resistance, suggesting that the sclerophyllous habitus does not per se lead to low efficiency in water transport within the leaf blade. A weak negative relationship (r² = 0.252) appeared to exist between K_SL and LSM. This might provide an explanation for the lower growth rates of sclerophylls with respect to malacophylls.     

Evergreens favored by higher responsiveness to increased CO₂

Physical CO(2) diffusion from sub-stomatal cavities to the chloroplasts where photosynthesis takes place is an important limitation of photosynthesis largely neglected in research related to global climate change. This limitation is particularly important in leaves with robust structures such as evergreen sclerophylls. In these leaves, photosynthesis is less sensitive to changes in stomatal openness, which is considered to be the primary limitation of photosynthesis. In this review we state that, because of large limitations in internal diffusion in C(3) plants, photosynthesis and the intrinsic efficiency of the use of plant water responds more strongly to elevated levels of CO(2) in leaves with more robust structures. This provides an additional explanation for the current apparent expansion of evergreen sclerophylls in many Earth ecosystems, and adds a new perspective to research of the biological effects of increasing atmospheric CO(2).     

Mediterranean sea cliff plants: morphological and physiological responses to environmental conditions

Aims The plants of Mediterranean sea cliff ecosystems are resistant to several environmental challenges. In this study, six species typical of the coastal rocky cliffs have been analyzed in order to evaluate their diverse morphological and physiological responses to their environment across the seasons, and to examine the strategy of the ecological group to which each species belongs. Since these species are widespread across the Mediterranean region, our aim was also to highlight their ecophysiological features in habitats where the direct influence of the sea is stronger.Methods The selected species are characteristic of the sea cliffs of Elba island (Tyrrhenian sea, Italy): the halophyte Crithmum maritimum, the semideciduous Helichrysum italicum and Lavandula stoechas and the sclerophylls Myrtus communis, Quercus ilex and Rhamnus alaternus. Four morphological traits—canopy height, leaf area, specific leaf area and leaf dry matter content—and two physiological traits—leaf water potential (LWP) and photosynthetic efficiency (PE), measured before the dawn and at midday—were analyzed. Water potential was measured by a pressure chamber and photosynthetic efficiency was determined by the analysis of chlorophyll fluorescence. Plant performance was also evaluated by calculating chronic (PI chr) and dynamic photoinhibition (PI dyn).Important findings Crithmum maritimum showed high resistance to the recurrent dry periods, because of the high water storage capacity of its leaves and its PE declined markedly only in July, under the harshest climatic conditions. Semideciduous taxa utilize primarily an avoidance strategy, which aims at reducing the overall leaf surface, while sclerophylls mostly show a tolerance strategy towards the prevailing stressors, as demonstrated by LWP and PE, that are lower in the sclerophylls than in the semideciduous taxa during summer, due to osmoregulation and photoinhibition, respectively. Furthermore, variability of physiological parameters was higher in the sclerophylls than in the semideciduous taxa, because the former had to withstand wider oscillations of their LWP and PE. The sclerophyllous taxa underwent a slight loss of PE also in winter, likely owing to the combined action of low temperature and high irradiance. In Mediterranean sea cliff ecosystems, the stressful combination of high irradiance, high temperatures and low rainfall typical of the summer season may have been intensified by the shallow soil which displays a poor water storage capacity. On the other hand, winter stress, caused by high solar radiation and low temperatures, does not seem to seriously affect the performance of the studied species.     

Comprehensive decision tree models in bioinformatics

Purpose

Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible.

Methods

This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree.

Results

The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree.

Conclusions

The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly redundant attributes that are very common in bioinformatics.     

Chloroplast movements in leaves of two evergreen sclerophyllous plants (Ilex aquifolium and Prunus laurocerasus)

ABSTRACT

Chloroplast movements provide a means for fine-tuning the absorption of radiation in leaves. Since evergreen sclerophylls may experience very different light levels during the seasons and at different locations either at the periphery or in the interior of a forest, such a mechanism must theoretically be of great importance for them. Detailed field and laboratory studies on sclerophylls are however lacking. We provide first evidence that chloroplasts in the leaf mesophyll of both Ilex aquifolium (holly) and Prunus laurocerasus (cherry laurel) may be stimulated by low light intensities. Even at winter temperatures close to freezing, chloroplasts move to a position where light absorption is increased. Effects of temperature, light pretreatment and light quality for the induction of movement are described.     

Caloric content in plants dominating maquis ecosystems in Greece

Summary Caloric content for 15 evergreen sclerophyllous and 8 deciduous plants dominating maquis ecosystems are presented on dry and ash-free dry weight basis. Leaves of evergreen sclerophylls contain 4,667±61, bark 4,207±78 and wood 4,250±37 cal.g^-1 d.w. On ash-free basis values are: 5,959±57, 4,560±71 and 4,325±32 cal.g^-1 ash-free d.w., respectively. On deciduous plants results show that leaves, bark and wood contain 4,375±47, 4,128±151 and 4,278±59 cal.g^-1 d.w. respectively. Values on ash-free dry weight are: 4,719±39, 4,529±124 and 4,371±67 cal.g^-1 ash-free d.w.     

模糊ＩＳＯＤＡＴＡ在草地植物群落分类上的应用

 模糊集合理论在元素与集合的关系中引入了连续变化的隶属度,因而能适应植物群落作连续和明显间断分布同时存在的情况。本文运用以模糊集合理论为基础的ISODATA聚类分析方法对松嫩平原草地植物群落进行了数量分类,结果说明模糊ISODATA聚类比传统的分类方法有更为客观、灵活的特点,是一种较为理想的植被数量分类方法。     

生物印迹:一个直接的酶修饰技术

生物印迹技术是一个简单、直接的酶修饰技术,已应用到有机合成、生物传感器制备和生物分离等领域,在推动化学品绿色合成方面具有潜在的应用价值。本文在生物印迹概念的提出与发展、分类、应用以及印迹技术策略的发展等方面综述近期研究成果,针对生物印迹研究过程的现实问题,展望其未来的发展趋势,为生物印迹相关研究提供有益的借鉴。     

Effective Automated Feature Construction and Selection for Classification of Biological Sequences

Background

Many open problems in bioinformatics involve elucidating underlying functional signals in biological sequences. DNA sequences, in particular, are characterized by rich architectures in which functional signals are increasingly found to combine local and distal interactions at the nucleotide level. Problems of interest include detection of regulatory regions, splice sites, exons, hypersensitive sites, and more. These problems naturally lend themselves to formulation as classification problems in machine learning. When classification is based on features extracted from the sequences under investigation, success is critically dependent on the chosen set of features.

Methodology

We present an algorithmic framework (EFFECT) for automated detection of functional signals in biological sequences. We focus here on classification problems involving DNA sequences which state-of-the-art work in machine learning shows to be challenging and involve complex combinations of local and distal features. EFFECT uses a two-stage process to first construct a set of candidate sequence-based features and then select a most effective subset for the classification task at hand. Both stages make heavy use of evolutionary algorithms to efficiently guide the search towards informative features capable of discriminating between sequences that contain a particular functional signal and those that do not.

Results

To demonstrate its generality, EFFECT is applied to three separate problems of importance in DNA research: the recognition of hypersensitive sites, splice sites, and ALU sites. Comparisons with state-of-the-art algorithms show that the framework is both general and powerful. In addition, a detailed analysis of the constructed features shows that they contain valuable biological information about DNA architecture, allowing biologists and other researchers to directly inspect the features and potentially use the insights obtained to assist wet-laboratory studies on retainment or modification of a specific signal. Code, documentation, and all data for the applications presented here are provided for the community at http://www.cs.gmu.edu/~ashehu/?q=OurTools.     

Growth, water relations and photosynthesis of seedlings and resprouts after fire

Seasonal patterns of growth, water relations, photosynthesis and leaf characteristics were compared between obligate seeders (Cistus monspeliensis and Cistus ladanifer) and resprouters (Arbutus unedo and Pistacia lentiscus) from the first to the second year after fire. We hypothesized that seedlings would be more water-limited than resprouts due to their shallower root systems. Regarding water use strategies, Cistus species are drought semi-deciduous and A. unedo and P. lentiscus are evergreen sclerophylls, therefore, comparisons were based on the relative deviation from mature conspecific plants. Seedlings and resprouts had higher shoot elongation and leaf production than mature plants, and over an extended period. Differences from mature plants were larger in resprouts, with two-fold transpiration, leaf conductance and photosynthesis in late spring/early summer. Seedlings of C. monspeliensis exhibited higher transpiration and leaf conductance than mature plants, while those of C. ladanifer only exhibited higher water potential. Growth increments and ameliorated water relations and photosynthesis after fire were attributed to an increase in water and nutrient availability. The small differences in water relations and photosynthesis between seedlings and mature conspecifics are in accordance with the prediction of seedlings experiencing higher water limitation than resprouts. We attribute these results to differences in root systems: resprouters benefited from an increase in root/shoot ratios and the presence of deep roots whereas Cistus seedlings relied on very shallow roots, which cannot provide assess to deep water during summer. Nevertheless, seedlings did not show evidence of experiencing a more severe water limitation than mature conspecifics, which we attributed to the presence of efficient mechanisms of avoiding and tolerating water stress. The results are discussed in relation to post-fire demography of seeders and resprouters in Mediterranean communities.     

河南禹县山西组中麟木属( Lepidodendron )的两个新种

本文对华夏植物群鳞木属植物的研究现状进行了综述,讨论了华夏木属是否废除的问题。根据华夏木属与鳞木属基本特征相同,只是叶座形态、叶痕形态与鳞木属不同,这些特征只能作鳞木属分种的依据,同意《中国古生代植物》的处理意见。本文还描述了河南禹县山西组鳞木属的两个新种,即:Lepidod endron huayanense Ma(spnov.), L. yuxianense. Ma(sp. nov.).     

北京维管植物编目和分布数据集

区域性维管植物编目对于该区域内植物多样性保护及植物资源可持续利用具有重要意义。北京作为中国首都, 尽管编目工作早在20世纪60年代就得以开展, 但近30年来没有进行系统更新。现有数据零散、不系统, 相关编目进展甚至已经落后于周边地区。本文在《北京植物志(1992年修订版)》的基础上, 结合多年实际野外调查, 通过系统检索文献资料对现有编目数据进行查漏补缺(补充新分类群、新记录)、修订名称(基于新分类修订成果)、更新分类系统(采用基于分子数据的新分类系统), 并添加物种等级、分布状态、生长状态、室内/室外、分布区、了解程度及保护状况等相关信息, 最终完成北京维管植物编目和分布数据集(分为本土植物和外来植物两个表单, 其中外来植物主要基于志书和文献记载)。截至2021年12月31日, 该数据集共有数据2,883条(本土1,680条, 外来1,203条), 其中包含北京本土野生维管植物134科611属1,597个类群(1,440种3天然杂交种46亚种97变种11变型), 与《北京植物志(1992年修订版)》相比增加3科26属173种4亚种28变种11变型, 其中列入《国家重点保护野生植物名录(2021)》的有16种(一级仅1种), 列入《北京市重点保护野生植物名录(2008)》的有90种3亚种4变种; 收录外来维管植物137科581属1,184个类群(含992种及其他种下等级), 其中栽培植物854种19杂交种15亚种29变种2变型87栽培品种38栽培群, 逸生植物132种1亚种, 归化植物77种2变种, 入侵植物27种。编目数据显示, 北京本土野生维管植物多样性整体上并不高, 主要以广泛分布的常见种为主, 特有种、狭域种以及珍稀濒危种数量不多; 同时, 北京存在大量的外来植物(许多种类在《北京植物志》各版中已经收录), 这些植物也是北京维管植物多样性的重要组成部分, 但现有数据尚不完整。     

民间植物分类系统与区域性物种多样性快速评估——以西双版纳傣族为例

生物多样性的快速流失 ,使传统分类工作在热带物种多样性评估中显出不足 ,而民间分类系统在区域性物种多样性快速评估中的作用已经引起人们的重视。前人对西双版纳傣族民间植物命名和分类系统已做过研究 ,该文在此基础上 ,探讨能否将这种知识用于区域性物种多样性快速评估。利用生物多样性快速编目、样方调查及民族植物学中民间访谈的方法 ,考察了三个傣族村寨原住民的植物识别能力。结果表明 ,傣族原住民的植物识别程度与其年龄呈显著正相关 ,中年以后识别能力趋于稳定 ,识别率高达 91 %以上。通过与长期在西双版纳地区工作的野外植物分类学家相比较 ,我们发现傣族原住民的植物识别率不低于分类学家 ,且所需时间比分类学家少。作者认为 ,民间植物分类系统可以用于局部地区的物种多样性快速评估。     

A geomorphic approach to global classification for natural inland wetlands and rationalization of the system used by the Ramsar Convention – a discussion

Globally, the most widely used wetland classification is that adopted by the contracting parties of the Ramsar Convention, which is the Convention on Wetlands of International Importance especially as Waterfowl Habitat. A review of the Inland Wetland component of this system shows that mixed criteria are used to separate the wetlands, and that not all natural inland wetlands have been addressed. A classification system using landform and hydro-period, which results in 13 primary geomorphically non-emergent types for natural wetlands, is proposed to describe the full variety of wetlands at a primary level around the globe, and is suggested to be incorporated as the first-tier of the Ramsar classification.The proposed classification has been designed so wetlands can be described, classified and compared systematically. This paper attempts to reconcile the Ramsar Classification system with the proposed approach. The intention in this paper is not to displace the Ramsar Classification, but rather to indicate its inherent underlying geomorphic structure, and hence re-order its hierarchical framework. This adjustment to the existing classification system would highlight underlying similarities between wetlands so that global comparisons can be more readily made. It also has considerable advantages for a staged, systematic discrimination and classification of the vast array of differing wetlands globally.The use of geomorphic and hydrologic elements as the primary and secondary divisions with the more commonly used Ramsar Classification terms as a tertiary division, provides a logical structure to compare and contrast wetlands globally.     

Higher recall in metagenomic sequence classification exploiting overlapping reads

Background

In recent years several different fields, such as ecology, medicine and microbiology, have experienced an unprecedented development due to the possibility of direct sequencing of microbioimic samples. Among problems that researchers in the field have to deal with, taxonomic classification of metagenomic reads is one of the most challenging. State of the art methods classify single reads with almost 100% precision. However, very often, the performance in terms of recall falls at about 50%. As a consequence, state-of-the-art methods are indeed capable of correctly classify only half of the reads in the sample. How to achieve better performances in terms of overall quality of classification remains a largely unsolved problem.

Results

In this paper we propose a method for metagenomics CLassification Improvement with Overlapping Reads (CLIOR), that exploits the information carried by the overlapping reads graph of the input read dataset to improve recall, f-measure, and the estimated abundance of species. In this work, we applied CLIOR on top of the classification produced by the classifier Clark-l. Experiments on simulated and synthetic metagenomes show that CLIOR can lead to substantial improvement of the recall rate, sometimes doubling it. On average, on simulated datasets, the increase of recall is paired with an higher precision too, while on synthetic datasets it comes at expenses of a small loss of precision. On experiments on real metagenomes CLIOR is able to assign many more reads while keeping the abundance ratios in line with previous studies.

Conclusions

Our results showed that with CLIOR is possible to boost the recall of a state-of-the-art metagenomic classifier by inferring and/or correcting the assignment of reads with missing or erroneous labeling. CLIOR is not restricted to the reads classification algorithm used in our experiments, but it may be applied to other methods too. Finally, CLIOR does not need large computational resources, and it can be run on a laptop.

     

Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases

ATP(CTP):tRNA nucleotidyl transferases, tRNA maturing enzymes found in all organisms, and eubacterial poly(A) polymerases, enzymes involved in mRNA degradation, are so similar that until now their biochemical functions could not be distinguished by their amino acid sequence. BLAST searches and analysis with the program "Sequence Space" for the prediction of functional residues revealed sequence motifs which define these two protein families. One of the poly(A) polymerase defining motifs specifies a structure that we propose to function in binding the 3' terminus of the RNA substrate. Similar motifs are found in other homopolyribonucleotidyl transferases. Phylogenetic classification of nucleotidyl tranferases from sequenced genomes reveals that eubacterial poly(A) polymerases have evolved relatively recently and are found only in a small group of bacteria and surprisingly also in plants, where they may function in organelles.     

A preliminary review of the modern classification systems of the flowering plants

The present paper is divided into three parts: 1. The first part is devoted to the review of the historical origin of the modern classification systems of the flowering plants. Early systems of classification since the Aristotelian time provided a basis for the modern schemes of classification. This paper has reviewed briefly the history of plant systematics, which is divided into three periods: the period of mechanical systems of classification, of natural systems of classification, and of phylogenetic systems of classification. The historical development of the plant systems and the basic idea for three periods is discussed respectively. This paper also considers that the studies of the modern classification system have been entering a new period which primarily aims at overall evolutionary respects. 2. Comparison of the modern classification systems of the flowering plants. Four main modern systems (i. e. A. Cronquist 1979, A. Takhtajan 1980, J. Hutchinson 1973 and A. Engler^,s system as revised by H. Melchior in Engler^,s Syllabus der Pflanzenfamilien 1964) which have greatly influenced the systemstics of plants are compared as to their systematical principles, basic concepts and systematic positions of higher taxa (orders and families) of the flowering plants. The paper is of the opinion that there is still much important work to be done in every field. 3. A review for the modern classification systems of the flowering plants. The paper reviews the modern classification of angiosperms from six aspects: a). The flowers plants are originated from a common ancestral stock; b). The flowers of angiosperms are homogeneous, stamen and carpel are phylletic sporangiophores, all flowers of angiosperms are comparable; c). Monocotyledons are originated from primitive dicotyledons, and represent phylogenetically monophyletic branch; d). The idea advocating the subdivision of Dicotyledoneae into Lignosae and Herbaceae should be rejected as pointed out by many authors; e). The systematical position of Hamamelidae is still a crucial subject for further research; f). The evolutional trends and evaluation of taxonomic characters must be considered in connection with the cor-relation to other characters in question.