Applications of mitochondrial DNA analysis in conservation: a critical review

Patterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) 'gene conservation' - the identification and management of genetic diversity, and (ii) 'molecular ecology' - the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time-frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long-term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within-population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short-term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource-intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long-term planning and short-term execution of species recovery plans.     

Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth

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Does environmental management improve enterprise's value? – An empirical research based on Chinese listed companies

The company's environmental management behaviors can improve the relationship between the company stakeholders, help companies to sustainably develop. But it is more seen as an obligation and cost of the company's environmental protection in developing countries. So what kind of impact the environmental protection have on the value of the company? Taking Chinese listing Corporation as a sample. This paper analyzes the impact of enterprises’ environmental management and its disclosure on corporate value. We conclude that environmental management excluding independent environment report can improve corporate value. In specific environmental management measures, producing environmental friendly products can help environmental friendly products gain recognition and improve corporate value significantly.     

inSPIRE: An Open-Source Tool for Increased Mass Spectrometry Identification Rates Using Prosit Spectral Prediction

Rescoring of mass spectrometry (MS) search results using spectral predictors can strongly increase peptide spectrum match (PSM) identification rates. This approach is particularly effective when aiming to search MS data against large databases, for example, when dealing with nonspecific cleavage in immunopeptidomics or inflation of the reference database for noncanonical peptide identification. Here, we present inSPIRE (in silico Spectral Predictor Informed REscoring), a flexible and performant open-source rescoring pipeline built on Prosit MS spectral prediction, which is compatible with common database search engines. inSPIRE allows large-scale rescoring with data from multiple MS search files, increases sensitivity to minor differences in amino acid residue position, and can be applied to various MS sample types, including tryptic proteome digestions and immunopeptidomes. inSPIRE boosts PSM identification rates in immunopeptidomics, leading to better performance than the original Prosit rescoring pipeline, as confirmed by benchmarking of inSPIRE performance on ground truth datasets. The integration of various features in the inSPIRE backbone further boosts the PSM identification in immunopeptidomics, with a potential benefit for the identification of noncanonical peptides.     

Use of pollution risk and ecosystem service values in marine management strategies in Bohai Sea,China

Different coastal areas possess different pollution risks and ecosystem service values. The management strategies in these areas also differ. With limited environmental funds available, it is necessary to conduct in-depth study of pollution risks and ecosystem service values for developing marine conservation and management strategies. This paper proposes a management method that combines marine pollution risks and ecosystem service values to identify the management priorities of different sites, which are used to determine the appropriate management strategies. The management priorities of different bays in China's Bohai Sea were determined, and management strategies were recommended. The method can be used to determine effective management strategies for oceans around the world, especially in developing countries with limited environmental protection funds.     

Ralstonia eutropha H16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools

Ralstonia eutropha strain H16 is a Gram-negative non-pathogenic betaproteobacterium ubiquitously found in soils and has been the subject of intensive research for more than 50 years. Due to its remarkable metabolically versatility, it utilizes a broad range of renewable heterotrophic resources. The substrate utilization range can be further extended by metabolic engineering as genetic tools are available. It has become the best studied “Knallgas” bacterium capable of chemolithoautotrophic growth with hydrogen as the electron donor and carbon dioxide as the carbon source. It also serves as a model organism to study the metabolism of poly(β-hydroxybutyrate), a polyester which is accumulated within the cells for storage of both carbon and energy. Thermoplastic and biodegradable properties of this polyhydroxyalkanoate (PHA) have attracted much biotechnical interest as a replacement for fossil resource-based plastics. The first applications of R. eutropha aimed at chemolithoautotrophic production of single cell protein (SCP) for food and feed and the synthesis of various PHAs. The complete annotated genome is available allowing systematic biology approaches together with data provided by available omics studies. Besides PHAs, novel biopolymers of 2-hydroxyalkanoates and polythioesters or cyanophycin as well as chemicals such as alcohols, alkanes, alkenes, and further interesting value added chemicals significantly recently extended the range of products synthesized by R. eutropha. High cell density cultivations can be performed without too much effort and the available repertoire of genetic tools is rapidly growing. Altogether, this qualifies R. eutropha strain H16 to become a production platform strain for a large spectrum of products.     

The “capacity to reason” in conservation biology and policy: the southern elephant seal branding controversy

Modern environmental research is typically governed by a number of protocols designed to embrace the epistemological and ethical values of society. These protocols evolve in response to changing values, and few disciplines in environmental science have received as much attention as biological conservation. This paper describes the events leading to a controversy regarding a particular research technique used to investigate the cause of a long-term population decline of southern elephant seals (Mirounga leonina) at Macquarie Island, south of Australia – hot-iron branding of individuals. We discuss procedures and protocols that were in place at the time the controversy erupted, the subsequent reflection of the researchers and authorities involved, and the steps taken to avoid future occurrences. Our treatment of the issue is framed within a discussion of modern ethical philosophy, and our aim is to identify the true source of the controversy. We offer several suggestions as to how such events can be avoided in the future, and provide a model framework for incorporating changing ethical values into important biological conservation objectives.     

Random dispersion in excitatory synapse response

The excitatory synaptic function is subject to a huge amount of researches and fairly all the structural elements of the synapse are investigated to determine their specific contribution to the response. A model of an excitatory (hippocampal) synapse, based on time discretized Langevin equations (time-step = 40 fs), was introduced to describe the Brownian motion of Glutamate molecules (GLUTs) within the synaptic cleft and their binding to postsynaptic receptors. The binding has been computed by the introduction of a binding probability related to the hits of GLUTs on receptor binding sites. This model has been utilized in computer simulations aimed to describe the random dispersion of the synaptic response, evaluated from the dispersion of the peak amplitude of the excitatory post-synaptic current. The results of the simulation, presented here, have been used to find a reliable numerical quantity for the unknown value of the binding probability. Moreover, the same results have shown that the coefficient of variation decreases when the number of postsynaptic receptors increases, all the other parameters of the process being unchanged. Due to its possible relationships with the learning and memory, this last finding seems to furnish an important clue for understanding the basic mechanisms of the brain activity.