Using connectivity to identify climatic drivers of local adaptation

Understanding the climatic drivers of local adaptation is vital. Such knowledge is not only of theoretical interest but is critical to inform management actions under climate change, such as assisted translocation and targeted gene flow. Unfortunately, there are a vast number of potential trait–environment combinations, and simple relationships between trait and environment are ambiguous: representing either plastic or evolved variation. Here, we show that by incorporating connectivity as an index of gene flow, we can differentiate trait–environment relationships reflecting genetic variation vs. phenotypic plasticity. In this way, we rapidly shorten the list of trait–environment combinations that are of significance. Our analysis of an existing data set on geographic variation in a tropical lizard shows that we can effectively rank climatic variables by the strength of their role in local adaptation. The promise of our method is a rapid and general approach to identifying the environmental drivers of local adaptation.     

Mining of genomic databases to identify novel biodesulfurizing microorganisms

The commercialization of the biocatalytic desulfurization process does not seem to be realistic in the near future because of the low desulfurization rate of the known microorganisms. Hence, the future development will depend on either genetically modifying the currently available bacteria or identifying novel biodesulfurizers. In this study an in silico method to identify new biodesulfurizing microorganisms was adopted. By screening the available genomic databases, 13 novel desulfurizing microorganisms belonging to 12 genera were identified. Several of these could be of immense utility as they have both environment pollutant and industrial waste degrading capability.     

A new concept for reduction of diffuse contamination by simultaneous application of pesticide and pesticide-degrading microorganisms

Pesticide residues and their transformation products are frequently found in groundwater and surface waters. This study examined whether adding pesticide-degrading microorganisms simultaneously with the pesticide at application could significantly reduce diffuse contamination from pesticide use. Degradation of the phenoxyacetic acid herbicides MCPA (4-chloro-2-methylphenoxyacetic acid) and 2,4-D (2,4-dichlorophenoxyacetic acid) was studied in soil microcosm experiments after simultaneous spraying of herbicide and herbicide-degrading bacteria on an agricultural soil and on a sand with low degradation potential. The latter represented pesticide use on non-agricultural soils poor in microbial activity. Degradation and possible loss of herbicidal effect were also tested in a system with plants and the amounts of bacteria needed to give satisfactory MCPA-degradation rate and the survival of degrading bacteria in formulated MCPA were determined. The results showed >80–99% degradation of 2,4-D and MCPA in soil within 1 day and >99% within 3 days after inoculation with 10⁵–10⁷ herbicide-degrading bacteria g⁻¹ dry weight of soil. Enhanced degradation of MCPA was also obtained in the presence of winter wheat and white mustard without loss of the intended herbicidal effect on white mustard. The survival of an isolated MCPA-degrading Sphingomonas sp. in three realistic concentrations of formulated MCPA was very poor, showing that in practical applications direct contact between the microorganisms and the pesticide formulation must be precluded. The applicability and economic feasibility of the method and the information needed to obtain a useable product for field use are discussed.     

The three steps to cancer: A new concept of cancerigenesis

A new theory of carcinogenesis is presented. It is based on the premise that the initial step in the development of cancer is injury by a carcinogen of the coding units in the specialized cells which direct or control the elaboration of a specific “product” or “function”. Carcinogens are varied and number in the thousands, yet the end result, following exposure to them by target stem cells, is always the same, i.e. unbridled cell multiplication with invasion and metastasis. There must be one common denominator which, as stated, is the injury of the coding units of the specialist cells. This is the first step toward cancer; the carcinogen need no longer be present. The second is the uninhibited activity by a pertinent stimulator on functionally deficient cells which remain refractory to the demands for the differentiated “product” or “function”. However, the cells do remain responsive to the second aspect of the dual-roled stimulator, namely, the stimulus to divide. This results in hyperplasia and neoplasia. The events characterizing the third step are coincidental or accidental. There is cellular overcrowding, but the neovasculature is often initially or eventually inadequate. As a result, foci deficient in nutrients form, some cells die, and others become detached and thrive in the culture medium provided by the host through the rupture of capillaries, venules and/or arterioles, forming an area of hemorrhage and necrosis. Surviving cells become autonomous, anaplastic, cataplastic, cannibalistic, invasive and metastatic, i.e. cancer (Fig. 4). Since cancer is only possible in multicellular organisms, the author traces evolution of multicells from unicells. The latter are autonomous and cancer among them is a nonentity. The multicellular organism, on the other hand, is composed of inter-dependent organs, whose component cells are specialists by virtue of contained specific coding apparatuses. Concomitant with this development, an exquisitely sensitive “checks and balances” system of Inductors, Differentiators, Stimulators and Inhibitors, involving Neuroendocrine, Immune and other humeral factors evolved whereby harmonious orchestration of functions was attained and chaos avoided. The article includes clinical and experimental evidence in support of the thesis that the defective stem cell represents the initial step in the development of cancer. A discussion of the characteristics of the cancer cell follows, and an evaluation of the present modalities of treatment. Some of the shortcomings and failures are reviewed and suggestions for a completely different approach to therapy is presented. The essence of new therapy is the realization that cancer is not an infection, is not caused by foreign predators, but is the manifestation of the response of the body to its own, i.e. idiosomatic, predators. The cancer cell mass is not a cause but an effect, and its total eradication or destruction following spread is not feasible. The future may lie in measures which “reform”, rehabilitate and differentiate the anaplastic cell.     

Integrated analysis of recurrent properties of cancer genes to identify novel drivers

The heterogeneity of cancer genomes in terms of acquired mutations complicates the identification of genes whose modification may exert a driver role in tumorigenesis. In this study, we present a novel method that integrates expression profiles, mutation effects, and systemic properties of mutated genes to identify novel cancer drivers. We applied our method to ovarian cancer samples and were able to identify putative drivers in the majority of carcinomas without mutations in known cancer genes, thus suggesting that it can be used as a complementary approach to find rare driver mutations that cannot be detected using frequency-based approaches.     

The max bin regression method to identify maximum bioindicator responses to ecological drivers

A need in environmental science is to determine the response range of a bioindicator to environmental drivers. A common problem with regression based approaches is the indicator response may be obfuscated by many zero or low-value observations when the organisms are not present because of life history characteristics. A method is described for determining the maximum response of an ecological variable to environmental drivers using a median approach. A regression is performed on the relationship histogram after taking the maximum ecological response value from a set of evenly spaced bins. This technique is an alternative to quantile regression at the 95% level and is analyzed on general examples and specific applications in coastal ecology using benthic macroinfauna as bioindicators. This new technique is useful for ecosystem management purposes where the maximum response of a biological indicator to an environmental driver is desired and is analogous to determining the ‘area under the curve’ of a regression.     

Selective breeding of conventional and new industrial microorganisms: from sake microorganisms to green algae

World Journal of Microbiology and Biotechnology - The basis for science and technology in advanced nations might be considered to have come from Egypt, Babylonia, China or ancient countries. Thus,...     

Using connectivity to identify climatic drivers of local adaptation: a response to Macdonald et al.

Macdonald et al. (Ecol. Lett., 21, 2018, 207–216) proposed an analytical framework for identifying evolutionary processes underlying trait‐environment relationships observed in natural populations. Here, we propose an expanded and refined framework based on simulations and bootstrap‐based approaches, and we elaborate on an important statistical caveat common to most datasets.     

A functional genomics approach to identify new regulators of Wnt signaling

A recent study by used a genome-wide RNAi screen in Drosophila cells to identify 238 candidate regulators of the Wnt-signaling pathway, most of which had not been previously connected to Wnt signaling. Supporting in vivo studies are in progress. The fact that such an impressive number of potential modulators had eluded detection in genetic screens underscores the potential of applying new, high-throughput approaches to old problems.     

A new concept for DNA-arrays

We will insert a cleavage site in an oligodeoxynucleotide, which can be used for a selective and quantitative cleavage. For that reason we synthesized the four 5'-S-(4,4'-dimethoxytrityl)-mercapto-2'-deoxynucleotide-3'-O-(2-cyanoethoxydiisopropylamino)-phosphites (5a-d). The cleavage of P-S and C-S bonds is described (Mag, M.; Lücking, S.; Engels, J.W. Synthesis and selective cleavage of an oligodeoxy-nucleotide containing a bridged internucleotide 5'-phosphorthioate linkage. Nucleic Acids Res. 1991, 19 (7), 1437-1441; Marriott, J.H.; Mottahedeh, M.; Reese, C.B. 9-(4-methoxyphenyl)xanthen-9-thiol: A useful reagent for the preparation of thiols. Tetrahedron Lett. 1990, 31 (51), 7485-7488; Divakar, K.J.; Mottoh, A.; Reese, C.B.; Shanghvi, Y.S. Approaches to the synthesis of 2' thio analogues of pyrimidine ribosides. J. Chem. Sc., Perkin Trans. 1 1990, 969-974). The oligodeoxynucleotides with an achiral bridged 5'-phosphorothioate linkage 5'-O-P-S-3' are synthesized by the phosphoramidite procedure.     

A new concept of paleoamygdala substrate

We put forward a new concept of paleoamygdala substrate, a complex of gray matter located in the periventricular zone of the lateral ventricle underhorn in the posterior segment of the phylogenetically ancient cortical/medial group of the amygdaloid complex. The argumentation is based on the cytoarchitectonic analysis, the consideration of specific neural organization and ontogenetic features as well as the literature data characterizing the results of hodological and functional studies.     

A new approach to identify species in Xiphinema americanum sensu lato

Four putative species belonging to the X. americanum group are known to transmit American nepoviruses and these nematodes and viruses are listed in European quarantine legislation. Identification of species in this group is therefore of particular importance for phytosanitary purposes, but is problematic because of the similar morphology of the putative species. As part of the Synthesys project BE-TAF 1769, eight collaborative institutions contributed material to Fera for study. Video technology allowed the best records of type material and in conjunction with photographic images created a 'virtual' collection of images that relies less on the deteriorating quality of museum specimens. Revised definitions of lip region and tail shape are considered to be the most stable characters for differentiation. Position of the amphidial aperture, development of the odontostyle collar and some established morphometric characters are considered of limited use although they retain value for latter stages of identification.     

生态系统途径——生态系统管理的一种新理念

介绍了生态系统途径的概念和内涵．生态系统途径最早由西方生态学家提出。随后得到一系列国际学术组织和国家的认同和支持,其中《生物多样性公约》、世界自然保护联盟和世界野生动物基金发挥了重要作用,．生态系统途径的实质是对土地、水和生物资源进行综合管理,旨在生态系统保护、生物资源可持续利用和共享生物资源三者之间达到平衡．作为生态系统管理的一种方法论,它以生物为核心。将人类及文化的多样性视为生态系统的一个组成部分,2000年《生物多样性公约》缔约国会议上制定的生态系统管理的12条基本原则和5项行动指南,丰富了生态系统途径的内涵,明确了实施的办法,我国在生态系统管理方面有着丰富的学术储备和经验总结。但也存在一定问题。

     

A new concept to guide timing of nitrogen fertilisation for sugarcane

Summary The pattern of nutrient uptake and development of roots form important factors in timing and placement of fertiliser. Characteristic differences between crops in these two aspects may fix up critical time and mode of application. Studies conducted on sugarcane at the Indian Institute of Sugarcane Research, Lucknow on the pattern of uptake of nitrogen and rooting revealed a trend where high rates of accumulation per unit plant mass precedes a phase of relatively small uptake before the boom period of growth sets in, where dilution in the composition takes place. The enrichment of the composition in itself has been held to be the main justification for applying fertiliser at the earliest which alone has been seen to ensure good yield. A critical look at the approach will expose that this explanation hitherto held is untenable. The reason for early fertilisation seems to be influenced by the smaller root foraging capacity in the early phase. This seems to suggest an entirely different concept in rationalisation of fertiliser application.     

Using multilevel models to identify drivers of landscape‐genetic structure among management areas

Landscape genetics offers a powerful approach to understanding species' dispersal patterns. However, a central obstacle is to account for ecological processes operating at multiple spatial scales, while keeping research outcomes applicable to conservation management. We address this challenge by applying a novel multilevel regression approach to model landscape drivers of genetic structure at both the resolution of individuals and at a spatial resolution relevant to management (i.e. local government management areas: LGAs) for the koala (Phascolartos cinereus) in Australia. Our approach allows for the simultaneous incorporation of drivers of landscape‐genetic relationships operating at multiple spatial resolutions. Using microsatellite data for 1106 koalas, we show that, at the individual resolution, foliage projective cover (FPC) facilitates high gene flow (i.e. low resistance) until it falls below approximately 30%. Out of six additional land‐cover variables, only highways and freeways further explained genetic distance after accounting for the effect of FPC. At the LGA resolution, there was significant variation in isolation‐by‐resistance (IBR) relationships in terms of their slopes and intercepts. This was predominantly explained by the average resistance distance among LGAs, with a weaker effect of historical forest cover. Rates of recent landscape change did not further explain variation in IBR relationships among LGAs. By using a novel multilevel model, we disentangle the effect of landscape resistance on gene flow at the fine resolution (i.e. among individuals) from effects occurring at coarser resolutions (i.e. among LGAs). This has important implications for our ability to identify appropriate scale‐dependent management actions.