bluuebunny/crossref_metadata_2025 huggingface dataset:
Microcirculation versus Macrocirculation for the Management of Septic Shock: Is Hyperoxia any Good?
Authors: Mahmoodpoor Ata , Sheikhzadeh Daryoush , Golzari Samad EJ
Published: April 2017

Macrovascular indices such as hemodynamic parameters and conventional cardiovascular support measures are commonly, yet mistakenly used, for the clinical management of septic shock. Nevertheless, it is the microcirculatory dysfunction that contributes immensely to the development of septic shock. Approaches focusing on macrocirculation rather than microcirculation utterly neglect 'what lies beneath' in the microcirculation (1). The most important known mechanisms contributing to the pathophysiology of severe sepsis are but not limited to"microcirculatory and mitochondrial distress syndrome" (MMDS) (2), global tissue rather than arterial hypoxia (3), generalized endothelial cell injury (4), and activation of the coagulation cascade (5). Therefore, setting macrocirculation parameters such as arterial oxygen saturation as the ultimate goal of resuscitation in septic patients (6) not only would not be associated with any benefits but also harm the patients. Moreover, it might falsely reassure the clinicians that the patients are in clinically stable state and overlook ‘what lies beneath'.Hyperoxia was initially believed to exert vasoconstrictor properties, thus potentially allowing for haemodynamic stabilisation in vasodilatory shock. Nevertheless, it has been shown that normobaric hyperoxia decreases the capillary perfusion and VO2 max (the maximum rate of oxygen consumption) and increases the heterogenisity of perfusion (7). Accordingly, some studies revealed that hyperoxia increases the risk of multi-organ failure in sepsis (8). Microcirculatory and cellular factors and tissue diffusion influence oxygen status of cells and supranormal O2 delivery can compensate for neither the diffusion impairment existing between capillaries and cells, nor for the intracellular metabolic dysfunction (9). Therefore, oxygen therapy should be managed cautiously during sepsis to minimize its probable deleterious effects (8). This might be achieved through personalized oxygenation based on the repeated assessments of ongoing oxygen requirements and implementation of strategies reducing metabolic rate and improving tissue oxygenation.
Performance of interferon-γrelease assay in the diagnosis of tuberculous lymphadenitis: a meta-analysis
Authors: Liu Qianqian , Li Wenzhang , Chen Yunfeng , Du Xinmiao , Wang Chengdi , Liang Binmiao , Tang Yin , Feng Yulin , Tao Chuanmin , He Jian-Qing
Published: April 2017

Background

The diagnostic values of interferon-gamma release assays (IGRA) in tuberculosis (TB) vary a lot with different site of infections, with especially higher sensitivities in chronic forms of TB such as tuberculosis of the lymph node. We conducted a meta-analysis to comprehensively evaluate the overall accuracy of diagnostic IGRA for tuberculous lymphadenitis.

Methods

Pubmed, Web of Science, EMBASE, Wanfang and CNKI databases up to February 17, 2017 were searched to identify published studies. The study quality was evaluated using the QUADAS-2 checklist. The pooled estimates of diagnostic parameters were generated using a bivariate random-effects model and summary receiver operating characteristic (SROC) curves were used to summarize global performance.

Results

A total of ten qualified studies, performed in Korea or China, including 1,084 patients, were enrolled in this meta-analysis. The pooled estimates of diagnostic accuracy were as follows: sensitivity, 0.89 (95% CI [0.85–0.92]); specificity, 0.81 (95% CI [0.77–0.83]); positive likelihood ratio (PLR), 4.25 (95% CI [2.79–6.47]); negative likelihood ratio (NLR), 0.16 (95% CI [0.12–0.22]); and area under the curve (AUC) was 0.93. According to subgroup analyses, studies conducted using QuantiFERON-TB, in Korean population and focusing on cervical lymphadenitis exhibited relative higher specificity while lower sensitivity. No evidence of publication bias was identified.

Conclusions

IGRA exhibits high diagnostic accuracy in tuberculous lymphadenitis. The diagnostic value of IGRA differed by different IGRA methods, ethnicity and lymphadenitis location. Our conclusion may be more applicable to population from TB prevalent areas.
gb4gv: a genome browser forgeminivirus
Authors: Ho Eric S. , Newsom-Stewart Catherine M. , Diarra Lysa , McCauley Caroline S.
Published: April 2017

Background

Geminiviruses (familyGeminiviridae) are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, the NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes with no explicit association in linking them. Thus, our goal is to build a comprehensiveGeminivirusgenomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc.

Methods

We have employed manual and automatic methods to curate 508 genomes from four major genera ofGeminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases.

Results

These data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser.

Discussion

With the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in theGeminiviridae.

Availability and Implementation

The database can be found at:http://gb4gv.lafayette.edu.
The use of food imports to overcome local limits to growth
Authors: Porkka Miina , Guillaume Joseph H. A. , Siebert Stefan , Schaphoff Sibyll , Kummu Matti
Published: April 2017

There is a fundamental tension between population growth and carrying capacity, i.e., the population that could potentially be supported using the resources and technologies available at a given time. When population growth outpaces improvements in food production locally, food imports can avoid local limits and allow growth to continue. This import strategy is central to the debate on food security with continuing rapid growth of the world population. This highlights the importance of a quantitative global understanding of where the strategy is implemented, whether it has been successful, and what drivers are involved. We present an integrated quantitative analysis to answer these questions at sub‐national and national scale for 1961–2009, focusing on water as the key limiting resource and accounting for resource and technology impacts on local carrying capacity. According to the sub‐national estimates, food imports have nearly universally been used to overcome local limits to growth, affecting 3.0 billion people—81% of the population that is approaching or already exceeded local carrying capacity. This strategy is successful in 88% of the cases, being highly dependent on economic purchasing power. In the unsuccessful cases, increases in imports and local productivity have not kept pace with population growth, leaving 460 million people with insufficient food. Where the strategy has been successful, food security of 1.4 billion people has become dependent on imports. Whether or not this dependence on imports is considered desirable, it has policy implications that need to be taken into account.
Quantifying the role of urbanization on airflow perturbations and dunefield evolution
Authors: Smith Alexander B. , Jackson Derek W. T. , Cooper J. Andrew G. , Hernández‐Calvento L.
Published: April 2017

Rapid urban development has been widespread in many arid regions of the world during the Anthropocene. Such development has the potential to affect, and be affected by, local and regional dunefield dynamics. While urban design often includes consideration of the wind regime, the potential impact of construction on the surrounding environment is seldom considered and remains poorly understood. In this study, regional airflow modeling during successive stages of urbanization at Maspalomas, Gran Canaria, Spain, indicates significant and progressive flow perturbations that have altered the adjacent dunefield. Significant modifications to the boundary layer velocity, mean wind directionality, turbulence intensity, and sediment flux potential are attributed to the extension of the evolving urban geometry into the internal boundary layer. Two distinct process/response zones were identified: (1) the urban shadow zone where widespread dune stabilization is attributed to the sheltering effect of the urban area on surface wind velocity; and (2) the acceleration zone where airflow is deflected away from the urbanized area, causing an increase in sediment transport potential and surface erosion. Consistent coherent turbulent structures were identified at landform and dunefield scales: counter‐rotating vortices develop in the lee‐side flow of dune crests and shedding off the buildings on the downwind edge of the urban area. This study illustrates the direct geomorphic impact of urbanization on aeolian dunefield dynamics, a relationship that has received little previous attention. The study provides a template for investigations of the potential impact of urbanization in arid zones.
Paleoenvironment change and its impact on carbon and nitrogen accumulation in the Zoige wetland, northeastern Qinghai‐Tibetan Plateau over the past 14,000 years
Authors: Zeng Mengxiu , Zhu Cheng , Song Yougui , Ma Chunmei , Yang Zhenjing
Published: April 2017

As the largest alpine wetland and peat deposition area in China, the Zoige wetland is climatically sensitive. The organic matter (OM) in peat stores copious environmental information. Here we report new data on the organic geochemistry of a 4.5 m peat profile HY2014 from southern Zoige wetland. Based on closely spaced accelerator mass spectrometry (AMS) 14C dating, we established a high‐resolution geochronological framework beginning at 14,057 a BP. Moreover, we estimated the sedimentation flux of TOC and TN (SFs) and their influencing factors. Before 10,916 a BP, the lake shrunk and peat began to develop under cold and dry conditions, and SFs were at their lowest values due to low productivity. More OM originated from hydrophyte and marsh plants. From 10,916 to 3050 a BP, peat was widely and well developed, and the climate was warm and humid, despite a cooling and drying trend. The HY2014 profile experienced an optimum climate during 10,916 − 6000 a BP, when SFs had the highest values that benefited from high productivity, and OM mainly originated from terrestrial plants. After 3050 a BP, the climate was the coldest and driest. The high SFs over the past 2000 a BP were mainly resulted from the low decomposition rate. The plant community, primary productivity, and decomposition rate were closely linked with the temporal variation of SFs. The environment change was mainly controlled by summer solar insolation, and the Zoige wetland was significantly influenced by the Indian summer monsoon.
Evaluation of retrieval methods of daytime convective boundary layer height based on lidar data
Authors: Li Hong , Yang Yi , Hu Xiao‐Ming , Huang Zhongwei , Wang Guoyin , Zhang Beidou , Zhang Tiejun
Published: April 2017

The atmospheric boundary layer height is a basic parameter in describing the structure of the lower atmosphere. Because of their high temporal resolution, ground‐based lidar data are widely used to determine the daytime convective boundary layer height (CBLH), but the currently available retrieval methods have their advantages and drawbacks. In this paper, four methods of retrieving the CBLH (i.e., the gradient method, the idealized backscatter method, and two forms of the wavelet covariance transform method) from lidar normalized relative backscatter are evaluated, using two artificial cases (an idealized profile and a case similar to real profile), to test their stability and accuracy. The results show that the gradient method is suitable for high signal‐to‐noise ratio conditions. The idealized backscatter method is less sensitive to the first estimate of the CBLH; however, it is computationally expensive. The results obtained from the two forms of the wavelet covariance transform method are influenced by the selection of the initial input value of the wavelet amplitude. Further sensitivity analysis using real profiles under different orders of magnitude of background counts show that when different initial input values are set, the idealized backscatter method always obtains consistent CBLH. For two wavelet methods, the different CBLH are always obtained with the increase in the wavelet amplitude when noise is significant. Finally, the CBLHs as measured by three lidar‐based methods are evaluated by as measured from L‐band soundings. The boundary layer heights from two instruments coincide with ±200 m in most situations.
Comparing mass balance and adjoint methods for inverse modeling of nitrogen dioxide columns for global nitrogen oxide emissions
Authors: Cooper Matthew , Martin Randall V. , Padmanabhan Akhila , Henze Daven K.
Published: April 2017

Satellite observations offer information applicable to top‐down constraints on emission inventories through inverse modeling. Here we compare two methods of inverse modeling for emissions of nitrogen oxides (NOx) from nitrogen dioxide (NO2) columns using the GEOS‐Chem chemical transport model and its adjoint. We treat the adjoint‐based 4D‐Var modeling approach for estimating top‐down emissions as a benchmark against which to evaluate variations on the mass balance method. We use synthetic NO2 columns generated from known NOx emissions to serve as “truth.” We find that error in mass balance inversions can be reduced by up to a factor of 2 with an iterative process that uses finite difference calculations of the local sensitivity of NO2 columns to a change in emissions. In a simplified experiment to recover local emission perturbations, horizontal smearing effects due to NOx transport are better resolved by the adjoint approach than by mass balance. For more complex emission changes, or at finer resolution, the iterative finite difference mass balance and adjoint methods produce similar global top‐down inventories when inverting hourly synthetic observations, both reducing the a priori error by factors of 3–4. Inversions of simulated satellite observations from low Earth and geostationary orbits also indicate that both the mass balance and adjoint inversions produce similar results, reducing a priori error by a factor of 3. As the iterative finite difference mass balance method provides similar accuracy as the adjoint method, it offers the prospect of accurately estimating top‐down NOx emissions using models that do not have an adjoint.
Development of an advanced eco‐hydrologic and biogeochemical coupling model aimed at clarifying the missing role of inland water in the global biogeochemical cycle
Authors: Nakayama Tadanobu
Published: April 2017

Recent research showed that inland water including rivers, lakes, and groundwater may play some role in carbon cycling, although its contribution has remained uncertain due to limited amount of reliable data available. In this study, the author developed an advanced model coupling eco‐hydrology and biogeochemical cycle (National Integrated Catchment‐based Eco‐hydrology (NICE)‐BGC). This new model incorporates complex coupling of hydrologic‐carbon cycle in terrestrial‐aquatic linkages and interplay between inorganic and organic carbon during the whole process of carbon cycling. The model could simulate both horizontal transports (export from land to inland water 2.01 ± 1.98 Pg C/yr and transported to ocean 1.13 ± 0.50 Pg C/yr) and vertical fluxes (degassing 0.79 ± 0.38 Pg C/yr, and sediment storage 0.20 ± 0.09 Pg C/yr) in major rivers in good agreement with previous researches, which was an improved estimate of carbon flux from previous studies. The model results also showed global net land flux simulated by NICE‐BGC (−1.05 ± 0.62 Pg C/yr) decreased carbon sink a little in comparison with revised Lund‐Potsdam‐Jena Wetland Hydrology and Methane (−1.79 ± 0.64 Pg C/yr) and previous materials (−2.8 to −1.4 Pg C/yr). This is attributable to CO2 evasion and lateral carbon transport explicitly included in the model, and the result suggests that most previous researches have generally overestimated the accumulation of terrestrial carbon and underestimated the potential for lateral transport. The results further implied difference between inverse techniques and budget estimates suggested can be explained to some extent by a net source from inland water. NICE‐BGC would play an important role in reevaluation of greenhouse gas budget of the biosphere, quantification of hot spots, and bridging the gap between top‐down and bottom‐up approaches to global carbon budget.
Rock record and magnetic response to large earthquakes within Wenchuan Earthquake Fault Scientific Drilling cores
Authors: Zhang Lei , Sun Zhiming , Li Haibing , Zhao Laishi , Song Sheng‐Rong , Chou Yu‐Min , Cao Yong , Ye Xiaozhou , Wang Huan , He Xiangli
Published: April 2017

Fault‐related pseudotachylytes are often considered to be produced by large seismic events. To investigate the rock record and magnetic response to large earthquakes within cores from the Wenchuan Earthquake Fault Scientific Drilling borehole 2 (WFSD‐2), we carried out microstructural, geochemical, and rock‐magnetic analyses of representative cores. Based on microstructural observations and powder X‐ray diffraction analyses, we found 21 layers of melt‐origin pseudotachylytes from 579.62 to 599.31 m‐depth in the cores. The presence of early‐formed pseudotachylyte fragments in the new layer suggests that seismic faulting processes exploited the same fault strand more than once. Pseudotachylyte veins have higher values of magnetic susceptibility relative to wall rocks. Rock‐magnetic results indicate that the magnetic minerals within the pseudotachylyte veins are magnetite with varying amounts of paramagnetic minerals. Magnetic hysteresis loops show that a reduction of the grain size of ferromagnetic minerals is not a plausible explanation for the higher magnetic susceptibility values in pseudotachylyte veins. Rock‐magnetic analyses indicate that frictional heating (>500°C) occurred in the pseudotachylyte veins during large earthquakes. The resulting high temperatures induced thermal decomposition of paramagnetic minerals, forming magnetite and contributing to the higher magnetic susceptibility values. Different generations of pseudotachylytes and numerous high magnetic susceptibility zones together demonstrate that ancient powerful earthquakes may have occurred repeatedly in the Longmen Shan thrust belt.
Putting
Physcomitrella Patens
on the Tree of Life: The Evolution and Ecology of Mosses
Authors: Mishler Brent D. , Oliver Melvin J.
Published: April 2017

Physcomitrella patens
is an important model system for studies of genetics and physiology, and with its newly sequenced genome, it is perfectly placed phylogenetically to serve as a point of comparison for angiosperms. This chapter addresses three main questions: (1) How typical of a moss is
P. patens
? It is rather atypical, given the reasons that it was selected as a model system, such as its rapid life cycle and reduced morphology, yet it is representative in many ways. (2) Where does it belong in the phylogenetic history of land plants? The mosses are monophyletic, and share a common ancestor with hornworts and tracheophytes, with
P. patens
nesting within the ‘true mosses’. (3) What are the special attributes of moss ecology and evolution that can lend special interest to the study of
P. patens
? When comparing
P. patens
with tracheophytes, it is important to understand both its similarities and differences with its larger cousins – we discuss how many processes influencing their physiology, ecology and evolutionary diversification seem to be quite different from the tracheophytes.
Gene Targeting
Authors: Kamisugi Yasuko , Cuming Andrew C.
Published: April 2017

Physcomitrella patens
is a model plant for comparative genomic analysis, and is the only plant model in which ‘gene targeting’ – the replacement of an endogenous gene by a genetically altered variant transgene – occurs with high efficiency. We describe the parameters that determine the efficiency of gene targeting and discuss the nature of the integration events that occur following transformation of
P. patens
. Integration of transgenes utilises endogenous mechanisms for the repair of DNA double‐strand breaks, and the preferential integration of transforming DNA at homologous sites by
P. patens
indicates that the predominating mechanism for DNA repair is based on homologous recombination, rather than non‐homologous end joining, as is the case in flowering plants.
P. patens
thus provides a useful experimental model for the study of the HR‐mediated DNA repair pathway in plants, and understanding how this mechanism operates in
P. patens
may pave the way for the development of more efficient gene targeting strategies for the genetic modification of crop species.
Chloroplasts
Authors: Sugita Mamoru , Aoki Setsuyuki
Published: April 2017

InPhyscomitrella patens, chloronemal and leaf cells contain numerous large round chloroplasts while caulonemal cells contain fewer and smaller spindle‐shaped chloroplasts. Unlike seed plants, plastid differentiation is not usually observed inP. patensand the gametophytes always contain chloroplasts that develop even in the dark. TheP. patensplastid genome (122 890 bp) possesses at least 118 genes. The most interesting feature is that therpoAgene encoding the α subunit of the plastid‐encoded plastid RNA polymerase (PEP) is absent from the plastid genome ofP. patens. Instead, two nuclear counterparts encode the α subunits of PEP enzyme and modulate transcription of the plastid genes. WhetherP. patenschloroplasts contain a second RNA polymerase, the nuclear‐encoded plastid RNA polymerase (NEP), continues to be debated. Here, we provide biochemical evidence supporting the existence of NEP activity inP. patens. Plastid transformation, which has been achieved inP. patens, allows further investigation of the regulation of plastid gene expression and over‐production of foreign polypeptides in the moss chloroplasts. Molecular techniques with the complete genome informatics open a way to study the molecular basis of plastid division and movement, chloroplast import, or circadian rhythm inP. patens.
Hormonal Regulation of Development by Auxin and Cytokinin in Moss
Authors: von Schwartzenberg Klaus
Published: April 2017

Since the early days of plant hormone research, bryophytes have attracted studies on developmental and reproductive processes. It is a striking characteristic of bryophytes that they respond to several plant hormones, and model plants such as the moss
Physcomitrella patens
therefore offer insights into the hormonal signalling processes that were established in a land plant lineage which has diverged from seed plants ca. 430 million years ago. This review aims to summarise knowledge on auxin and cytokinin in mosses, thereby outlining hormonal action on a morphogenetic and molecular level as well as biosynthesis and metabolism of these hormones. In this respect, the recent assembly of the
P. patens
genome sequence provides extremely valuable data enabling comparative approaches to decipher the evolution of hormone‐mediated regulatory networks in plants.
Carpel Evolution
Authors: Vialette‐Guiraud Aurélie C.M. , Scutt Charlie P.
Published: April 2017

The carpel is the progenitor organ to the fruit and a defining feature of the flowering plants, or angiosperms. This organ has evolved in the angiosperms to generate a wide diversity of forms, often related to breeding strategies and seed distribution mechanisms. In this chapter, we focus on a number of key stages in the evolution of the carpel and fruit, about which something can be said of the molecular mechanisms underlying evolutionary change. In particular, we describe hypotheses for the evolutionary origin of the carpel in the first flowering plants and attempt to reconstruct the history of its structural diversification in various major angiosperm groups. In doing so, we concentrate on the genes and mechanisms whose presence can be deduced at key evolutionary stages in the angiosperms, and on molecular‐evolutionary processes such as neo‐ and sub‐functionalization, which have moulded these genes and the developmental processes they regulate. We also review the literature on the evolution of syncarpy – a phenomenon of enormous adaptive significance in the angiosperms. Lastly, we describe some examples of convergent evolution that have led to the development of fruit‐like structures both within and outside the flowering plants.
Fertilization and Fruit Initiation
Authors: Fuentes Sara , Vivian‐Smith Adam
Published: April 2017

Angiosperms have evolved the unique processes of double fertilization and fruit development as key steps of their survival and dispersal strategies. In this chapter, we will examine fertilization and fruit initiation as central restriction points to fruit and seed development. Pollination and fertilization appear essential for fruit initiation, since angiosperm flowers universally enter terminal senescence and abscission phases if pollination is prevented. We review key developmental processes, pathways and genes that were recruited to control and restrict the reproductive growth of the carpel and ovule until fertilization is achieved. Ever since the discovery that exogenous application of phytohormones results in the development of seedless fruit without fertilization (termed parthenocarpy), most research has concentrated on the role of endogenous phytohormones as triggers for fruit initiation after fertilization. We will highlight how uncoupling of fruit initiation from fertilization through mutational studies can further contribute to the understanding of these complex processes. Initial analysis shows that strict local control of auxin signalling, through a transcription factor network, forms one of the decisive and primary events that leads to the hierarchical control over gibberellin metabolism and perception. Testing and challenging these assumptions will provide further knowledge indispensable for controlling fruit set and yield in agriculture.
Long‐Distance Seed Dispersal
Authors: Schurr Frank M. , Spiegel Orr , Steinitz Ofer , Trakhtenbrot Ana , Tsoar Asaf , Nathan Ran
Published: April 2017

Most seeds of most plant species are dispersed over distances shorter than a few dozen metres, and only very few seeds travel over long distances. While the long‐distance dispersal (LDD) of seeds is, thus, typically rare, it has disproportionately large effects on the long‐term and large‐scale dynamics of plants. Here, we first highlight the importance of LDD for various aspects of plant biology, discuss problems with quantifying LDD, and advocate a new vector‐based framework for LDD research that may help to overcome some of these problems. We then present six generalizations about LDD mechanisms that can be derived using this framework. While the framework and the generalizations are also highlighted in Nathan, R., Schurr, F.M., Spiegel, O.,et al.(2008) Mechanisms of long‐distance seed dispersal.Trends in Ecology and Evolution23, 638–647, this chapter provides a more in‐depth derivation of the framework and additional evidence for the generalizations. In particular, we present here a new meta‐analysis validating an innovative model for the allometry of seed dispersal by animals. In the second part of the chapter, we extend Nathanet al.'s (2008) discussion of the implications of the framework and generalizations for understanding LDD evolution and forecasting large‐scale dynamics of plants. In particular, we use the vector‐based framework to address two fundamental questions about LDD: can we identify all relevant LDD vectors and can plant traits influence LDD? We conclude by suggesting directions for future research on LDD.
Factors Influencing the Ripening and Quality of Fleshy Fruits
Authors: Barry Cornelius S.
Published: April 2017

Fleshy fruits have a dual function in the reproductive strategies of plants. Initially, fleshy fruits protect the developing seeds from predation and then, once the seeds are mature, they facilitate dispersal of the enclosed seeds. Plants have evolved numerous chemical and physical barriers that discourage seed predation from fleshy fruits. Similarly, the ripening of fleshy fruits occurs through a range of coordinated biochemical processes that convert an unpalatable unripe fruit into a fruit that is nutritious and desirable to seed‐dispersing fauna. The biochemical changes that occur at the onset of ripening are species specific but several general processes occur that are common to many fruits, suggesting that the mechanisms that control ripening may be evolutionarily conserved. For example, fruit ripening is often accompanied by the accumulation of brightly coloured pigments, the synthesis of aroma volatiles and the conversion of complex carbohydrates into sugars. These changes facilitate seed dispersal strategies. The genetic and biochemical pathways that lead to fruit ripening are not fully understood. However, significant progress has been made in identifying some of the components of these pathways. This review highlights recent research that has contributed to the understanding of the ripening process at the molecular level and outlines the development of genomics‐based resources for fleshy fruit‐bearing species.
Parthenocarpy in Crop Plants
Authors: Pandolfini Tiziana , Molesini Barbara , Spena Angelo
Published: April 2017

Fruit set and growth in the absence of fertilization (parthenocarpy) is a useful trait in plants grown for the value of their fruit. Auxins and gibberellins are widely used to spray flowers to chemically confer parthenocarpy. In recent years, genetic modifications of either auxin or gibberellin biology have been used to confer parthenocarpy to tomato and other crops. Present knowledge indicates that parthenocarpy can be achieved by genetic modification of either auxin synthesis (iaaM), auxin sensitivity (rolB), auxin content (Aucsia) or auxin signal transduction (IAA9 or ARF8). Genetic modification of gibberellin signal transduction (DELLA) has also been shown to confer parthenocarpy. Available data, obtained under both open field and protected cultivation, show that genetic parthenocarpy can be used to improve fruit production and/or fruit quality. The mechanisms, genetically modified to confer parthenocarpy, are active also in other plant organs. Observations consistent with the Euanthial theory that envisages the fruit as a modified leaf predict that the mechanisms underlying fruit initiation have been recruited from molecular machineries present and controlling other plant developmental processes. The flower/fruit represents the last evolutionary innovation of the green plant lineage, and yet genes (i.e. Aucsia) controlling fruit initiation are most likely older than 1 billion years being present in Prasinophytes (i.e. probable ancestors of Charophytes, which themselves are considered ancestors of all land plants).
Molecular Modes of Action of Defensive Secondary Metabolites
Authors: Wink Michael , Schimmer Oskar
Published: April 2017

Secondary metabolites (SM) have been shaped by evolution for more than 500 million years. As a result, many of them have distinctive biochemical and pharmacological properties. The molecular modes of action of the main groups of SM are reviewed in this chapter. Details are given on interactions of SM with proteins that can induce conformational changes and thus a modification of their bioactivity. The fluidity and permeability of biomembranes constitute another important target, which is influenced by many lipophilic and amphiphilic SM. A number of SM can either alkylate or intercalate DNA, which can cause mutations and in consequence cancer or malformations. Many SM are cytotoxic because they interfere with biomembranes, proteins of the cytoskeleton or DNA; they often induce programmed cell death (apoptosis). A large number of SM, especially alkaloids modulate neuronal signal transduction by interfering with ion channels, ion pumps, neuroreceptors, choline esterase, monoamine oxidase and other enzymes related to signal transduction pathways. A typical feature of SM is their ability to modulate more than one molecular target; thus, additive and even synergistic activities can be expected.
Chemical Defence in Marine Ecosystems (FromAPRVolume 39)
Authors: Putz Annika , Proksch Peter
Published: April 2017

Nature has provided a broad arsenal of structurally diverse and pharmacologically active compounds that serve as highly effective drugs or lead structures for the development of novel drugs to combat a multitude of diseases. Traditionally, terrestrial organisms represent the richest source of natural drugs. Considering the fact that over 70% of the surface of the earth is covered by oceans that harbour a rich biodiversity, aspiration in marine bioprospecting as a viable counterpart for the discovery of bioactive compounds from the terrestrial environment seems justified. Interestingly, the majority of marine natural products involved in clinical or preclinical trials is produced by invertebrates, which is in contrast to compounds derived from the terrestrial environment where plants by far exceed animals with respect to the production of bioactive metabolites. The fact that bioactive metabolites are predominantly found in sessile or slow‐moving marine organisms that lack physical defence structures thus appears to reflect the ecological importance of these compounds with respect to inter‐ as well as intraspecific interactions, for example predation, competition for space and fouling. Numerous natural products from marine invertebrates show striking structural similarities to known metabolites of microbial origin. This fact suggests that microorganisms such as bacteria and microalgae that often live associated with marine invertebrates are at least involved in the biosynthesis or are in fact the true sources of these respective metabolites in many cases.
Production of Natural Products by Plant Cell and Organ Cultures
Authors: Alfermann August‐Wilhelm
Published: April 2017

Natural products have been used as medicines, food additives or in technical applications by humans since thousands of years. Due to various reasons, a sufficient supply of the plant raw material has become increasingly difficult in recent years. Since more than 30 years, laboratories worldwide are trying to produce natural products for commercial application with plant cell and organ cultures. The commercial success of this research is still very limited, due to too low product yields resulting into production costs, which are not acceptable. Among organ cultures, root and hairy root cultures are the most promising for the production of secondary metabolites in good yields. This chapter describes the methods used to overcome these intrinsic problems in product yields and the hopes which are set on the new developments to transfer the appropriate plant genes into microorganisms, which may become more applicable for large scale production of plant natural products than plant cells themselves. First results in this field, e.g. the synthesis of benzylisoquinoline alkaloids in recombinant yeast cells, are already very promising.
Introduction: Biochemistry, Physiology and Ecological Functions of Secondary Metabolites
Authors: Wink Michael
Published: April 2017

Secondary metabolites (SM) occur in plants in a high structural diversity. The different classes of SM and their biosynthetic pathways are summarized in this introduction. A typical feature of SM is their storage in relatively high concentrations, sometimes in organs which do not produce them. A long‐distance transport via the phloem or xylem is then required. Whereas hydrophilic substances are stored in the vacuole, lipophilic metabolites can be found in latex, resin ducts, oil cells or cuticle. SM are not necessarily end products and some of them, especially if they contain nitrogen, are metabolically recycled. Biosynthesis, transport and storage are energy‐dependent processes which include the costs for the replication and transcription of the corresponding genes and the translation of proteins. The intricate biochemical and physiological features are strongly correlated with the function of SM: SM are not useless waste products (as assumed earlier), but important tools against herbivores and microbes. Some of them also function as signal molecules to attract pollinating arthropods or seed‐dispersing animals and as signal compounds in other plant – plant, plant – animal and plant – microbe relationships.
Biosynthesis of Phenylpropanoids and Related Compounds (FromAPRVolume 40)
Authors: Petersen Maike , Hans Joachim , Matern Ulrich
Published: April 2017

Phenolic compounds are ubiquitous in the plant kingdom. A main pathway for the formation of these compounds starts with the aromatic amino acidsl‐phenylalanine and – to a lesser extent –l‐tyrosine. In the general phenylpropanoid pathway, these are transformed to coenzyme A‐activated 4‐coumaric acid by phenylalanine ammonia‐lyase, cinnamic acid 4‐hydroxylase and 4‐coumarate CoA‐ligase. 4‐Coumaroyl‐CoA gives rise to a large number of different natural products, e.g. flavonoids, lignans, coumarins, tannins, hydroxycinnamic acid esters and amides as well as lignin monomers. This review gives an insight into recent findings concerning the general phenylpropanoid pathway as well as the biosyntheses of hydroxycinnamoyl conjugates, phenolic aroma and fragrance compounds, lignans, coumarins and gallo‐/ellagitannins.
Gibberellins in Fungi, Bacteria and Lower Plants: Biosynthesis, Function and Evolution
Authors: Tudzynski Bettina , Studt Lena , Rojas María Cecilia
Published: April 2017

The rice pathogenFusarium fujikuroi, as well as two distantly related fungi,Sphaceloma manihoticolaandPhaeosphaeriaesp., contains clusters of gibberellin (GA) biosynthesis genes and produces GAs. Fungal GAs are structurally identical to those synthesised by higher plants, although the respective biosynthetic pathways, genes and enzymes differ. Besides fungi, some bacteria synthesise GAs. An operon of GA biosynthesis genes was found in the symbiotic rhizobacteriumBradyrhizobium japonicumand in otherRhizobiumspecies. This operon encodes the enzymes of GA9biosynthesis and includes a reductase or alcohol dehydrogenase gene not present in fungal clusters. Differences between genes and enzymes indicate convergent evolution of the GA biosynthesis pathway in higher plants, fungi and bacteria. In contrast to higher plants, GAs are not produced by all lower plants. Mosses or liverworts synthesiseent‐kaurenoids, but not GAs, while lycophytes and ferns synthesise GAs or GA‐related products that participate in the regulation of reproductive development.
Flexible Inorganic Ferroelectric Thin Films for Nonvolatile Memory Devices
Authors: Yu Hyeonggeun , Chung Ching‐Chang , Shewmon Nate , Ho Szuheng , Carpenter Joshua H. , Larrabee Ryan , Sun Tianlei , Jones Jacob L. , Ade Harald , O'Connor Brendan T. , So Franky
Published: April 2017

Next‐generation wearable electronics call for flexible nonvolatile devices for ubiquitous data storage. Thus far, only organic ferroelectric materials have shown intrinsic flexibility and processability on plastic substrates. Here, it is shown that by controlling the heating rate, ferroelectric hafnia films can be grown on plastic substrates. The resulting highly flexible capacitor with a film thickness of 30 nm yields a remnant polarization of 10 µC cm−2. Bending tests show that the film ferroelectricity can be retained under a bending radius below 8 mm with up to 1000 bending cycles. The excellent flexibility is due to the extremely thin hafnia film thickness. Using the ferroelectric film as a gate insulator, a low voltage nonvolatile vertical organic transistor is demonstrated on a plastic substrate with an extrapolated date retention time of up to 10 years.
Self‐Organized Epitaxial Vertically Aligned Nanocomposites with Long‐Range Ordering Enabled by Substrate Nanotemplating
Authors: Fan Meng , Zhang Bruce , Wang Han , Jian Jie , Sun Xing , Huang Jijie , Li Leigang , Zhang Xinghang , Wang Haiyan
Published: April 2017

Vertically aligned nanocomposites (VAN) thin films present as an intriguing material family for achieving novel functionalities. However, most of the VAN structures tend to grow in a random fashion, hindering the future integration in nanoscale devices. Previous efforts for achieving ordered nanopillar structures have been focused on specific systems, and rely on sophisticated lithography and seeding techniques, making large area ordering quite difficult. In this work, a new technique is presented to produce self‐assembled nanocomposites with long‐range ordering through selective nucleation of nanocomposites on termination patterned substrates. Specifically, SrTiO3 (001) substrates have been annealed to achieve alternating chemical terminations and thus enable selective epitaxy during the VAN growth. La0.7Sr0.3MnO3:CeO2 (LSMO):CeO2 nanocomposites, as a prototype, are demonstrated to form well‐ordered rows in matrix structure, with CeO2 (011) domains selectively grown on SrO terminated area, showing enhanced functionality. This approach provides a large degree of long‐range ordering for nanocomposite growth that could lead to unique functionalities and takes the nanocomposites one step closer toward future nanoscale device integration.
Unidirectional Wetting Properties on Multi‐Bioinspired Magnetocontrollable Slippery Microcilia
Authors: Cao Moyuan , Jin Xu , Peng Yun , Yu Cunming , Li Kan , Liu Kesong , Jiang Lei
Published: April 2017

Here, a smart fluid‐controlled surface is designed, via the rational integration of the unique properties of three natural examples, i.e., the unidirectional wetting behaviors of butterfly's wing, liquid‐infused “slippery” surface of the pitcher plant, and the motile microcilia of micro‐organisms. Anisotropic wettability, lubricated surfaces, and magnetoresponsive microstructures are assembled into one unified system. The as‐prepared surface covered by tilted microcilia achieves significant unidirectional droplet adhesion and sliding. Regulating by external magnet field, the directionality of ferromagnetic microcilia can be synergistically switched, which facilitates a continuous and omnidirectional‐controllable water delivery. This work opens an avenue for applications of anisotropic wetting surfaces, such as complex‐flow distribution and liquid delivery, and extend the design approach of multi‐bioinspiration integration.
Few‐Layer Black Phosphorus Carbide Field‐Effect Transistor via Carbon Doping
Authors: Tan Wee Chong , Cai Yongqing , Ng Rui Jie , Huang Li , Feng Xuewei , Zhang Gang , Zhang Yong‐Wei , Nijhuis Christian A. , Liu Xinke , Ang Kah‐Wee
Published: April 2017

Black phosphorus carbide (b‐PC) is a new family of layered semiconducting material that has recently been predicted to have the lightest electrons and holes among all known 2D semiconductors, yielding a p‐type mobility (≈105 cm2 V−1 s−1) at room temperature that is approximately five times larger than the maximum value in black phosphorus. Here, a high‐performance composite few‐layer b‐PC field‐effect transistor fabricated via a novel carbon doping technique which achieved a high hole mobility of 1995 cm2 V−1 s−1 at room temperature is reported. The absorption spectrum of this material covers an electromagnetic spectrum in the infrared regime not served by black phosphorus and is useful for range finding applications as the earth atmosphere has good transparency in this spectral range. Additionally, a low contact resistance of 289 Ω µm is achieved using a nickel phosphide alloy contact with an edge contacted interface via sputtering and thermal treatment.
Akt inhibitor MK‐2206 in combination with bendamustine and rituximab in relapsed or refractory chronic lymphocytic leukemia: Results from the N1087 alliance study
Authors: Larsen Jeremy T. , Shanafelt Tait D. , Leis Jose F. , LaPlant Betsy , Call Tim , Pettinger Adam , Hanson Curtis , Erlichman Charles , Habermann Thomas Matthew , Reeder Craig , Nikcevich Daniel , Bowen Deborah , Conte Michael , Boysen Justin , Secreto Charla , Lesnick Connie , Tschumper Renee , Jelinek Diane , Kay Neil E. , Ding Wei
Published: April 2017

Akt is a downstream target of B cell receptor signaling and is a central regulator of CLL cell survival. We aim to investigate the safety and efficacy of the Akt inhibitor MK‐2206 in combination with bendamustine and rituximab (BR) in relapsed and/or refractory CLL in a phase I/II study. A standard phase I design was used with cohorts of three plus three patients to determine the maximum tolerated dose (MTD) of MK‐2206 in combination with BR in relapsed CLL. Single‐agent MK‐2206 (weekly dosed) was administered one‐week in advance before BR on cycle 1 and subsequently was given with BR at the same time for cycle 2‐6. Phase II employed the MTD of MK‐2206 with BR to evaluate safety and efficacy of this study combination. Thirteen relapsed/refractory CLL were treated for maximal 6‐cycle of therapy. The maximum tolerated dose of MK‐2206 was 90 mg by mouth once weekly. The most common grade 3/4 adverse events were neutropenia (46%), febrile neutropenia (23%), rash (15%), diarrhea (15%), and thrombocytopenia (15%). Overall response rate was 92% with a median progression free survival and treatment free survival of 16 and 24 months, respectively. Five patients (38%) achieved complete remission or complete remission with incomplete count recovery, two of whom were MRD negative. The efficacy and tolerability of this combination indicates that Akt inhibition combined with chemoimmunotherapy is a promising novel treatment combination in CLL and deserves further prospective clinical trial.
Biotin‐thiamine responsive basal ganglia disease: Identification of a pyruvate peak on brain spectroscopy, novel mutation in SLC19A3, and calculation of prevalence based on allele frequencies from aggregated next‐generation sequencing data
Authors: Ferreira Carlos R. , Whitehead Matthew T. , Leon Eyby
Published: April 2017

Biotin‐thiamine responsive basal ganglia disease is an inborn error of metabolism caused by mutations in SLC19A3, encoding a transporter of thiamine across the plasma membrane. We report a novel mutation identified in the homozygous state in a patient with typical brain MRI changes. In addition, this patient had markedly elevated CSF pyruvate, a low lactate‐to‐pyruvate molar ratio, and an abnormal pyruvate peak at 2.4 ppm on brain magnetic resonance spectroscopy. Using aggregated exome sequencing data, we calculate the carrier frequency of mutations in SLC19A3 as 1 in 232 individuals in the general population, for an estimated prevalence of the disease of approximately 1 in 215,000 individuals. The disease is thus more frequent than previously recognized, and the presence of a pyruvate peak on spectroscopy could serve as an important diagnostic clue.