bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inverse correlation between heme synthesis and the Warburg effect in cancer cells
Authors: Sugiyama Yuta , Takahashi Erika , Takahashi Kiwamu , Nakajima Motowo , Tanaka Tohru , Ogura Shun-ichiro 
Published: August 2019

AbstractsCancer cells show a bias toward the glycolytic system over the conventional mitochondrial electron transfer system for obtaining energy. This biased metabolic adaptation is called the Warburg effect. Cancer cells also exhibit a characteristic metabolism, a decreased heme synthesizing ability. Here we show that heme synthesis and the Warburg effect are inversely correlated. We used human gastric cancer cell lines to investigate glycolytic metabolism and electron transfer system toward promotion/inhibition of heme synthesis. Under hypoxic conditions, heme synthesis was suppressed and the glycolytic system was enhanced. Addition of a heme precursor for the promotion of heme synthesis led to an enhanced electron transfer system and inhibited the glycolytic system and vice versa. Enhanced heme synthesis leads to suppression of cancer cell proliferation by increasing intracellular reactive oxygen species levels. Collectively, the promotion of heme synthesis in cancer cells eliminated the Warburg effect by shifting energy metabolism from glycolysis to oxidative phosphorylation.
A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies sub-telomeric regions as drivers of virulence
Authors: Wyatt Nathan A. , Richards Jonathan K. , Brueggeman Robert S. , Friesen Timothy L. 
Published: August 2019

AbstractPyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in sub-telomeric regions of chromosomes with 10 of the 14 accessory region QTL localizing to sub-telomeric regions. Comparative analysis of the sub-telomeric regions of P. teres f. teres chromosomes revealed translocation events where homology was detected between non-homologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the sub-telomeric accessory genomic compartments not only harbor most of the known virulence loci, but also that these regions have the capacity to rapidly evolve.
Nanoscale distribution of nuclear sites analyzed by superresolution STED-ICCS
Authors: Oneto M. , Scipioni L. , Sarmento M.J. , Cainero I. , Pelicci S. , Furia L. , Pelicci P.G. , Dellino G.I. , Bianchini P. , Faretta M. , Gratton E. , Diaspro A. , Lanzanò L. 
Published: August 2019

AbstractDeciphering the spatiotemporal coordination between nuclear functions is important to understand its role in the maintenance of human genome. In this context, superresolution microscopy has gained considerable interest as it can be used to probe the spatial organization of functional sites in intact single cell nuclei in the 20-250 nm range. Among the methods that quantify colocalization from multicolor images, image cross-correlation spectroscopy (ICCS) offers several advantages, namely it does not require a pre-segmentation of the image into objects and can be used to detect dynamic interactions. However, the combination of ICCS with super-resolution microscopy has not been explored yet.Here we combine dual color stimulated emission depletion (STED) nanoscopy with ICCS (STED-ICCS) to quantify the nanoscale distribution of functional nuclear sites. We show that STED-ICCS provides not only a value of colocalized fraction but also the characteristic distances associated to correlated nuclear sites. As a validation, we quantify the nanoscale spatial distribution of three different pairs of functional nuclear sites in MCF10A cells. As expected, transcription foci and a transcriptionally repressive histone marker (H3K9me3) are not correlated. Conversely, nascent DNA replication foci and the Proliferating cell nuclear antigen (PCNA) protein have a high level of proximity and are correlated at a nanometer distance which is close to the limit of our experimental approach. Finally, transcription foci are found at a distance of 130 nm from replication foci, indicating a spatial segregation at the nanoscale. Overall, our data demonstrate that STED-ICCS can be a powerful tool for the analysis of nanoscale distribution of functional sites in the nucleus.Statement of significanceSeveral methods are available to quantify the proximity of two labeled molecules from dual color images. Among them, image cross-correlation spectroscopy (ICCS) is attractive as it does not require a pre-segmentation of the image into objects and can be used to detect dynamic interactions. Here, we combine for the first time ICCS with superresolution stimulated emission depletion (STED) microscopy (STED-ICCS) to quantify the spatial distribution of functional sites in the nucleus. Our results show that STED-ICCS, in addition to quantifying the colocalized fraction, detects characteristic nanometer distances associated to correlated nuclear sites. This work shows that STED-ICCS can be a powerful tool to quantify the nanoscale distribution of functional sites in the nucleus.
The Cannabis Multi-Omics Draft Map Project
Authors: Jenkins Conor , Orsburn Ben 
Published: August 2019

AbstractRecently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources we have developed from proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources. All data for this project is available to view or download at www.CannabisDraftMap.Org
Winter is coming: pathogen emergence in seasonal environments
Authors: Carmona Philippe , Gandon Sylvain 
Published: August 2019

AbstractMany infectious diseases exhibit seasonal dynamics driven by periodic fluctuations of the environment. Predicting the risk of pathogen emergence at different points in time is key for the development of effective public health strategies. Here we study the impact of seasonality on the probability of emergence of directly transmitted pathogens under different epidemiological scenarios. We show that when the period of the fluctuation is large relative to the duration of the infection, the probability of emergence varies dramatically with the time at which the pathogen is introduced in the host population. In particular, we identify a new effect of seasonality (the winter is coming effect) where the probability of emergence is vanishingly small even though pathogen transmission is high. We use this theoretical framework to compare the impact of different control strategies on the average probability of emergence. We show that, when pathogen eradication is not attainable, the optimal strategy is to act intensively in a narrow time interval. Interestingly, the optimal control strategy is not always the strategy minimizing R0, the basic reproduction ratio of the pathogen. This theoretical framework is extended to study the probability of emergence of vector borne diseases in seasonal environments and we show how it can be used to improve risk maps of Zika virus emergence.
Paucity of adaptive selection in PmrAB two-component system may resist emergence of colistin resistance in Acinetobacter baumannii
Authors: Pagal Sudhakar , Saranathan Rajagopalan , Rani Anshu , Tomar Archana , Arunkumar K. P. , Prashanth K. 
Published: August 2019

AbstractInvestigations on the selection pressure acting on point mutations in PmrAB two-component system may provide insights into the future of colistin therapy in Acinetobacter baumannii, since mutations in pmrAB are implicated in colistin resistance. We performed adaptive selection analysis of pmrAB and compared with the available data on colistin resistant strains. We analysed PmrAB sequences in 3113 draft genomes of A. baumannii obtained from RefSeq database. Adaptive selection analysis was performed by two widely used programs namely, HyPhy and PAML. In addition, to examine the reliability of the approach, the same analysis was performed on gyrA of Escherichia coli and Salmonella enterica, since adaptive mutations on gyrA confer quinolone resistance. Mutations that had caused colistin resistance were found to be neither adaptive nor polymorphic, rather they occur at sites that are either under neutral or purifying selection. Strong negative evolutionary selection pressure is also observed at sites throughout both PmrA and PmrB. Sites with high levels of polymorphisms in PmrAB were found to be under neutral selection. Notably, there was no sign of positive selection. Some of them are rather deleterious. These conditions might be maintaining the incidence of colistin resistance in A. baumannii under check. Therefore, in the context of colistin resistance, natural selection plays only a minor role and we assert that in future, A. baumannii may not be able to sustain and successfully disseminate colistin resistance. Therefore, at present the concerns raised about continuing the usage of colistin for the treatment against A. baumannii infections appears to be unnecessary.
A winner in the Anthropocene: changing host plant distribution explains geographic range expansion in the gulf fritillary butterfly
Authors: Halsch Christopher A. , Shapiro Arthur M. , Thorne James H. , Waetjen David P. , Forister Matthew L. 
Published: August 2019

AbstractThe changing climate is altering the geographic distributions of species around the world with consequences for population dynamics, resulting in winners and losers in the Anthropocene.Agraulis vanillae, the gulf fritillary butterfly, has expanded its range in the past one hundred years in the western United States. We combine time series analysis with species distribution modeling to investigate factors limiting the distribution ofA. vanillaeand to predict future shifts under warming scenarios.In the western US, where we have time series and geographic data, urban development has a positive influence (the host plant is an ornamental in gardens), being associated with year of colonization. Colonization was also associated to a lesser extent with winter maximum temperatures, while a negative impact of minimum temperatures and precipitation was apparent on population growth rates.Across the country, the butterfly is primarily limited by host availability and positively affected by human presence. Perhaps counter-intuitively for a largely tropical ectotherm, current effects of a warming climate (in the years post-colonization) are either negative (on population growth rate) or indirect, likely mediated through availability of areas that can support the host.Under future climate scenarios, conditions are predicted to become more suitable forPassiflorain many urban areas, which would likely result in further expansion ofA. vanillaeduring the dispersive season. These results illustrate the value of combining time series with spatial modeling to understand and predict shifting geographic ranges in the Anthropocene.
Horizontal transmission and recombination maintain forever young bacterial symbiont genomes
Authors: Russell Shelbi L. , Pepper-Tunick Evan , Svedberg Jesper , Byrne Ashley , Castillo Jennie Ruelas , Vollmers Christopher , Beinart Roxanne A. , Corbett-Detig Russ 
Published: August 2019

AbstractBacterial symbionts bring a wealth of functions to the associations they participate in, but by doing so, they endanger the genes and genomes underlying these abilities. When bacterial symbionts become obligately associated with their hosts, their genomes are thought to decay towards an organelle-like fate due to decreased homologous recombination and inefficient selection. However, numerous associations exist that counter these expectations, especially in marine environments, possibly due to ongoing horizontal gene flow. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine chemosynthetic bacterial-bivalve endosymbioses that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory. We found that transmission mode strongly predicts homologous recombination rates, and that exceedingly low recombination rates are associated with moderate genome degradation in the marine symbionts with nearly strict vertical transmission. Nonetheless, even the most degraded marine endosymbiont genomes are occasionally horizontally transmitted and are much larger than their terrestrial insect symbiont counterparts. Therefore, horizontal transmission and recombination enable efficient natural selection to maintain intermediate symbiont genome sizes and substantial functional genetic variation.Author summarySymbiotic associations between bacteria and eukaryotes are ubiquitous in nature and have contributed to the evolution of radically novel phenotypes and niches for the involved partners. New metabolic or physiological capacities that arise in these associations are typically encoded by the bacterial symbiont genomes. However, the association itself endangers the retention of bacterial genomic coding capacity. Endosymbiont genome evolution theory predicts that when bacterial symbionts become restricted to host tissues, their populations cannot remove deleterious mutations efficiently. This ultimately results in their genomes degrading to small, function-poor states, reminiscent of organellar genomes. However, many ancient marine endosymbionts do not fit this prediction, but instead retain relatively large, gene-rich genomes, indicating that the evolutionary dynamics of this process need more thorough characterization. Here we show that on-going symbiont gene flow via horizontal transmission between bivalve hosts and recombination among divergent gammaproteobacterial symbiont lineages are sufficient to maintain large and dynamic bacterial symbiont genomes. These findings indicate that many obligately associated symbiont genomes may not be as isolated from one another as previously assumed and are not on a one way path to degradation.
Are trade‐offs really the key drivers of ageing and life span?
Authors: Cohen Alan A. , Coste Christophe F. D. , Li Xiang‐Yi , Bourg Salomé , Pavard Samuel 
Published: August 2019

Abstract

Current thinking in life‐history theory and the biology of ageing suggests that ageing rates, and consequently life spans, evolve largely as a function of trade‐offs with reproduction. While various evolutionary constraints are generally acknowledged to exist, their potential role in determining ageing rates is rarely considered.

This review integrates three types of information to assess the relative importance of constraints and trade‐offs in shaping ageing rates: (a) empirical work on the presence of intraspecific trade‐offs; (b) theoretical work on factors limiting the force of trade‐offs; and (c) consideration of the biological mechanisms of ageing, as currently understood.

At the empirical level, evidence for intraspecific trade‐offs is mixed, including some surprising failures to observe a trade‐off in model organisms. At the theoretical level, the presence of multiple currencies and nonlinearity can weaken the strength and/or generality of trade‐offs. Additionally, trade‐offs among lower‐level functions, such as between sources of mortality, can create constraints at higher organizational levels, for example such that reductions in reproduction are unable to produce decreases in ageing rate. In terms of ageing mechanisms, some mechanisms, such as the regulation of IGF‐1 and related pathways, seem to agree quite well with trade‐offs as a driving force; however, other mechanisms, such as dysregulation of the vertebrate stress response and stem cell exhaustion, seem more likely to impose constraints than to mediate trade‐offs.

Taken together, these findings suggest that trade‐offs alone are insufficient to understand how ageing rates evolve; instead, both trade‐offs and constraints likely play important roles in shaping evolutionary patterns, with their relative importance varying across taxa. Accordingly, it is time to revisit the broad assumption that survival–reproduction trade‐offs are the key force structuring much of life‐history variation and the evolution of ageing rates.

A free Plain Language Summary can be found within the Supporting Information of this article.
P‐wave complex‐valued traveltimes in homogeneous attenuating transversely isotropic media
Authors: Hao Qi , Waheed Umair bin , Alkhalifah Tariq 
Published: August 2019

ABSTRACTComputation of complex‐valued traveltimes provides an efficient approach to describe the seismic wave attenuation for applications like attenuation tomography, inverse Q filtering and Kirchhoff migration with absorption compensation. Attenuating acoustic transverse isotropy can be used to describe the directional variation of velocity and attenuation of P‐waves in thin‐bedding geological structures. We present an approximate method to solve the acoustic eikonal equation for an attenuating transversely isotropic medium with a vertical symmetry axis. We take into account two similar parameterizations of an attenuating vertical symmetry axis medium. The first parameterization uses the normal moveout velocity, whereas the second parameterization uses the horizontal velocity. For each parameterization, we combine perturbation theory and the Shanks transform in different ways to derive analytic solutions. Numerical examples show that the analytic solutions derived from the second parameterization yield better accuracy. The Shanks transform solution with respect to only the anellipticity parameter from the second parameterization is demonstrated numerically to be the most accurate among all the analytic solutions.
‘Are we there yet?’ Australian HR professionals and the Fourth Industrial Revolution
Authors: Nankervis Alan , Connell Julia , Cameron Roslyn , Montague Alan , Prikshat Verma 
Published: August 2019

Although still in its early stages, the Fourth Industrial Revolution (FIR), which involves a broad range of artificial intelligence, robotics and machine learning technologies, will fundamentally change the way many of us work and relate to one another. Driven by technology, this transformation presents a range of challenges, as well as opportunities, where we might expect Human Resource (HR) professionals would lead the way. However, little is currently known in relation to how prepared HR professionals in Australia are to ready their organisations for this new era of work and associated resourcing. Consequently, this paper goes some way towards closing that gap. Specifically, the study reported here sets out to explore the levels of preparedness amongst Australian HRM professionals for the impact of the FIR on organisations, workplaces, jobs and skills, as well as on their own professional roles and competencies. The study utilised a sequential mixed methods research design with two phases, the first was qualitative focus groups (n = 5) followed by a quantitative online survey of selected senior HR practitioners (n = 150). The findings indicate that, while most believe that FIR technologies might be useful for their organisations and assist with improving job performance, increasing productivity and making jobs easier for employees, contrarily many did not intend to use them in the foreseeable future. Marginal support was also evident in relation to the potential contributions of FIR technologies to HR process enhancement and overall HR effectiveness. Most respondents were also not impressed with the lack of current Australian government FIR strategies and policies.
Are Earnings Forecasts Informed by Proxy Statement Compensation Disclosures?
Authors: Larocque Stephannie A. , Martin Melissa A. , Walther Beverly R. 
Published: August 2019

ABSTRACTWe investigate the extent to which market participants use compensation payouts released in the DEF 14A proxy statement (DEF14A) to assess future firm performance by examining sell‐side analysts' earnings forecasts. Consistent with prior work, we confirm that CEO compensation unexplained by current observable economic factors is positively associated with future firm performance. We find that both the likelihood that analysts revise their forecasts following release of the DEF14A and the magnitude and direction of analysts' forecast revisions are positively associated with unexplained CEO compensation. These associations are stronger after the SEC required additional compensation‐related disclosures in late 2006 but lower if the firm has weak corporate governance or more precise other information. Analysts' reactions are not complete, however. Analysts' forecast errors measured months after the DEF14A release are associated with past unexplained compensation, especially in the pre‐2006 period and for analysts who do not revise at the DEF14A release. Taken together, our results suggest that compensation payouts released in the DEF14A contain useful forward‐looking information that is recognized by at least some sophisticated market participants and that the increased disclosure regulations assisted market participants in incorporating this information.