bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporary pond loss as a result of pasture abandonment: exploring the social-ecological drivers and consequences on amphibians
Authors: Erős Nándor , Malos Cristian , Horváth Csaba , Hartel Tibor 
Published: September 2019

AbstractAmphibian conservation in farming landscapes should address two challenges. First, to understand the relationship between landuse and amphibian habitat quality and second, to understand and support of the capacity of the local communities to continue those farming practices which supports amphibian friendly habitats. While the first challenge is addressed by several studies, there is virtually no study addressing the socio-economic drivers of landuse change. The major aim of this study to fill this knowledge gap by (i) documenting the temporary pond loss in 10 years in a traditionally managed pasture as a result of land abandonment and (ii) exploring the socio-economic and environmental drivers of abandonment. The results show a dramatic increase of scrub cover in the study area as a result of land abandonment. The formation of temporary ponds was negatively influenced by the increase of scrub cover in the vicinity of ponds. There were no differences between the amphibian species assemblages nor the species richness between the lost- and persisting ponds. The social component of the research highlights possible maladaptive paths in pasture management reinforced by the village depopulation, wrong interpretation of nature protection law by officials, scrub encroachment caused decrease in pasture quality and the demotivation of locals to restart traditional grazing. Conservation efforts in traditional farming landscapes facing land abandonment should (i) target the maximization of the quality of the remaining ponds for amphibians and (ii) should support reviving traditional farming practices within the local community.
A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production
Authors: Fouladiha Hamideh , Marashi Sayed-Amir , Torkashvand Fatemeh , Mahboudi Fereidoun , Lewis Nathan E. , Vaziri Behrouz 
Published: September 2019

AbstractChinese hamster ovary (CHO) cells are the main workhorse in the biopharmaceutical industry for the production of recombinant proteins, such as monoclonal antibodies. To date, a variety of metabolic engineering approaches have been used to improve the productivity of CHO cells. While genetic manipulations are potentially laborious in mammalian cells, rational design of CHO cell culture medium or efficient fed-batch strategies are more popular approaches for bioprocess optimization. In this study, a genome-scale metabolic network model of CHO cells was used to design feeding strategies for CHO cells to improve monoclonal antibody (mAb) production. A number of metabolites, including threonine and arachidonate, were suggested by the model to be added into cell culture medium. The designed composition has been experimentally validated, and then optimized, using design of experiment methods. About a two-fold increase in the total mAb expression has been observed using this strategy. Our approach can be used in similar bioprocess optimization problems, in order to suggest new ways of increasing production in different cell factories.
Eco-ethology and trait distribution of two congeneric species – different strategies for the plague pestAcanthoplus discoidalisand the long-leggedA. longipes(Orthoptera: Tettigoniidae)
Authors: Conti Erminia , Costa Giovanni , Mulder Christian 
Published: September 2019

AbstractHigh trait variability among insects reflects a combination of intra- and inter-phenotype variations. Our aim was to assess if the trait distribution of body measurements can be more significantly influenced by sex (intraspecific variance) or by species (interspecific variance). To achieve this, we collected in Namibia tettigoniids belonging to two congeneric species of armoured ground crickets:Acanthoplus discoidalis(a significant pest in African croplands) and the long-leggedAcanthoplus longipes. We measured in the field the total body length, the maximal pronotal width and length, and the femur and tibia lengths of the hind legs in 106 adults. We also derived the body mass from length and width values of the sampled specimens. No significant differences emerged in the two species by sex. A discriminant analysis clearly shows that at species level the locomotory traits as captured by tibia and femur lengths and the size traits as captured by body and pronotal lengths account for 99% of the total variance and clearly separate this pest from its congeneric species. In essence, it is not primarily the body size that differentiates the two species, but rather the pronotum and hind leg larger sizes ofA. longipes. Different eco-ethological requirements, like the peculiarity of the calling song and the movements within the vegetation (and the consequently needed energy), independently force these functional traits.
KIT ligand protects against both light-induced and genetic photoreceptor degeneration
Authors: Li Huirong , Lian Lili , Liu Bo , Chen Yu , Yang Jinglei , Jian Shuhui , Zhou Jiajia , Xu Ying , Ma Xiaoyin , Qu Jia , Hou Ling 
Published: September 2019

AbstractPhotoreceptor cell degeneration is a major cause of blindness and a considerable health burden during aging but effective therapeutic or preventive strategies have not so far become commercially available. Here we show in mouse models that signaling through the tyrosine kinase receptor KIT protects photoreceptor cells against both light-induced and inherited retinal degeneration. Upon light damage, photoreceptor cells upregulate Kit ligand (KITL) and activate KIT signaling, which in turn induces nuclear accumulation of the transcription factor NRF2 and stimulates the expression of the antioxidant geneHmox1. Conversely, a viableKitmutation promotes light-induced photoreceptor damage, which is reversed by experimental expression ofHmox1. Furthermore, overexpression of KITL from a viral AAV8 vector prevents photoreceptor cell death and partially restores retinal function after light damage or in genetic models of human retinitis pigmentosa. Hence, application of KITL may provide a novel therapeutic avenue for prevention or treatment of retinal degenerative diseases.
Bayesian analysis of GWAS summary data reveals differential signatures of natural selection across human complex traits and functional genomic categories
Authors: Zeng Jian , Xue Angli , Jiang Longda , Lloyd-Jones Luke R , Wu Yang , Wang Huanwei , Zheng Zhili , Yengo Loic , Kemper Kathryn E , Goddard Michael E , Wray Naomi R , Visscher Peter M , Yang Jian 
Published: September 2019

AbstractUnderstanding how natural selection has shaped the genetic architecture of complex traits and diseases is of importance in medical and evolutionary genetics. Bayesian methods have been developed using individual-level data to estimate multiple features of genetic architecture, including signatures of natural selection. Here, we present an enhanced method (SBayesS) that only requires GWAS summary statistics and incorporates functional genomic annotations. We analysed GWAS data with large sample sizes for 155 complex traits and detected pervasive signatures of negative selection with diverse estimates of SNP-based heritability and polygenicity. Projecting these estimates onto a map of genetic architecture obtained from evolutionary simulations revealed relatively strong natural selection on genetic variants associated with cardiorespiratory and cognitive traits and relatively small number of mutational targets for diseases. Averaging across traits, the joint distribution of SNP effect size and MAF varied across functional genomic regions (likely to be a consequence of natural selection), with enrichment in both the number of associated variants and the magnitude of effect sizes in regions such as transcriptional start sites, coding regions and 5’- and 3’-UTRs.
Derivation of endometrial gland organoids from term post-partum placenta
Authors: Marinić Mirna , Lynch Vincent J. 
Published: September 2019

ABSTRACTA major limitation of recently developed methods for the generation of endometrial gland organoids is their reliance on decidua isolated from endometrial biopsies or elective termination of pregnancies. Here we report the successful establishment of endometrial gland organoids from decidua isolated from term placental membranes, as well as the identification of potential survival factors for the co-culture of gland organoids and endometrial stromal fibroblasts. These modifications facilitate the generation of patient-specific endometrial gland organoids with known pregnancy outcomes, such as term vs. preterm birth.
Gray whale transcriptome reveals longevity adaptations associated with DNA repair and ubiquitination
Authors: Toren Dmitri , Kulaga Anton , Jethva Mineshbhai , Rubin Eitan , Snezhkina Anastasia V , Kudryavtseva Anna V , Nowicki Dmitry , Tacutu Robi , Moskalev Alexey A , Fraifeld Vadim E 
Published: September 2019

AbstractOne important question in aging research is how differences in genomics and transcriptomics determine the maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in non-model organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking-based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that of other long- and short-lived mammals. Gray whales are among the top 1% longest-lived mammals. Despite the extreme environment, or maybe due to a remarkable adaptation to its habitat (intermittent hypoxia, Arctic water, and high pressure), gray whales reach at least the age of 77 years. In this work, we show that long-lived mammals share common gene expression patterns between themselves, including high expression of DNA maintenance and repair, ubiquitination, apoptosis, and immune responses. Additionally, the level of expression for gray whale orthologs of pro- and anti-longevity genes found in model organisms is in support of their alleged role and direction in lifespan determination. Remarkably, among highly expressed pro-longevity genes many are stress-related, reflecting an adaptation to extreme environmental conditions. The conducted analysis suggests that the gray whale potentially possesses high resistance to cancer and stress, at least in part ensuring its longevity. This new transcriptome assembly also provides important resources to support the efforts of maintaining the endangered population of gray whales.
Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining
Authors: Suárez Gabriel A. , Dugan Kyle R. , Renda Brian A. , Leonard Sean P. , Gangavarapu Lakshmi S. , Barrick Jeffrey E. 
Published: September 2019

ABSTRACTOne goal of synthetic biology is to improve the efficiency and predictability of living cells by removing extraneous genes from their genomes. We demonstrate improved methods for engineering the genome of the metabolically versatile and naturally transformable bacterium Acinetobacter baylyi ADP1 and apply them to a genome streamlining project. In Golden Transformation, linear DNA fragments constructed by Golden Gate Assembly are directly added to cells to create targeted deletions, edits, or additions to the chromosome. We tested the dispensability of 55 regions of the ADP1 chromosome using Golden Transformation. The 19 successful multiple-gene deletions ranged in size from 21 to 183 kilobases and collectively accounted for 24.6% of its genome. Deletion success could only be partially predicted on the basis of a single-gene knockout strain collection and a new Tn-Seq experiment. We further show that ADP1’s native CRISPR/Cas locus is active and can be retargeted using Golden Transformation. We reprogrammed it to create a CRISPR-Lock, which validates that a gene has been successfully removed from the chromosome and prevents it from being reacquired. These methods can be used together to implement combinatorial routes to further genome streamlining and for more rapid and assured metabolic engineering of this versatile chassis organism.
Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Authors: Samuels Tamsin J. , Järvelin Aino I. , Ish-Horowicz David , Davis Ilan 
Published: September 2019

ABSTRACTThe numerous neurons and glia that form the brain originate from tightly controlled growth and division of neural stem cells, regulated systemically by known extrinsic signals. However, the intrinsic mechanisms that control the characteristic proliferation rates of individual neural stem cells are unknown. Here, we show that the size and division rates of Drosophila neural stem cells (neuroblasts) are controlled by the highly conserved RNA binding protein Imp (IGF2BP), via one of its top binding targets in the brain, myc mRNA. We show that Imp stabilises myc mRNA leading to increased Myc protein levels, larger neuroblasts, and faster division rates. Declining Imp levels throughout development limit myc mRNA stability to restrain neuroblast growth and division, while heterogeneous Imp expression correlates with myc mRNA stability between individual neuroblasts in the brain. We propose that Imp-dependent regulation of myc mRNA stability fine-tunes individual neural stem cell proliferation rates.Abstract Figure
Life history genomic regions explain differences in Atlantic salmon marine diet specialization
Authors: Aykanat Tutku , Rasmussen Martin , Ozerov Mikhail , Niemelä Eero , Paulin Lars , Vähä Juha-Pekka , Hindar Kjetil , Wennevik Vidar , Pedersen Torstein , Svenning Martin-A. , Primmer Craig R. 
Published: September 2019

AbstractAnimals employ various foraging strategies along their ontogeny to acquire energy, and with varying degree of efficiencies, to support growth, maturation and subsequent reproduction events. Individuals that can efficiently acquire energy early are more likely to mature at an earlier age, as a result of faster energy gain which can fuel maturation and reproduction.We aimed to test the hypothesis that heritable resource acquisition variation that co-varies with efficiency along the ontogeny would influence maturation timing of individuals.To test this hypothesis, we utilized Atlantic salmon as a model which exhibit a simple, hence trackable, genetic control of maturation age. We then monitored the variation in diet acquisition (quantified as the stomach fullness and composition) of individuals with different ages, and linked it genomic regions (haploblocks) that were previously identified to be associated with age-at-maturity.Consistent with the hypothesis, we demonstrated that one of the life history genomic regions tested (six6) was indeed associated with age-dependent differences in stomach fullness. Prey composition was marginally linked to both genomic regions (six6andvgll3). We further showed Atlantic salmon switched to the so-called “feast and famine” strategy along the ontogeny, where older age groups exhibited heavier stomach content, but that came at the expense of running on empty more often.These results suggest genetic variation underlying resource utilization variation may explain the genetic basis of age structure in Atlantic salmon. Given that ontogenetic diet has a genetic component and the strong spatial diversity associated with these genomic regions, we predict populations with diverse maturation age will have diverse evolutionary responses to future changes in marine food-web structures.
Architecture of the Mto1/2 microtubule nucleation complex
Authors: Thakur Harish C. , Lynch Eric M. , Borek Weronika E. , Bao Xun X. , Ashraf Sanju , Zou Juan , Rappsilber Juri , Cook Atlanta G. , Sawin Kenneth E. 
Published: September 2019

ABSTRACTProteins that contain a Centrosomin Motif 1 (CM1) domain are key regulators ofγ-tubulin complex-dependent microtubule nucleation, but how they are organized in higher-order structures is largely unknown. Mto1[bonsai], a truncated functional version of theSchizosaccharomyces pombeCM1 protein Mto1, interacts with Mto2 to form an Mto1/2[bonsai] complexin vivo. Here we show that recombinant Mto1/2[bonsai] forms higher-order multimersin vitroand that Mto2 alone can also multimerize. We demonstrate that Mto2 multimerization involves two separate homodimerization domains, the near N-terminal domain (NND) and the twin-cysteine domain (TCD). The TCD crystal structure reveals a stable homodimer with a novel dimerization interface. While the NND homodimer is intrinsically less stable, using crosslinking mass spectrometry we show that within Mto1/2[bonsai] complexes, it can be reinforced by additional cooperative interactions involving both Mto2 and Mto1[bonsai]. We propose a model for Mto1/2[bonsai] complex architecture that is supported by functional analysis of mutantsin vivo.
Tree aboveground biomass and species richness of the mature tropical forests of Darien, Panama, and their role in global climate change mitigation and biodiversity conservation
Authors: Mateo‐Vega Javier , Arroyo‐Mora J. Pablo , Potvin Catherine 
Published: September 2019

AbstractThe remote forests of the Darien region in eastern Panama are among the last remnants of relatively undisturbed forest habitat in the Central American isthmus. Despite decades of efforts by the government, nongovernmental organizations, and civil society, including Indigenous peoples, to protect the region's natural heritage, it remains under significant threat due to widespread illegal logging. Now, the Panamanian government is considering the mechanism, Reducing Emissions from Deforestation and Forest Degradation (REDD+), as another option to limit forest loss. Central to the proper functioning of REDD+ is the need to reduce uncertainties in estimates of aboveground biomass (AGB). These estimates are used to establish realistic reference levels against which additional contributions to reducing carbon dioxide emissions from the loss and degradation of forests can be financially compensated. Also, highly desirable to REDD+ is the achievement of biodiversity cobenefits. REDD+ investments will likely be directed primarily to areas where the potential to simultaneously mitigate climate change and conserve biodiversity is highest. Here, we present the results of a field‐based forest carbon inventorying method tested in Darien's mature forests with the participation of Embera and Wounaan Indigenous peoples. We also explore whether variations in field‐based estimates of AGB across mature forests, in both undisturbed and disturbed areas, are detectable through free and readily‐available remote sensing data sources. Furthermore, we examine and compare AGB and tree species richness in Darien with other well‐studied forest sites across the tropics. Our findings reveal that Darien's forests play a crucial role globally and regionally in storing carbon and housing biodiversity, and support the imperative need to protect these forests in a culturally appropriate manner with the region's Indigenous peoples.
Relationships between coarse woody debris habitat quality and forest maturity attributes
Authors: van Galen Laura G. , Jordan Gregory J. , Baker Susan C. 
Published: September 2019

AbstractCoarse woody debris (CWD) is an important contributor to forest biodiversity because it provides essential habitat for saproxylic (dead wood‐dependent) species. However, CWD is frequently overlooked in forest management and restoration decisions around the world. We have therefore developed an index of CWD habitat quality that integrates four important characteristics of saproxylic habitat. We apply this index to wet eucalypt forests in Tasmania, Australia. The relationships between the CWD index and standing forest structural and floristic maturity metrics were weak (R2< .09), highlighting the necessity to explicitly factor CWD habitat into conservation planning. A hump‐shaped relationship between current CWD habitat quality and variables linked to future quality (standing tree basal area and the number of old‐growth eucalypts) implies that stands with medium current quality provide better potential future habitat than stands with high current quality. CWD habitat quality was lower in previously harvested stands. We present a web app that calculates CWD habitat quality scores from raw field measurements. Our approach can be applied in conservation assessments to determine habitat availability for biodiversity, and to quantify the impacts of management actions and restoration activities.
The on‐ground feasibility of a waterless barrier to stop the spread of invasive cane toads in Western Australia
Authors: Gregg Emily A. , Tingley Reid , Phillips Benjamin L. 
Published: September 2019

AbstractModeling suggests that excluding invasive cane toads from artificial water points (e.g., pastoral dams) along an arid coastal corridor in Western Australia would create a “waterless barrier” halting their spread. In this study, we explored one critical assumption of these models: that toads cannot persist in the corridor during the dry season without access to artificial water points. We explicitly tested this assumption by translocating and radio‐tracking 78 male cane toads in the proposed barrier region during the dry season. Telemetered toads moved substantial distances (maximum distance >2.5 km/night) and were adept at finding shelter. Nonetheless, toads experienced high water loss rates (1.89%/hr) and rapid mortality in both desert (mean ± SD = 43.6 hr ±1.4) and coastal (24.5 hr ±1.2) habitats. Survival analysis suggested that toads could survive a maximum of 5 days without access to surface water and would move a maximum of 5.35 km in this time. Our results confirm that artificial water points are a critical resource for toads in the proposed barrier region and provide further evidence that the waterless barrier could successfully halt toad expansion in Western Australia.
Of cowboys, fish, and pangolins: US trade in exotic leather
Authors: Heinrich Sarah , Ross Joshua V. , Cassey Phill 
Published: September 2019

AbstractIllegal wildlife trade is a lucrative business, which is driving many species towards extinction. Pangolins (Manis spp.) and arapaimas (Arapaima spp.) are two CITES listed genera coveted in the leather fashion industry for their unique skin pattern. The US has contributed to the decline of pangolin species and was historically a large market for pangolin leather products. While the US trade in pangolin products has declined since 2000, we suspect that pangolin leather may now be substituted by arapaima products. Arapaima leather trade has increased significantly since the year 2011. We found a strong positive correlation between the US states trading in both arapaima and pangolin leather products. The US states that were most involved in this trade had a lower population density and were comparatively wealthier than others. Leather items of both arapaima and pangolin were found for sale on eBay, with 75% of incidents in breach of eBay policy, and potentially illegal. Pangolin leather products were also falsely advertised as arapaima products. We conclude that arapaima leather is increasingly used to satisfy the persisting demand for exotic leather, and further research is urgently needed to determine the effect of the trade on wild arapaima populations.