bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are fungal strains from salinized streams adapted to salt-rich conditions?
Authors: Gonçalves Ana Lúcia , Carvalho Adriana , Bärlocher Felix , Canhoto Cristina 
Published: December 2018

Anthropogenic salinization of freshwater is a global problem with largely unknown consequences for stream functions. We compared the effects of salt addition (6 g l−1NaCl) in microcosms on leaf mass loss and microbial parameters in single- and multispecies assemblages of fungal strains (Heliscus lugdunensis, HELU;Tetracladium marchalianum, TEMA;Flagellospora curta, FLCU) isolated from a reference (R) or salinized (S) stream. Fungal growth and interactions were also assessed. Salinization inhibited leaf decomposition and fungal biomass, but no differences were observed between species, strains or species combinations. Sporulation rates in monocultures were not affected by added salt, but differed among species (FLCU > HELU > TEMA), with S strains releasing more conidia. Fungal assemblages did not differ significantly in total conidia production (either between strains or medium salt concentration). HELU was the dominant species, which also had highest growth and most pronounced antagonistic behaviour. Fungal species, irrespective of origin, largely maintained their function in salinized streams. Strains from salt-contaminated streams did not trade-off conidial production for vegetative growth at high salt levels. The expected reduction of fungal diversity and potential changes in nutritional litter quality owing to salinization may impact leaf incorporation into secondary production in streams.This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Regulations are needed to protect freshwater ecosystems from salinization
Authors: Schuler Matthew S. , Cañedo-Argüelles Miguel , Hintz William D. , Dyack Brenda , Birk Sebastian , Relyea Rick A. 
Published: December 2018

Anthropogenic activities such as mining, agriculture and industrial wastes have increased the rate of salinization of freshwater ecosystems around the world. Despite the known and probable consequences of freshwater salinization, few consequential regulatory standards and management procedures exist. Current regulations are generally inadequate because they are regionally inconsistent, lack legal consequences and have few ion-specific standards. The lack of ion-specific standards is problematic, because each anthropogenic source of freshwater salinization is associated with a distinct set of ions that can present unique social and economic costs. Additionally, the environmental and toxicological consequences of freshwater salinization are often dependent on the occurrence, concentration and ratios of specific ions. Therefore, to protect fresh waters from continued salinization, discrete, ion-specific management and regulatory strategies should be considered for each source of freshwater salinization, using data from standardized, ion-specific monitoring practices. To develop comprehensive monitoring, regulatory, and management guidelines, we recommend the use of co-adaptive, multi-stakeholder approaches that balance environmental, social, and economic costs and benefits associated with freshwater salinization.
This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Why are mayflies (Ephemeroptera) lost following small increases in salinity? Three conceptual osmophysiological hypotheses
Authors: Kefford Ben J. 
Published: December 2018

The salinity of many freshwaters is increasing globally as a result of human activities. Associated with this increase in salinity are losses of Ephemeroptera (mayfly) abundance and richness. The salinity concentrations at which Ephemeroptera decline in nature are lower than their internal salinity or haemolymph osmolality. Many species also suffer substantial mortality in single species laboratory toxicity tests at salinities lower than their internal salinity. These findings are problematic as conventional osmoregulation theory suggests that freshwater animals should not experience stress where external osmolality is greater than haemolymph osmolality. Here I explore three hypotheses to explain salt sensitivity in Ephemeroptera. These conceptual hypotheses are based on the observations that as the external sodium ion (Na+) concentration increases so does the Na+turnover rate (both uptake and elimination rates increase). Sulphate () uptake in mayflies also increases with increasing externalalthough, unlike Na+, its rate of increase decreases with increasing external. The first hypothesis is premised on ion turnover being energetically costly. The first hypothesis proposes that individuals must devote a greater proportion of their energy to ion homeostasis at the expense of other uses including growth and development. Lethal levels of salinity presumably result from individuals not being able to devote enough energy to maintain ion homeostasis without critical loss of other vital functions. The second hypothesis is premised on the uptake of Na+exchanged for (an outgoing) H+, leading to (localized) loss of pH regulation. The third hypothesis is premised on localized Na+toxicity or poisoning with increased Na turnover as salinity increases. None of the proposed hypotheses is without potential problems, yet all are testable, and research effort should be focused at attempting to falsify them.This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Authors: Estévez Edurne , Rodríguez-Castillo Tamara , González-Ferreras Alexia María , Cañedo-Argüelles Miguel , Barquín José 
Published: December 2018

The salinization of freshwaters is a global water quality problem that leads to the biological degradation of aquatic ecosystems. However, little is known about the spatial extent of freshwater salinization and the relative contribution of each human activity (e.g. agriculture, urbanization, mining or shale-gas extraction). Here, we investigated environmental factors that explain spatio-temporal patterns of water salinity and examined the causes, the extent and the degree of salinization of Spanish rivers. Results showed a strong variation in water salinity among river typologies and between river reaches in good and poor ecological status according to the Water Framework Directive. The variation in water salinity was largely explained by a combination of natural (i.e. climate and geology) and anthropogenic (i.e. land use) factors. By contrast, land use factors as urbanization and agriculture were the main drivers of salinization, which affected more than one quarter of the rivers and streams in Spain, especially those in the most arid regions (central and southern regions) and in the main courses of the largest rivers such as the Ebro, Douro and Tajo rivers. The information provided here can be relevant to set priority regions and actions to ameliorate freshwater salinization.
This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Multiple riparian–stream connections are predicted to change in response to salinization
Authors: Entrekin Sally A. , Clay Natalie A. , Mogilevski Anastasia , Howard-Parker Brooke , Evans-White Michelle A. 
Published: December 2018

Secondary freshwater salinization, a common anthropogenic alteration, has detrimental, lethal and sub-lethal effects on aquatic biota. Ions from secondary salinization can become toxic to terrestrial and aquatic organisms when exposed to salinized runoff that causes periodic high-concentration pulses. Gradual, low-level (less than 1000 ppm salinity) increases in salt concentrations are also commonly documented in regions with urbanization, agriculture, drilling and mining. Despite widespread low-level salt increases, little is known about the biological and ecological consequences in coupled riparian–stream systems. Recent research indicates lethal and even sub-lethal levels of ions can subsidize or stress microbial decomposer and macroinvertebrate detritivores that could lead to alterations of three riparian–stream pathways: (i) salinized runoff that changes microbial decomposer and macroinvertebrate detritivore and algae performance leading to changes in composition and processing of detrital pools; (ii) riparian plant salt uptake and altered litter chemistry, and litterfall for riparian and aquatic detritivores and their subsequent enrichment, stimulating decomposition rates and production of dissolved and fine organic matter; and (iii) salt consumption in salinized soils could increase riparian detritivore growth, decomposition and dissolved organic matter production. Subsidy–stress and reciprocal flows in coupled riparian–stream connections provide frameworks to identify the extent and magnitude of changes in detrital processing from salinization.This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Salinization effects on coastal ecosystems: a terrestrial model ecosystem approach
Authors: Pereira C. S. , Lopes I. , Abrantes I. , Sousa J. P. , Chelinho S. 
Published: December 2018

In coastal areas, intrusion/irrigation with seawater can threaten biodiversity along with crop yields, and the leaching of salts from areas affected by these processes can increase the salinity of water bodies nearby. The aims of this study were to evaluate the effects of salinization on coastal soil ecosystems due to saline intrusion/irrigation. Terrestrial model ecosystems were used to simulate two soil salinization scenarios: (i) seawater intrusion and irrigation with distilled water and (ii) seawater intrusion and irrigation with saline water. Three sampling periods were established: T0—after acclimation period; T1—salinization effects; and T2—populations' recovery. In each sampling period, the abundance of nematodes, enchytraeids, springtails, mites and earthworms, and plant biomass were measured. Immediate negative effects on enchytraeid abundance were detected, especially at the higher level of saltwater via intrusion+irrigation. Eight weeks after the cessation of saline irrigation, the abundance of enchytraeids fully recovered, and some delayed effects were observed in earthworm abundance and plant biomass, especially at the higher soil conductivity level. The observed low capacity of soil to retain salts suggests that, particularly at high soil conductivities, nearby freshwater bodies can also be endangered. Under saline conditions similar to the ones assayed, survival of some soil communities can be threatened, leading to the loss of biodiversity.
This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Challenges and future prospects for developing Ca and Mg water quality guidelines: a meta-analysis
Authors: Bogart Sarah J. , Azizishirazi Ali , Pyle Greg G. 
Published: December 2018

Anthropogenic activities have the potential to increase water hardness (Ca + Mg) in receiving waters to toxic concentrations, and thus, water quality guidelines (WQG) for Ca and Mg are warranted. However, Ca can modify Mg toxicity in Ca-poor water and additional interactions with other major ions (Na+, K+, HCO3−/CO32−, SO42−and Cl−) may occur, potentially obscuring the water hardness–effect relationship. In a meta-analysis of toxicological studies, we: (i) evaluate the performance of three WQG derivation methods, and (ii) determine the influence of several variables (acute/chronic data, anions, Ca:Mg ratios, non-geographically relevant species) on the models. We find that the most sensitive species- or species sensitivity distribution (SSD)-based WQG derivation methods greatly overestimate water hardness toxicity, particularly if non-resident species are included. Broad-scale implementation of most sensitive species- or SSD-based WQG is impractical because water hardness varies beyond and within the regional scale. Anion type does not affect water hardness toxicity across species, but the Ca : Mg ratio is toxicologically relevant, underscoring the importance of considering ion ratios when developing major ion WQG. Although data supporting formal water hardness WQG are unavailable, we suggest using a two-component background condition approach that supports simultaneous management of water hardness and Ca : Mg ratio, and WQG that are applicable beyond the regional scale.This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
Landscape-scale forest loss as a catalyst of population and biodiversity change
Authors: Daskalova Gergana N. , Myers-Smith Isla H. , Bjorkman Anne D. , Blowes Shane A. , Supp Sarah R. , Magurran Anne , Dornelas Maria 
Published: December 2018

AbstractGlobal assessments have highlighted land-use change as a key driver of biodiversity change. However, we lack real-world global-scale estimates of how habitat transformations such as forest loss and gain are reshaping biodiversity over time. Here, we quantify the influence of 150 years of forest cover change on populations and ecological assemblages worldwide and across taxa by analyzing change in 6,667 time series. We found that forest loss simultaneously intensified ongoing increases and decreases in abundance, species richness and temporal species replacement (turnover) by up to 48%. Temporal lags in these responses extended up to 50 years and increased with species’ generation time. Our findings demonstrate that land-use change precipitates divergent population and biodiversity change, highlighting the complex biotic consequences of deforestation and afforestation.One Sentence SummaryDeclines in forest cover amplify both gains and losses in population abundance and biodiversity over time.
MAU2 and NIPBL variants in Cornelia de Lange syndrome reveal MAU2-independent loading of cohesin and uncover a protective mechanism against early truncating mutations in NIPBL
Authors: Parenti Ilaria , Diab Farah , Gil Sara Ruiz , Mulugeta Eskeatnaf , Casa Valentina , Berutti Riccardo , Brouwer Rutger W.W. , Dupé Valerie , Eckhold Juliane , Graf Elisabeth , Puisac Beatriz , Ramos Feliciano , Schwarzmayr Thomas , van Staveren Thomas , van IJcken Wilfred F. J. , Strom Tim M. , Pié Juan , Watrin Erwan , Kaiser Frank J. , Wendt Kerstin S. 
Published: December 2018

ABSTRACTCornelia de Lange syndrome (CdLS) is a rare developmental disorder caused by mutations in genes related to the cohesin complex. For its association with chromatin, cohesin depends on a heterodimer formed by NIPBL and MAU2, which interact via their respective N-termini. Variants in NIPBL are the main cause of CdLS and result in NIPBL haploinsufficiency.Using CRISPR, we generated cells homozygous for an out-of-frame duplication in NIPBL. Remarkably, alternative translation initiation rescued NIPBL expression in these cells and produced an N-terminally truncated NIPBL that lacks MAU2-interaction domain, causing a dramatic reduction of MAU2 protein levels. Strikingly, this protective mechanism allows nearly normal amounts of cohesin to be loaded onto chromatin in a manner that is independent of functional NIPBL/MAU2 complexes and therefore in contrast to previous findings.We also report the first pathogenic variant in MAU2, a deletion of seven amino acids important for wrapping the N-terminus of NIPBL within MAU2. The mutation causes dramatic reduction of MAU2 heterodimerization with NIPBL, hence undermining the stability of both proteins.Our data confirm NIPBL haploinsufficiency as the major pathogenic mechanism of CdLS and give new insights into the molecular mechanisms responsible for this neurodevelopmental disorder. Our work also unveils an alternative translation-based mechanism that protects cells from out-of-frame variants of NIPBL and that may be of relevance in other genetic conditions.
Stress, novel sex genes and epigenetic reprogramming orchestrate socially-controlled sex change
Authors: Todd Erica V , Ortega-Recalde Oscar , Liu Hui , Lamm Melissa S , Rutherford Kim M , Cross Hugh , Black Michael A , Kardailsky Olga , Marshall Graves Jennifer A , Hore Timothy A , Godwin John R , Gemmell Neil J 
Published: December 2018

AbstractBluehead wrasses undergo dramatic, socially-cued female to male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis, that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression, and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.One Sentence SummaryOvary to testis transformation in a sex-changing fish involves transcriptomic and epigenomic reprogramming.
GRIBCG: A software for selection of sgRNAs in the design of balancer chromosomes
Authors: Merritt Brian B. , Cheung Lily S. 
Published: December 2018

AbstractBackgroundBalancer chromosomes are tools used by fruit fly geneticists to prevent meiotic recombination. Recently, CRISPR/Cas9 genome editing has been shown capable of generating inversions similar to the chromosomal rearrangements present in balancer chromosomes. Extending the benefits of balancer chromosomes to other multicellular organisms could significantly accelerate biomedical and plant genetics research.ResultsHere, we present GRIBCG (Guide RNA Identifier for Balancer Chromosome Generation), a tool for the rational design of balancer chromosomes. GRIBCG identifies single guide RNAs (sgRNAs) for use withStreptococcus pyogenesCas9 (SpCas9). These sgRNAs would efficiently cut a chromosome multiple times while minimizing off-target cutting in the rest of the genome. We describe the performance of this tool on six model organisms and compare our results to two routinely used fruit fly balancer chromosomes.ConclusionGRIBCG is the first of its kind tool for the design of balancer chromosomes using CRISPR/Cas9. GRIBCG can accelerate genetics research by providing a fast, systematic and simple to use framework to induce chromosomal rearrangements.
Discovery of Novel Glycerolated Quinazolinones from Streptomyces sp. MBT27
Authors: Machushynets Nataliia , Wu Changsheng , Elsayed Somayah S. , Hankemeier Thomas , van Wezel Gilles P. 
Published: December 2018

AbstractActinobacteria are a major source of novel bioactive natural products. A challenge in the screening of these microorganisms lies in finding the favorable growth conditions for secondary metabolite production and dereplication of known molecules. Here, we report that Streptomyces sp. MBT27 produces 4-quinazolinone alkaloids in response to elevated levels of glycerol, whereby quinazolinones A (1) and B (2) form a new sub-class of this interesting family of natural products. Global Natural Product Social molecular networking (GNPS) resulted in a quinazolinone-related network that included anthranilic acid (3), anthranilamide (4), 4(3H)-quinazolinone (5) and 2,2-dimethyl-1,2-dihydroquinazolin-4(3H)-one (6). Actinomycins D (7) and X2 (8) were also identified in the extracts of Streptomyces sp. MBT27. The induction of quinazolinone production by glycerol combined with biosynthetic insights provide evidence that glycerol is integrated into the chemical scaffold. The unprecedented 1,4-dioxepane ring that is spiro-fused into the quinazolinone backbone, is most likely formed by intermolecular etherification of two units of glycerol. Our work underlines the importance of varying the growth conditions for the discovery of novel natural products and for understanding their biosynthesis.
New perspectives into the evolutionary pressures acting on the Human intrinsically disordered proteins
Authors: Forcelloni Sergio , Giansanti Andrea 
Published: December 2018

AbstractThe codon usage bias is the well-known phenomenon of an unequal use of synonymous codons in coding DNA. These patterns reflect the action of weak selection working at the molecular level and allows to quantify the effects of natural selection, which tend to increase the fitness of the organisms. The prevailing hypothesis to explain the origin of codons usage bias is the selection-mutation-drift theory, according to which it results from a balance between the natural selection favoring optimal codons and combined action of random mutations and genetic drift which allow the persistence of nonoptimal codons. The main focus of this study is to quantify the extent of evolutionary pressures shaping the human genome. We found distinct patterns of mutational bias and natural selection in the human genes, depending on the structural properties of the encoded proteins (e.g. well-structured proteins, proteins with a long disordered segment embedded in a folded structure, or mostly unfolded proteins). Intrinsically disordered proteins are generally thought to evolve more rapidly, largely attributed to relaxed purifying selection due to the lack of structural constraint. Interestingly we observed that mostly unstructured proteins are not only affected by a basic mutational bias as the structured ones but are under a specific selective pressure underlining the important role of these proteins during evolution being freer to accept mutations, both neutral and selective. Our results provide new insight into understanding general laws and unknown aspects of protein evolution and they could be very useful in protein search and design.
UNC-16/JIP3 negatively regulates actin dynamics dependent on DLK-1 and microtubule dynamics independent of DLK-1 in regenerating neurons
Authors: Kulkarni Sucheta S. , Sabharwal Vidur , Sheoran Seema , Basu Atrayee , Matsumoto Kunihiro , Hisamoto Naoki , Ghosh-Roy Anindya , Koushika Sandhya P. 
Published: December 2018

AbstractNeuronal regeneration after injury depends on the intrinsic growth potential of neurons. UNC-16, aC. elegansJIP3 homologue, inhibits axonal regeneration by regulating regrowth initiation and rate of regrowth. UNC-16/JIP3 inhibits the regeneration promoting activity of DLK-1 long but acts additively to and independently of inhibitory DLK-1 short isoform. UNC-16/JIP3 promotes DLK-1 punctate localization in a concentration dependent manner limiting DLK-1 long availability at the cut site minutes after injury. UNC-16 negatively regulates actin dynamics dependent on DLK-1 and microtubule dynamics independent of DLK-1. The faster regeneration seen inunc-16does not lead to functional recovery. We propose a model where UNC-16/JIP3 plays its inhibitory role through tight temporal and spatial control of DLK-1 function. The dual inhibitory control by both UNC-16 and DLK-1 short calibrate the intrinsic growth promoting function of DLK-1 long in vivo.