bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing extraction methods and diversity of anthocyanins from purple-fleshed sweet potatoes grown in cooler climates
Authors: Bennett Alexandra A. , Fan Kai , Moghe Gaurav D. 
Published: August 2020

AbstractAnthocyanins are economically valuable phytochemicals of significant relevance to human health. Multiple fruit and vegetable sources for industrial-scale anthocyanin purification exist, however, each source has distinct anthocyanin levels and profiles conferred by modifications to the central anthocyanidin core. In this study, we assessed three purple-fleshed and one orange-fleshed cultivars of sweet potato, with the goal of studying their anthocyanin yield and diversity when this warm-weather crop is grown in cooler, northern latitudes. Comparison of multiple anthocyanin extraction methods revealed acidified ethanol extraction of lyophilized roots as the optimal method, producing a high, average yield of ∼800 mg anthocyanins/100g dry weight. Mass spectrometric analysis of sweet potato extracts identified eighteen high-confidence anthocyanins – all derived from peonidin and cyanidin cores – contributing to over 90% of the total anthocyanin signal. The concentrations of different anthocyanins were variable between the three purple-fleshed cultivars, while low anthocyanin accumulation was observed in the orange-fleshed cultivar. Further assessment of the untargeted high-resolution mass spectrometry data using MS/MS molecular networking revealed existence of low-abundance anthocyanins with delphinidin and pelargonidin cores, as well as over 250 peaks comprising of potential anthocyanins and flavonoids. These results provide a comprehensive insight into anthocyanin yields of purple-fleshed sweet potato grown in the northern latitudes and reveal the large diversity of anthocyanins and flavonoids in this popular crop.
A Non-stop identity complex (NIC) supervises enterocyte identity and protects from pre-mature aging
Authors: Erez Neta , Israitel Lena , Bitman-Lotan Eliya , Wong Wing Hing , Raz Gal , Danial Salwa , Brodsly Na’ama Flint , Belova Elena , Maksimenko Oksana , Georgiev Pavel , Druley Todd , Mohan Ryan , Orian Amir 
Published: August 2020

SummaryA hallmark of aging is the inability of differentiated cells to maintain their identity. In the agedDrosophilamidgut differentiated enterocytes (ECs) lose their identity, and the integrity of the midgut tissue and its homeostasis are impaired. To discover regulators of EC identity relevant to aging we performed an RNAi screen targeting 453 ubiquitin-related genes in fully differentiated ECs. Seventeen genes were identified, including the de-ubiquitinase Non-stop (Not/dUSP22; CG4166). Acute loss of Non-stop in young ECs phenotypically resembled aged ECs. Lineage tracing experiments established that Non-stop-deficient young ECs as well as wild-type aged ECs are no longer differentiated. Aging or acute loss of Non-stop also resulted in progenitor cell hyperproliferation and mis-differentiation, loss of gut integrity, and reduced organismal survival. Proteomic analysis unveiled that Non-stop maintains identity as part of a Non-stop identity complex (NIC) that contains E(y)2, Sgf11, Cp190, (Mod) mdg4, and Nup98. Transcriptionally, Non-stop ensured chromatin accessibility at EC genes, maintained an EC-specific gene expression signature, and silenced non-EC-relevant transcriptional programs. Within the NIC, Non-stop was required for stabilizing of NIC subunits. Upon aging, the levels of Non-stop and NIC subunits declined, and the large-scale organization of the nucleus was distorted. Maintaining youthful levels of Non-stop in wildtype aged ECs safeguarded the protein level of NIC subunits, restored the large-scale organization of the differentiated nucleus, and suppressed aging phenotypes and tissue integrity. Thus, the isopeptidase Non-stop, and NIC, supervise EC identity and protects from premature aging.
Host age shapes virome abundance and diversity in birds
Authors: Wille Michelle , Shi Mang , Hurt Aeron C. , Klaassen Marcel , Holmes Edward C. 
Published: August 2020

AbstractHost age influences the ecology of many microorganisms. This is evident in one-host – one virus systems, such as influenza A virus in Mallards, but also in community studies of parasites and microbiomes. We used a meta-transcriptomic approach to assess whether host age is associated with differences in the abundance and diversity of avian viromes. We used samples from cohabiting Ruddy Turnstones (Arenaria interpres) across three age groups, collected at two contrasting points in their annual migratory cycle. Overall, we identified 14 viruses that likely infect birds, 11 of which were novel, including members of theReoviridae,Astroviridae,Picornaviridae, andPhenuiviridae. Strikingly, 12 of the viruses identified were from juvenile birds sampled in the first year of their life, compared to only two viruses in adult birds. Similarly, both viral abundance and alpha diversity were higher in juvenile than adult birds. Notably, time of sampling had no association with virome structure such that the migratory period may not play a major role in structuring avian viromes. As well as informing studies of virus ecology, that host age impacts viral assemblages is a critical consideration for the future surveillance of novel and emerging viruses.
Intra and inter-annual climatic conditions have stronger effect than grazing intensity on root growth of permanent grasslands
Authors: Picon-Cochard Catherine , Vassal Nathalie , Martin Raphaël , Herfurth Damien , Note Priscilla , Louault Frédérique 
Published: August 2020

AbstractBackground and AimsUnderstanding how direct and indirect changes in climatic conditions, management, and species composition affect root production and root traits is of prime importance for the delivery of carbon sequestration services of grasslands. This study considers the effects of climatic variability and gradients of herbage utilisation by grazing on root production over the course of two years. The root and leaf traits of the plant communities were determined to detect their capacity to predict above- and below-ground net primary production, ANPP and BNPP, respectively.MethodsA long-term field experiment was used to compare the effects of abandonment and low (Ca-) and high (Ca+) grazing intensities (resulting in mean residual plant heights of 15.2 cm and 7.7 cm, respectively) induced by grazing rotations on upland fertile grasslands after 10 years of treatment application. Ingrowth cores and exclusion cages were used to measure, respectively, the root and shoot mass production several times each year and at an annual scale. The root and leaf traits of the communities were measured near the vegetation’s peak growing season.ResultsWe observed strong seasonal root production across treatments in both a wet and a dry year, but the response to grazing intensity was hardly observable within growing seasons. In the abandonment treatment, the spring and autumn root growth peaks were delayed by approximately one month compared to the two cattle treatments, possibly due to a late plant canopy green-up induced by lower soil temperatures and an accumulation of litter. The BNPP was slightly lower in the abandonment treatment compared to the cattle treatments only during the dry year, whereas a decline of the ANPP in the abandonment treatment compared to the Ca+ treatment was observed during the wet year. In response to drought, which occurred during the second year, the root-to-shoot biomass ratio was stable in the cattle treatments but declined in the abandonment treatment. The higher allocation to root mass could benefit plant communities under drier conditions.ConclusionsRotational grazing pressures and climatic condition variabilities had limited effects on root growth seasonality, although drought had stronger effects on the BNPP than on the ANPP. The stability of the root-to-shoot biomass ratio during the dry year evidenced a higher resistance to drought by grazed versus abandoned grassland communities.
Rearing medium dictates variability across replicates in untreated and arsenic challenged zebrafish larvae
Authors: Nair Anjana Ramdas , Delaney Patrice , Ranjan Shashi , Khan Nouf , Palmer Catherine , Sadler Kirsten C. 
Published: August 2020

ABSTRACTReproducibility and consistency are hallmarks of scientific integrity. Biological systems are inherently noisy, posing a challenge to reproducibility. This is particularly relevant to the field of environmental toxicology, where many unaccounted experimental parameters can have a marked influence on the biological response to exposure. Here, we extend the use of zebrafish as a robust toxicological model for studying the effects of inorganic arsenic (iAs) on liver biology. We observed that iAs toxicity in this system is not influenced by important parameters including genetic background, rearing container material or rearing volume but the dose response to iAs is influenced by the rearing medium. We compared mortality as a measure of iAs toxicity to embryos cultured in two standard rearing media: egg water made from dehydrated ocean salts dissolved in water and a defined embryo medium which is a pH adjusted, buffered salt solution. Larvae reared in egg water were more susceptible to iAs compared to those reared in embryo medium. This effect was independent of the pH differences between these solutions. These culture conditions did not cause any difference in the global hepatic transcriptome of control zebrafish. Further, no difference in the expression of genes involved in the unfolded protein response (UPR) in larvae exposed to iAs treatment or in a stress independent system to activate UPR genes by transgenic overexpression of activating transcription factor 6 (nAtf6) in hepatocytes was observed. However, the clutch-to-clutch variation in gene expression was significantly greater in larvae reared in egg water compared to those in embryo medium. These data demonstrate that egg water affects reproducibility across replicates in terms of gene expression and exacerbates iAs mediated toxic response. This highlights the importance of rigorous evaluation of experimental conditions to assure reproducibility.
Population Dynamic Regulators In An Empirical Predator-Prey System
Authors: Frank Anna S. , Subbey Sam , Kobras Melanie , Gjøsæter Harald 
Published: August 2020

ABSTRACTThis paper investigates stability conditions of an empirical predator-prey system using a model that includes a single delay term,τ, in description of the predator dynamics. We derive theoretical conditions onτ, in terms of other model parameters, and determine how changes in these conditions define different stability regimes of the system. We derive optimal model parameters by fitting model to empirical data, using unconstrained optimization. The optimization results are combined with those from the theoretical analysis, to make inference about the empirical system stability.Our results show that Hopf bifurcation occurs in the predatory-prey system whenτexceeds a theoretically derived valueτ* > 0. This value represents the critical time for prey availability in advance of the optimal predator growth period. Set into an ecological context, our findings provide mathematical evidence for validity of the match-mismatch hypothesis, for this particular species.
The Japan Monkey Centre Primates Brain Imaging Repository of high-resolution postmortem magnetic resonance imaging: the second phase of the archive of digital records
Authors: Sakai Tomoko , Hata Junichi , Shintaku Yuta , Ohta Hiroki , Sogabe Kazumi , Mori Susumu , Okano Hirotaka James , Hamada Yuzuru , Hirabayashi Toshiyuki , Minamimoto Takafumi , Sadato Norihiro , Okano Hideyuki , Oishi Kenichi 
Published: August 2020

AbstractA comparison of neuroanatomical features of the brain between humans and our evolutionary relatives, nonhuman primates, is key to understanding the human brain system and the neural basis of mental and neurological disorders. Although most comparative MRI studies of human and nonhuman primate brains have been based on brains of primates that had been used as subjects in experiments, it is essential to investigate various species of nonhuman primates in order to elucidate and interpret the diversity of neuroanatomy features among humans and nonhuman primates. To develop a research platform for this purpose, it is necessary to harmonize the scientific contributions of studies with the standards of animal ethics, animal welfare, and the conservation of brain information for long-term continuation of the field. In previous research, we first developed an open-resource repository of anatomical images obtained using 9.4-Tex vivoMRI of postmortem brain samples from 12 nonhuman primate species, and which are stored at the Japan Monkey Centre. In the present study, as a second phase, we released a collection of T2-weighted images and diffusion tensor images obtained in nine species: white-throated capuchin, Bolivian squirrel monkey, stump-tailed macaque, Tibet monkey, Sykes’ monkey, Assamese macaque, pig-tailed macaque, crested macaque, and chimpanzee. Our image repository should facilitate scientific discoveries in the field of comparative neuroscience. This repository can also promote animal ethics and animal welfare in experiments with nonhuman primate models by optimizing methods forin vivoandex vivoMRI scanning of brains and supporting veterinary neuroradiological education. In addition, the repository is expected to contribute to conservation, preserving information about the brains of various primates, including endangered species, in a permanent digital form.
Evolution and antiviral activity of a human protein of retroviral origin
Authors: Frank John A. , Singh Manvendra , Cullen Harrison B. , Kirou Raphael A. , Benkaddour-Boumzaouad Meriem , Cortes Jose L. , Garcia-Perez Jose , Coyne Carolyn B. , Feschotte Cédric 
Published: August 2020

AbstractEndogenous retroviruses are abundant components of mammalian genomes descended from ancient germline infections. In several mammals, the envelope proteins encoded by these elements protect against exogenous viruses, but this activity has not been documented in human. We report that our genome harbors a large pool of envelope-derived sequences with the potential to restrict retroviral infection. To further test this, we characterize in detail the envelope-derived protein,Suppressyn. We found thatSuppressynis expressed in preimplantation embryos and developing placenta using its ancestral retroviral promoter. Restriction assays in cell culture show thatSuppressyn, and its hominoid orthologs, can restrict infection by extant mammalian type D retroviruses. Our data support a generalizable model of retroviral envelope cooption for host immunity and genome defense.SummaryWe found that the human genome expresses a vast pool of envelope sequences of retroviral origin and provide proof of principle that such proteins can restrict zoonotic viruses.
Anatomical and cellular heterogeneity in the mouse oviduct-- its potential roles in reproduction and preimplantation development
Authors: Harwalkar Keerthana , Ford Matthew J , Teng Katie , Yamanaka Nobuko , Yang Brenna , Burtscher Ingo , Lickert Heiko , Yamanaka Yojiro 
Published: August 2020

ABSTRACTThe oviduct/fallopian tube is a tube-like structure that extends from the uterus to the ovary. It is an essential reproductive tissue that provides an environment for internal fertilization and preimplantation development. However, our knowledge of its regional and cellular heterogeneity is still limited. Here, we examined the anatomical complexity of mouse oviducts using modern imaging techniques and fluorescence reporter lines. We found that there are basic coiling patterns and turning points in the coiled mouse oviduct can serve as reliable landmarks for luminal morphological regionalities. We identified previously unrecognized anatomical structures in the isthmus and uterotubal junction (UTJ) that likely play important roles in reproduction. Interestingly, during ovulation, the isthmus was transiently plugged by a thick mucus, keeping the oocytes within the ampulla. Preimplantation embryos travelled along the oviduct and formed a queue within small compartments of the UTJ before uterine entry. Taken together, the oviduct luminal epithelium had highly diverse luminal structures with distinct cell populations reflecting its complex functions in reproduction.
Population ecology ofTrigoniulus corallinus(Gervais) (Diplopoda: Spirobolida)
Authors: Bhakat S. 
Published: August 2020

AbstractA population ofTrigoniulus corallinus(Gervis) in an open land rich in organic matter is studied for a year. Population density and biomass ranged from 2.13 to 56.31per m2and 1026.38 to 8494.38 per m2respectively. Various indices showed that population ofT. corallinusis aggregated in distribution in the peak period of their abundance and this is due to patchy distribution of food, soil moisture and sexual attraction. Monthly age structure showed adult and late stadia are abundant in June, October and November while August population covered all the stadia.In the developmental stages, length and width progression factor ofT. corallinusranged from 1.11 to 1.98 (mean 1.43) and 1.10 to 1.56 (mean 1.31) respectively. Weight progression factor in female is higher compared to that of male and this may due to more accumulation of egg forming tissue in female. Population density and biomass is significantly correlated with minimum temperature and rainfall.
PKS-A Clade of Oil Palm Might Play Role During Defense AgainstGanoderma boninenseInfection
Authors: Tanjung Zulfikar Achmad , Aditama Redi , Utomo Condro , Liwang Tony , Tryono Reno 
Published: August 2020

ABSTRACTSPolyketide synthase (PKS) is an essential catalyzing enzyme in the polyketide (PK) biosynthesis pathway of bacteria, fungi and plants which have diverse beneficial functions such as antibiotic and antiparasitic. This study was aimed to identify specific plant type III PKSs in the African oil palm,Elaeis guineensis, and predict its biosynthesized metabolites as plant defense compounds against the most threatening fungal pathogen,Ganoderma boninensethat causing the basal stem rot disease. We used the oil palm protein database to detect the presence of type III PKS domains using the HMMER version V3.1b2. An artificial inoculation was made on oil palm root tissues and RNA sequencing was performed to obtain the transcriptome profile after 7 days exposure toG. boninense. Among 40,421 proteins, we identified 38 of which containing type III PKS domains. Signal peptide signature motifs were absence in all PKSs suggesting their intracellular functions during the polyketide biosynthesis. A molecular phylogeny analysis reflected the relationships among these PKSs that clustered into PKS-A, -B and -C clades. Most of the PKS-A members were up-regulated afterG. boninenseinfection, indicating their essential role in the biosynthesis of PK products which might needed for defense.
When and why an essential popular mineral—calcium—is an effective antifungal adjuvant against the human pathogen?
Authors: Zhang Chi , Ren Yiran , Gu Huiyu , Gao Lu , Zhang Yuanwei , Lu Ling 
Published: August 2020

AbstractIn eukaryotes, calcium not only is an essential mineral nutrient but also serves as an intracellular second messenger that is necessary for many physiological processes. Here, we show that exogenous calcium is toxic when fungal cells lack functional calcineurin, a calcium-dependent protein phosphatase that acts as the central regulator of the calcium signaling pathway. By monitoring intracellular calcium, particularly by tracking vacuolar calcium dynamics in living cells through a novel procedure using modified aequorin, we found that calcineurin dysfunction perturbed calcium homeostasis in intracellular compartments including the cytosol, mitochondria, and vacuole, leading to drastic autophagy global organelle fragmentation, and even lastly resulting in cell death upon an extracellular calcium stimulus. Notably, the defective phenotypes seen with calcineurin mutants can be significantly suppressed by alleviating a cytosolic calcium overload or increasing vacuolar calcium storage capacity, suggesting toxicity of exogenous calcium to calcineurin mutants is tightly associated with abnormal cytosolic calcium accumulation and vacuolar calcium storage capacity deficiency. Our findings provide insights into how calcineurin regulates intracellular calcium homeostasis for cell survival and may have important implications for antifungal therapy and clinical drug administration.
Overexpression of the transcription factor GROWTH-REGULATING FACTOR5 improves transformation of dicot and monocot species
Authors: Kong Jixiang , Martín-Ortigosa Susana , Finer John , Orchard Nuananong , Gunadi Andika , Batts Lou Ann , Thakare Dhiraj , Rush Bradford , Schmitz Oliver , Stuiver Maarten , Olhoft Paula , Pacheco-Villalobos David 
Published: August 2020

1AbstractSuccessful regeneration of genetically modified plants from cell culture is highly dependent on the species, genotype, and tissue-type being targeted for transformation. Studies in some plant species have shown that when expression is altered, some genes regulating developmental processes are capable of triggering plant regeneration in a variety of plant cells and tissue-types previously identified as being recalcitrant to regeneration. In the present research, we report that developmental genes encoding GROWTH-REGULATING FACTORS positively enhance regeneration and transformation in both monocot and dicot species. In sugar beet (Beta vulgaris ssp. vulgaris), ectopic expression ofArabidopsis GRF5(AtGRF5) in callus cells accelerates shoot formation and dramatically increases transformation efficiency. More importantly, overexpression ofAtGRF5enables the production of stable transformants in recalcitrant sugar beet varieties. The introduction ofAtGRF5andGRF5orthologs into canola (Brassica napusL.), soybean (Glycine maxL.), and sunflower (Helianthus annuusL.) results in significant increases in genetic transformation of the explant tissue. A positive effect on proliferation of transgenic callus cells in canola was observed upon overexpression ofGRF5genes andAtGRF6andAtGRF9. In soybean and sunflower, the overexpression ofGRF5genes seems to increase the proliferation of transformed cells, promoting transgenic shoot formation. In addition, the transformation of two putativeAtGRF5orthologs in maize (Zea maysL.) significantly boosts transformation efficiency and resulted in fully fertile transgenic plants. Overall, the results suggest that overexpression ofGRFgenes render cells and tissues more competent to regeneration across a wide variety of crop species and regeneration processes. This sets GRFs apart from other developmental regulators and, therefore, they can potentially be applied to improve transformation of monocot and dicot plant species.