bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial-like nonribosomal peptide synthetases produce cyclopeptides in the zygomycetous fungusMortierella alpina
Authors: Wurlitzer Jacob M. , Stanišić Aleksa , Wasmuth Ina , Jungmann Sandra , Fischer Dagmar , Kries Hajo , Gressler Markus
Published: August 2020

Fungi are traditionally considered as reservoir of biologically active natural products. However, an active secondary metabolism has long not been attributed to early diverging fungi such asMortierella spec. Here, we report on the biosynthesis of two series of cyclic pentapeptides, the malpicyclins and malpibaldins, as products ofMortierella alpinaATCC32222. The molecular structures of malpicyclins were elucidated by HR-MS/MS, Marfey’s method, and 1D and 2D NMR spectroscopy. In addition, malpibaldin biosynthesis was confirmed by HR-MS. Genome mining and comparative qRT-PCR expression analysis pointed at two pentamodular nonribosomal peptide synthetases (NRPS), malpicyclin synthetase MpcA and malpibaldin synthetase MpbA, as candidate biosynthetic enzymes. Heterologous production of the respective adenylation domains and substrate specificity assays proved promiscuous substrate selection and confirmed their respective biosynthetic roles. In stark contrast to known fungal NRPSs, MpbA and MpcA contain bacterial-like dual epimerase/condensation domains allowing the racemization of enzyme-tetheredl-amino acids and the subsequent incorporation ofd-amino acids into the metabolites. Phylogenetic analyses of both NRPS genes indicate a bacterial origin and a horizontal gene transfer into the fungal genome. This is the first report of nonribosomal peptide biosynthesis in basal fungi which highlights this paraphylum as novel and underrated resource of natural products.

IMPORTANCE

Fungal natural compounds are industrially produced with application in antibiotic treatment, cancer medications and crop plant protection. Traditionally, higher fungi have been intensively investigated concerning their metabolic potential, but re-identification of already known compounds is frequently observed. Hence, alternative strategies to acquire novel bioactive molecules are required. We present the genusMortierellaas representative of the early diverging fungi as an underestimated resource of natural products.Mortierella alpinaproduces two families of cyclopeptides, denoted malpicyclins and malpibaldins, respectively, via two pentamodular nonribosomal peptide synthetases (NRPSs). These enzymes are much closer related to bacterial than to other fungal NRPSs, suggesting a bacterial origin of these NRPS genes inMortierella. Both enzymes are the first biochemically characterized natural product biosynthesis enzymes of basal fungi. Hence, this report establishes early diverging fungi as prolific natural compound producers and sheds light on the origin of their biosynthetic capacity.
Impaired cytotoxic CD8+ T cell response in elderly COVID-19 patients
Authors: Westmeier Jaana , Paniskaki Krystallenia , Karaköse Zehra , Werner Tanja , Sutter Kathrin , Dolff Sebastian , Overbeck Marvin , Limmer Andreas , Liu Jia , Zheng Xin , Brenner Thorsten , Berger Marc M. , Witzke Oliver , Trilling Mirko , Lu Mengji , Yang Dongliang , Babel Nina , Westhoff Timm , Dittmer Ulf , Zelinskyy Gennadiy
Published: August 2020

SARS-CoV-2 infection induces a T cell response that most likely contributes to virus control in COVID-19 patients, but may also induce immunopathology. Until now, the cytotoxic T cell response has not been very well characterized in COVID-19 patients.

Here, we analyzed the differentiation and cytotoxic profile of T cells in 30 cases of mild COVID-19 during acute infection. SARS-CoV-2 infection induced a cytotoxic response of CD8+ T cells, but not CD4+ T cells, characterized by the simultaneous production of granzyme A and B, as well as perforin within different effector CD8+ T cell subsets. PD-1 expressing CD8+ T cells also produced cytotoxic molecules during acute infection indicating that they were not functionally exhausted. However, in COVID-19 patients over the age of 80 years the cytotoxic T cell potential was diminished, especially in effector memory and terminally differentiated effector CD8+ cells, showing that elderly patients have impaired cellular immunity against SARS-CoV-2.

Our data provides valuable information about T cell responses in COVID-19 patients that may also have important implications for vaccine development.

Importance

Cytotoxic T cells are responsible for the elimination of infected cells and are key players for the control of viruses. CD8+ T cells with an effector phenotype express cytotoxic molecules and are able to perform target cell killing. COVID-19 patients with a mild disease course were analyzed for the differentiation status and cytotoxic profile of CD8+ T cells. SARS-CoV-2 infection induced a vigorous cytotoxic CD8+ T cell response. However, this cytotoxic profile of T cells was not detected in COVID-19 patients over the age of 80 years. Thus, the absence of a cytotoxic response in elderly patients might be a possible reason for the more frequent severity of COVID-19 in this age group in comparison to younger patients.
Detection of SARS-CoV-2 using non-commercial RT-LAMP reagents and raw samples
Authors: Alekseenko Alisa , Barrett Donal , Pareja-Sanchez Yerma , J Howard Rebecca , Strandback Emilia , Ampah-Korsah Henry , Rovšnik Urška , Zuniga-Veliz Silvia , Klenov Alexander , Malloo Jayshna , Ye Shenglong , Liu Xiyang , Reinius Björn , Elsässer Simon , Nyman Tomas , Sandh Gustaf , Yin Xiushan , Pelechano Vicent
Published: August 2020

Abstract

RT-LAMP detection of SARS-CoV-2 has been shown as a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validated the optimized RT-LAMP assay for the detection of SARS-CoV-2 in raw nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings with limited economic resources.
Adaptive learning under strategic and structural uncertainty: the case of auction games
Authors: Martinez-Saito Mario , Belianin Alexis , Shestakova Anna , Gutkin Boris , Klucharev Vasily
Published: August 2020

In games of incomplete information individual players make decisions facing a combination of structural uncertainty about the underlying parameters of the environment, and strategic uncertainty about the actions undertaken by their partners. How well are human actors able to cope with these uncertainties, and what models best describe their learning in such environments? We use a double auction task with different competitive and informational environments to characterize learning abilities of the single human participants (buyers) in a range of adaptive learning models covering reinforcement learning, directional learning and belief learning. Results show that real behaviour is best described using simple models of directional learning type with minimal knowledge assumptions about information efficiency of prices. This behavior is consistent with bounded rationality and risk aversion: human subjects try to maximize their chance for transaction, and do so using the simplest learning rule.
Dynamic nuclear structure emerges from chromatin crosslinks and motors
Authors: Liu Kuang , Patteson Alison E. , Banigan Edward J. , Schwarz J. M.
Published: August 2020

The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical mechanisms, we develop a model of an active, crosslinked Rouse chain bound to a polymeric shell. System-sized correlated motions occur but require both motor activityandcrosslinks. Contractile motors, in particular, enhance chromosome dynamics by driving anomalous density fluctuations. Nuclear shape fluctuations depend on motor strength, crosslinking, and chromosome-lamina binding. Therefore, complex chromatin dynamics and nuclear shape emerge from a minimal, active chromosome-lamina system.
Oxidative stress inducing agents’ copper and alloxan accelerate cell cycle re-entering of somatic plant cells in the presence of suboptimal exogenous auxin
Authors: Pasternak Taras
Published: August 2020

The physiological status of differentiated somatic plant cells and kinetics of re-entering in cell cycle were investigated in the case of Medicago sativa leaf protoplasts after the application of oxidative stress-inducing agents. Excess copper (30μM) and alloxan (0.5 mM) accelerated cell cycle re-entry at an exogenous auxin concentration that alone was insufficient to induce cell activation. Application of stress-inducing agents accelerated changes in the nuclei landscape with further faster re-entry in DNA replication and cytokinesis. This acceleration was accompanied by a lower level of reactive oxygen species (ROS) accumulations. At later stages, stress-agents treated cells resemble stem cells in planta with a smaller size, higher cell viability, lower ROS level, and lower activities of major ROS scavenging enzymes. A similar cellular response could be achieved by increasing the exogenous auxin concentration. Based on these experimental results, it is suggested that sub-lethal stress treatments evoke a transient cell state that accelerates cellular reprogramming. We also speculate that this transient cell state serves as an effective mechanism for protection against oxidative stress.
A novel 3D atomistic-continuum cancer invasion model: In silico simulations of an in vitro organotypic invasion assay
Authors: Franssen Linnea C. , Sfakianakis Nikolaos , Chaplain Mark A.J.
Published: August 2020

We develop a three-dimensional genuinely hybrid atomistic-continuum model that describes the invasive growth dynamics of individual cancer cells in tissue. The framework explicitly accounts for phenotypic variation by distinguishing between cancer cells of an epithelial-like and a mesenchymal-like phenotype. It also describes mutations between these cell phenotypes in the form ofepithelial-mesenchymal transition(EMT) and its reverse processmesenchymal-epithelial transition(MET). The model consists of a hybrid system of partial and stochastic differential equations that describe the evolution of epithelial-like and mesenchymal-like cancer cells, respectively, under the consideration of matrix-degrading enzyme concentrations and the extracellular matrix density. With the help of inverse parameter estimation and a sensitivity analysis, this three-dimensional model is then calibrated to anin vitroorganotypic invasion assay experiment of oral squamous cell carcinoma cells.
A novel fluorescence and DNA combination for complex, long-term marking of mosquitoes
Authors: Faiman Roy , Krajacich Benjamin J. , Graber Leland , Dao Adama , Yaro Alpha Seydou , Yossi Ousmane , Sanogo Zana Lamissa , Diallo Moussa , Samaké Djibril , Sylla Daman , Coulibaly Modibo , Kone Salif , Goita Sekou , Coulibaly Mamadou B. , Muratova Olga , McCormack Ashley , Gonçalves Bronner P. , Hume Jennifer , Duffy Patrick , Lehmann Tovi
Published: August 2020

Background

Current mark release recapture methodologies are limited in their ability to address complex problems in vector biology, such as studying multiple groups overlapping in space and time. Additionally, limited mark retention, reduced post-marking survival, and the large effort in marking, collection and recapture, all complicate effective insect tracking.

Method

We have developed and evaluated a marking method using a fluorescent dye (Smartwater®) combined with synthetic DNA tags to informatively and efficiently mark adult mosquitoes using an airbrush pump and nebulizer. Using handheld UV flashlights, the fluorescent marking enabled quick and simple initial detection of recaptures in a simple, field-ready, and non-destructive approach that when combined with a simple, extraction-free PCR on individual mosquito legs provides potentially unlimited marking information.

Results

This marking, first tested in the laboratory withAnopheles gambiaes.l. mosquitoes, did not affect survival (median ages 24-28 days,p-adj> 0.25), oviposition (median eggs/female of 28.8, 32.5, 33.3 for water, green, red dyes, respectively,p-adj> 0.44), orPlasmodiumcompetence (mean oocysts 5.56 to 10.6,p-adj> 0.95). DNA and fluorescence had 100% retention up to 3 weeks (longest time point tested) with high intensity, indicating marks would persist longer.

Conclusions

We describe a novel, simple, no/low-impact, and long-lasting marking method that allows separation of multiple insect subpopulations by combining unlimited length and sequence variation in the synthetic DNA tags. This method can be readily deployed in the field for marking multiple groups of mosquitoes or other insects.
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

Anthocyanins 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

A 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

Host 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

Abstract

Background and Aims

Understanding 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.

Methods

A 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.

Results

We 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.

Conclusions

Rotational 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

Reproducibility 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.
Self-generated persistent random forces drive phase separation in growing tumors
Authors: Sinha Sumit , Thirumalai D.
Published: August 2020

A single solid tumor, composed of nearly identical cells, exhibits heterogeneous dynamics. Cells dynamics in the core is glass-like whereas those in the periphery undergo diffusive or super-diffusive behavior. Quantification of heterogeneity using the mean square displacement or the self-intermediate scattering function, which involves averaging over the cell population, hides the complexity of the collective movement. Using the t-distributed stochastic neighbor embedding (t-SNE), a popular unsupervised machine learning dimensionality reduction technique, we show that the phase space structure of an evolving colony of cells, driven by cell division and apoptosis, partitions into nearly disjoint sets composed principally of core and periphery cells. The non-equilibrium phase separation is driven by the differences in the persistence of self-generated active forces induced by cell division. Extensive heterogeneity revealed by t-SNE paves way towards understanding the origins of intratumor heterogeneity using experimental imaging data.
Population Dynamic Regulators In An Empirical Predator-Prey System
Authors: Frank Anna S. , Subbey Sam , Kobras Melanie , Gjøsæter Harald
Published: August 2020

This 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

A 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

Endogenous 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.

We 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

The 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

A 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

ABSTRACTS

Polyketide 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

In 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

1

Successful 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.
Single cell BCR and transcriptome analysis after respiratory virus infection reveals spatiotemporal dynamics of antigen-specific B cell responses
Authors: Mathew Nimitha R. , Jayanthan Jayalal K. , Smirnov Ilya , Robinson Jonathan L. , Axelsson Hannes , Nakka Sravya S. , Emmanouilidi Aikaterini , Czarnewski Paulo , Yewdell William T. , Lebrero-Fernández Cristina , Bernasconi Valentina , Harandi Ali M. , Lycke Nils , Borcherding Nicholas , Yewdell Jonathan W. , Greiff Victor , Bemark Mats , Angeletti Davide
Published: August 2020

B cell responses are a critical component of anti-viral immunity. However, a comprehensive picture of antigen-specific B cell responses, differentiation, clonal proliferation and dynamics in different organs after infection is lacking. Here, we combined single-cell RNA sequencing with single-cell B cell receptor (BCR) characterization of antigen-specific cells in the draining lymph nodes, spleen and lungs after influenza infection. We identify several novel B cell subpopulations forming after infection and find organ-specific differences that persist over the course of the response. We discover important transcriptional differences between memory cells in lungs and lymphoid organs and describe organ-restricted clonal expansion. Strikingly, by combining BCR mutational analysis, monoclonal antibody expression and affinity measurements we find no differences between germinal center (GC)-derived memory and plasmacells, at odds with an affinity-based selection model. By linking antigen-recognition with transcriptional programming, clonal-proliferation and differentiation, these finding provide important advances in our understanding of antiviral B cell immunity.
How to limit the speed of a motor: The intricate regulation of the XPB ATPase and Translocase in TFIIH
Authors: Kappenberger J. , Koelmel W. , Schoenwetter E. , Scheuer T. , Woerner J. , Kuper J. , Kisker C.
Published: August 2020

The superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. In both processes the ATPase activity of XPB is essential. We investigated the interaction network that regulates XPB via the p52 and p8 subunits with functional mutagenesis based on a crystal structure of the full p52/p8 complex and current cryo-EM structures. Importantly, we show that XPB’s ATPase can be activated either by DNA or by the interaction with the p52/p8 proteins. Intriguingly, we observe that the ATPase activation by p52/p8 is significantly weaker than the activation by DNA and when both p52/p8 and DNA are present, p52/p8 dominates the maximum activation. We therefore define p52/p8 as the master regulator of XPB that acts as an activator and speed limiter at the same time. A correlative analysis of the ATPase and translocase activities of XPB shows that XPB only acts as a translocase within the context of complete core TFIIH and that XPA increases the processivity of the translocase complex without altering XPB’s ATPase activity. Our data unravel an intricate network that tightly controls the activity of XPB during transcription and nucleotide excision repair.
The assessment of the appraisal of records: case of the University of the Witwatersrand and the University of Venda
Authors: Netshakhuma Nkholedzeni Sidney
Published: August 2020

Purpose

The purpose of this study was to investigate the state of appraisal with regard to compliance with archives and records management legislations (ARML), the archives and records management policy (ARMP), reappraisal of records, capacity building, archives building and electronic records management (ERM) and to make a recommendation based on the research findings.

Design/methodology/approach

This study was based on the qualitative research technique. The research approach was a multiple case study comparing the previously advantaged and disadvantaged universities in South Africa.

Findings

The study found that ARML, ARMP, reappraisal of records and capacity building are essential for the appraisal of university records. The lack of appropriate appraisal theory/strategy led to a loss of institutional memory.

Research limitations/implications

This research was limited to the University of the Witwatersrand (WITS) and the University of Venda (UNIVEN). These two institutions are representatives of the state of archiving in South Africa.

Practical implications

This research will serve a benchmark for other South African universities, intending to implement systematic disposal of records in compliance with legislations and policies.

Social implications

Failure by universities to appraise records will lead to the loss of institutional memory. This implies that history of institution will be lost if necessary measures are not taken.

Originality/value

There is very little, if any, research on the appraisal of South African universities’ records. The outcome of this research will benefit universities that are seeking to develop and implement appraisal strategies.
Building trust in multi-stakeholder collaborations for new product development in the digital transformation era
Authors: Barrane Fatima Zahra , Ndubisi Nelson Oly , Kamble Sachin , Karuranga Gahima Egide , Poulin Diane
Published: August 2020

Purpose

The study aims to explore the critical approaches adopted by innovative organizations and to build an environment of trust between the multiple stakeholders collaborating for new product development (NPD).

Design/methodology/approach

A qualitative research approach is adopted in this study. Fifteen semi-structured interviews were conducted with experts from the wood product industry in Quebec, Canada. These organizations have successfully adopted the latest technological developments and have developed a strong collaboration with their stakeholders.

Findings

The study identified eleven strategies for the innovative organizations that included early involvement of the stakeholders in the design process, developing long-term relationships and fostering a transparent environment using Industry 4.0 technologies. A novel framework for using this strategy is presented with three stages of application, namely, planning, enactment and review.

Practical implications

Inter-organizational collaborations in NPD are more successful when imbued with trust. The NPD strategies must allow innovative organizations to achieve a balanced ecosystem in which value created through the adaption of new technology can be thoroughly captured through commercialization on time with no field failure.

Originality/value

The study adds to the body of knowledge in stakeholder theory and NPD research and practice.
Reclaiming the heterogeneity of the Arab states
Authors: Almutairi Shihanah , Heller Michael , Yen Dorothy
Published: August 2020

Purpose

This paper addresses the clustering of several Arab states on Hofstede's national culture dimensions and its implications for international firms targeting the Middle East and North African (MENA) region. It is imperative to distinguish the region's various national cultures, in order to enable enhanced segmenting strategies. The authors argue that reexamining the Arab states' national cultures can provide interested firms with a better understanding of their differences and similarities, so as to appropriately adjust their products and services to better serve their consumers.

Design/methodology/approach

Hofstede's Values Survey Module 2013 (VSM 13) questionnaire is employed. In total, 1400 surveys were disseminated to all the Arab states, 200 for each country.

Findings

find evidence that national cultural differences do exist for Arab states and discuss implications toward international firms expanding in the region.

Originality/value

Empirical contributions include the dissemination and translation of Hofstede's national culture survey, the VSM 13, on seven Arab states: Kuwait, the Kingdom of Saudi Arabia (KSA), the United Arab Emirates (UAE), Lebanon, Iraq, Libya and Egypt. Second, the VSM 13 survey measured the Arab states on two more dimensions which had not been previously measured before the present study's investigation. Last, the theoretical contribution of the present study offers empirical evidence that the MENA region's national culture profiles differ on all dimensions, and as such its findings are seen as an extension and validation of Hofstede's national culture theory.
Effects of search, experience and credence attributes versus suggestive brand names on product evaluations
Authors: Gunasti Kunter , Kara Selcan , Ross, Jr William T.
Published: August 2020

Purpose

This research aims to examine how credence, search and experience attributes compete with suggestive brand names that are incongruent with the attributes they cue (e.g. expensive EconoLodge Motel, short-lasting Duracell battery and joint-stiffening JointFlex pill).

Design/methodology/approach

This study relies on experimental studies, together with analyses of variance,t-tests and logistic regressions.

Findings

Incongruent suggestive brand names can distort product evaluations and alter perceptions of product performance in joint product judgments involving contradictory credence attributes; they can misdirect product evaluations even if the search attributes conflict with competitor brands. Furthermore, they are more likely to backfire if contradictory experience attributes are readily available to consumers.

Research limitations/implications

This test of the role of incongruence between suggestive brand names and actual product features includes key concepts that can inform continued studies, such as search attributes that consumers can readily observe, experience attributes that can be observed only after product use and credence attributes that might not be observed even after use.

Practical implications

This study provides applicable guidelines for managers, consumers and policymakers.

Originality/value

The findings expand beyond prior literature that focuses on memory-based, separate evaluations of advertised benefits and inferences or expectations of unavailable attributes. Specifically, this study details the implications of congruence between the suggestive brand names and different types of attributes observable at different consumption stages.