bluuebunny/crossref_metadata_2025_split huggingface dataset:
Right place, right time: Environmental sensing and signal transduction directs cellular differentiation and motility in Trypanosoma brucei
Authors: Walsh Breanna , Hill Kent L. 
Published: January 2021

AbstractTrypanosoma brucei and other African trypanosomes are vector‐borne parasites that cause substantial human suffering across sub‐Saharan Africa. The T. brucei life cycle is punctuated by numerous developmental stages, each occurring in a specific environmental niche and characterized by a unique morphology, metabolism, surface protein coat, and gene expression profile. The environmental cues and signaling pathways that drive transitions between these stages remain incompletely understood. Recent studies have started to fill this gap in knowledge. Likewise, several new studies have expanded our understanding of parasite movement through specific tissues and the parasite's ability to alter movement in response to external cues. Life cycle stage differentiation and motility are intimately integrated phenomena, as parasites must be at the right place (i.e., within a specific environmental milieu) at the right time (i.e., when they are appropriately staged and preadapted for perceiving and responding to signals) in order to complete their life cycle. In this review, we highlight some of the recent work that has transformed our understanding of signaling events that control parasite differentiation and motility. Increased knowledge of T. brucei environmental sensing and signal transduction advances our understanding of parasite biology and may direct prospective chemotherapeutic and transmission blockade strategies that are critical to eradication efforts.
Occurrence of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) off the Wild Coast of South Africa using photographic identification
Authors: Caputo Michelle , Bouveroux Thibaut , Froneman Pierre William , Shaanika Titus , Plön Stephanie 
Published: January 2021

AbstractThe present study represents the first reported boat‐based photographic identification study of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) off the Wild Coast of southeast South Africa. This area is known for the annual sardine run, which attracts apex predators to the region during the austral winter. Dedicated photo‐identification surveys were conducted along this coast at three different study sites in February, June, and November of each year from 2014 to 2016. During 47 surveys, 136 bottlenose dolphin groups were encountered, an estimated 4,474 dolphins observed, and 2,149 individuals were identified. Although most individuals (N = 1,770, 82.4%) were only observed once, some were resighted 2–7 times (N = 379, 17.6%), with an average of 305 days (range: 88–705 days) between resightings. The majority of bottlenose dolphins were resighted within the same study site (N = 192), indicating some degree of residency. However, 65 individuals were observed at two different study sites, indicating individual movements along the coast. Our findings contrast earlier suggestions that bottlenose dolphins only use the Wild Coast during the sardine run, as we found large number of animals year‐round with some level of site fidelity. This highlights the importance of the Wild Coast to bottlenose dolphins and provides further information on their status off southeastern South Africa.
A new species of baleen whale (Balaenoptera) from the Gulf of Mexico, with a review of its geographic distribution
Authors: Rosel Patricia E. , Wilcox Lynsey A. , Yamada Tadasu K. , Mullin Keith D. 
Published: January 2021

AbstractBryde's‐like whales are a complex of medium‐sized baleen whales that occur in tropical waters of all three major ocean basins. Currently, a single species of Bryde's whale, Balaenoptera edeni Anderson, 1879, is recognized, with two subspecies, Eden's whale, B. edeni edeni and Bryde's whale, B. edeni brydei (Olsen, 1913), although some authors have recognized these as separate species. Recently, a new, evolutionarily divergent lineage of Bryde's‐like whale was identified based on genetic data and was found to be restricted primarily to the northern Gulf of Mexico (GOMx). Here, we provide the first morphological examination of a complete skull from these whales and identify diagnostic characters that distinguish it from the other medium‐sized baleen whale taxa. In addition, we have increased the number of genetic samples of these Bryde's‐like whales in the GOMx from 23 to 36 individuals, all of which matched the GOMx lineage. A review of Bryde's‐like whale records in the Caribbean and greater Atlantic supports an isolated distribution for this unique lineage, augmenting the genetic and morphological body of evidence supporting the existence of an undescribed species of Balaenoptera from the Gulf of Mexico.
Reconstruction and analysis of a genome‐scale metabolic model for Agrobacterium tumefaciens
Authors: Xu Nan , Yang Qiyuan , Yang Xiaojing , Wang Mingqi , Guo Minliang 
Published: January 2021

AbstractThe plant pathogen Agrobacterium tumefaciens causes crown gall disease and is a widely used tool for generating transgenic plants owing to its virulence. The pathogenic process involves a shift from an independent to a living form within a host plant. However, comprehensive analyses of metabolites, genes, and reactions contributing to this complex process are lacking. To gain new insights about the pathogenicity from the viewpoints of physiology and cellular metabolism, a genome‐scale metabolic model (GSMM) was reconstructed for A. tumefaciens. The model, referred to as iNX1344, contained 1,344 genes, 1,441 reactions, and 1,106 metabolites. It was validated by analyses of in silico cell growth on 39 unique carbon or nitrogen sources and the flux distribution of carbon metabolism. A. tumefaciens metabolic characteristics under three ecological niches were modelled. A high capacity to access and metabolize nutrients is more important for rhizosphere colonization than in the soil, and substantial metabolic changes were detected during the shift from the rhizosphere to tumour environments. Furthermore, by integrating transcriptome data for tumour conditions, significant alterations in central metabolic pathways and secondary metabolite metabolism were identified. Overall, the GSMM and constraint‐based analysis could decode the physiological and metabolic features of A. tumefaciens as well as interspecific interactions with hosts, thereby improving our understanding of host adaptation and infection mechanisms.
Complementary effect of mechanism of multidrug resistance in Trichophyton mentagrophytes isolated from human dermatophytoses of animal origin
Authors: Gnat Sebastian , Łagowski Dominik , Nowakiewicz Aneta , Dyląg Mariusz , Osińska Marcelina 
Published: January 2021

AbstractBackgroundDermatophytoses have gained interest worldwide due to the increased resistance to terbinafine and azoles and difficulty in management of these refractory diseases.ObjectivesIn this study, we identified and analysed Trichophyton mentagrophytes clinical isolates obtained from humans with infections of animal origin.MethodsWe used quantitative real‐time PCR (qRT‐PCR) to examine the transcriptional modulation of three MDR genes (PDR1, MDR2 and MDR4) and analysed squalene epoxidase (SQLE) gene sequences from multidrug‐resistant Trichophyton mentagrophytes isolates.ResultsThe expression profile revealed a 2‐ to 12‐fold increase in mRNA accumulation in the presence of any of the antifungals, compared to cells incubated without drugs. A statistically significant relationship between the isolates exposed to itraconazole and increased expression of the tested genes was revealed. Substantially lower transcription levels were noted for cells exposed to luliconazole, that is, a third‐generation azole. Additionally, in the case of 50% of terbinafine‐resistant strains, Leu397Phe substitution in the SQLE gene was detected. Furthermore, the reduced susceptibility to itraconazole and voriconazole was overcome by milbemycin oxime.ConclusionsIn conclusion, our study shed more light on the role of the ABC transporter family in T. mentagrophytes, which, if overexpressed, can confer resistance to single azole drugs and even cross‐resistance. Finally, milbemycin oxime could be an interesting compound supporting treatment with azole drugs in the case of refractory dermatomycoses.
Zionism and Québécois nationalism: An initial comparative analysis
Authors: Daniel Rémi 
Published: January 2021

AbstractBased on several studies on each of these movements and on primary sources, I claim that Zionism and Québécois nationalism have a unique set of similarities. The first part of this article focuses on the redefinition of national identity made by both movements—the end of a religious‐ethnic identity and a new focus on language and territory—and on its various consequences. In the second part, I compare Zionists' and Québécois nationalists' arguments for sovereignty, demonstrating their similarities, with a shared wish to become a majority, a common fear from assimilation, the same aspiration towards normality, and the same claim that national independence will bring with it a new era of progress. By doing so, I point to possible directions of more thorough comparative analyses bringing these two movements together.
Waved and unwaved flags: Nation and sexuality in a social media debate in Cyprus
Authors: Kadianaki Irini , Figgou Lia , Kyprianou Marina 
Published: January 2021

AbstractThis article focuses on the ways in which LGBT+ flag raising in a university at the Republic of Cyprus was debated in a social media environment. It aims to examine the ways in which discourses around sexuality intersect with discourses around the nation in a postcolonial, ethnically divided, European context. One hundred four comments posted on the university Facebook page were analysed through Thematic and Rhetorical analysis. Analysis revealed three main ways of accounting for the flag incident in which sexuality and LGBT+ issues are represented as (a) inferior to national issues, (b) symbolic and/or tangible threat to the nation and (c) personal (instead of collective) identity that should not be waved in public. The discussion focuses on the ways in which the findings differentiate from literature on homonationalism and on their implications for constructing collectiveness and understanding citizenship.
Mechanisms underlying the promotion of 5‐hydroxytryptamine secretion in enterochromaffin cells of constipation mice by Bifidobacterium and Lactobacillus
Authors: Lu Youyou , Zhang Zhe , Tong Lingjun , Zhou Xiaohong , Liang Xi , Yi Huaxi , Gong Pimin , Liu Tongjie , Zhang Lanwei , Yang Liuqing , Shi Hanping 
Published: January 2021

AbstractBackground5‐Hydroxytryptamine (5‐HT) could play a role in alleviating symptoms in constipation. However, the mechanism underlying the role of intestinal flora in the promotion of 5‐HT secretion by enterochromaffin cells (ECs) and regulation of the gastrointestinal endocrine system remains unclear.MethodsA constipation mouse model was constructed, and the 5‐HT, chromogranin A (CGA), substance P (SP), motilin (MTL), dopamine, and noradrenaline expression levels were measured using enzyme‐linked immunosorbent assay(Elisa) and immunofluorescence, and key proteins, such as the transient receptor potential (TRP) ion channels/tryptophan hydroxylase (TPH) and olfactory receptor (OR), were determined using western blot. Flow cytometry and in vivo imaging were used to observe microbial colonization in the intestinal tracts of mice.Key ResultsBifidobacterium animalis F1‐7 (F1‐7), Lactobacillus paraccasei F34‐3 (F34‐3), and Lactobacillus plantarum FWDG (FWDG) promoted 5‐HT secretion. F1‐7 and F34‐3 induced CGA expression, increased catecholamine secretion, and activated the CGA/α2A adrenoreceptor (ADRα2A) cascade signal in ECs. FWDG increased noradrenaline levels and activated the ADRα2A signal in ECs. SP content increased in F1‐7 and F34‐3, and MTL expression increased in FWDG via the above signal. F1‐7 and F34‐3 downregulated TRPV4 and upregulated TPH, whereas FWDG upregulated OR2A4 for promoting 5‐HT secretion by ECs. Finally, we observed that F1‐7, F34‐3, and FWDG were well colonized in the large intestine.Conclusions and InferencesF1‐7, F34‐3, and FWDG promoted 5‐HT secretion in ECs of constipation mice by activating the CGA/ADRα2A cascade signal and regulating the TRP/TPH–OR pathways.
A blueprint for gene function analysis through Base Editing in the model plant Physcomitrium (Physcomitrella) patens
Authors: Guyon‐Debast Anouchka , Alboresi Alessandro , Terret Zoé , Charlot Florence , Berthier Floriane , Vendrell‐Mir Pol , Casacuberta Josep M. , Veillet Florian , Morosinotto Tomas , Gallois Jean‐Luc , Nogué Fabien 
Published: January 2021

Summary

CRISPR‐Cas9 has proven to be highly valuable for genome editing in plants, including the model plant Physcomitrium patens. However, the fact that most of the editing events produced using the native Cas9 nuclease correspond to small insertions and deletions is a limitation.

CRISPR‐Cas9 base editors enable targeted mutation of single nucleotides in eukaryotic genomes and therefore overcome this limitation. Here, we report two programmable base‐editing systems to induce precise cytosine or adenine conversions in P. patens.

Using cytosine or adenine base editors, site‐specific single‐base mutations can be achieved with an efficiency up to 55%, without off‐target mutations. Using the APT gene as a reporter of editing, we could show that both base editors can be used in simplex or multiplex, allowing for the production of protein variants with multiple amino‐acid changes. Finally, we set up a co‐editing selection system, named selecting modification of APRT to report gene targeting (SMART), allowing up to 90% efficiency site‐specific base editing in P. patens.

These two base editors will facilitate gene functional analysis in P. patens, allowing for site‐specific editing of a given base through single sgRNA base editing or for in planta evolution of a given gene through the production of randomly mutagenised variants using multiple sgRNA base editing.
Adaptation of Arabidopsis halleri to extreme metal pollution through limited metal accumulation involves changes in cell wall composition and metal homeostasis
Authors: Corso Massimiliano , An Xinhui , Jones Catherine Yvonne , Gonzalez‐Doblas Verónica , Schvartzman M. Sol , Malkowski Eugeniusz , Willats William G. T. , Hanikenne Marc , Verbruggen Nathalie 
Published: January 2021

Summary

Metallophytes constitute powerful models for the study of metal homeostasis, adaptation to extreme environments and the evolution of naturally selected traits. Arabidopsis halleri is a pseudometallophyte which shows constitutive zinc/cadmium (Zn/Cd) tolerance and Zn hyperaccumulation but high intraspecific variability in Cd accumulation.

To examine the molecular basis of the variation in metal tolerance and accumulation, ionome, transcriptome and cell wall glycan array profiles were compared in two genetically close A. halleri populations from metalliferous and nonmetalliferous sites in Northern Italy. The metallicolous population displayed increased tolerance to and reduced hyperaccumulation of Zn, and limited accumulation of Cd, as well as altered metal homeostasis, compared to the nonmetallicolous population. This correlated well with the differential expression of transporter genes involved in trace metal entry and in Cd/Zn vacuolar sequestration in roots. Many cell wall‐related genes were also more highly expressed in roots of the metallicolous population.

Glycan array and histological staining analyses demonstrated that there were major differences between the two populations in terms of the accumulation of specific root pectin and hemicellulose epitopes.

Our results support the idea that both specific cell wall components and regulation of transporter genes play a role in limiting accumulation of metals in A. halleri at contaminated sites.
Dual roles of the serine/arginine‐rich splicing factor SR45a in promoting and interacting with nuclear cap‐binding complex to modulate the salt‐stress response in Arabidopsis
Authors: Li Ying , Guo Qianhuan , Liu Peng , Huang Jinguang , Zhang Shizhong , Yang Guodong , Wu Changai , Zheng Chengchao , Yan Kang 
Published: January 2021

Summary

Alternative splicing (AS) is emerging as a critical co‐transcriptional regulation for plants in response to environmental stresses. Although multiple splicing factors have been linked to the salt‐sensitive signaling network, the molecular mechanism remains unclear.

We discovered that a conserved serine/arginine‐rich (SR)‐like protein, SR45a, as a component of the spliceosome, was involved in post‐transcriptional regulation of salinity tolerance in Arabidopsis thaliana. Furthermore, SR45a was required for the AS and messenger RNA (mRNA) maturation of several salt‐tolerance genes. Two alternatively spliced variants of SR45a were induced by salt stress, full‐length SR45a‐1a and the truncated isoform SR45a‐1b, respectively. Lines with overexpression of SR45a‐1a and SR45a‐1b exhibited hypersensitive to salt stress.

Our data indicated that SR45a directly interacted with the cap‐binding complex (CBC) subunit cap‐binding protein 20 (CBP20) which mediated salt‐stress responses. Instead of binding to other spliceosome components, SR45a‐1b promoted the association of SR45a‐1a with CBP20, therefore mediating salt‐stress signal transduction pathways. Additionally, the mutations in SR45a and CBP20 led to different salt‐stress phenotypes.

Together, these results provide the evidence that SR45a‐CBP20 acts as a regulatory complex to regulate the plant response to salt stress, through a regulatory mechanism to fine‐tune the splicing factors, especially in stressful conditions.
Growth‐regulating factor 5 (GRF5)‐mediated gene regulatory network promotes leaf growth and expansion in poplar
Authors: Wu Wenqi , Li Jiang , Wang Qiao , Lv Kaiwen , Du Kang , Zhang Wenli , Li Quanzi , Kang Xiangyang , Wei Hairong 
Published: January 2021

Summary

Although polyploid plants have larger leaves than their diploid counterparts, the molecular mechanisms underlying this difference (or trait) remain elusive.

Differentially expressed genes (DEGs) between triploid and full‐sib diploid poplar trees were identified from two transcriptomic data sets followed by a gene association study among DEGs to identify key leaf growth regulators. Yeast one‐hybrid system, electrophoretic mobility shift assay, and dual‐luciferase assay were employed to substantiate that PpnGRF5‐1 directly regulated PpnCKX1. The interactions between PpnGRF5‐1 and growth‐regulating factor (GRF)‐interacting factors (GIFs) were experimentally validated and a multilayered hierarchical regulatory network (ML‐hGRN)‐mediated by PpnGRF5‐1 was constructed with top‐down graphic Gaussian model (GGM) algorithm by combining RNA‐sequencing data from its overexpression lines and DAP‐sequencing data.

PpnGRF5‐1 is a negative regulator of PpnCKX1. Overexpression of PpnGRF5‐1 in diploid transgenic lines resulted in larger leaves resembling those of triploids, and significantly increased zeatin and isopentenyladenine in the apical buds and third leaves. PpnGRF5‐1 also interacted with GIFs to increase its regulatory diversity and capacity. An ML‐hGRN‐mediated by PpnGRF5‐1 was obtained and could largely elucidate larger leaves.

PpnGRF5‐1 and the ML‐hGRN‐mediated by PpnGRF5‐1 were underlying the leaf growth and development.
Recent developments in using the molecular decay dating method: a review
Authors: Tintner Johannes 
Published: January 2021

AbstractThe dating of organic findings is a fundamental task for many scientific fields. Radiocarbon dating is currently the most commonly used method. For wood, dendrochronology is another state‐of‐the‐art method. Both methods suffer from systematic restrictions, leading to samples that have not yet been able to be dated. Molecular changes over time are reported for many materials under different preservation conditions. Many of them are intrinsically monotonous. These monotonous molecular decay (MD) patterns can be understood as clocks that start at the time when a given molecule was formed. Factors that influence these clocks include input material composition and preservation conditions. Different wood species, degrees of pyrolysis, and pretreatments lead to different prediction models. Preservation conditions might change the speed of a given clock and lead to different prediction models. Currently published models for predicting the age of wood, paper, and parchment depend on infrared spectroscopy. In contrast to radiocarbon dating, dating via MD does not comprise a single methodology. Some clocks may deliver less precise results than the others. Ultimately, developing a completely different, new dating strategy‐such as MD dating–will help to bring to light a treasure trove of information hidden in the darkness of organic findings.
Perceptions of local community members towards foreign aid: A case study of Vava'u, Tonga
Authors: Haak Edgar , Nakamura Naohiro 
Published: January 2021

AbstractForeign aid has arguably played a significant role in the economic development of the Pacific Island countries. Tonga is deemed to have succeeded in implementing the principles of the Paris Declaration of 2005, especially Ownership, Alignment and Harmonisation, by aid funding channelled through state institutions. Nevertheless, it is still unknown if the aid effect has reached civil society, and how community members perceive aid. This article examines the perceptions of community members towards foreign aid, using the case study of the archipelago of Vava'u, Tonga.
Efficacy of hypermethylated DNA biomarkers in saliva and oral swabs for oral cancer diagnosis: Systematic review and meta‐analysis
Authors: Adeoye John , Alade Azeez Arisekola , Zhu Wang‐yong , Wang Weilan , Choi Siu‐Wai , Thomson Peter 
Published: January 2021

AbstractObjectivesThis study aims to determine the diagnostic test accuracy (DTA) of hypermethylated DNA biomarkers in saliva and oral swabs for oral squamous cell carcinoma (OSCC) detection from the prevalidation studies available.Materials and MethodsElectronic database searching of PubMed, EMBASE, Cochrane Library, Scopus, Web of Science, and LILACS was conducted to identify relevant articles that were published between January 1, 2000, and August 1, 2020.ResultsMeta‐analysis was conducted based on 11 of 20 studies selected for review. Included studies had high bias concerns on the QUADAS‐2 study assessment tool. We found that salivary and oral swab hypermethylation markers had better specificity than sensitivity for oral cancer detection. Summary sensitivity and specificity (95% CI) of hypermethylation panels were 86.2% (60–96.2) and 90.6% (85.9–93.9) while for individual markers, summary sensitivity and specificity (95% CI) were 70% (56.9–80.5) and 91.9% (80.3–96.9), respectively. Respective positive and negative likelihood ratios for combined markers were 9.2 (5.89–14.36) and 0.15 (0.05–0.5), and 8.61 (3.39–21.87) and 0.33 (0.22–0.49) for single‐application biomarkers.ConclusionDNA hypermethylation biomarkers especially in combination have acceptable DTA that warrants further optimization with rigorous biomarker evaluation methods for conclusive determination of their efficacy.