bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved reference genome annotation of Brassica rapa by PacBio RNA sequencing
Authors: Zhang Zhicheng , Guo Jing , Cai Xu , Li Yufang , Xi Xi , Lin Runmao , Liang Jianli , Wang Xiaowu , Wu Jian 
Published: November 2021

AbstractThe species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the UTR regions of 20,340 annotated genes and corrected 886 wrongly-spliced genes. We also identified 28,564 alternative splicing (AS) events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.
Ionotropic glutamate receptors in the retina – a bioinformatical meta-analysis
Authors: Pircher Bianca , Pircher Thomas , Feigenspan Andreas 
Published: November 2021

ABSTRACTGlutamate is an essential neurotransmitter for signal processing in the vertical pathway of the mammalian retina, where it is involved in the distribution of visual information into several parallel channels. The excitatory effects of glutamate are mediated by AMPA-, kainate-, and NMDA-type ionotropic glutamate receptors (iGluRs). The expression patterns of these receptors in the vertebrate retina have been investigated so far with mainly immunocytochemical, in-situ hybridization, and electrophysiological/pharmacological techniques. Here, we have used scRNA sequencing data from chicken, mouse, macaque, and human retina to describe and compare the profile of iGluR expression in major retinal cell types across species. Our results suggest that major retinal cell types each express a unique set of iGluRs with substantial differences between non-mammalian and mammalian retinae. Expression of iGluRs has been investigated in more detail for amacrine and bipolar cell types of the human retina, each showing minor variations of a common pattern. The differential expression of iGluRs is likely to convey unique signal processing properties to individual elements of the retinal circuitry.
Development and characterization of a high fat diet-streptozotocin induced type 2 diabetes model in nude athymic rats
Authors: Sun Xuetao , Nunes Sara S 
Published: November 2021

AbstractPeople with diabetes mellitus (DM) are at an increased risk for myocardial infarction (MI) than age matched people without DM. However, assays for pre-clinical therapy are performed in animal models of ischemia that lack the co-morbid conditions present in patients with MI, such as DM. This contributes to the failure to translate pre-clinical trials results to the clinic. Thus, to increase the clinical relevance of xenograft studies in pre-clinical models, it is important to have a DM model in animals that are immunodeficient. Here, we developed a type 2 diabetes mellitus (T2D) model in nude athymic rats using high-fat diet and streptozotocin (HFD-STZ). Nude athymic rats were randomized into a control group (normal chow) or a HFD (45% fat, 20% protein and 35% carbohydrate)-STZ group. STZ (35 mg/kg i.v.) or vehicle was administered 8 weeks after HFD feeding started. Assessments were done longitudinally and at week 9 (endpoint). The HFD-STZ group showed mild hyperglycemia pre STZ administration (7.7 ± 0.3 mM vs 5.8 ± 0.2 mM in control) by week 8. In addition, plasma insulin levels were increased and the HOMA index was 2.5-times higher in the HFD-STZ. The HFD-STZ group showed increased fasting (147%) triglycerides. After STZ-administration, blood glucose levels increased substantially (23.6 ± 1.4 mM vs 5.5 ± 0.3 mM in control). The HFD-STZ treated animals also showed increased left ventricular wall thickness, cardiac hypertrophy and fibrosis, reduced cardiac function compared to normal chow control. In line with the HFD-STZ model in immunocompetent rats, the HFD-STZ treatment of athymic rats recapitulates key features of T2D, including aspects of established clinical diabetic cardiomyopathy and should be suitable for xenograft studies in the context of T2D.
Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis
Authors: Buijs Valerie A. , Groenewald Johannes Z. , Haridas Sajeet , LaButti Kurt M. , Lipzen Anna , Martin Francis M. , Barry Kerrie , Grigoriev Igor V. , Crous Pedro W. , Seidl Michael F. 
Published: November 2021

AbstractMembers of the fungal genus Phyllosticta can colonize a variety of plant hosts, including several Citrus species such as Citrus sinensis (orange), Citrus limon (lemon), and Citrus maxima (pomelo). Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. Furthermore, the lifestyle of Phyllosticta citrichinaensis is ambiguous, as it has been described as a weak pathogen but Koch’s postulates may not have been established and the presence of this species was never reported to cause any crop or economic losses. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or endophytes. We also observed that species, based on their carbohydrate active enzymes, group independent of their phylogenetic association, and this clustering correlated with trophy prediction. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. We thus present the first genomic comparison of multiple citrus-colonizing pathogens and endophytes of the genus Phyllosticta, and therefore provide the basis for further comparative studies into the lifestyle adaptations within this genus.
High throughput screening of a new fluorescent G-quadruplex ligand having telomerase inhibitory activity in human A549 cells
Authors: Ghosh Sourav , De Debapriya , Banerjee Victor , Biswas Soumyajit , Ghosh Utpal 
Published: November 2021

AbstractGenome-wide analysis showed that putative G-quadruplex DNA structures are prevalent in the human genome. The presence of G-quadruplex structure in the telomere and promoter region of certain oncogenes inspired people to use G-quadruplex ligand as anti-cancer agents. G-quadruplex structures, stabilized by ligand at telomere are resolved by telomerase making the cancer cells resistant to G-quadruplex ligand. So, identification of a new G-quadruplex ligand having anti-telomerase activity would be a promising strategy for cancer therapy as about 85% of human cancers are telomerase positive. A set of the drug-like compounds were screened from the ZINC database randomly and 2284 ligands were chosen following Lipinski’s rule of five that were docked with five different G-quadruplex DNA sequences in idock. We screened 43 potential G-quadruplex binders using Z-score as a normalization scoring function. The compound (ZINC ID-05220992) gave the best score (average idock = −10.17 kcal/mol, average normalized idock = −3.42). We performed G4 FID assay, CD analysis to understand its binding with three different G-quadruplex DNA sequences, and checked its anti-telomerase activity in A549 cells using TRAP assay. We observed that this compound had an intrinsic fluorescence, capability to stain live cells with a blue fluorescence, and a specific affinity to only 22AG out of three different G-quadruplex DNA sequences under study. It showed cytotoxicity, good permeability to live cells, and a significant reduction of telomerase activity in human A549 cells at a very low dose. So, this compound has strong potential to be an anti-cancer drug.Graphical AbstractHighlightsA set of compounds were screened randomly by a High throughput method and Lipinski’s rule of five from ZINC database to identify potential G4-binders.The compound (ZINC ID-05220992) was screened after docking with five G-quadruplex DNAIt binds G-quadruplex DNA 22AG as detected by TO displacement and CD spectroscopy.It inhibits telomerase activity in A549 cells and also cytotoxic to this cell.It penetrates live A549 cell in culture and stains it with blue fluorescence
Deletion of two genes improves heterologous secretion of fungal lignin-degrading heme peroxidases in S. cerevisiae
Authors: Khlystov Nikita A. 
Published: November 2021

AbstractEfficient, large-scale heterologous production of enzymes is a crucial component of the biomass valorization industry. Whereas cellulose utilization has been successful in applications such as bioethanol, its counterpart lignin remains significantly underutilized despite being an abundant potential source of aromatic commodity chemicals. Fungal lignin-degrading heme peroxidases are thought to be the major agents responsible for lignin depolymerization in nature, but their large-scale production remains inaccessible due to the genetic intractability of basidiomycete fungi and the challenges in the heterologous production of these enzymes. In this study, we employ a strain engineering approach based on functional genomics to identify mutants of the model yeast Saccharomyces cerevisiae with enhanced heterologous production of lignin-degrading heme peroxidases. We show that our screening method coupling an activity-based readout with fluorescence-assisted cell sorting enables identification of two single null mutants of S. cerevisiae, pmt2 and cyt2, with up to 11-fold improved secretion of a versatile peroxidase from the lignin-degrading fungus Pleurotus eryngii. We demonstrate that the double deletion strain pmt2cyt2 displays positive epistasis, improving and even enabling production of members from all three classes of lignin-degrading fungal peroxidases. We anticipate that these mutant strains will be broadly applicable for improved heterologous production of this biotechnologically important class of enzymes.
Leveraging information in spatial transcriptomics to predict super-resolution gene expression from histology images in tumors
Authors: Pang Minxing , Su Kenong , Li Mingyao 
Published: November 2021

ABSTRACTRecent developments in spatial transcriptomics (ST) technologies have enabled the profiling of transcriptome-wide gene expression while retaining the location information of measured genes within tissues. Moreover, the corresponding high-resolution hematoxylin and eosin-stained histology images are readily available for the ST tissue sections. Since histology images are easy to obtain, it is desirable to leverage information learned from ST to predict gene expression for tissue sections where only histology images are available. Here we present HisToGene, a deep learning model for gene expression prediction from histology images. To account for the spatial dependency of measured spots, HisToGene adopts Vision Transformer, a state-of-the-art method for image recognition. The well-trained HisToGene model can also predict super-resolution gene expression. Through evaluations on 32 HER2+ breast cancer samples with 9,612 spots and 785 genes, we show that HisToGene accurately predicts gene expression and outperforms ST-Net both in gene expression prediction and clustering tissue regions using the predicted expression. We further show that the predicted super-resolution gene expression also leads to higher clustering accuracy than observed gene expression. Gene expression predicted from HisToGene enables researchers to generate virtual transcriptomics data at scale and can help elucidate the molecular signatures of tissues.
Inference of Rift Valley Fever pathogenesis in Bos taurus using a gene co-expression network
Authors: Gitau John K. , Macharia Rosaline W. , Mwangi Kennedy W. , Ongeso Nehemiah M. , Murungi Edwin 
Published: November 2021

AbstractBackgroundRift Valley Fever (RVF) is a viral disease caused by the Rift Valley Fever virus and spread mainly by the Aedes and Culex mosquito species. The disease primarily infects domestic animals such as sheep, goats, and cattle, resulting in a spectrum of clinical outcomes including morbidity, massive storm abortions, and neonatal fatalities. RVF outbreaks are closely linked to above-average rainfall and flooding, which create an ideal environment for mosquitos to breed, multiply, and transmit the virus to animals. The outcomes of human RVF infection range from self-limiting febrile illness to potentially fatal hemorrhagic diatheses and miscarriage in pregnant women. Collectively, the economic losses due to the zoonotic RVF disease is immense.MethodsUsing the Weighted Gene Co-expression Network Analysis (WGCNA) package, RNA-Seq data generated from five healthy Bos taurus steer calves aged 4-6 months was obtained from the Gene Expression Omnibus (GEO) database (Accession number GSE71417). The data was utilized to construct a gene co-expression network. Enriched modules containing genes potentially involved in RVF infection progression were identified. Moreover, using the Multiple Expectation Maximizations for Motif Elicitation (MEME) suite, consensus regulatory motifs of enriched gene clusters were deciphered and the most abundant putative regulatory motif in each enriched module unveiled by comparative analysis with publicly available motifs using the TOMTOM motif comparison tool. The potential roles of the identified regulatory motifs were inferred by literature mining.ResultsThe constructed gene co-expression network revealed thirty-three (33) modules, nine of which were enriched for Gene Ontology terms linked to RVF pathogenesis. Functional enrichment in two (red and turquoise) of the nine modules was significant. ASH1-like histone lysine methyltransferase and Astrotactin were the hub genes for the red and turquoise modules respectively. ASH1-like histone lysine methyltransferase gene is involved in chromatin epigenetic modification while Astrotactin is a vertebrate-specific gene that plays an important role in neurodevelopment. Additionally, consensus regulatory motifs located on the 3' end of genes in each enriched module was identified.ConclusionsIn this study, we have developed a gene co-expression network that has aided in the unveiling of functionally related genes, intramodular hub genes, and immunity genes potentially involved in RVF pathogenesis. The discovery of functional genes with putative critical roles in the establishment of RVF infection establishment will contribute to the understanding of the molecular mechanism of RVF pathogenesis. Importantly, the putative regulatory motifs identified are plausible targets for RVF drug and vaccine development.
The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind
Authors: Hintikka Sanni , Carlsson Jeanette E.L. , Carlsson Jens 
Published: November 2021

ABSTRACTEnvironmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies have displayed high levels of nontarget amplification. To date, enrichment methods bypassing amplification have not been able to match the detection levels of conventional metabarcoding. This study evaluated the use of universal metabarcoding primers as capture probes to either isolate target DNA or to remove nontarget DNA, prior to amplification, by using biotinylated versions of universal metazoan and bacterial barcoding primers, namely metazoan COI (mlCOIintF) and bacterial 16S (515F). Additionally, each step of the protocol was assessed by amplifying for both metazoan COI (mlCOIintF/jgHCO2198) and bacterial 16S (515F/806R) to investigate the effect on the metazoan and bacterial communities. Bacterial read abundance increased significantly in response to the captures (COI library), while the quality of the captured DNA was also improved. The metazoan-based probe captured bacterial DNA in a range that was also amplifiable with the 16S primers, demonstrating the ability of universal capture probes to isolate larger fragments of DNA from eDNA. Although the use of the tested COI probe cannot be recommended for metazoan enrichment, based on the experimental results, the concept of capturing longer fragments could be applied to metazoan metabarcoding. By using a truly conserved site without a high-level taxonomic resolution as a target for capture, it may be possible to isolate DNA fragments large enough to span over a nearby barcoding region (e.g., COI), which can then be processed through a conventional metabarcoding-by-amplification protocol.
Convergent evolution of mevalonate pathway in Inonotus obliquus and Betula pendula
Authors: Safronov Omid , Bal Guleycan Lutfullahoglu , Sipari Nina , Wilkens Maya , Safdari Pezhman , Smolander Olli-Pekka , Lihavainen Jenna , Silvan Niko , Rajaraman Sitaram , Laine Pia K. , Paulin Lars G , Auvinen Petri , Sarjala Tytti , Overmyer Kirk , Kangasjärvi Jaakko , Battersby Brendan , Richter Uwe , Salojärvi Jarkko 
Published: November 2021

AbstractInonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses revealed a lineage-specific whole genome duplication event and an expansion of Cytochrome P450 superfamily. Fungal biosynthetic clusters were enriched for tandemly duplicated genes, suggesting that biosynthetic pathway evolution has proceeded through small-scale duplications. Metabolomic fingerprinting confirmed a highly complex terpene biosynthesis chemistry when compared against related fungal species lacking the genome duplication event.
The membrane-actin linker ezrin acts as a sliding anchor
Authors: Korkmazhan Elgin , Dunn Alexander R. 
Published: November 2021

ABSTRACTProtein linkages to filamentous (F)-actin provide the cell membrane with mechanical resiliency and give rise to intricate membrane architectures. However, the actin cytoskeleton is highly dynamic, and undergoes rapid changes in shape during cell motility and other processes. The molecular mechanisms that underlie the mechanically robust yet fluid connection between the membrane and actin cytoskeleton remain poorly understood. Here, we used a single-molecule optical trap assay to examine how the prototypical membrane-actin linker ezrin acts to anchor F-actin to the cell membrane. Remarkably, we find that ezrin forms a complex that slides along F-actin over micron distances while resisting mechanical detachment. The ubiquity of ezrin and analogous proteins suggests that sliding anchors such as ezrin may constitute an important but overlooked element in the construction of the actin cytoskeleton.
Intravenous haloperidol and cocaine alter the distribution of T CD4+ and B lymphocytes and NKT cells in rats
Authors: Jankowski Maciej M. , Ignatowska-Jankowska Bogna M. , Glac Wojciech , Wiergowski Marek , Kaźmierska-Grębowska Paulina , Świergiel Artur H. 
Published: November 2021

AbstractModulation of dopamine transmission evokes strong behavioral effects that can be achieved by psychoactive drugs such as haloperidol or cocaine. Cocaine non-specifically increases dopamine transmission by blocking dopamine active transporter (DAT) and evokes behavioral arousal, while haloperidol is a non-specific dopamine D2 receptor antagonist with sedative effects. Interestingly, dopamine has been found to affect immune cells in addition to its action in the central nervous system. Here we address the possible interactions between haloperidol and cocaine and their effects on both immune cells and behavior in freely moving rats. We use an intravenous model of haloperidol and binge cocaine administration to evaluate the drugs’ impact on the distribution of lymphocyte subsets in both the peripheral blood and the spleen. We assess the drugs’ behavioral effects by measuring locomotor activity. Cocaine evoked a pronounced locomotor response and stereotypic behaviors, both of which were completely blocked after pretreatment with haloperidol. The results suggest that blood lymphopenia which was induced by haloperidol and cocaine (except for NKT cells), is independent of dopaminergic activity and most likely results from the massive secretion of corticosterone. Haloperidol pretreatment prevented the cocaine-induced decrease in NKT cell numbers. On the other hand, the increased systemic dopaminergic activity after cocaine administration is a significant factor in retaining T CD4+ and B lymphocytes in the spleen.Abstract Figure
propeller: testing for differences in cell type proportions in single cell data
Authors: Phipson Belinda , Sim Choon Boon , Porrello Enzo R. , Hewitt Alex W , Powell Joseph , Oshlack Alicia 
Published: November 2021

AbstractMotivationSingle cell RNA Sequencing (scRNA-seq) has rapidly gained popularity over the last few years for profiling the transcriptomes of thousands to millions of single cells. This technology is now being used to analyse experiments with complex designs including biological replication. One question that can be asked from single cell experiments, which has been difficult to directly address with bulk RNA-seq data, is whether the cell type proportions are different between two or more experimental conditions. As well as gene expression changes, the relative depletion or enrichment of a particular cell type can be the functional consequence of disease or treatment. However, cell type proportions estimates from scRNA-seq data are variable and statistical methods that can correctly account for different sources of variability are needed to confidently identify statistically significant shifts in cell type composition between experimental conditions.ResultsWe have developed propeller, a robust and flexible method that leverages biological replication to find statistically significant differences in cell type proportions between groups. Using simulated cell type proportions data we show that propeller performs well under a variety of scenarios. We applied propeller to test for significant changes in proportions of cell types related to human heart development, ageing and COVID-19 disease severity.Availability and implementationThe propeller method is publicly available in the open source speckle R package (https://github.com/phipsonlab/speckle). All the analysis code for the paper is available at https://github.com/phipsonlab/propeller-paper-analysis/, and the associated analysis website is available at https://phipsonlab.github.io/propeller-paper-analysis/.ContactAlicia Oshlack: Alicia.Oshlack@petermac.orgBelinda Phipson: phipson.b@wehi.edu.auSupplementary informationYes.