bluuebunny/crossref_metadata_2025_split huggingface dataset:
OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival
Authors: Lv Jun , Shang Lianguang , Chen Yun , Han Yao , Yang Xiaoyan , Xie Shuzhang , Bai Wenqin , Hu Mingyu , Wu Hong , Lei Kairong , Yang Ya’nan , Ge Shengzhen , Trinh Hai Phuong , Zhang Yi , Guo Longbiao , Wang Zhongwei 
Published: April 2020

AbstractBackgroundThe large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice.ResultsIn this study, we raised a mutant from tissue-culture-derived plants ofOryza sativa subsp. japonica‘Zhonghua 11’, which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designatedseedling-lethal chlorosis 1(slc1). Theslc1mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning ofOsSLC1revealed that a single base (G) deletion was detected in the first exon ofOs06g0710800in theslc1mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed thatOsSLC1is responsible for the seedling-lethal chlorosis phenotype in theslc1mutant.OsSLC1was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function ofOsSLC1affected the intron splicing of multiple group II introns, and especially precluded the intron splicing ofrps16, and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes.ConclusionWe characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially therps16intron, and is essential for early chloroplast development and seedling survival in rice.
Study on the influence mechanism of underground mineral element Fe(II) on Cr(VI) transformation under subsurface and groundwater interaction zones
Authors: Zheng Yiru , Liu Shuguang , Dai Chaomeng , Duan Yanping , Makhinov Aleksei Nikolavich , Hon Leong Kah , Araruna Júnior José Tavares 
Published: April 2020

Abstract
Background
With the acceleration of urbanization, heavy metal contamination in subsurface water and groundwater is becoming more and more serious, and the interaction between surface water and underground water is an important factor that cannot be ignored. Based on the change of oxygen content in surface water and groundwater environment, this research mainly studied the influencing factors and mechanism of underground mineral element Fe(II) on the morphological transformation of heavy metal Cr(VI) under the condition of surface–groundwater interaction, and simulates the interaction process of subsurface–groundwater by changing the dissolved oxygen content in the redox reaction system of dissolved Fe(II) and Cr(VI). The influence mechanism of pH, Fe(II):Cr(VI), groundwater hardness ion and humic acid on the morphological transformation of Cr(VI) was investigated.

Results
The results showed that the content of DO did affect the conversion of Cr(VI) by Fe(II). pH had a great influence on the redox reaction: while pH = 3–5, the reaction rate of Fe(II) and Cr(VI) and the removal rate of Cr(VI) decreased with the increase of pH; while pH = 6–8, the reaction rate and the removal of Cr(VI) increased with the increase of pH. When Fe(II):Cr(VI) = 3:1, the reaction of Fe(II) and Cr(VI) is affected by DO; when Fe(II):Cr(VI) is 1:1, 2:1, 4:1 and 5:1, DO has no obvious effect on the reaction. Groundwater hardness ions can greatly promote the redox reaction. When humic acid exists in the reaction system, the Fe(III) formed by the oxidation of Fe(II) by Cr(VI) will once again be converted into soluble Fe(II), the reduction of humic acid further promotes the redox reaction between Fe(II) and Cr(VI), and promotes the conversion of Cr(VI) by Fe(II) more effectively. Moreover, the higher the concentration of humic acid, the higher the removal rate of Cr(VI).

Conclusions
The research results have practical guiding significance for groundwater contamination prediction, pollution control and remediation, integrated water resources management and the construction of sponge city in China.
Reconstruction of a gene regulatory network of the induced systemic resistance defense response in Arabidopsis using boolean networks
Authors: Timmermann Tania , González Bernardo , Ruz Gonzalo A. 
Published: April 2020

Abstract
Background
An important process for plant survival is the immune system. The induced systemic resistance (ISR) triggered by beneficial microbes is an important cost-effective defense mechanism by which plants are primed to an eventual pathogen attack. Defense mechanisms such as ISR depend on an accurate and context-specific regulation of gene expression. Interactions between genes and their products give rise to complex circuits known as gene regulatory networks (GRNs). Here, we explore the regulatory mechanism of the ISR defense response triggered by the beneficial bacterium Paraburkholderia phytofirmans PsJN in Arabidopsis thaliana plants infected with Pseudomonas syringae DC3000. To achieve this, a GRN underlying the ISR response was inferred using gene expression time-series data of certain defense-related genes, differential evolution, and threshold Boolean networks.

Results
One thousand threshold Boolean networks were inferred that met the restriction of the desired dynamics. From these networks, a consensus network was obtained that helped to find plausible interactions between the genes. A representative network was selected from the consensus network and biological restrictions were applied to it. The dynamics of the selected network showed that the largest attractor, a limit cycle of length 3, represents the final stage of the defense response (12, 18, and 24 h). Also, the structural robustness of the GRN was studied through the networks’ attractors.

Conclusions
A computational intelligence approach was designed to reconstruct a GRN underlying the ISR defense response in plants using gene expression time-series data of A. thaliana colonized by P. phytofirmans PsJN and subsequently infected with P. syringae DC3000. Using differential evolution, 1000 GRNs from time-series data were successfully inferred. Through the study of the network dynamics of the selected GRN, it can be concluded that it is structurally robust since three mutations were necessary to completely disarm the Boolean trajectory that represents the biological data. The proposed method to reconstruct GRNs is general and can be used to infer other biologically relevant networks to formulate new biological hypotheses.
PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease
Authors: Thejer Bashar M. , Adhikary Partho P. , Teakel Sarah L. , Fang Johnny , Weston Paul A. , Gurusinghe Saliya , Anwer Ayad G. , Gosnell Martin , Jazayeri Jalal A. , Ludescher Marina , Gray Lesley-Ann , Pawlak Michael , Wallace Robyn H. , Pant Sameer D. , Wong Marie , Fischer Tamas , New Elizabeth J. , Fehm Tanja N. , Neubauer Hans , Goldys Ewa M. , Quinn Jane C. , Weston Leslie A. , Cahill Michael A. 
Published: April 2020

Abstract
Background
Progesterone receptor membrane component 1 (PGRMC1) is often elevated in cancers, and exists in alternative states of phosphorylation. A motif centered on PGRMC1 Y180 was evolutionarily acquired concurrently with the embryological gastrulation organizer that orchestrates vertebrate tissue differentiation.

Results
Here, we show that mutagenic manipulation of PGRMC1 phosphorylation alters cell metabolism, genomic stability, and CpG methylation. Each of several mutants elicited distinct patterns of genomic CpG methylation. Mutation of S57A/Y180/S181A led to increased net hypermethylation, reminiscent of embryonic stem cells. Pathways enrichment analysis suggested modulation of processes related to animal cell differentiation status and tissue identity, as well as cell cycle control and ATM/ATR DNA damage repair regulation. We detected different genomic mutation rates in culture.

Conclusions
A companion manuscript shows that these cell states dramatically affect protein abundances, cell and mitochondrial morphology, and glycolytic metabolism. We propose that PGRMC1 phosphorylation status modulates cellular plasticity mechanisms relevant to early embryological tissue differentiation.
CHD9 upregulates RUNX2 and has a potential role in skeletal evolution
Authors: Newton Axel H. , Pask Andrew J. 
Published: April 2020

Abstract
Background
Changes in gene regulation are widely recognized as an important driver of adaptive phenotypic evolution. However, the specific molecular mechanisms that underpin such changes are still poorly understood. Chromatin state plays an essential role in gene regulation, by influencing the accessibility of coding loci to the transcriptional machinery. Changes in the function of chromatin remodellers are therefore strong candidates to drive changes in gene expression associated with phenotypic adaptation. Here, we identify amino acid homoplasies in the chromatin remodeller CHD9, shared between the extinct marsupial thylacine and eutherian wolf which show remarkable skull convergence. CHD9 is involved in osteogenesis, though its role in the process is still poorly understood. We examine whether CHD9 is able to regulate the expression of osteogenic target genes and examine the function of a key substitution in the CHD9 DNA binding domain.

Results
We examined whether CHD9 was able to upregulate its osteogenic target genes, RUNX2, Osteocalcin (OC) and ALP in HEK293T cells. We found that overexpression of CHD9 upregulated RUNX2, the master regulator of osteoblast cell fate, but not the downstream genes OC or ALP, supporting the idea that CHD9 regulates osteogenic progenitors rather than terminal osteoblasts. We also found that the evolutionary substitution in the CHD9 DNA binding domain does not alter protein secondary structure, but was able to drive a small but insignificant increase in RUNX2 activation. Finally, CHD9 was unable to activate an episomal RUNX2 promoter-reporter construct, suggesting that CHD9 requires the full chromatin complement for its function.

Conclusions
We provide new evidence to the role of CHD9 in osteogenic differentiation through its newly observed ability to upregulate the expression of RUNX2. Though we were unable to identify significant functional consequences of the evolutionary substitution in HEK293T cells, our study provides important steps forward in the functional investigation of protein homoplasy and its role in developmental processes. Mutations in coding genes may be a mechanism for driving adaptive changes in gene expression, and their validation is essential towards determining the functional consequences of evolutionary homoplasy.
Analyses of the folding sites of irregular β-trefoil fold proteins through sequence-based techniques and Gō-model simulations
Authors: Kimura Risako , Aumpuchin Panyavut , Hamaue Shoya , Shimomura Takumi , Kikuchi Takeshi 
Published: April 2020

Abstract
Background
The details of the folding mechanisms have not yet been fully understood for many proteins, and it is believed that the information on the folding mechanism of a protein is encoded in its amino acid sequence. β-trefoil proteins are known to have the same 3D scaffold, namely, a three-fold symmetric scaffold, despite the proteins’ low sequence identity among superfamilies. In this study, we extract an initial folding unit from the amino acid sequences of irregular β-trefoil proteins by constructing an average distance map (ADM) and utilizing inter-residue average distance statistics to determine the relative contact frequencies for residue pairs in terms of F values. We compare our sequence-based prediction results with the packing between hydrophobic residues in native 3D structures and a Gō-model simulation.

Results
The ADM and F-value analyses predict that the N-terminal and C-terminal regions are compact and that the hydrophobic residues at the central region can be regarded as an interaction center with other residues. These results correspond well to those of the Gō-model simulations. Moreover, our results indicate that the irregular parts in the β-trefoil proteins do not hinder the protein formation. Conserved hydrophobic residues on the β5 strand are always the interaction center of packing between the conserved hydrophobic residues in both regular and irregular β-trefoil proteins.

Conclusions
We revealed that the β5 strand plays an important role in β-trefoil protein structure construction. The sequence-based methods used in this study can extract the protein folding information from only amino acid sequence data, and well corresponded to 3D structure-based Gō-model simulation and available experimental results.
A unified nomenclature for vertebrate olfactory receptors
Authors: Olender Tsviya , Jones Tamsin E. M. , Bruford Elspeth , Lancet Doron 
Published: April 2020

Abstract
Background
Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights.

Results
Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature.

Conclusions
We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.
Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues
Authors: Berglund Emelie , Saarenpää Sami , Jemt Anders , Gruselius Joel , Larsson Ludvig , Bergenstråhle Ludvig , Lundeberg Joakim , Giacomello Stefania 
Published: April 2020

Abstract
Background
Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and co-expression of cells in tissues. Unfortunately, manual preparation of high-quality sequencing libraries is time-consuming and subject to technical variability due to human error during manual pipetting, which results in sample swapping and the accidental introduction of batch effects. All these factors complicate the production and interpretation of biological datasets.

Results
We have integrated an Agilent Bravo Automated Liquid Handling Platform into the Spatial Transcriptomics workflow. Compared to the previously reported Magnatrix 8000+ automated protocol, this approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples. The new approach is also shown to be highly accurate and almost completely free from technical variability between prepared samples.

Conclusions
The new automated Spatial Transcriptomics protocol using the Agilent Bravo Automated Liquid Handling Platform rapidly generates high-quality Spatial Transcriptomics libraries. Given the wide use of the Agilent Bravo Automated Liquid Handling Platform in research laboratories and facilities, this will allow many researchers to quickly create robust Spatial Transcriptomics libraries.
Identification and application of piwi-interacting RNAs from seminal plasma exosomes in Cynoglossus semilaevis
Authors: Zhang Bo , Zhao Na , Jia Lei , Che Jinyuan , He Xiaoxu , Liu Kefeng , Bao Baolong 
Published: April 2020

Abstract
Background
Piwi-interacting RNAs (piRNAs) have been linked to epigenetic and post-transcriptional gene silencing of retrotransposons in germ line cells, particularly in spermatogenesis. Exosomes are important mediators of vesicle transport, and the piRNAs in exosomes might play an important role in cell communication and signal pathway regulation. Moreover, exosomic piRNAs are promising biomarkers for disease diagnosis and physiological status indication. We used Cynoglossus semilaevis because of its commercial value and its sexual dimorphism, particularly the sex reversed “pseudomales” who have a female karyotype, produce sperm, and copulate with normal females to produce viable offspring.

Results
To determine whether piRNAs from fish germ line cells have similar features, seminal plasma exosomes from half-smooth tongue sole, C. semilaevis, were identified, and their small RNAs were sequenced and analysed. We identified six signature piRNAs as biomarkers in exosomes of seminal plasma from males and pseudomale C. semilaevis. Bioinformatic analysis showed that all six signatures were sex-related, and four were DNA methylation-related and transposition-related piRNAs. Their expression profiles were verified using real-time quantitative PCR. The expression of the signature piRNAs was markedly higher in males than in pseudomales. The signature piRNAs could be exploited as male-specific biomarkers in this fish.

Conclusions
These signatures provide an effective tool to explore the regulatory mechanism of sex development in C. semilaevis and may provide guidance for future research on the function of piRNAs in the generative mechanism of sex reversed “pseudomales” in C. semilaevis.
Transcriptomic diversity in seedling roots of European flint maize in response to cold
Authors: Frey Felix P. , Pitz Marion , Schön Chris-Carolin , Hochholdinger Frank 
Published: April 2020

AbstractBackgroundLow temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resource for genes and alleles conferring cold tolerance which they acquired during their adaptation to the agroecological conditions in Europe.ResultsBased on a phenotyping experiment of 276 doubled haploid lines derived from the European flint landrace “Petkuser Ferdinand Rot” diverging for cold tolerance, we selected 21 of these lines for an RNA-seq experiment. The different genotypes showed highly variable transcriptomic responses to cold. We identified 148, 3254 and 563 genes differentially expressed with respect to cold treatment, cold tolerance and growth rate at cold, respectively. Gene ontology (GO) term enrichment demonstrated that the detoxification of reactive oxygen species is associated with cold tolerance, whereas amino acids might play a crucial role as antioxidant precursors and signaling molecules.ConclusionDoubled haploids representing a European maize flint landrace display genotype-specific transcriptome patterns associated with cold response, cold tolerance and seedling growth rate at cold. Identification of cold regulated genes in European flint germplasm, could be a starting point for introgressing such alleles in modern breeding material for maize improvement.
Identification and analysis of the FAD gene family in walnuts (Juglans regia L.) based on transcriptome data
Authors: Liu Kai , Zhao Shugang , Wang Shuang , Wang Hongxia , Zhang Zhihua 
Published: April 2020

Abstract
Background
Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main function of fatty acid desaturase (FAD), which is widely distributed in organisms, is to remove hydrogen from carbon chains in the biosynthesis of unsaturated fatty acids to generate C=C bonds.

Results
By performing a series of bioinformatics analysis, 24 members of the JrFAD gene family were identified from the genome database of walnut, and then compared with the homologous genes from Arabidopsis. Phylogenetic analysis showed that JrFADs were classified into four subfamilies: the SAD desaturase subfamily, Δ7/Δ9 desaturase subfamily, Δ12/ω-3 desaturase subfamily and “front-end” desaturase subfamily. Meanwhile, the expression of fatty acid synthesis genes in walnut kernels at different developmental stages was analysed by transcriptome sequencing, with expression of JrFAD3-1, which encodes an enzyme involved in linolenic acid synthesis, being particularly prominent. The relative expression level of JrFAD3-1 changed dramatically with the kernel development stages and exhibited a Bell-Shaped Curve. A significant positive correlation was observed between the expression of JrFAD3-1 during 70–100 DAF (Days after flowering) and the content of alpha-linolenic acid during 100–130 DAF, with a correlation coefficient of 0.991. Additionally, JrFAD3-1 was proved closely related to homologous genes in Betula pendula and Corylus heterophylla, indicating that the conserved structure of FADs is consistent with classical plant taxonomy.

Conclusion
Twenty-four members JrFADs in walnut were identified and classified into four subfamilies. JrFAD3-1 may play significant roles in the biosynthesis of polyunsaturated fatty acids in walnut.