title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=773 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects link: https://peerj.com/articles/12676 last-modified: 2022-01-05 description: Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the clone CCN 51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao industry will be discussed highlighting the major challenges for flavor enhancement and its relevance as a platform for the identification of novel genetic markers for cultivar improvement in breeding programs. creator: Ramon E. Jaimez creator: Luigy Barragan creator: Miguel Fernández-Niño creator: Ludger A. Wessjohann creator: George Cedeño-Garcia creator: Ignacio Sotomayor Cantos creator: Francisco Arteaga uri: https://doi.org/10.7717/peerj.12676 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jaimez et al. title: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog link: https://peerj.com/articles/12712 last-modified: 2022-01-05 description: The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection. creator: Roland A. Knapp creator: Maxwell B. Joseph creator: Thomas C. Smith creator: Ericka E. Hegeman creator: Vance T. Vredenburg creator: James E. Erdman Jr creator: Daniel M. Boiano creator: Andrea J. Jani creator: Cheryl J. Briggs uri: https://doi.org/10.7717/peerj.12712 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Knapp et al. title: Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study link: https://peerj.com/articles/12715 last-modified: 2022-01-05 description: BackgroundImproved detection of hepatocellular carcinoma (HCC) is needed, as current detection methods, such as alpha fetoprotein (AFP) and ultrasound, suffer from poor sensitivity. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate many cellular functions and impact cancer development and progression. Notably, miRNAs are detectable in saliva and have shown potential as non-invasive biomarkers for a number of cancers including breast, oral, and lung cancers. Here, we present, to our knowledge, the first report of salivary miRNAs in HCC and compare these findings to patients with cirrhosis, a high-risk cohort for HCC.MethodsWe performed small RNA sequencing in 20 patients with HCC and 19 with cirrhosis. Eleven patients with HCC had chronic liver disease, and analyses were performed with these samples combined and stratified by the presence of chronic liver disease. P values were adjusted for multiple comparisons using a false discovery rate (FDR) approach and miRNA with FDR P < 0.05 were considered statistically significant. Differential expression of salivary miRNAs was compared to a previously published report of miRNAs in liver tissue of patients with HCC vs cirrhosis. Support vector machines and leave-one-out cross-validation were performed to determine if salivary miRNAs have predictive potential for detecting HCC.ResultsA total of 4,565 precursor and mature miRNAs were detected in saliva and 365 were significantly different between those with HCC compared to cirrhosis (FDR P < 0.05). Interestingly, 283 of these miRNAs were significantly downregulated in patients with HCC. Machine-learning identified a combination of 10 miRNAs and covariates that accurately classified patients with HCC (AUC = 0.87). In addition, we identified three miRNAs that were differentially expressed in HCC saliva samples and in a previously published study of miRNAs in HCC tissue compared to cirrhotic liver tissue.ConclusionsThis study demonstrates, for the first time, that miRNAs relevant to HCC are detectable in saliva, that salivary miRNA signatures show potential to be highly sensitive and specific non-invasive biomarkers of HCC, and that additional studies utilizing larger cohorts are needed. creator: Arshiya Mariam creator: Galen Miller-Atkins creator: Amika Moro creator: Alejandro I. Rodarte creator: Shirin Siddiqi creator: Lou-Anne Acevedo-Moreno creator: J. Mark Brown creator: Daniela S. Allende creator: Federico Aucejo creator: Daniel M. Rotroff uri: https://doi.org/10.7717/peerj.12715 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Mariam et al. title: Genome-wide sequence identification and expression analysis of N6-methyladenosine demethylase in sugar beet (Beta vulgaris L.) under salt stress link: https://peerj.com/articles/12719 last-modified: 2022-01-05 description: In eukaryotes, N6-methyladenosine (m6A) is the most abundant and highly conserved RNA modification. In vivo, m6A demethylase dynamically regulates the m6A level by removing the m6A marker where it plays an important role in plant growth, development and response to abiotic stress. The confirmed m6A demethylases in Arabidopsis thaliana include ALKBH9B and ALKBH10B, both belonging to the ALKB family. In this study, BvALKB family members were identified in sugar beet genome-wide database, and their conserved domains, gene structures, chromosomal locations, phylogeny, conserved motifs and expression of BvALKB genes were analyzed. Almost all BvALKB proteins contained the conserved domain of 2OG-Fe II-Oxy. Phylogenetic analysis suggested that the ten proteins were clustered into five groups, each of which had similar motifs and gene structures. Three Arabidopsis m6A demethylase-homologous proteins (BvALKBH6B, BvALKBH8B and BvALKBH10B) were of particular interest in our study. Expression profile analysis showed that almost all genes were up-regulated or down-regulated to varying degrees under salt stress. More specifically, BvALKBH10B homologous to AtALKBH10B was significantly up-regulated, suggesting that the transcriptional activity of this gene is responsive to salt stress. This study provides a theoretical basis for further screening of m6A demethylase in sugar beet, and also lays a foundation for studying the role of ALKB family proteins in growth, development and response to salinity stress. creator: Jie Cui creator: Junli Liu creator: Junliang Li creator: Dayou Cheng creator: Cuihong Dai uri: https://doi.org/10.7717/peerj.12719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cui et al. title: Identification of FEZ2 as a potential oncogene in pancreatic ductal adenocarcinoma link: https://peerj.com/articles/12736 last-modified: 2022-01-05 description: Pancreatic ductal adenocarcinoma (PDAC) is one of the common malignant tumors with high lethal rate and poor prognosis. Dysregulation of many genes have been reported to be involved in the occurrence and development of PDAC. However, as a highly conserved gene in eukaryotes, the role of Fasciculation and Elongation protein Zeta 2 (FEZ2) in pancreatic cancer progression is not clear. In this study, we identified the oncogenic effect of FEZ2 on PDAC. By mining of The Cancer Genome Atlas (TCGA) database, we found that FEZ2 was upregulated in PDAC tissues and FEZ2 expression was negatively regulated by its methylation. Moreover, high expression and low methylation of FEZ2 correlated with poor prognosis in PDAC patients. Besides, we found that FEZ2 could promote PDAC cells proliferation, migration and 5-FU resistance in vitro. Furthermore, Gene pathway enrichment analysis demonstrated a positive correlation between Wnt signaling activation and FEZ2 expression in PDAC patients. Western blot showed that FEZ2 knockdown significantly suppressed β-catenin expression. Collectively, our finding revealed that FEZ2 functioned as a potential oncogene on PDAC progression and migration, and the expression of FEZ2 had guidance value for the treatment and chemotherapy program of PDAC patients. creator: Chaozhi Yang creator: Xuebing Wang creator: Chenjie Qiu creator: Ziruo Zheng creator: Kai Lin creator: Min Tu creator: Kai Zhang creator: Kuirong Jiang creator: Wentao Gao uri: https://doi.org/10.7717/peerj.12736 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Discovery of potential protein biomarkers associated with sugarcane white leaf disease susceptibility using a comparative proteomic approach link: https://peerj.com/articles/12740 last-modified: 2022-01-05 description: Sugarcane white leaf disease (SCWLD) is caused by phytoplasma, a serious sugarcane phytoplasma pathogen, which causes significant decreases in crop yield and sugar quality. The identification of proteins involved in the defense mechanism against SCWLD phytoplasma may help towards the development of varieties resistant to SCWLD. We investigated the proteomes of four sugarcane varieties with different levels of susceptibility to SCWLD phytoplasma infection, namely K88-92 and K95-84 (high), KK3 (moderate), and UT1 (low) by quantitative label-free nano-liquid chromatography-tandem mass spectrometry (nano LC-MS/MS). A total of 248 proteins were identified and compared among the four sugarcane varieties. Two potential candidate protein biomarkers for reduced susceptibility to SCWLD phytoplasma were identified as proteins detected only in UT1. The functions of these proteins are associated with protein folding, metal ion binding, and oxidoreductase. The candidate biomarkers could be useful for further study of the sugarcane defense mechanism against SCWLD phytoplasma, and in molecular and conventional breeding strategies for variety improvement. creator: Kantinan Leetanasaksakul creator: Sittiruk Roytrakul creator: Narumon Phaonakrop creator: Suthathip Kittisenachai creator: Siriwan Thaisakun creator: Nitiya Srithuanok creator: Klanarong Sriroth creator: Laurent Soulard uri: https://doi.org/10.7717/peerj.12740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Leetanasaksakul et al. title: Beyond the prey: male spiders highly invest in silk when producing worthless gifts link: https://peerj.com/articles/12757 last-modified: 2022-01-05 description: In the spider Paratrechalea ornata, males have two gift-giving mating tactics, offering either a nutritive (prey) or a worthless (prey leftovers) silk wrapped gift to females. Both gift types confer similar mating success and duration and afford males a higher success rate than when they offer no gift. If this lack of difference in the reproductive benefits is true, we would expect all males to offer a gift but some males to offer a worthless gift even if prey are available. To test this, we allowed 18 males to court multiple females over five consecutive trials. In each trial, a male was able to produce a nutritive gift (a live housefly) or a worthless gift (mealworm exuviae). We found that, in line with our predictions, 20% of the males produced worthless gifts even when they had the opportunity to produce a nutritive one. However, rather than worthless gifts being a cheap tactic, they were related to a higher investment in silk wrapping. This latter result was replicated for worthless gifts produced in both the presence and absence of a live prey item. We propose that variation in gift-giving tactics likely evolved initially as a conditional strategy related to prey availability and male condition in P. ornata. Selection may then have favoured silk wrapping as a trait involved in female attraction, leading worthless gift-giving to invade. creator: Camila Pavón-Peláez creator: Valentina Franco-Trecu creator: Irene Pandulli-Alonso creator: Therésa M. Jones creator: Maria J. Albo uri: https://doi.org/10.7717/peerj.12757 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pavón-Peláez et al. title: Protection of catalpol against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway link: https://peerj.com/articles/12759 last-modified: 2022-01-05 description: Catalpol significantly reduces triptolide-induced hepatotoxicity, which is closely related to autophagy. The aim of this study was to explore the unclear protective mechanism of catalpol against triptolide. The detoxification effect of catalpol on triptolide was investigated in HepaRG cell line. The detoxification effects were assessed by measuring cell viability, autophagy, and apoptosis, as well as the endoplasmic reticulum stress protein and mRNA expression levels. We found that 5–20 µg/L triptolide treatments increased the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH), as well as the expression of autophagy proteins including LC3 and Beclin1. The expression of P62 was downregulated and the production of autophagosomes was increased, as determined by transmission electron microscope and monodansylcadaverine staining. In contrast, 40 µg/L catalpol reversed these triptolide-induced changes in the liver function index, autophagy level, and apoptotic protein expression, including Cleaved-caspase3 and Cleaved-caspase9 by inhibiting excessive autophagy. Simultaneously, catalpol reversed endoplasmic reticulum stress, including the expression of PERK, which regulates autophagy. Moreover, we used the PERK inhibitor GSK2656157 to prove that the PERK-ATF4-CHOP pathway of the unfolded protein response is an important pathway that could induce autophagy. Catalpol inhibited excessive autophagy by suppressing the PERK pathway. Altogether, catalpol protects against triptolide-induced hepatotoxicity by inhibiting excessive autophagy via the PERK-ATF4-CHOP pathway. The results of this study are beneficial to clarify the detoxification mechanism of catalpol against triptolide-induced hepatotoxicity and to promote the application of triptolide. creator: Linluo Zhang creator: Changqing Li creator: Ling Fu creator: Zhichao Yu creator: Gengrui Xu creator: Jie Zhou creator: Meiyu Shen creator: Zhe Feng creator: Huaxu Zhu creator: Tong Xie creator: Lingling Zhou creator: Xueping Zhou uri: https://doi.org/10.7717/peerj.12759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma link: https://peerj.com/articles/12493 last-modified: 2022-01-04 description: BackgroundClear cell renal cell carcinoma (ccRCC) is a tumor that frequently shows the hematogenous pathway and tends to be resistant to radiotherapy and chemotherapy. However, the exact mechanism of ccRCC metastasis remains unknown.MethodsDifferentially expressed genes (DEGs) of three gene expression profiles (GSE85258, GSE105288 and GSE22541) downloaded from the Gene Expression Omnibus (GEO) database were analyzed by GEO2R analysis, and co-expressed DEGs among the datasets were identified using a Venn drawing tool. The co-expressed DEGs were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and hub genes were determined based on the protein-protein interaction network established by STRING. After survival analysis performed on UALCAN website, possible key genes were selected and verified in ccRCC cell lines and ccRCC tissues (n = 44). Statistical analysis was conducted using GraphPad Prism (Version 8.1.1).ResultsA total of 104 co-expressed DEGs were identified in the three datasets. Pathway analysis revealed that these genes were enriched in the extracellular matrix (ECM)–receptor interaction, protein digestion and absorption and focal adhesion. Survival analysis on 17 hub genes revealed that four key genes with a significant impact on survival: procollagen C-endopeptidase enhancer (PCOLCE), prolyl 4-hydroxylase subunit beta (P4HB), collagen type VI alpha 2 (COL6A2) and collagen type VI alpha 3 (COL6A3). Patients with higher expression of these key genes had worse survival than those with lower expression. In vitro experiments revealed that the mRNA expression levels of PCOLCE, P4HB and COL6A2 were three times higher and that of COL6A3 mRNA was 16 times higher in the metastatic ccRCC cell line Caki-1 than the corresponding primary cell line Caki-2. Immunohistochemistry revealed higher expression of the proteins encoded by these four genes in metastatic ccRCC compared with tumors from the corresponding primary sites, with statistical significance.ConclusionPCOLCE, P4HB, COL6A2 and COL6A3 are upregulated in metastatic ccRCC and might be related to poor prognosis and distant metastases. creator: Tingting Zhong creator: Zeying Jiang creator: Xiangdong Wang creator: Honglei Wang creator: Meiyi Song creator: Wenfang Chen creator: Shicong Yang uri: https://doi.org/10.7717/peerj.12493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhong et al. title: Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola link: https://peerj.com/articles/12558 last-modified: 2022-01-04 description: BackgroundMembers of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available.MethodsIn the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed.ResultsEight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development. creator: Chengru Li creator: Na Dong creator: Liming Shen creator: Meng Lu creator: Junwen Zhai creator: Yamei Zhao creator: Lei Chen creator: Zhiting Wan creator: Zhongjian Liu creator: Hui Ren creator: Shasha Wu uri: https://doi.org/10.7717/peerj.12558 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al.