title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=632 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients link: https://peerj.com/articles/13986 last-modified: 2022-10-18 description: An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time. creator: Anna A. Valyaeva creator: Maria A. Tikhomirova creator: Daria M. Potashnikova creator: Alexandra N. Bogomazova creator: Galina P. Snigiryova creator: Aleksey A. Penin creator: Maria D. Logacheva creator: Eugene A. Arifulin creator: Anna A. Shmakova creator: Diego Germini creator: Anastasia I. Kachalova creator: Aleena A. Saidova creator: Anastasia A. Zharikova creator: Yana R. Musinova creator: Andrey A. Mironov creator: Yegor S. Vassetzky creator: Eugene V. Sheval uri: https://doi.org/10.7717/peerj.13986 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Valyaeva et al. title: Fossil Sirenia from the Pleistocene of Qatar: new questions about the antiquity of sea cows in the Gulf Region link: https://peerj.com/articles/14075 last-modified: 2022-10-18 description: One of the largest and least documented populations of dugongs (Dugong dugon) resides in the coastal waters of the United Arab Emirates, and waters surrounding Saudi Arabia, Bahrain, and Qatar. The archaeological record of dugongs in the Gulf Region is abundant, but little is known about their fossil record in the region. Here we report an isolated sirenian rib fragment from the Futaisi Member of the Fuwayrit Formation near the town of Al Ruwais, in northern Qatar. The Fuwayrit Formation is a marine Pleistocene deposit exposed onshore in Qatar and the United Arab Emirates. Based on the correlative dating of the basal Futaisi Member with other onshore platforms, the rib fragment is approximately 125 ka. We propose that this isolated rib (likely the first rib from the right side) belongs to Dugongidae, with strong similarities to extant Dugong. We cannot, however, eliminate the possibility that it belongs to an extinct taxon, especially given its similarities with other fossil dugongid material from both Qatar and elsewhere in the world. Aside from reflecting the presence of Gulf seagrass communities in the Pleistocene, this occurrence also suggests that different (and potentially multiple) lineages of sirenians inhabited the Gulf Region in the geologic past. creator: Nicholas D. Pyenson creator: Mehsin Al-Ansi creator: Clare M. Fieseler creator: Khalid Hassan Al Jaber creator: Katherine D. Klim creator: Jacques LeBlanc creator: Ahmad Mujthaba Dheen Mohamed creator: Ismail Al-Shaikh creator: Christopher D. Marshall uri: https://doi.org/10.7717/peerj.14075 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew link: https://peerj.com/articles/14114 last-modified: 2022-10-18 description: Psychotria viridis (Rubioideae: Rubiaceae), popularly known as chacrona, is commonly found as a shrub in the Amazon region and is well-known to produce psychoactive compounds, such as the N,N-dimethyltryptamine (DMT). Together with the liana Banisteropsis caapi, P. viridis is one of the main components of the Amerindian traditional, entheogenic beverage known as ayahuasca. In this work, we assembled and annotated the organellar genomes (ptDNA and mtDNA), presenting the first genomics resources for this species. The P. viridis ptDNA exhibits 154,106 bp, encoding all known ptDNA gene repertoire found in angiosperms. The Psychotria genus is a complex paraphyletic group, and according to phylogenomic analyses, P. viridis is nested in the Psychotrieae clade. Comparative ptDNA analyses indicate that most Rubiaceae plastomes present conserved ptDNA structures, often showing slight differences at the junction sites of the major four regions (LSC-IR-SSC). For the mitochondrion, assembly graph-based analysis supports a complex mtDNA organization, presenting at least two alternative and circular mitogenomes structures exhibiting two main repeats spanning 24 kb and 749 bp that may symmetrically isomerize the mitogenome into variable arrangements and isoforms. The circular mtDNA sequences (615,370 and 570,344 bp) encode almost all plant mitochondrial genes (except for the ccmC, rps7, rps10, rps14, rps19, rpl2 and rpl16 that appears as pseudogenes, and the absent genes sdh3, rps2, rsp4, rsp8, rps11, rpl6, and rpl10), showing slight variations related to exclusive regions, ptDNA integration, and relics of previous events of LTR-RT integration. The detection of two mitogenomes haplotypes is evidence of heteroplasmy as observed by the complex organization of the mitochondrial genome using graph-based analysis. Taken together, these results elicit the primary insights into the genome biology and evolutionary history of Psychotria viridis and may be used to aid strategies for conservation of this sacred, entheogenic species. creator: Alessandro M. Varani creator: Saura R. Silva creator: Simone Lopes creator: Jose Beethoven Figueiredo Barbosa creator: Danilo Oliveira creator: Maria Alice Corrêa creator: Ana Paula Moraes creator: Vitor F.O. Miranda creator: Francisco Prosdocimi uri: https://doi.org/10.7717/peerj.14114 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Varani et al. title: Clinical associations and genetic interactions of oncogenic BRAF alleles link: https://peerj.com/articles/14126 last-modified: 2022-10-18 description: BRAF is a serine/threonine-specific protein kinase that regulates the MAPK/ERK signaling pathway, and mutations in the BRAF gene are considered oncogenic drivers in diverse types of cancer. Based on the signaling mechanism, oncogenic BRAF mutations can be assigned to three different classes: class 1 mutations constitutively activate the kinase domain and lead to RAS-independent signaling, class 2 mutations induce artificial dimerization of BRAF and RAS-independent signaling and class 3 mutations display reduced or abolished kinase function and require upstream signals.Despite the importance of BRAF mutations in cancer, the clinical associations, genetic interactions and therapeutic implications of non-V600 BRAF mutations have not been explored comprehensively yet. In this study, the author analyzed publically available data from the AACR Project GENIE to further understand clinical associations and genetic interactions of oncogenic BRAF mutations. The analyses identified 93 recurrent BRAF mutations, out of which 50 could be assigned to a functional class based on literature review. The author could show that the frequency of BRAF mutations varies across cancer types and subtypes, and that the BRAF mutation classes are unequally distributed across cancer types and subtypes. Using permutation testing-based co-occurrence analyses, the author defined the genetic interactions of BRAF mutations in multiple cancer types and revealed unexplored genetic interactions that might define clinically relevant subgroups. With non-small cell lung cancer as example, the author further showed that the genetic interactions are BRAF mutation class-specific. The presented analyses explore the properties of oncogenic BRAF mutations and will help to further delineate the complex role of BRAF in cancer. creator: Sebastian A. Wagner uri: https://doi.org/10.7717/peerj.14126 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wagner title: WRKY transcription factor family in lettuce plant (Lactuca sativa): Genome-wide characterization, chromosome location, phylogeny structures, and expression patterns link: https://peerj.com/articles/14136 last-modified: 2022-10-18 description: WRKY transcription factors (TF) have been identified in many plant species and play critical roles in multiple stages of growth and development and under various stress conditions. As one of the most popular vegetable crops, asparagus lettuce has important medicinal and nutritional value. However, study of WRKY TFs family in asparagus lettuce is limited. With the lettuce (Lactuca sativa L.) genome publication, we identified 76 WRKY TFs and analyzed structural characteristics, phylogenetic relationships, chromosomal distribution, interaction network, and expression profiles. The 76 LsWRKY TFs were phylogenetically classified as Groups I, II (IIa-IIe), and III. Cis element analysis revealed complex regulatory relationships of LsWRKY genes in response to different biological progresses. Interaction network analysis indicated that LsWRKY TFs could interact with other proteins, such as SIB (sigma factor binding protein), WRKY TFs, and MPK. The WRKYIII subfamily genes showed different expression patterns during the progress of asparagus lettuce stem enlargement. According to qRT-PCR analysis, abiotic stresses (drought, salt, low temperature, and high temperature) and phytohormone treatment could induce specific LsWRKYIII gene expression. These results will provide systematic and comprehensive information on LsWRKY TFs and lay the foundation for further clarification of the regulatory mechanism of LsWRKY, especially LsWRKYIII TFs, involved in stress response and the progress of plant growth and development. creator: Ping Du creator: Qinglian Wu creator: Yihua Liu creator: Xue Cao creator: Wenyi Yi creator: Tikun Jiao creator: Mengqi Hu creator: Ying Huang uri: https://doi.org/10.7717/peerj.14136 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Du et al. title: Computer vision supports primary access to meat by early Homo 1.84 million years ago link: https://peerj.com/articles/14148 last-modified: 2022-10-18 description: Human carnivory is atypical among primates. Unlike chimpanzees and bonobos, who are known to hunt smaller monkeys and eat them immediately, human foragers often cooperate to kill large animals and transport them to a safe location to be shared. While it is known that meat became an important part of the hominin diet around 2.6–2 Mya, whether intense cooperation and food sharing developed in conjunction with the regular intake of meat remains unresolved. A widespread assumption is that early hominins acquired animal protein through klepto-parasitism at felid kills. This should be testable by detecting felid-specific bone modifications and tooth marks on carcasses consumed by hominins. Here, deep learning (DL) computer vision was used to identify agency through the analysis of tooth pits and scores on bones recovered from the Early Pleistocene site of DS (Bed I, Olduvai Gorge). We present the first objective evidence of primary access to meat by hominins 1.8 Mya by showing that the most common securely detectable bone-modifying fissipeds at the site were hyenas. The absence of felid modifications in most of the carcasses analyzed indicates that hominins were the primary consumers of most animals accumulated at the site, with hyenas intervening at the post-depositional stage. This underscores the role of hominins as a prominent part of the early Pleistocene African carnivore guild. It also stresses the major (and potentially regular) role that meat played in the diet that configured the emergence of early Homo. creator: Lucía Cobo-Sánchez creator: Marcos Pizarro-Monzo creator: Gabriel Cifuentes-Alcobendas creator: Blanca Jiménez García creator: Natalia Abellán Beltrán creator: Lloyd A. Courtenay creator: Audax Mabulla creator: Enrique Baquedano creator: Manuel Domínguez-Rodrigo uri: https://doi.org/10.7717/peerj.14148 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cobo-Sánchez et al. title: Proteomic analysis of IgM antigens from mammary tissue under pre- and post-cancer conditions using the MMTV-PyVT mouse model link: https://peerj.com/articles/14175 last-modified: 2022-10-18 description: We analyzed the recognition of tumor antigens by IgM in transgenic MMTV-PyVT mice. PyVT female mice are a model of breast cancer that simulates its counterpart in humans. The PyVT model allows studying antigen recognition in two conditions: before and during tumor expression. We attempted to identify by sequence, the antigens recognized by IgM that are expressed or disappear in the membrane of breast transgenic tissue during the transition “No tumor-Tumor”. 2D immunoblots were obtained of isolated membranes from the breast tissue in the fifth, sixth, and seventh week (transition point). Proteins recognized by IgM were sequenced in duplicate by MALDI-TOF. In the transition, we observed the disappearance of antigens in transgenic mice with respect to non-transgenic ones. We believe that in the diagnosis of cancer in its early stages, the expression of early antigens is as important as their early delocalization, with the latter having the advantage that, under normal conditions, we can know which proteins should be present at a given time. Therefore, we could consider that also the absence of antigens could be considered as a biomarker of cancer in progress. creator: Ricardo Hernández Ávila creator: Mariana Díaz-Zaragoza creator: Pedro Ostoa-Saloma uri: https://doi.org/10.7717/peerj.14175 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hernández Ávila et al. title: A retrospective study of prevalence and pattern of international consensus on ANA patterns among patients with hepatitis C virus infection link: https://peerj.com/articles/14200 last-modified: 2022-10-18 description: BackgroundA previous study reported a 30% prevalence of various autoantibodies among patients with hepatitis C virus (HCV) infection. The International Consensus on Anti-Nuclear Antibody (ANA) Patterns was recently introduced to classify ANA patterns based on immunoassay on HEp-2 cells. There is no previous report with this newly developed classification to evaluate patients with HCV infection. The study aims to study the prevalence and pattern of ANA patterns among HCV-infected patients.MethodsWe retrospectively analyzed the medical records of patients with HCV infection from September 2020 to June 2021 at our institution. A positive ANA is defined as a titer of more than 1:320. We compared patient features among the positive and negative groups.ResultsOverall, 258 patients were enrolled—184 patients with negative ANA and 74 patients (28.7%) with positive ANA. The mean age was 67.3 in ANA positive group and 61.2 ANA negative group. Female was prominent with ANA positive and accounted for 63.5%. The most detected ANA pattern was AC-1(homogeneous) (25.9%), followed by AC-4(fine speckled) (25.2%) and AC-21(anti-mitochondrial antibody) (9.6%). In ANA positive group, we found a trend of lower HCV viral load (5.72 log10 IU/ML vs. 6.02 log10 IU/ML), lower alanine aminotransferase level (39.5 U/L vs. 44 U/L), and higher advanced fibrosis (F3 and F4) (38.5% vs. 26.1%). In addition, higher positive ANA (more than 1:640) is significantly associated with lower estimated glomerular filtration rate (eGFR) (77.76 vs. 87.94 mL/min/1.73 m2, P = 0.044).ConclusionsA high prevalence (28.7%) of ANA was found in patients with chronic hepatitis C. The presence of positive ANA is not related to the severity of their hepatic manifestation. However, higher positive ANA was significantly associated with lower eGFR. creator: Shun-Wen Hsiao creator: Chuan-San Fan creator: Hsu-Heng Yen creator: Siou-Ping Huang creator: Yang-Yuan Chen creator: Pei-Yuan Su uri: https://doi.org/10.7717/peerj.14200 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hsiao et al. title: IQGAP3 in clear cell renal cell carcinoma contributes to drug resistance and genome stability link: https://peerj.com/articles/14201 last-modified: 2022-10-18 description: BackgroundClear cell renal clear cell carcinoma (ccRCC) is resistant to most chemotherapeutic drugs and the molecular mechanisms have not been fully revealed. Genomic instability and the abnormal activation of bypass DNA repair pathway is the potential cause of tumor resistance to radiotherapy and chemotherapy. IQ-motif GTPase activating protein 3 (IQGAP3) regulates cell migration and intercellular adhesion. This study aims to analysis the effects of IQGAP3 expression on cell survival, genome stability and clinical prognosis in ccRCC.MethodsMultiple bioinformatics analysis based on TCGA database and IHC analysis on clinical specimens were included. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) were used to determine protein expression level. MTT assay and 3D spheroid cell growth assay were used to assess cell proliferation and drug resistance in RNAi transfected ccRCC cells. Cell invasion capacity was evaluated by transwell assay. The influence of IQGAP3 on genome instability was revealed by micronuclei number and γ H2AX recruitment test.ResultsThe highly expressed IQGAP3 in multiple subtypes of renal cell carcinoma has a clear prognostic value. Deletion of IQGAP3 inhibits cell growth in 3D Matrigel. IQGAP3 depletion lso increases accumulated DNA damage, and improves cell sensitivity to ionizing radiation and chemotherapeutic drugs. Therefore, targeting DNA damage repair function of IQGAP3 in tumorigenesis can provide ideas for the development of new targets for early diagnosis. creator: Wen Li creator: Zhifeng Wang creator: Hanlin Wang creator: Jian Zhang creator: Xiaobin Wang creator: Shaojun Xing creator: Si Chen uri: https://doi.org/10.7717/peerj.14201 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease link: https://peerj.com/articles/14217 last-modified: 2022-10-18 description: Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn’s disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient’s individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients. creator: Efe Sezgin creator: Gamze Terlemez creator: Berkay Bozkurt creator: Göksel Bengi creator: Hale Akpinar creator: İlker Büyüktorun uri: https://doi.org/10.7717/peerj.14217 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sezgin et al.