title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=850 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Development and validation of a novel survival model for acute myeloid leukemia based on autophagy-related genes link: https://peerj.com/articles/11968 last-modified: 2021-08-12 description: BackgroundAcute myeloid leukemia (AML) is one of the most common blood cancers, and is characterized by impaired hematopoietic function and bone marrow (BM) failure. Under normal circumstances, autophagy may suppress tumorigenesis, however under the stressful conditions of late stage tumor growth autophagy actually protects tumor cells, so inhibiting autophagy in these cases also inhibits tumor growth and promotes tumor cell death.MethodsAML gene expression profile data and corresponding clinical data were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, from which prognostic-related genes were screened to construct a risk score model through LASSO and univariate and multivariate Cox analyses. Then the model was verified in the TCGA cohort and GEO cohorts. In addition, we also analyzed the relationship between autophagy genes and immune infiltrating cells and therapeutic drugs.ResultsWe built a model containing 10 autophagy-related genes to predict the survival of AML patients by dividing them into high- or low-risk subgroups. The high-risk subgroup was prone to a poorer prognosis in both the training TCGA-LAML cohort and the validation GSE37642 cohort. Univariate and multivariate Cox analysis revealed that the risk score of the autophagy model can be used as an independent prognostic factor. The high-risk subgroup had not only higher fractions of CD4 naïve T cell, NK cell activated, and resting mast cells but also higher expression of immune checkpoint genes CTLA4 and CD274. Last, we screened drug sensitivity between high- and low-risk subgroups.ConclusionThe risk score model based on 10 autophagy-related genes can serve as an effective prognostic predictor for AML patients and may guide for patient stratification for immunotherapies and drugs. creator: Li Huang creator: Lier Lin creator: Xiangjun Fu creator: Can Meng uri: https://doi.org/10.7717/peerj.11968 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Huang et al. title: Muvi schmallenbergi gen. nov., sp. nov. (Crustacea, Tanaidacea) from the southeast Australian coast, with comments on the distribution and habitat preferences of Chondropodinae link: https://peerj.com/articles/11607 last-modified: 2021-08-11 description: Based on material collected from the shelf off southeast Australia (offshore of Portland), a new genus and new species, Muvi schmallenbergi gen. nov., sp. nov., of the tanaidacean family Metapseudidae, is described. Muvi is distinguishable from other genera within the subfamily Chondropodinae by having equally long antennular flagella. It also differs from other Chondropodinae by a combination of characters such as eyelobes with a group of visual elements, rostrum with smooth lateral edges, pereonites with lateral processes and pleotelson lacking lateral process, antennule article-1 with a single apophysis, maxillule inner lobe well-developed, labial palp bearing three distal setae, cheliped exopod well-developed and setose, pereopod-1 coxa with distinct apophysis, pleopods in five pairs, and uropod basis without apophysis. The genus Deidamiapseudes Sganga & Roccatagliata, 2016 is moved from Chondropodinae (Metapseudidae) to Apseudoidea incertae sedis. An identification key for the genera within Chondropodinae is given, and their distribution is discussed. creator: Piotr Jóźwiak creator: Magdalena Błażewicz uri: https://doi.org/10.7717/peerj.11607 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jóźwiak and Błażewicz title: Genome-wide identification and characterization of the Lateral Organ Boundaries Domain (LBD) gene family in polyploid wheat and related species link: https://peerj.com/articles/11811 last-modified: 2021-08-11 description: BackgroundWheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species.MethodsUsing a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a–e, II a and II b).ResultsThe gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat. creator: Jun Xu creator: Ping Hu creator: Ye Tao creator: Puwen Song creator: Huanting Gao creator: Yuanyuan Guan uri: https://doi.org/10.7717/peerj.11811 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Xu et al. title: Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India link: https://peerj.com/articles/11846 last-modified: 2021-08-11 description: To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm. creator: Vikas Vohra creator: Narendra Pratap Singh creator: Supriya Chhotaray creator: Varinder Singh Raina creator: Alka Chopra creator: Ranjit Singh Kataria uri: https://doi.org/10.7717/peerj.11846 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Vohra et al. title: Transport of biodeposits and benthic footprint around an oyster farm, Damariscotta Estuary, Maine link: https://peerj.com/articles/11862 last-modified: 2021-08-11 description: The benthic impact of aquaculture waste depends on the area and extent of waste accumulation on the sediment surface below and around the farm. In this study we investigated the effect of flow on biodeposit transport and initial deposition by calculating a rough aquaculture “footprint” around an oyster aquaculture farm in the Damariscotta River, ME. We also compared a site under the farm to a downstream “away” site calculated to be within the footprint of the farm. We found similar sediment biogeochemical fluxes, geochemical properties and macrofaunal communities at the site under the farm and the away site, as well as low organic enrichment at both sites, indicating that biodeposition in this environment likely does not have a major influence on the benthos. To predict accumulation of biodeposits, we measured sediment erodibility under a range of shear stresses and found slightly higher erosion rates at the farm than at the away site. A microalgal mat was observed at the sediment surface in many sediment cores. Partial failure of the microalgal mat was observed at high shear velocity, suggesting that the mat may fail and surface sediment erode at shear velocities comparable to or greater than those calculated fromin situ flow measurements. However, this study took place during neap tide, and it is likely that peak bottom velocities during spring tides are high enough to periodically “clear” under-farm sediment of recent deposits. creator: Kara Gadeken creator: William C. Clemo creator: Will Ballentine creator: Steven L. Dykstra creator: Mai Fung creator: Alexis Hagemeyer creator: Kelly M. Dorgan creator: Brian Dzwonkowski uri: https://doi.org/10.7717/peerj.11862 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gadeken et al. title: Biogeography, diversity and environmental relationships of shelf and deep-sea benthic Amphipoda around Iceland link: https://peerj.com/articles/11898 last-modified: 2021-08-11 description: The waters around Iceland, bounding the Northern North Atlantic and the Nordic seas, are a region characterized by complex hydrography and seabed topography. This and the presence of the Greenland-Iceland-Faroe-Scotland ridge (GIFR) are likely to have a major impact on the diversity and distribution of the benthic fauna there. Biodiversity in this region is also under increasing threat from climate-induced changes, ocean warming and acidification in particular, affecting the marine realm. The aim of the present study was to investigate the biodiversity and distributional patterns of amphipod crustaceans in Icelandic waters and how it relates to environmental variables and depth. A comprehensive data set from the literature and recent expeditions was compiled constituting distributional records for 355 amphipod species across a major depth gradient (18–3,700 m). Using a 1° hexagonal grid to map amphipod distributions and a set of environmental factors (depth, pH, phytobiomass, velocity, dissolved oxygen, dissolved iron, salinity and temperature) we could identify four distinct amphipod assemblages: A Deep-North, Deep-South, and a Coastal cluster as well as one restricted to the GIFR. In addition to depth, salinity and temperature were the main parameters that determined the distribution of amphipods. Diversity differed greatly between the depth clusters and was significantly higher in coastal and GIFR assemblages compared to the deep-sea clusters north and south of the GIFR. A variety of factors and processes are likely to be responsible for the perceived biodiversity patterns, which, however, appear to vary according to region and depth. Low diversity of amphipod communities in the Nordic basins can be interpreted as a reflection of the prevailing harsh environmental conditions in combination with a barrier effect of the GIFR. By contrast, low diversity of the deep North Atlantic assemblages might be linked to the variable nature of the oceanographic environment in the region over multiple spatio-temporal scales. Overall, our study highlights the importance of amphipods as a constituent part of Icelandic benthos. The strong responses of amphipod communities to certain water mass variables raise the question of whether and how their distribution will change due to climate alteration, which should be a focus of future studies. creator: Anne-Nina Lörz creator: Stefanie Kaiser creator: Jens Oldeland creator: Caroline Stolter creator: Karlotta Kürzel creator: Saskia Brix uri: https://doi.org/10.7717/peerj.11898 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lörz et al. title: The composition, geography, biology and assembly of the coastal flora of the Cape Floristic Region link: https://peerj.com/articles/11916 last-modified: 2021-08-11 description: The Cape Floristic Region (CFR) is globally recognized as a hotspot of plant diversity and endemism. Much of this diversity stems from radiations associated with infertile acid sands derived from sandstones of the geologically ancient Cape Fold Belt. These ancient montane floras acted as the source for most subsequent radiations on the Cape lowlands during the Oligocene (on silcretes) and Mio–Pliocene (on shales). The geomorphic evolution of the CFR during the Plio–Pleistocene led to the first large-scale occurrence of calcareous substrata (coastal dunes and calcarenites) along the Cape coast, providing novel habitats for plant colonization and ensuing evolution of the Cape coastal flora—the most recent diversification event in the Cape. Few studies have investigated the CFR’s dune and calcarenite floras, and fewer still have done so in an evolutionary context. Here, we present a unified flora of these coastal calcareous habitats of the CFR and analyze the taxonomic, biological and geographical traits of its component species to gain insights into its assembly. The Cape coastal flora, comprising 1,365 species, is taxonomically dominated by the Asteraceae, Fabaceae and Iridaceae, with Erica, Aspalathus and Agathosma being the most speciose genera. In terms of growth-form mix, there is a roughly equal split between herbaceous and woody species, the former dominated by geophytes and forbs, the latter by dwarf and low shrubs. Species associated with the Fynbos biome constitute the bulk of the flora, while the Subtropical Thicket and Wetland biomes also house a substantial number of species. The Cape coastal flora is a distinctly southern African assemblage, with 61% of species belonging to southern African lineages (including 35% of species with Cape affinity) and 59% being endemic to the CFR. Unique among floras from the Cape and coastal Mediterranean-climate regions is the relatively high proportion of species associated with tropical lineages, several of which are restricted to calcareous substrata of the CFR. The endemic, calcicolous component of the flora, constituting 40% of species, represents 6% of the Cape’s regional plant diversity—high tallies compared to other biodiversity hotspots. Most coastal-flora endemics emerged during the Plio–Pleistocene as a product of ecological speciation upon the colonization of calcareous substrata, with the calcifugous fynbos floras of montane acid substrata being the most significant source of this diversification, especially on the typically shallow soils of calcarenite landscapes. On the other hand, renosterveld floras, associated with edaphically benign soils that are widespread on the CFR lowlands, have not been a major source of lineages to the coastal flora. Our findings suggest that, over and above the strong pH gradient that exists on calcareous substrata, soil depth and texture may act as important edaphic filters to incorporating lineages from floras on juxtaposed substrata in the CFR. creator: B. Adriaan Grobler creator: Richard M. Cowling uri: https://doi.org/10.7717/peerj.11916 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Grobler and Cowling title: Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids link: https://peerj.com/articles/11933 last-modified: 2021-08-11 description: SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 incidence in sewersheds and therefore, there is a strong interest in using these measurements to augment traditional disease surveillance methods. A wastewater surveillance program should provide rapid turn around for sample measurements (ideally within 24 hours), but storage of samples is necessary for a variety of reasons including biobanking. Here we investigate how storage of wastewater solids at 4 °C, −20 °C, and −80 °C affects measured concentrations of SARS-CoV-2 RNA. We find that short term (7 or 8 d) storage of raw solids at 4 °C has little effect on measured concentrations of SARS-CoV-2 RNA, whereas longer term storage at 4 °C (35–122 d) or freezing reduces measurements by 60%, on average. We show that normalizing SARS-CoV-2 RNA concentrations by concentrations of pepper mild mottle virus (PMMoV) RNA, an endogenous wastewater virus, can correct for changes during storage as storage can have a similar effect on PMMoV RNA as on SARS-CoV-2 RNA. The reductions in SARS-CoV-2 RNA in solids during freeze thaws is less than those reported for the same target in liquid influent by several authors. creator: Adrian Simpson creator: Aaron Topol creator: Bradley J. White creator: Marlene K. Wolfe creator: Krista R. Wigginton creator: Alexandria B. Boehm uri: https://doi.org/10.7717/peerj.11933 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Simpson et al. title: Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum) link: https://peerj.com/articles/11939 last-modified: 2021-08-11 description: BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat. creator: Jiali Zhao creator: Hongyou Li creator: Juan Huang creator: Taoxiong Shi creator: Ziye Meng creator: Qingfu Chen creator: Jiao Deng uri: https://doi.org/10.7717/peerj.11939 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhao et al. title: Herbivory and misidentification of target habitat constrain region-wide restoration success of spekboom (Portulacaria afra) in South African subtropical succulent thicket link: https://peerj.com/articles/11944 last-modified: 2021-08-11 description: Restoration of degraded subtropical succulent thicket, via the planting of Portulacaria afra (spekboom) truncheons, is the focus of a public works programme funded by the South African government. The goals of the programme, which started in 2004, are to create jobs, sequester carbon, restore biodiversity, reduce erosion, improve soil water holding capacity and catalyse private sector investment for upscaling of restoration. Here we report on a region-wide experiment to identify factors that can improve project success. Measures of success were survivorship and annual aboveground biomass carbon sequestration (ABCsr) of spekboom truncheons some 33–57 months after planting—starting in March 2008—into 173 fenced plots (0.25 ha) located throughout the global extent of spekboom thicket vegetation. We also collected data for 18 explanatory variables under the control of managers, and an additional 39 variables reflecting soil physical and chemical characteristics and rainfall patterns post restoration, all beyond the influence of managers. Since the latter covariates were available for only 83 plots, we analysed the two data sets separately. We used a prediction rule ensemble to determine the most important predictors of restoration success. There was great variation in percentage survivorship (median = 24, range = 0–100%) and ABCsr (median = 0.009, range = 0–0.38 t C ha−1 yr−1). The model using management variables explained less variance (53%) in survivorship than the model incorporating additional soil and rainfall covariates (62%). ABCsr models were better fits (78 and 88% variance explained, respectively). All model configurations identified browse intensity as a highly influential predictor of restoration success. Predicted success was highest for plots located in target habitat; however, only 45% were thus located, suggesting the need for expert input and habitat modelling for improving target habitat identification. Frost exposure was another important predictor influencing all models but was likely a consequence of locating sites off target habitat. Sites planted on equatorward slopes during the warm season showed reduced carbon sequestration, possibly due to elevated soil moisture stress associated with high radiation loads. Physiographic factors associated with improved restoration success were location on sloping ground (reduced frost exposure), increasing longitude (more warm-season rainfall) and increasing latitude (less frost coastwards). Few trends were evident among post-restoration climatic factors beyond the control of managers. Higher rainfall during the year post restoration had a negative impact on carbon sequestration while higher rain during the early months post restoration had a positive effect on both carbon sequestration and survivorship. Soil factors showed little importance for the survivorship model, whereas silt content, % K and Mg CEC emerged as predictors of carbon sequestration. Our results have direct relevance for improving the success of landscape-scale restoration projects envisioned for the ca. 8,930 km2 of degraded spekboom thicket. creator: Marius L. van der Vyver creator: Anthony J. Mills creator: Mark Difford creator: Richard M. Cowling uri: https://doi.org/10.7717/peerj.11944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 van der Vyver et al.