title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=714 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation link: https://peerj.com/articles/13115 last-modified: 2022-05-16 description: Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern SCS. creator: Jinpeng Zhang creator: Andrzej Witkowski creator: Michał Tomczak creator: Chao Li creator: Kevin McCartney creator: Zhen Xia uri: https://doi.org/10.7717/peerj.13115 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna link: https://peerj.com/articles/13251 last-modified: 2022-05-16 description: The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins) OMM assemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale. creator: Gabriel Aguirre-Fernández creator: Jürg Jost creator: Sarah Hilfiker uri: https://doi.org/10.7717/peerj.13251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aguirre-Fernández et al. title: Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park link: https://peerj.com/articles/13302 last-modified: 2022-05-16 description: BackgroundThe reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia’s Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies.MethodsThis study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models.ResultsA total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Conversely, a higher proportion of immature manta rays used the northern site, Cauldron, where foraging was commonly observed. Fishing gear-related injuries were noted on 56 individuals (~5%), and predatory injuries were present on 32 individuals (~3%). Tourism within the park increased from 2014 to 2017, with 34% more dive boats per survey at Karang Makassar and Mawan.DiscussionThe Komodo NP contains several distinct critical habitats for manta rays that encompass all demographics and accommodate seasonal manta ray movements. While the present study has not examined population trends, it does provide foundational data for such work. Continued research into manta ray abundance, long-range movements, and identifying and protecting other critical aggregation areas within the region is integral to securing the species’ recovery. We provide management recommendations to limit undue pressure on manta rays and their critical habitats from tourism. creator: Elitza S. Germanov creator: Simon J. Pierce creator: Andrea D. Marshall creator: I. Gede Hendrawan creator: Ande Kefi creator: Lars Bejder creator: Neil Loneragan uri: https://doi.org/10.7717/peerj.13302 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Germanov et al. title: Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries link: https://peerj.com/articles/13426 last-modified: 2022-05-16 description: IntroductionThe consumption of dairy products contributes to health, nutrition, and livelihoods globally. However, dairy products do not come without microbiological food safety risks for consumers. Despite this risk, common hygiene measures in high-income countries, particularly pasteurisation, ensures that milk is safe, and is indeed frequently mandated by law. Nevertheless, over the past two decades, there has been a global increase in the number of consumers in high-income developed countries actively seeking out unpasteurised milk in liquid and product forms for perceived nutritional and health benefits, and improved taste. The often-anecdotal claims upon which consumers make such choices are not all supported by scientific evidence; however, some recent research studies have investigated (and in some cases demonstrated) the positive impact of unpasteurised milk consumption on the prevalence of asthma, atopy, rectal cancer and respiratory illness.MethodsTo investigate the significance of unpasteurised milk and milk product consumption for human health in high-income countries, outbreak data between the years 2000 and 2018 were obtained for the United States of America, Canada, the European Union, the United Kingdom, Japan, New Zealand and Australia, which were then categorized into three World Health Organisation subregions: AMR A, EUR A and WPR A. Outbreak dynamic variables such as pathogens, the place of consumption, numbers of outbreaks and deaths per million capita, the average number of cases per outbreak and regulations were described and analysed using R Studio. To provide an overview of unpasteurised milk-related disease outbreaks, a rapid evidence review was also undertaken to establish an overview of what is known in the current literature about hazards and drivers of consumption.ResultsFoodborne outbreaks associated with unpasteurised dairy consumption have risen in high-income countries over the period 2000 to 2018, with Campylobacter spp. being the most common aetiological agent responsible, followed by Escherichia coli and Salmonella spp. The most common places of consumption are on farms or in households, indicating individuals choose to drink unpasteurised milk, rather than a widespread distribution of the product, for example, at social events and in schools. Further study is needed to better understand contributing factors, such as cultural differences in the consumption of dairy products.ConclusionThere are several observable health benefits linked to consuming raw milk, but outbreaks associated with unpasteurised milk and milk products are on the rise. It cannot be definitively concluded whether the benefits outweigh the risks, and ultimately the decision lies with the individual consumer. Nevertheless, many countries have regulations in place to protect consumer health, acknowledging the definite risks to human health that unpasteurised dairy foods may pose, particularly from microbial hazards. creator: Joanna N. de Klerk creator: Philip A. Robinson uri: https://doi.org/10.7717/peerj.13426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 de Klerk and Robinson title: Search for morphological indicators that predict implantation by principal component analysis using images of blastocyst link: https://peerj.com/articles/13441 last-modified: 2022-05-16 description: BackgroundAlthough the current evaluation of human blastocysts is based on the Gardner criteria, there may be other notable parameters. The purpose of our study was to clarify whether the morphology of blastocysts has notable indicators other than the Gardner criteria.MethodsTo find such indicators, we compared blastocysts that showed elevated human chorionic gonadotropin (hCG) levels after transplantation (hCG-positive group; n = 129) and those that did not (hCG-negative group; n = 105) using principal component analysis of pixel brightness of the images.ResultsThe comparison revealed that the hCG-positive group had grainy morphology and the hCG-negative group had non-grainy morphology. Classification of the blastocysts by this indicator did not make a difference in Gardner score. Interestingly, all embryos with ≥20% fragmentation were non-grainy. The visual classification based on this analysis was significantly more accurate than the prediction of implantation using the Gardner score ≥3BB. As graininess can be used in combination with the Gardner score, this indicator will enhance current reproductive technologies. creator: Daisuke Mashiko creator: Mikiko Tokoro creator: Masae Kojima creator: Noritaka Fukunaga creator: Yoshimasa Asada creator: Kazuo Yamagata uri: https://doi.org/10.7717/peerj.13441 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mashiko et al. title: Malformations in Late Devonian brachiopods from the western Junggar, NW China and their potential causes link: https://peerj.com/articles/13447 last-modified: 2022-05-16 description: Although malformations are found in both extant organisms and the fossil record, they are more rarely reported in the fossil record than in living organisms, and the environmental factors causing the malformations are much more difficult to identify for the fossil record. Two athyrid brachiopod taxa from the Upper Devonian Hongguleleng Formation in western Junggar (Xinjiang, NW China) show distinctive shell malformation. Of 198 Cleiothyridina and 405 Crinisarina specimens, 18 and 39 individuals were malformed, respectively; an abnormality ratio of nearly 10%. Considering the preservation status and buried environment of the abnormal specimens, and analysis of trace elements and rare earth elements from whole-rock and brachiopod shells, we conclude that the appearance of malformed athyrids is likely related to epi/endoparasites, or less likely the slightly higher content of heavy metal in the sea. creator: Ruiwen Zong creator: Yiming Gong uri: https://doi.org/10.7717/peerj.13447 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zong and Gong title: Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.) link: https://peerj.com/articles/13189 last-modified: 2022-05-13 description: Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree. creator: Bingbing Guo creator: Hong Yang creator: Longjun Dai creator: Xizhu Zhao creator: Li-feng Wang uri: https://doi.org/10.7717/peerj.13189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Guo et al. title: Anatomical indicators of Eucalyptus spp. resistance to Glycaspis brimblecombei (Hemiptera: Aphalaridae) link: https://peerj.com/articles/13346 last-modified: 2022-05-13 description: The total area of forest crops in Brazil is 9.55 million hectares, of which 7.5 million hectares are Eucalyptus. These crops are the most productive in the world, but may suffer losses due to exotic pests, including Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae) found in Brazil since 2003. Interactions between Eucalyptus plants and insect pests may led to the selection of resistant genotypes. Eucalyptus species are either susceptible or resistant to this pest group, but the damage they suffer needs to be evaluated. The objective was to determine possible leaf anatomy indicators of different Eucalyptus species associated with G. brimblecombei infestations, focusing on plant resistance to this pest. The study was carried out with Eucalyptus camaldulensis, Eucalyptus grandis, Eucalyptus saligna and Eucalyptus urophylla saplings infested or not by G. brimblecombei eggs and nymphs. Eighteen anatomical characteristics of the leaves of these plants were analyzed. The number of stomata on the adaxial and abaxial sides and the glandular area in the central leaf vein are associated with greater or lesser infestation by G. brimblecombei in the Eucalyptus genotypes. creator: Fernando Henrique Moreno de Oliveira Del Piero creator: Carlos Frederico Wilcken creator: Maurício Magalhães Domingues creator: Ana Laura Favoreto creator: Roberto Antonio Rodella creator: Alexandre Igor Azevedo Pereira creator: Wiane Meloni Silva creator: José Eduardo Serrão creator: José Cola Zanuncio uri: https://doi.org/10.7717/peerj.13346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Del Piero et al. title: Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L. link: https://peerj.com/articles/13372 last-modified: 2022-05-13 description: BackgroundCotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development.MethodsUsing genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum.ResultsChromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton. creator: Kun Liu creator: Nosheen Kabir creator: Zhenzhen Wei creator: Zhuojing Sun creator: Jian Wang creator: Jing Qi creator: Miaoyang Liu creator: Ji Liu creator: Kehai Zhou uri: https://doi.org/10.7717/peerj.13372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Prevalence of hyperglycemia in masters athletes link: https://peerj.com/articles/13389 last-modified: 2022-05-13 description: BackgroundAgeing is associated with decreased physical activity, obesity and subsequently an increased risk of developing type 2 diabetes mellitus (T2dm). Master athletes (MA) have initiated exercise or sport later in life or pursued a physically active lifestyle for an extended period. Subsequently, MAs have been proposed as a model of successful ageing as this active lifestyle is associated with health benefits including decreased health risk of chronic diseases and a reduction in premature mortality. Given long-term physical activity/exercise has previously been shown to be protective against hyperglycemia, a risk factor for T2dm, it is plausible that MA may have protective benefit against developing hyperglycemia. Therefore, the aim of this study was to investigate the prevalence of hyperglycemia via fasting plasma glucose (FPG) in MAs competing at the World Masters Games (WMG).MethodsThis cross-sectional, observational survey utilized an online survey using open-source web-based software was used to investigate MAs physiological and medical-related parameters. Over 28,000 MAs competed in the WMG, of which 8,072 MAs completed the survey. Of these MAs, a total of 486 (males 277, females 209; range 27 to 91 years, mean age 55.1 ± 10.2 years) attained recent pathology results which included FPG which was subsequently analyzed for this study. FPG and other outcome variables were compared between genders and to the Australian and United States general population.ResultsMean FPG for MAs was 5.03 mmol (±1.2, 95% CI [4.9–5.1] mmol) with majority (75.5%) of MAs reporting a normal (<5.5 mmol) FPG, followed by pre-diabetes (20.2%, >5.51 to <5.99 mmol) and abnormal (4.3%, >7.0 mmol). There was no significant difference (P = 0.333) in FPG between genders however, males had a slightly higher (+2.1%) FPG as compared to females (5.08 ± 1.2 mmol (95% CI [4.9–5.22] mmol) versus 4.98 ± 1.1 mmol (95% CI 4.8-5.1 mmol)). The majority of males (71.8%) and females (80.3%) were classified with a normal FPG. With regard to an abnormal FPG level, only 4.0% of males and 4.9% of females were classified abnormal which was suggestive of undiagnosed T2dm. With regard to age by decade, there was no significant difference (P = 0.06–1.00) between age groups and no relationship between the MAs’ age and FPG (r = .054, P = 0.24). As a group, MAs had a significantly lower FPG as compared to the Australian (−3.2%, P = 0.005) and United States general populations (−13.9%, P < 0.001).ConclusionsMost, however not all, MAs were found to have normal glycaemia, with only a small percentage indicating a risk of developing T2dm (i.e., impaired fasting glucose) and a smaller percentage identified with an abnormal FPG, suggestive of T2dm. These findings suggest MAs appear to be at low metabolic risk for developing T2dm based upon FPG and the physical activity/exercise they complete as MAs may indeed be protective against hyperglycemia whilst maintaining an active lifestyle. creator: Mike Climstein creator: Joe Walsh creator: Kent Adams creator: Trish Sevene creator: Tim Heazlewood creator: Mark DeBeliso uri: https://doi.org/10.7717/peerj.13389 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Climstein et al.