title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=998 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea link: https://peerj.com/articles/10538 last-modified: 2020-12-17 description: Massive floating green macroalgae have formed harmful green tides in the Yellow Sea since 2007. To study the early development and the associated environmental factors for the green tide, a field survey was carried out in the Subei Shoal, southwestern Yellow Sea. Multiple species were identified in both floating green macroalgae and micro-propagules , while their abundances showed distinct spatial variations. The floating macroalgal biomass was widespread in the northern Subei Shoal and most abundant at 34°N. Ulva prolifera dominated (91.2% in average) the floating macroalgae, and the majority (88.5%) of U. prolifera was the ‘floating type’. In comparison, the micro-propagules were most abundant around the aquaculture rafts, and decreased significantly with the distance to the rafts. The dominant species of micro-propagules was U. linza (48.5%), followed by U. prolifera (35.1%). Their distinct distribution patterns and species diversity suggested little direct contribution of micro-propagules for the floating macroalgae. The spatial variation of the floating macroalgae was probably a combined result from the biomass source and environmental factors, while the abundance of micro-propagules was closely associated with the rafts. A positive correlation between the floating macroalgae and DO was observed and suggested active photosynthesis of the initial biomass in Subei Shoal. This study revealed specific distributional pattern and relationships among the floating macroalgae, micro-propagules and the environmental factors in the source region, which helps understanding the early blooming dynamics of the green tides in Yellow Sea. creator: Xiaoxiang Miao creator: Jie Xiao creator: Qinzeng Xu creator: Shiliang Fan creator: Zongling Wang creator: Xiao Wang creator: Xuelei Zhang uri: https://doi.org/10.7717/peerj.10538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Miao et al. title: Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery link: https://peerj.com/articles/10554 last-modified: 2020-12-17 description: BackgroundPanulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region.MethodsThis study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus.ResultsUsing a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified. creator: J. Antonio Baeza uri: https://doi.org/10.7717/peerj.10554 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Baeza title: bmd: an R package for benchmark dose estimation link: https://peerj.com/articles/10557 last-modified: 2020-12-17 description: The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper’s objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R. It allows the rapid implementation of available, novel, and future statistical methods and the integration of other statistical analyses. creator: Signe M. Jensen creator: Felix M. Kluxen creator: Jens C. Streibig creator: Nina Cedergreen creator: Christian Ritz uri: https://doi.org/10.7717/peerj.10557 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jensen et al. title: Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas link: https://peerj.com/articles/10646 last-modified: 2020-12-17 description: Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism. creator: Timothy P. Driscoll creator: Victoria I. Verhoeve creator: Cassia Brockway creator: Darin L. Shrewsberry creator: Mariah Plumer creator: Spiridon E. Sevdalis creator: John F. Beckmann creator: Laura M. Krueger creator: Kevin R. Macaluso creator: Abdu F. Azad creator: Joseph J. Gillespie uri: https://doi.org/10.7717/peerj.10646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Driscoll et al. title: Observing animals and humans: dogs target their gaze to the biological information in natural scenes link: https://peerj.com/articles/10341 last-modified: 2020-12-16 description: BackgroundThis study examines how dogs observe images of natural scenes containing living creatures (wild animals, dogs and humans) recorded with eye gaze tracking. Because dogs have had limited exposure to wild animals in their lives, we also consider the natural novelty of the wild animal images for the dogs.MethodsThe eye gaze of dogs was recorded while they viewed natural images containing dogs, humans, and wild animals. Three categories of images were used: naturalistic landscape images containing single humans or animals, full body images containing a single human or an animal, and full body images containing a pair of humans or animals. The gazing behavior of two dog populations, family and kennel dogs, were compared.ResultsAs a main effect, dogs gazed at living creatures (object areas) longer than the background areas of the images; heads longer than bodies; heads longer than background areas; and bodies longer than background areas. Dogs gazed less at the object areas vs. the background in landscape images than in the other image categories. Both dog groups also gazed wild animal heads longer than human or dog heads in the images. When viewing single animal and human images, family dogs focused their gaze very prominently on the head areas, but in images containing a pair of animals or humans, they gazed more at the body than the head areas. In kennel dogs, the difference in gazing times of the head and body areas within single or paired images failed to reach significance.DiscussionDogs focused their gaze on living creatures in all image categories, also detecting them in the natural landscape images. Generally, they also gazed at the biologically informative areas of the images, such as the head, which supports the importance of the head/face area for dogs in obtaining social information. The natural novelty of the species represented in the images as well as the image category affected the gazing behavior of dogs. Furthermore, differences in the gazing strategy between family and kennel dogs was obtained, suggesting an influence of different social living environments and life experiences. creator: Heini Törnqvist creator: Sanni Somppi creator: Miiamaaria V. Kujala creator: Outi Vainio uri: https://doi.org/10.7717/peerj.10341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Törnqvist et al. title: Transcriptome profiling reveals Silibinin dose-dependent response network in non-small lung cancer cells link: https://peerj.com/articles/10373 last-modified: 2020-12-16 description: Silibinin (SIL), a natural flavonolignan from the milk thistle (Silybum marianum), is known to exhibit remarkable hepatoprotective, antineoplastic and EMT inhibiting effects in different cancer cells by targeting multiple molecular targets and pathways. However, the predominant majority of previous studies investigated effects of this phytocompound in a one particular cell line. Here, we carry out a systematic analysis of dose-dependent viability response to SIL in five non-small cell lung cancer (NSCLC) lines that gradually differ with respect to their intrinsic EMT stage. By correlating gene expression profiles of NSCLC cell lines with the pattern of their SIL IC50 response, a group of cell cycle, survival and stress responsive genes, including some prominent targets of STAT3 (BIRC5, FOXM1, BRCA1), was identified. The relevancy of these computationally selected genes to SIL viability response of NSCLC cells was confirmed by the transient knockdown test. In contrast to other EMT-inhibiting compounds, no correlation between the SIL IC50 and the intrinsic EMT stage of NSCLC cells was observed. Our experimental results show that SIL viability response of differently constituted NSCLC cells is linked to a subnetwork of tightly interconnected genes whose transcriptomic pattern can be used as a benchmark for assessment of individual SIL sensitivity instead of the conventional EMT signature. Insights gained in this study pave the way for optimization of customized adjuvant therapy of malignancies using Silibinin. creator: Jagan Mohan Kaipa creator: Vytaute Starkuviene creator: Holger Erfle creator: Roland Eils creator: Evgeny Gladilin uri: https://doi.org/10.7717/peerj.10373 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kaipa et al. title: Muscle strength and inflammatory response to the training load in rowers link: https://peerj.com/articles/10355 last-modified: 2020-12-16 description: BackgroundRegular exercise leads to changes in muscle metabolism. The consequence of this is the adaptation to higher training loads.The aim of this study was to evaluate biomechanical and biochemical parameters describing the functions of skeletal muscles in periods when changes in training forms were introduced.MethodsSeventeen male sweep-oar rowers, members of the Polish national rowing team, participated. The study was carried out at the beginning and at the end of the preparatory period. In the first and second examination measurements of torques of selected muscle groups and blood biochemical analysis were performed.ResultsThere was observed a statistically significant decrease in the relative global force of the right lower limb between both terms of examination. A statistically significant increase in maximum torque was found for torso flexors. In the case of muscles responsible for torso rotation, a statistically significant decrease in the torque values of right torso rotators was observed. A significant difference was found with respect to creatine kinase activity, total testosterone concentration, total testosterone to cortisol ratio and total phenolics concentration (p < 0.05).ConclusionThe study shows that the rowers’ training should be more focused on building the strength of lower limbs to prevent the overload of lumbar spine and that the amount of force developed may be significantly affected by the antioxidant potential of rowers. creator: Tomasz Podgórski creator: Alicja Nowak creator: Katarzyna Domaszewska creator: Jacek Mączyński creator: Magdalena Jabłońska creator: Jarosław Janowski creator: Małgorzata B. Ogurkowska uri: https://doi.org/10.7717/peerj.10355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Podgórski et al. title: Dysregulated levels of glycogen synthase kinase-3β (GSK-3β) and miR-135 in peripheral blood samples of cases with nephrotic syndrome link: https://peerj.com/articles/10377 last-modified: 2020-12-16 description: BackgroundGlycogen synthase kinase-3 (GSK-3β) is a serine/threonine kinase with multifunctions in various physiological procedures. Aberrant level of GSK-3β in kidney cells has a harmful role in podocyte injury.MethodsIn this article, the expression levels of GSK-3β and one of its upstream regulators, miR-135a-5p, were measured in peripheral blood mononuclear cells (PBMCs) of cases with the most common types of nephrotic syndrome (NS); focal segmental glomerulosclerosis (FSGS) and membranous glomerulonephritis (MGN). In so doing, fifty-two cases along with twenty-four healthy controls were included based on the strict criteria.ResultsLevels of GSK-3β mRNA and miR-135 were measured with quantitative real-time PCR. There were statistically significant increases in GSK-3β expression level in NS (P = 0.001), MGN (P = 0.002), and FSGS (P = 0.015) groups compared to the control group. Dysregulated levels of miR-135a-5p in PBMCs was not significant between the studied groups. Moreover, a significant decrease was observed in the expression level of miR-135a-5p in the plasma of patients with NS (P = 0.020), MGN (P = 0.040), and FSGS (P = 0.046) compared to the control group. ROC curve analysis approved a diagnostic power of GSK-3β in discriminating patients from healthy controls (AUC: 0.72, P = 0.002) with high sensitivity and specificity.ConclusionsDysregulated levels of GSK-3β and its regulator miR-135a may participate in the pathogenesis of NS with different etiology. Therefore, more research is needed for understanding the relationship between them. creator: Mohammadreza Ardalan creator: Seyyedeh Mina Hejazian creator: Hassan Fazlazar Sharabiyani creator: Farahnoosh Farnood creator: Amirhossein Ghafari Aghdam creator: Milad Bastami creator: Elham Ahmadian creator: Sepideh Zununi Vahed creator: Magali Cucchiarini uri: https://doi.org/10.7717/peerj.10377 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Ardalan et al. title: Long-term administration of vitamin B12 and adenosine triphosphate for idiopathic sudden sensorineural hearing loss: a retrospective study link: https://peerj.com/articles/10406 last-modified: 2020-12-16 description: BackgroundIn idiopathic sudden sensorineural hearing loss (ISSNHL), the relationship between the administration duration of vitamin B12 (vit B12) with adenosine triphosphate (ATP) and their therapeutic effect is not fully understood.ObjectiveTo investigate the therapeutic effect of long-term 16 (≥weeks) administration of vit B12 with ATP on the prognosis of ISSNHL patients and compare it with those of short-term (<8 weeks) and middle-term (≥8 weeks, <16 weeks) administration.MethodsWe retrospectively reviewed the medical records of 117 patients with ISSNHL treated between 2015 and 2018.ResultsThe overall recovery rate was 32.5%. Initial higher hearing threshold and initial higher grade of hearing loss (HL) were associated with a poor prognosis. However, the administration duration of vit B12 and ATP did not influence the overall hearing improvement. With regard to the time course of hearing recovery, there was no significant difference in hearing recovery among the long-, middle-, and short-term administration groups until 16 weeks after treatment. However, at 16–24 weeks after initial treatment, the short-term administration group exhibited significantly lower hearing recovery than did the long-term administration groups.ConclusionsThe administration duration of vit B12 and ATP did not influence the overall hearing prognosis in ISSNHL, but long-term administration of vit B12 and ATP helped prevent the progression of HL after ISSNHL. Our results suggest that long-term administration of vit B12 and ATP is not necessarily required to treat ISSNHL patients, except for slowly progressing HL in the affected ears. creator: Takaomi Kurioka creator: Hajime Sano creator: Shogo Furuki creator: Taku Yamashita uri: https://doi.org/10.7717/peerj.10406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kurioka et al. title: Characterization of DNA methylation in Malawian Mycobacterium tuberculosis clinical isolates link: https://peerj.com/articles/10432 last-modified: 2020-12-16 description: BackgroundAlthough Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized.MethodsWe completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date.ResultsWe replicate and confirm four methylation disrupting mutations in 4 lineages of Mtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in the MamB gene of Indo-oceanic lineage of Mtb. Additionally, we report a novel missense mutation G454A (G152S) in the MamA gene of the Euro-American lineage which could potentially be attributed to total disruption of methylation in the CCCAG motif but partial loss in a partner motif. Through a genomic and methylome comparative analysis with a global sample of sixteen, we report previously unknown mutations affecting the pks15/1 locus in L6 isolates. We confirm that methylation in Mtb is lineage specific although some unresolved issues still remain. creator: Victor Ndhlovu creator: Anmol Kiran creator: Derek J. Sloan creator: Wilson Mandala creator: Marriott Nliwasa creator: Dean B. Everett creator: Benjamin Kumwenda creator: Mphatso Mwapasa creator: Konstantina Kontogianni creator: Mercy Kamdolozi creator: Elizabeth Corbett creator: Maxine Caws creator: Gerry Davies uri: https://doi.org/10.7717/peerj.10432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ndhlovu et al.