title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=993 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Consistency of dark skeletal muscles in Thai native black-bone chickens (Gallus gallus domesticus) link: https://peerj.com/articles/10728 last-modified: 2021-01-13 description: Black-bone chickens (Gallus gallus domesticus) have become economically valuable, particularly in Southeast Asia as a consequence of popular traditional Chinese medical practices. Chickens with whole body organ darkness are considered to have higher value and are, therefore, more often requested. This research study aimed to investigate the darkness in 34 skeletal muscles of 10 Thai black-bone chickens (five males and five females). The evaluation of muscle darkness was done on two levels: (i) a color chart was employed at the macroanatomical level and (ii) by using melanin pigment to evaluate the structure at the microanatomy level. The results revealed that the accumulation of melanin pigment in the muscle tissue was observed in the endomysium, perimysium and epimysium. With respect to the results of the color chart test, iliotibialis lateralis pars preacetabularis, gastrocnemius, fibularis longus and puboischiofemoralis pars medialis showed the highest degree of darkness, while serratus profundus, pectoralis, iliotibialis cranialis, flexor cruris lateralis, and flexor cruris medialis appeared to be the least dark. In addition, we found that the highest and lowest amounts of melanin pigment was noted in the flexor carpi ulnaris and pectoralis (p < 0.05), respectively; however, there was no significant difference (p > 0.05) observed between the sexes. These results reveal that the 34 specified muscles of black-bone chickens showed uneven distribution of darkness due to the differing accumulations of melanin pigments of each muscle.This information may provide background knowledge for a better understanding of melanin accumulation and lead to breeding improvements in Thai black-bone chickens. creator: Wannapimol Kriangwanich creator: Promporn Piboon creator: Wirakorn Sakorn creator: Kittisak Buddhachat creator: Varankpicha Kochagul creator: Kidsadagon Pringproa creator: Supamit Mekchay creator: Korakot Nganvongpanit uri: https://doi.org/10.7717/peerj.10728 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kriangwanich et al. title: Records of ctenophores from South Africa link: https://peerj.com/articles/10697 last-modified: 2021-01-12 description: Although ctenophores can be conspicuous components of the plankton in coastal marine ecosystems, only six species have been formally described from around South Africa. Using photographs from local community scientists, we add a further three species (Cestum veneris, Beroe forskalii?, Ocyropsis maculata?) and six morphospecies to the regional fauna. These additions suggest that South Africa has a ctenophore fauna that is amongst the most diverse, globally; an observation in agreement with information from other taxa. Tips on how community scientists can improve their photographic contributions to understanding ctenophore diversity are provided. creator: Mark J. Gibbons creator: Steve H.D. Haddock creator: George I. Matsumoto creator: Craig Foster uri: https://doi.org/10.7717/peerj.10697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gibbons et al. title: Present practices and emerging opportunities in bioengineering for slope stabilization in Malaysia: An overview link: https://peerj.com/articles/10477 last-modified: 2021-01-12 description: Population increase and the demand for infrastructure development such as construction of highways and road widening are intangible, leading up to mass land clearing. As flat terrains become scarce, infrastructure expansions have moved on to hilly terrains, cutting through slopes and forests. Unvegetated or bare slopes are prone to erosion due to the lack of or insufficient surface cover. The combination of exposed slope, uncontrolled slope management practices, poor slope planning and high rainfall as in Malaysia could steer towards slope failures which then results in landslides under acute situation. Moreover, due to the tropical weather, the soils undergo intense chemical weathering and leaching that elevates soil erosion and surface runoff. Mitigation measures are vital to address slope failures as they lead to economic loss and loss of lives. Since there is minimal or limited information and investigations on slope stabilization methods in Malaysia, this review deciphers into the current slope management practices such as geotextiles, brush layering, live poles, rock buttress and concrete structures. However, these methods have their drawbacks. Thus, as a way forward, we highlight the potential application of soil bioengineering methods especially on the use of whole plants. Here, we discuss the general attributions of a plant in slope stabilization including its mechanical, hydrological and hydraulic effects. Subsequently, we focus on species selection, and engineering properties of vegetation especially rooting structures and architecture. Finally, the review will dissect and assess the ecological principles for vegetation establishment with an emphasis on adopting the mix-culture approach as a slope failure mitigation measure. Nevertheless, the use of soil bioengineering is limited to low to moderate risk slopes only, while in high-risk slopes, the use of traditional engineering measure is deemed more appropriate and remain to be the solution for slope stabilization. creator: Deivaseeno Dorairaj creator: Normaniza Osman uri: https://doi.org/10.7717/peerj.10477 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Dorairaj and Osman title: Comment on Pescott & Jitlal 2020: Failure to account for measurement error undermines their conclusion of a weak impact of nitrogen deposition on plant species richness link: https://peerj.com/articles/10632 last-modified: 2021-01-12 description: Estimation of the impacts of atmospheric nitrogen (N) deposition on ecosystems and biodiversity is a research imperative. Analyses of large-scale spatial gradients, where an observed response is correlated with measured or modelled deposition, have been an important source of evidence. A number of problems beset this approach. For example, if responses are spatially aggregated then treating each location as statistically independent can lead to biased confidence intervals and a greater probably of false positive results. Using methods that account for residual spatial autocorrelation, Pescott & Jitlal (2020) re-analysed two large-scale spatial gradient datasets from Britain where modelled N deposition at 5 × 5 km resolution had been previously correlated with species richness in small quadrats. They found that N deposition effects were weaker than previously demonstrated leading them to conclude that “previous estimates of Ndep impacts on richness from space-for-time substitution studies are likely to have been over-estimated”. We use a simulation study to show that their conclusion is unreliable despite them recognising that an influential fraction of the residual spatially structured variation could itself be attributable to N deposition. This arises because the covariate used was modelled N deposition at 5 × 5 km resolution leaving open the possibility that measured or modelled N deposition at finer resolutions could explain more variance in the response. Explicitly treating this as spatially auto-correlated error ignores this possibility and leads directly to their unreliable conclusion. We further demonstrate the plausibility of this scenario by showing that significant variation in N deposition at the 1 km square resolution is indeed averaged at 5 × 5 km resolution. Further analyses are required to explore whether estimation of the size of the N deposition effect on plant species richness and other measures of biodiversity is indeed dependent on the accuracy and hence measurement error of the N deposition covariate. Until then the conclusions of Pescott & Jitlal (2020) should be considered premature. creator: Simon M. Smart creator: Carly J. Stevens creator: Sam J. Tomlinson creator: Lindsay C. Maskell creator: Peter A. Henrys uri: https://doi.org/10.7717/peerj.10632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Smart et al. title: Calcineurin subunit B is involved in shell regeneration in Haliotis diversicolor link: https://peerj.com/articles/10662 last-modified: 2021-01-12 description: Abalone shells are mainly composed of two major polymorphs of CaCO3 that are distributed in different layers of the shell. The process of shell biomineralization is controlled by genes and proteins expressed within the mantle epithelium. In this present paper, we conducted a shell regeneration experiment to study the role of HcCNA and HcCNB (individual subunits of calcineurin) in shell biomineralization in H. diversicolor. The results of qPCR showed that HcCNB is upregulated to a greater extent than HcCNA in the mantle after shell notching. In vivo study of the effects of rHcCNB injection showed a significantly higher percentage of regenerated shell length, but not area, in the injected group compared to the control group. In addition, SEM observation of the inner surface of the regenerated shells revealed three different zones including prismatic, nacreous, and a distinct transition zone. Changes in the crystal organization and ultrastructure are clearly evident in these three zones, particularly after 3 weeks of rHcCNB administration. We hypothesize that this is due to faster biomineralization rates in the rHcCNB treated group. Taken together, our results demonstrate that HcCNB participates in shell regeneration in H. diversicolor. As calcineurin subunits have also been implicated in shell formation in bivalves, these findings suggest that calcineurin subunits may play important roles in biomineralization in all conchiferans. creator: Tiranan Buddawong creator: Somluk Asuvapongpatana creator: Chanyatip Suwannasing creator: Valainipha Habuddha creator: Chompoonut Sukonset creator: Chanyarak Sombutkayasith creator: Carmel McDougall creator: Wattana Weerachatyanukul uri: https://doi.org/10.7717/peerj.10662 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Buddawong et al. title: Effects of subjective and objective autoregulation methods for intensity and volume on enhancing maximal strength during resistance-training interventions: a systematic review link: https://peerj.com/articles/10663 last-modified: 2021-01-12 description: BackgroundMaximal strength is a critical determinant of performance in numerous sports. Autoregulation is a resistance training prescription approach to adjust training variables based on the individuals’ daily fluctuations in performance, which are a result of training-induced fitness and fatigue, together with readiness from daily non-training stressors.ObjectiveThis review aimed to summarise the effects of different subjective and objective autoregulation methods for intensity and volume on enhancing maximal strength.Materials and MethodsA comprehensive literature search was conducted through SPORTDiscus, PubMed and Google Scholar. Studies had to meet the following criteria to be included in the review: (1) estimation of 1-RM or a 1-RM test for both pre-test and post-test to measure progression in strength assessment during the training intervention, (2) a training comparison group, (3) participants were healthy, (4) the article had a detailed description of training intensity, training volume, and training frequency during the training intervention, (5) the training intervention lasted for more than four weeks, (6) studies with objective autoregulation methods utilised a validated measuring tool to monitor velocity, (7) English-language studies.ResultsFourteen studies met the inclusion criteria, comprising 30 training groups and 356 participants. Effect size and percentage differences were calculated for 13 out of 14 studies to compare the effects of different training interventions. All autoregulation training protocols resulted in an increase in 1-RM, from small ES to large ES.ConclusionOverall, our findings suggest that using both subjective autoregulation methods for intensity, such as repetitions in reserve rating of perceived exertion and flexible daily undulation periodisation, together with objective autoregulation methods for autoregulation intensity and volume, such as velocity targets and velocity loss, could be effective methods for enhancing maximal strength. It is speculated that this is because the implementation of autoregulation into a periodised plan may take into account the athletes’ daily fluctuations, such as fluctuations in fitness, fatigue, and readiness to train. When training with a validated measuring tool to monitor velocity, this may provide objective augmented intra- and interset feedback during the resistance exercise who could be beneficial for increasing maximal strength. Coaches, practitioners, and athletes are encouraged to implement such autoregulation methods into a periodised plan when the goal is to enhance maximal strength. creator: Stian Larsen creator: Eirik Kristiansen creator: Roland van den Tillaar uri: https://doi.org/10.7717/peerj.10663 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Larsen et al. title: Molecular systematics of the Sicista tianschanica species complex: a contribution from historical DNA analysis link: https://peerj.com/articles/10759 last-modified: 2021-01-12 description: The Tianshan birch mouse Sicista tianschanica is an endemic of the Central Asian mountains and has previously been shown to include several karyomorphs (“Terskey”, “Talgar”, “Dzungar”); however, the taxonomic status of these forms has remained uncertain. We examined the genetic variation in S. tianschanica based on historical DNA samples from museum collections, including the type series. Mitochondrial and nuclear data indicated that the species complex includes two major clades: Northern (N) and Southern (S) (cytb distance 13%). The N clade corresponds to the “Dzungar” karyomorph (Dzungar Alatau, Tarbagatay). The S clade is comprised of four lineages (S1–S4) divergent at 6–8%; the relationships among which are resolved incompletely. The S1 lineage is found in eastern Tianshan and corresponds to the nominal taxon. The S2 is distributed in central and northern Tianshan and corresponds to the “Terskey” karyomorph. The S3 is restricted to Trans-Ili Alatau and belongs to the “Talgar” karyomorph. The S4 is represented by a single specimen from southeastern Dzungar Alatau with "Talgar" karyotype. No interlineage gene flow was revealed. The validity of S. zhetysuica (equivalent to the N clade) is supported. Based on genetic and karyotypic evidence, lineages S2 and S3 are described as distinct species. The status of the S4 requires further investigation. creator: Vladimir S. Lebedev creator: Yulia Kovalskaya creator: Evgeniya N. Solovyeva creator: Elena D. Zemlemerova creator: Anna A. Bannikova creator: Mikhail Yu Rusin creator: Vera A. Matrosova uri: https://doi.org/10.7717/peerj.10759 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lebedev et al. title: New distributional records of the Samana least gecko (Sphaerodactylus samanensis, Cochran, 1932) with comments on its morphological variation and conservation status link: https://peerj.com/articles/10404 last-modified: 2021-01-11 description: We report here five new localities across the distribution of the lizard Sphaerodactylus samanensis, extending its current geographic range to the west, in the Cordillera Central of Hispaniola. We also report phenotypic variation in the color pattern and scutellation on throat and pelvic regions of males from both eastern and western populations, which is described below. Furthermore, based on these new data, we confirm that the species is not fitting in its current IUCN category, and in consequence propose updating its conservation status. creator: Germán Chávez creator: Miguel A. Landestoy T creator: Gail S. Ross creator: Joaquín A. Ugarte-Núñez uri: https://doi.org/10.7717/peerj.10404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chávez et al. title: Evaluation of resistance to powdery mildew and identification of resistance genes in wheat cultivars link: https://peerj.com/articles/10425 last-modified: 2021-01-11 description: Wheat powdery mildew, caused by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a serious disease of wheat worldwide that can cause significant yield losses. Growing resistant cultivars is the most cost-effective and eco-soundly strategy to manage the disease. Therefore, a high breeding priority is to identify genes that can be readily used either singly or in combination for effective resistance to powdery mildew and also in combination with genes for resistance to other diseases. Yunnan Province, with complex and diverse ecological environments and climates, is one of the main wheat growing regions in China. This region provides initial inoculum for starting epidemics of wheat powdery mildew in the region and other regions and thus, plays a key role in the regional and large-scale epidemics of the disease throughout China. The objectives of this study were to evaluate seedling resistance of 69 main wheat cultivars to powdery mildew and to determine the presence of resistance genes Pm3, Pm8, Pm13, Pm16, and Pm21in these cultivars using gene specific DNA markers. Evaluation of 69 wheat cultivars with six Bgt isolates showed that only four cultivars were resistant to all tested isolates, indicating that the overall level of powdery mildew resistance of Yunnan wheat cultivars is inadequate. The molecular marker results showed that 27 cultivars likely have at least one of these genes. Six cultivars were found likely to have Pm3,18 likely to have Pm8,5 likely to have Pm16,and 3 likely to have Pm21. No cultivar was found to carry Pm13. The information on the presence of the Pmresistance genes in Yunnan wheat cultivars can be used in future wheat disease breeding programs. In particular, cultivars carrying Pm21, which is effective against all Bgtraces in China, should be pyramided with other effective genes to developing new cultivars with durable resistance to powdery mildew. creator: Xianxin Wu creator: Qiang Bian creator: Yue Gao creator: Xinyu Ni creator: Yanqiu Sun creator: Yuanhu Xuan creator: Yuanyin Cao creator: Tianya Li uri: https://doi.org/10.7717/peerj.10425 license: https://creativecommons.org/licenses/by/4.0/ rights: 2021 Wu et al. title: Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen link: https://peerj.com/articles/10463 last-modified: 2021-01-11 description: BackgroundThe rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen.MethodWe aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage’s chemical characteristics and community structure of biofilm-embedded microbiota.ResultsRumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen.ConclusionOur findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen. creator: Mohammad Farhad Vahidi creator: Javad Gharechahi creator: Mehrdad Behmanesh creator: Xue-Zhi Ding creator: Jian-Lin Han creator: Ghasem Hosseini Salekdeh uri: https://doi.org/10.7717/peerj.10463 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Vahidi et al.