title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=684
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Wide space sowing achieved high productivity and effective nitrogen use of irrigated wheat in South Shanxi, China
link: https://peerj.com/articles/13727
last-modified: 2022-07-11
description: Wheat (Triticum aestivum L.) is a staple crop worldwide, and its yield has improved since the green revolution, which was attributed to chemical nitrogen (N) fertilizer application. However, regular N application decreases N use efficiency (NUE, the ratio of grain dry matter yield to N supply from soil and fertilizer). Various practices have been implemented to maintain high crop yield and improve NUE. Nowadays, the enhanced sowing method, i.e., wide space sowing (WS), has improved the productivity of wheat crops. However, how the sowing method and N application rate affect N use and yield productivity has not been fully elucidated. Field experiments with treatments using two sowing methods (WS, and drill sowing, DS) and four N application rates (0, 180, 240, and 300 kg ha−1, represented as N0, N180, N240, and N300, respectively) were conducted from 2017 to 2019. The results showed that grain yield under WS was 13.57–16.38% higher than that under DS. The yield advantage under WS was attributed to an increased ear number. Both the higher stem and productive stem percentage accounted for the increased ear number under WS. Higher total N quantity and larger leaf area index at anthesis under WS contributed to higher dry matter production, resulting in higher grain yield. Higher dry matter production was due to pre-anthesis dry weight and post-anthesis dry weight. The wheat crop under WS had a 12.44–15.00% higher NUE than that under DS. The increased NUE under WS was attributed to higher N uptake efficiency (the ratio of total N quantity at maturity to N supply from soil and fertilizer), which was the result of greater total N quantity. The higher total N quantity under WS was due to both higher pre-anthesis N uptake and post-anthesis N uptake. Remarkably, compared to DS with 240 kg N ha−1, WS with 180 kg N ha−1 had almost equal grain yield, dry matter, and total N quantity. Therefore, wheat crops under WS could achieve both high NUE and grain yield simultaneously with only moderate N fertilizer in South Shanxi, China.
creator: Qiang Wang
creator: Hafeez Noor
creator: Min Sun
creator: Aixia Ren
creator: Yu Feng
creator: Peng Qiao
creator: Jingjing Zhang
creator: Zhiqiang Gao
uri: https://doi.org/10.7717/peerj.13727
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wang et al.

title: Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México
link: https://peerj.com/articles/13235
last-modified: 2022-07-08
description: BackgroundThe gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.MethodsWe employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.ResultsAs hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6–V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.
creator: David Ramirez-Delgado
creator: Francesco Cicala
creator: Ricardo A. Gonzalez-Sanchez
creator: Rosalia Avalos-Tellez
creator: Elena Solana-Arellano
creator: Alexei Licea-Navarro
uri: https://doi.org/10.7717/peerj.13235
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Ramirez-Delgado et al.

title: Identification and subcellular localization analysis of membrane protein Ycf 1 in the microsporidian Nosema bombycis
link: https://peerj.com/articles/13530
last-modified: 2022-07-08
description: Microsporidia are obligate intracellular parasites that can infect a wide range of vertebrates and invertebrates including humans and insects, such as silkworm and bees. The microsporidium Nosema bombycis can cause pebrine in Bombyx mori, which is the most destructive disease in the sericulture industry. Although membrane proteins are involved in a wide range of cellular functions and part of many important metabolic pathways, there are rare reports about the membrane proteins of microsporidia up to now. We screened a putative membrane protein Ycf 1 from the midgut transcriptome of the N. bombycis-infected silkworm. Gene cloning and bioinformatics analysis showed that the Ycf 1 gene contains a complete open reading frame (ORF) of 969 bp in length encoding a 322 amino acid polypeptide that has one signal peptide and one transmembrane domain. Indirect immunofluorescence results showed that Ycf 1 protein is distributed on the plasma membrane. Expression pattern analysis showed that the Ycf 1 gene expressed in all developmental stages of N. bombycis. Knockdown of the Ycf 1 gene by RNAi effectively inhibited the proliferation of N. bombycis. These results indicated that Ycf 1 is a membrane protein and plays an important role in the life cycle of N. bombycis.
creator: Yong Chen
creator: Erjun Wei
creator: Ying Chen
creator: Ping He
creator: Runpeng Wang
creator: Qiang Wang
creator: Xudong Tang
creator: Yiling Zhang
creator: Feng Zhu
creator: Zhongyuan Shen
uri: https://doi.org/10.7717/peerj.13530
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Chen et al.

title: Ecological restoration stimulates environmental outcomes but exacerbates water shortage in the Loess Plateau
link: https://peerj.com/articles/13658
last-modified: 2022-07-08
description: Restoration is the natural and intervention-assisted set of processes designed to promote and facilitate the recovery of an ecosystem that has been degraded, damaged, or destroyed. However, it can also have an adverse effect on the environment. Thus, assessing an ecological restoration project’s impact is crucial to determining its success and optimum management strategies. We performed a meta-analysis concerning the environmental outcomes during the years 2000–2015 resulting from the “Grain for Green” Project (GFGP) implementation in the Loess Plateau (LP). Data were gathered from 40 peer-reviewed English-language articles chosen from a pool of 332 articles. The results showed that, on average, GFGP increased forest coverage by 35.7% (95% CI [24.15–47.52%]), and grassland by 1.05% (95% CI [0.8–1.28%]). At the same time, GFGP has a positive impact on soil carbon (C) sequestration, net ecosystem production (NEP), and net primary production (NPP), from the years 2000 to 2015 by an average of 36% (95% CI [28.96–43.18%]), 22.7% (95% CI [9.10–36.79%]), and 13.5% (95% CI [9.44–17.354%]), respectively. Soil erosion, sediment load, runoff coefficient, and water yield were reduced by 13.3% (95% CI [0.27–25.76%]), 21.5% (95% CI [1.50–39.99%]), 22.4% (95% CI [5.28–40.45%]) and 43.3% (95% CI [27.03–82.86%]), respectively, from the years 2000 to 2015. Our results indicate that water supply decreased with the increase of vegetation coverage. Therefore, to balance the needs for green space, GFGP policies and strategies should recover, enhance, and sustain more resilient ecosystems.
creator: Mbezele Junior Yannick Ngaba
creator: Yves Uwiragiye
creator: Hongzhi Miao
creator: Zhiqin Li
creator: Paulo Pereira
creator: Jianbin Zhou
uri: https://doi.org/10.7717/peerj.13658
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Ngaba et al.

title: Evaluating pharmacists’ knowledge, attitude, and practices toward amiodarone cross-reactivity with iodine: a cross-sectional pilot study
link: https://peerj.com/articles/13665
last-modified: 2022-07-08
description: IntroductionIodine is a vital mineral of the human body that acts by maintaining the health of the thyroid gland. Research has shown that iodine-rich food allergy (i.e., seafood allergy) is not caused by iodine itself; instead, it is caused by other proteins including tropomyosin and parvalbumin in shellfish and fish, respectively. Amiodarone is a commonly used antiarrhythmic agent containing a significant amount of iodine.ObjectiveThis study’s objective was to assess pharmacists’ knowledge, attitude, and practices toward the misconception of iodine allergy and the cross-reactivity with amiodarone.MethodsIn February 2020, a cross-sectional study was conducted by sending out an online survey to three pharmaceutical organizations (Saudi Pharmaceutical Society, Kuwait Pharmaceutical Association, and Oman Pharmaceutical Society). Additionally, an electronic questionnaire was administered to pharmacists attending the Dubai International Pharmaceuticals and Technologies Conference and Exhibition 2020 (DUPHAT). Chi-square or Fisher’s exact test, when appropriate, were used to compare categorical variables. The statistical analyses were carried out using SPSS software.ResultsData were collected from 66 respondents. However, only 61 (92.4%) were included in the final analysis following the exclusion of incomplete responses. The mean age of participants was 35 ± 8.48 years. The majority of participants did not have the Board of Pharmacy Specialties Certification (54.1%). Moreover, (41%) of participants licensed as pharmacists with more than 10 years of initial pharmacy licensure. Forty-three (70.5%) of participants had the misconception that iodine allergy should be considered before amiodarone administration, 20/32 (62.5%) of whom considered iodine allergy alone thought that premedication with corticosteroids and/or antihistamines is necessary. Concerning iodine allergy and amiodarone use, there was no significant difference in knowledge between the pharmacists who have board certification and those who did not.ConclusionPharmacists’ misconception concerning iodine allergy and cross-reactivity with amiodarone was evident. Implementation of educational programs targeting pharmacists is necessary to correct these misconceptions.
creator: Nura Abdullah Alshehab
creator: Munirah Abdullah Alhumaid
creator: Mohammed Abdulrazaq Alabdulwahed
creator: Abdulaziz Saleh Almulhim
uri: https://doi.org/10.7717/peerj.13665
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Alshehab et al.

title: Optimizing human coronavirus OC43 growth and titration
link: https://peerj.com/articles/13721
last-modified: 2022-07-08
description: Coronaviruses have been at the forefront of the news for the last 2 years. Unfortunately, SARS-CoV-2, the etiologic agent for the COVID-19 pandemic, must be manipulated in biosecurity level 3 settings, which significantly limits research. Meanwhile, several less pathogenic human coronaviruses (HCoV) exist and can be studied in much more common biosafety level 2 laboratories. Among them, HCoV-OC43 is a good surrogate candidate for SARS-CoV-2 since both are phylogenetically related human Betacoronaviruses. However, one issue has been the lack of standardized means among laboratories to propagate and titer this less virulent coronavirus. The present study probes the optimal parameters to propagate HCoV-OC43. First, testing of five different cell lines (MRC-5, Huh7.5, Vero, HCT-8, HRT-18) indicated that the physiologically relevant MRC-5 human lung cell line produced among the highest viral titers. HRT-18 may however be an interesting alternative as they are quick growing cells that also led to higher viral titers and a better tropism for various HCoV-OC43 variants. We also probed the impact of serum and temperature during viral expansion and confirmed that the normal temperature of the upper respiratory track (33 °C) improves viral yields over the typical 37 °C used to grow many other viruses. Meanwhile, we did not notice any evidence that serum concentrations significantly affected the virus but interestingly noted that the virus grew quite efficiently in a serum-free media formulation. Meanwhile sonication of viral stocks somewhat improved viral titers. Four titration methods (plaque assays, TCID50-CPE, TCID50-IFA and TCID50–IPA) were also probed using two cell lines (VeroE6 and HRT-18). In our hands, plaque assays proved unreliable and quantification of the virus by scoring CPE positive wells was significantly less sensitive than antibody-based assays (IFA and IPA). While the latter methods were equally sensitive, we favor the TCID50-IPA method since simpler, faster and cheaper than the IFA protocol. Moreover, the HRT-18 cells appeared more sensitive to quantify the virus. Perhaps most importantly, these optimized protocols routinely led to high titer viral stocks in the order of 108 TCID50/ml magnitude, which should fulfill the requirements of most experimental settings.
creator: Christopher Savoie
creator: Roger Lippé
uri: https://doi.org/10.7717/peerj.13721
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Savoie and Lippé

title: Effects of school-based neuromuscular training on fundamental movement skills and physical fitness in children: a systematic review
link: https://peerj.com/articles/13726
last-modified: 2022-07-08
description: ObjectivesThe primary purpose of this review was to clarify the effects of school-based integrated neuromuscular training (INT) on fundamental movement skills and physical fitness in children. The secondary purpose was to examine whether school-based INT intervention is superior to physical education (PE) intervention in enhancing motor skills and fitness.MethodsA systematic literature search was performed in four electronic databases: PubMed, Web of Science, MEDLINE (EBSCOhost), and Cochrane Central Register of Controlled Trials. The last search was performed on December 21, 2021, and was limited to the English language, human species, and peer reviewed journals. Randomized controlled trials and cluster randomized controlled trials that examine the effects of school-based INT on motor skills and/or fitness in healthy children who were aged up to 14 years old were included. Moreover, studies included in this study should compare school-based INT-induced adaptions with those generated by PE interventions. Studies that involve athletic children and additional exercise training were excluded. The Physiotherapy Evidence Database (PEDro) scale was used to assess the quality of the study.ResultsOf 1,026 studies identified, seven original trials that meet the inclusion criteria were included in this review. Based on the PEDro scale, the PEDro score of seven studies was between six and eight points with a mean score of 5.29. Among the seven studies included in this study, four studies assessed physical fitness including muscular fitness (n = 4), speed (n = 3), endurance (n = 2), and flexibility (n = 2). Three studies examined the effects of INT on postural control and three studies explored its effects on motor skills. Concerning movement competence, significant and greater improvements in postural control and fundamental motor skills were observed following school-based INT interventions compared to PE intervention in two and three studies, respectively. Regarding physical fitness, neuromuscular training significantly increased muscular fitness, speed, endurance, flexibility in three, two, one, and one studies, respectively. However, only greater improvements in muscle fitness were observed in school-based INT group compared to PE group. The main limitations of this review were the lack of descriptions of training intensity and volume and the low methodological quality of the included studies.ConclusionThis review provides evidence that school-based neuromuscular training programs are superior to PE lessons in improving postural control, fundamental motor skills and muscular strength. Therefore, INT could be incorporated into traditional physical education classes in school. Trial registration number: CRD42022297349.
creator: Junlei Lin
creator: Ruofei Zhang
creator: Jie Shen
creator: Aiguo Zhou
uri: https://doi.org/10.7717/peerj.13726
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Lin et al.

title: The osteology and affinities of Eotyrannus lengi, a tyrannosauroid theropod from the Wealden Supergroup of southern England
link: https://peerj.com/articles/12727
last-modified: 2022-07-07
description: Eotyrannus lengiHutt et al., 2001 from the Lower Cretaceous Wessex Formation (part of the Wealden Supergroup) of the Isle of Wight, southern England, is described in detail, compared with other theropods, and evaluated in a new phylogenetic analysis. Eotyrannus is represented by a single individual that would have been c. 4.5 m long; it preserves the anterior part of the skull, a partial forelimb and pectoral girdle, various cervical, dorsal and caudal vertebrae, rib fragments, part of the ilium, and hindlimb elements excluding the femur. Lack of fusion with regard to both neurocentral and sacral sutures indicates subadult status. Eotyrannus possesses thickened, fused, pneumatic nasals with deep lateral recesses, elongate, tridactyl forelimbs and a tyrannosaurid-like scapulocoracoid. The short preantorbital ramus of the maxilla and nasals that are approximately seven times longer than they are wide show that Eotyrannus was not longirostrine. A posterodorsally inclined ridge on the ilium’s lateral surface fails to reach the dorsal margin: a configuration seen elsewhere in Juratyrant. Eotyrannus is not arctometatarsalian. Autapomorphies include the presence of curving furrows on the dentary, a block-like humeral entepicondyle, and a distoproximally aligned channel close to the distolateral border of the tibia. Within Tyrannosauroidea, E. lengi is phylogenetically intermediate between Proceratosauridae and Yutyrannus and the clade that includes Xiongguanlong, Megaraptora, Dryptosaurus and Tyrannosauridae. We do not find support for a close affinity between Eotyrannus and Juratyrant. Our analysis supports the inclusion of Megaraptora within Tyrannosauroidea and thus increases Cretaceous tyrannosauroid diversity and disparity. A proposal that Eotyrannus might belong within Megaraptora, however, is based on character states not present in the taxon. Several theropods from the Wessex Formation are based on material that overlaps with the E. lengi holotype but none can be shown to be synonymous with it.
creator: Darren Naish
creator: Andrea Cau
uri: https://doi.org/10.7717/peerj.12727
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Naish and Cau

title: The expanding roles of neuronal nitric oxide synthase (NOS1)
link: https://peerj.com/articles/13651
last-modified: 2022-07-07
description: The nitric oxide synthases (NOS; EC 1.14.13.39) use L-arginine as a substrate to produce nitric oxide (NO) as a by-product in the tissue microenvironment. NOS1 represents the predominant NO-producing enzyme highly enriched in the brain and known to mediate multiple functions, ranging from learning and memory development to maintaining synaptic plasticity and neuronal development, Alzheimer’s disease (AD), psychiatric disorders and behavioral deficits. However, accumulating evidence indicate both canonical and non-canonical roles of NOS1-derived NO in several other tissues and chronic diseases. A better understanding of NOS1-derived NO signaling, and identification and characterization of NO-metabolites in non-neuronal tissues could become useful in diagnosis and prognosis of diseases associated with NOS1 expression. Continued investigation on the roles of NOS1, therefore, will synthesize new knowledge and aid in the discovery of small molecules which could be used to titrate the activities of NOS1-derived NO signaling and NO-metabolites. Here, we address the significance of NOS1 and its byproduct NO in modifying pathophysiological events, which could be beneficial in understanding both the disease mechanisms and therapeutics.
creator: Kundan Solanki
creator: Sajjan Rajpoot
creator: Evgeny E. Bezsonov
creator: Alexander N. Orekhov
creator: Rohit Saluja
creator: Anita Wary
creator: Cassondra Axen
creator: Kishore Wary
creator: Mirza S. Baig
uri: https://doi.org/10.7717/peerj.13651
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Solanki et al.

title: Quantification of water requirement of some major crops under semi-arid climate in Turkey
link: https://peerj.com/articles/13696
last-modified: 2022-07-07
description: The Southeastern Anatolian Region of Turkey is located in semi arid climate zone and therefore requires an efficient water use. Well-planned irrigation with optimum water required by the crops is essential for the limited water resources of the region. The numerical tool CROPWAT of the Food and Agriculture Organization (FAO) was used for modelling efficient irrigation of local crops pistachio, olive, almond and grape without reducing the yield. Local climatic, soil, plant and rainfall information were used as inputs to CROPWAT model to predict the reference evapotranspiration (ETo) values. The crop water requirement (CWR) for pistachio, olive, almond, and grape was calculated as 1,294.0 mm, 659.4 mm, 790.2 mm, and 752.0 mm, respectively, The number of irrigation needed during growth stages was determined as eight for pistachio, three for olive, six for almond and five for grape.
creator: Yusuf Aydın
uri: https://doi.org/10.7717/peerj.13696
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Aydın