title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1366 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize link: https://peerj.com/articles/6815 last-modified: 2019-05-03 description: BackgroundThe spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation.MethodsWe used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals.ResultsIntrogression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize.DiscussionAlthough there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized. creator: Eric Gonzalez-Segovia creator: Sergio Pérez-Limon creator: G. Carolina Cíntora-Martínez creator: Alejandro Guerrero-Zavala creator: Garrett M. Janzen creator: Matthew B. Hufford creator: Jeffrey Ross-Ibarra creator: Ruairidh J. H. Sawers uri: https://doi.org/10.7717/peerj.6815 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gonzalez-Segovia et al. title: Genome-wide identification and expression profile analysis of the Hsp20 gene family in Barley (Hordeum vulgare L.) link: https://peerj.com/articles/6832 last-modified: 2019-05-03 description: In plants, heat shock proteins (Hsps) play important roles in response to diverse stresses. Hsp20 is the major family of Hsps, but their role remains poorly understood in barley (Hordeum vulgare L.). To reveal the mechanisms of barley Hsp20s (HvHsp20s) response to stress conditions, we performed a comprehensive genome-wide analysis of the HvHsp20 gene family using bioinformatics-based methods. In total, 38 putative HvHsp20s were identified in barley and grouped into four subfamilies (C, CP, PX, and MT) based on predicted subcellular localization and their phylogenetic relationships. A sequence analysis indicated that most HvHsp20 genes have no intron or one with a relatively short length. In addition, the same group of HvHsp20 proteins in the phylogenetic tree shared similar gene structure and motifs, indicating that they were highly conserved and might have similar function. Based on RNA-seq data analysis, we showed that the transcript levels of HvHsp20 genes could be induced largely by abiotic and biotic stresses such as heat, salt, and powdery mildew. Three HvHsp20 genes, HORVU7Hr1G036540, HORVU7Hr1G036470, and HORVU3Hr1G007500, were up-regulated under biotic and abiotic stresses, suggesting their potential roles in mediating the response of barley plants to environment stresses. These results provide valuable information for further understanding the complex mechanisms of HvHsp20 gene family in barley. creator: Jie Li creator: Xinhao Liu uri: https://doi.org/10.7717/peerj.6832 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li and Liu title: Prefrontal cortical activation measured by fNIRS during walking: effects of age, disease and secondary task link: https://peerj.com/articles/6833 last-modified: 2019-05-03 description: BackgroundCognitive processes are required during walking to appropriately respond to environmental and task demands. There are now many studies that have used functional Near-Infrared Spectroscopy (fNIRS) to record brain activation to investigate neural bases of cognitive contributions in gait. The aim of this systematic review was to summarize the published research regarding Prefrontal cortical (PFC) activation patterns during simple and complex walking tasks in young adults, older adults and clinical groups with balance disorders using fNIRS. Our secondary aim was to evaluate each included study based on methodological reporting criteria important for good data quality.MethodsWe conducted searches in June 2018 using four databases: Embase, PubMed, Scopus and PsycINFO. The strategy search used was: (((((near infrared spectroscopy) OR functional near infrared spectroscopy) OR nirs) OR fnirs) AND (((gait) OR walking) OR locomotion) AND (((((young) OR adult) OR older) OR elderly) NOT children)) AND (((Brain) OR cortex) OR cortical) for our search. The papers included met the specific review criteria: (i) used fNIRS to measure PFC activation patterns; (ii) included walking tasks (simple and complex) and; (iii) assessed young people, older people and/or clinical groups with balance disorders.ResultsThirty five (describing 75 brain activation comparisons) of the 308 studies retrieved through our search met the inclusion criteria. Based on 6 methodological reporting considerations, 20 were of high quality, 10 were of medium quality and 5 were of low quality. Eleven/20 comparisons in young people, 23/37 comparisons in older people and 15/18 comparisons in clinical groups reported increased PFC activation with increased walking task complexity. The majority of comparisons that used verbal fluency, counting backwards or secondary motor tasks reported increases in PFC activation (83%, 64% and 58% of these studies, respectively). In contrast, no studies found secondary visual tasks increased PFC activation.ConclusionIncreased PFC activation was most common in studies that involved walks comprising secondary verbal fluency and arithmetic tasks. Clinical groups generally showed increased PFC activation irrespective of type of secondary task performed during walking which suggests these groups require more attentional resources for safe walking. Systematic review registration number: PROSPERO 2017 - CRD42017059501. creator: Paulo H.S. Pelicioni creator: Mylou Tijsma creator: Stephen R. Lord creator: Jasmine Menant uri: https://doi.org/10.7717/peerj.6833 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pelicioni et al. title: Leptin-a mediates transcription of genes that participate in central endocrine and phosphatidylinositol signaling pathways in 72-hour embryonic zebrafish (Danio rerio) link: https://peerj.com/articles/6848 last-modified: 2019-05-03 description: We analyzed microarray expression data to highlight biological pathways that respond to embryonic zebrafish Leptin-a (lepa) signaling. Microarray expression measures for 26,046 genes were evaluated from lepa morpholino oligonucleotide “knockdown”, recombinant Leptin-a “rescue”, and uninjected control zebrafish at 72-hours post fertilization. In addition to KEGG pathway enrichment for phosphatidylinositol signaling and neuroactive ligand-receptor interactions, Gene Ontology (GO) data from lepa rescue zebrafish include JAK/STAT cascade, sensory perception, nervous system processes, and synaptic signaling. In the zebrafish lepa rescue treatment, we found changes in the expression of homologous genes that align with mammalian leptin signaling cascades including AMPK (prkaa2), ACC (acacb), Ca2+/calmodulin-dependent kinase (camkk2), PI3K (pik3r1), Ser/Thr protein kinase B (akt3), neuropeptides (agrp2, cart1), mitogen-activated protein kinase (MAPK), and insulin receptor substrate (LOC794738, LOC100537326). Notch signaling pathway and ribosome biogenesis genes respond to knockdown of Leptin-a. Differentially expressed transcription factors in lepa knockdown zebrafish regulate neurogenesis, neural differentiation, and cell fate commitment. This study presents a role for zebrafish Leptin-a in influencing expression of genes that mediate phosphatidylinositol and central endocrine signaling. creator: Matthew Tuttle creator: Mark R. Dalman creator: Qin Liu creator: Richard L. Londraville uri: https://doi.org/10.7717/peerj.6848 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tuttle et al. title: Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations link: https://peerj.com/articles/6861 last-modified: 2019-05-03 description: AimIn this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application.ResultNo deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region.ConclusionThis study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations. creator: Weian Du creator: Chunlei Feng creator: Ting Yao creator: Cheng Xiao creator: Hongyan Huang creator: Weibin Wu creator: Linnan Zhu creator: Honghua Qiao creator: Chao Liu creator: Ling Chen uri: https://doi.org/10.7717/peerj.6861 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Du et al. title: Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci link: https://peerj.com/articles/6864 last-modified: 2019-05-03 description: The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web. creator: Marshal Hedin creator: Shahan Derkarabetian creator: Adan Alfaro creator: Martín J. Ramírez creator: Jason E. Bond uri: https://doi.org/10.7717/peerj.6864 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hedin et al. title: Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center link: https://peerj.com/articles/6868 last-modified: 2019-05-03 description: BackgroundThe objective of this study is to investigate small cell neuroendocrine carcinoma of the cervix (SCCC), using a retrospective clinicopathological characteristic and treatment approach.MethodWe retrospectively analyzed cases of early-stage SCCC, identified between 2006 and 2016, in women who received radical surgery and adjuvant chemotherapy with or without radiotherapy. Kaplan–Meier and one-way ANOVA analyses were performed.ResultA total of 37 cases of SCCC are presented in this study, of which 21 had stage IB1 SCCC, 12 had stage IB2, 3 had stage IIA1, and 1 had stage IIA2. All patients were treated with radical surgery and adjuvant chemotherapy, specifically, 26 with radical surgery followed by adjuvant chemotherapy plus radiation and 11 with neoadjuvant chemotherapy (NACT) followed by radical surgery. After a median follow-up time of 27 months (range, 8–115 months), the 2-year and 5-year disease-free survival rate for all patients was 51.9% and 34.1%, respectively, and the overall survival rate was 60.3% and 38.6%, respectively. Univariate analysis showed that International Federation of Gynecology and Obstetrics (FIGO) stage and tumor size may be a predictor of a poor prognosis. NACT and adjuvant radiation did not improve survival over adjuvant chemotherapy alone but should not be a significant independent prognostic factor for survival.ConclusionEven in patients with early-stage SCCC, the prognosis is poor, although FIGO stage and tumor size may act as surrogate factors prognostic of survival. creator: Dandan Zhang creator: Xiaoxin Ma uri: https://doi.org/10.7717/peerj.6868 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang and Ma title: Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis link: https://peerj.com/articles/6871 last-modified: 2019-05-03 description: BackgroundElaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown.MethodsIn order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus, and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing).ResultsA total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase (DESA1), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis. creator: Jiayue Wu creator: Linlin Peng creator: Shubin Dong creator: Xiaofei Xia creator: Liangcheng Zhao uri: https://doi.org/10.7717/peerj.6871 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wu et al. title: Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China link: https://peerj.com/articles/6897 last-modified: 2019-05-03 description: BackgroundPatchy vegetation is a very common phenomenon due to long-term overgrazing in degraded steppe grasslands, which results in substantial uncertainty associated with soil carbon (C) and nitrogen (N) dynamics because of changes in the amount of litter accumulation and nutrition input into soil.MethodsWe investigated soil C and N stocks beneath three types of monodominant species patches according to community dominance. Stipa krylovii patches, Artemisia frigida patches, and Potentilla acaulis patches represent better to worse vegetation conditions in a grassland in northern China.ResultsThe results revealed that the soil C stock (0–40 cm) changed significantly, from 84.7 to 95.7 Mg ha−1, and that the soil organic carbon content (0–10 cm) and microbial biomass carbon (0–10 and 10–20 cm) varied remarkably among the different monodominant species communities (P < 0.05). However, soil total nitrogen and microbial biomass nitrogen showed no significant differences among different plant patches in the top 0–20 cm of topsoil. The soil C stocks under the P. acaulis and S. krylovii patches were greater than that under the A. frigida patch. Our study implies that accurate estimates of soil C and N storage in degenerated grassland require integrated analyses of the concurrent effects of differences in plant community composition. creator: Yujuan Zhang creator: Shiming Tang creator: Shu Xie creator: Kesi Liu creator: Jinsheng Li creator: Qian Chen creator: Ding Huang creator: Kun Wang uri: https://doi.org/10.7717/peerj.6897 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China link: https://peerj.com/articles/6919 last-modified: 2019-05-03 description: BackgroundThis study aims to describe the epidemiological patterns of influenza-like illness (ILI) in Huludao, China and seek scientific evidence on the link of ILI activity with weather factors.MethodsSurveillance data of ILI cases between January 2012 and December 2015 was collected in Huludao Central Hospital, meteorological data was obtained from the China Meteorological Data Service Center. Generalized additive model (GAM) was used to seek the relationship between the number of ILI cases and the meteorological factors. Multiple Smoothing parameter estimation was made on the basis of Poisson distribution, where the number of weekly ILI cases was treated as response, and the smoothness of weather was treated as covariates. Lag time was determined by the smallest Akaike information criterion (AIC). Smoothing coefficients were estimated for the prediction of the number of ILI cases.ResultsA total of 29, 622 ILI cases were observed during the study period, with children ILI cases constituted 86.77%. The association between ILI activity and meteorological factors varied across different lag periods. The lag time for average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity were 2, 2, 1, 1 and 0 weeks, respectively. Average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity could explain 16.5%, 9.5%, 18.0%, 15.9% and 7.7% of the deviance, respectively. Among the temperature indexes, the minimum temperature played the most important role. The number of ILI cases peaked when minimum temperature was around −13 °C in winter and 18 °C in summer. The number of cases peaked when the relative humidity was equal to 43% and then began to decrease with the increase of relative humidity. When the humidity exceeded 76%, the number of ILI cases began to rise.ConclusionsThe present study first analyzed the relationship between meteorological factors and ILI cases with special consideration of the length of lag period in Huludao, China. Low air temperature and low relative humidity (cold and dry weather condition) played a considerable role in the epidemic pattern of ILI cases. The trend of ILI activity could be possibly predicted by the variation of meteorological factors. creator: Ying-Long Bai creator: De-Sheng Huang creator: Jing Liu creator: De-Qiang Li creator: Peng Guan uri: https://doi.org/10.7717/peerj.6919 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bai et al.