Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci
Background Bacterial symbiosis is widespread in arthropods, especially in insects. Some of the symbionts undergo a long-term co-evolution with the host, resulting in massive genome decay. One particular consequence of genome decay is thought to be the elimination of transcriptional elements within both the coding region and intergenic sequences. In the whitefly Bemisia tabaci species complex, the obligate symbiont Candidatus Portiera aleyrodidarum is of vital importance in nutrient provision, and yet little is known about the regulatory capacities of it. Methods Portiera genomes of two whitefly species in China were sequenced and assembled. Gene content of these two Portiera genomes was predicted, and then subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis. Together with two other Portiera genomes from whitefly species available previously, four Portiera genomes were utilized to investigate regulatory capacities of Portiera, focusing on transcriptional elements, including genes related with transcription and functional elements within the intergenic spacers. Results Comparative analyses of the four Portiera genomes of whitefly B. tabaci indicate that the obligate symbionts Portiera is similar in different species of whiteflies, in terms of general genome features and possible functions in the biosynthesis of essential amino acids. The screening of transcriptional factors suggests compromised ability of Portiera to regulate the essential amino acid biosynthesis pathways. Meanwhile, thermal tolerance ability of Portiera is indicated with the detection of a σ32 factor, as well as two predicted σ32 binding sites. Within intergenic spacers, functional elements are predicted, including 37 Shine-Dalgarno sequences and 34 putative small RNAs.
Zhu et al. (2019) Conservation of transcriptional elements in the obligate symbiont of the whitefly Bemisia tabaci. PeerJ 7:e7477 https://doi.org/10.7717/peerj.7477
Risk and prognostic nomograms for hepatocellular carcinoma with newly-diagnosed pulmonary metastasis using SEER data
Purpose This research aimed to identify risk factors of pulmonary metastasis (PM) from hepatocellular carcinoma (HCC) and prognostic factors of patients with PM from HCC at initial diagnosis. Methods Patients diagnosed with HCC between 2010 and 2015 were reviewed retrospectively in the Surveillance, Epidemiology, and End Results (SEER) database. Patients with PM from HCC at initial diagnosis were identified from the entire cohort. Predictors for PM from HCC were identified by multivariate logistic regression analysis. Independent prognostic factors for patients with PM were determined by univariate and multivariate Cox regression analysis. Nomograms were also constructed for quantifying risk of metastasis and overall survival estimation visually. Results Our research included 30,641 patients diagnosed with HCC, of whom 1,732 cases were with PM from HCC at initial diagnosis. The risk factors causing PM from HCC were age (P = 0.001), race (P < 0.001), primary tumor size (P < 0.001), T stage (P < 0.001), N stage (P < 0.001), alpha-fetoprotein (P < 0.001), bone metastasis (P < 0.001), brain metastasis (P < 0.001), and intrahepatic metastasis (P < 0.001). The significantly prognostic factors for overall survival were age (P = 0.014), T stage (P = 0.009), surgical approach (P < 0.001), and chemotherapy (P < 0.001). Harrell’s C-index statistics of two nomograms were 0.768 and 0.687 respectively, indicating satisfactory predictive power. Conclusions This research provided evaluation of risk factors and prognosis for patients with PM from HCC. Two nomograms we developed can be convenient individualized tools to facilitate clinical decision-making.
Ye et al. (2019) Risk and prognostic nomograms for hepatocellular carcinoma with newly-diagnosed pulmonary metastasis using SEER data. PeerJ 7:e7496 https://doi.org/10.7717/peerj.7496
Factors affecting the composition of the gut microbiota, and its modulation
Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host fosters favorable microbiota by releasing specific factors, such as microRNAs, and nonspecific factors, such as antimicrobial peptides, mucus and immunoglobulin A that encourage the growth of specific types of bacteria and inhibit the growth of others. Diet, antibiotics, and age can change gut microbiota, and many studies have shown the relationship between disorders of the microbiota and several diseases and reported some ways to modulate that balance. In this review, we highlight how the host shapes its gut microbiota via specific and nonspecific factors, how environmental and nutritional factors affect it, and how to modulate it using prebiotics, probiotics, and fecal microbiota transplantation.
Hasan et al. (2019) Factors affecting the composition of the gut microbiota, and its modulation. PeerJ 7:e7502 https://doi.org/10.7717/peerj.7502
Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation
Protein aggregation into amyloid fibrils has been linked to multiple neurodegenerative disorders. Determining the kinetics of fibril formation, as well as their structural stability are important for the mechanistic understanding of amyloid aggregation. Tracking both fibril association and dissociation is usually performed by measuring light scattering of the solution or fluorescence of amyloid specific dyes, such as thioflavin-T. A possible addition to these methods is the recently discovered deep-blue autofluorescence (dbAF), which is linked to amyloid formation. In this work we explore the potential of this phenomenon to monitor amyloid fibril formation and dissociation, as well as show its possible relation to fibril size rather than amyloid structure.
Ziaunys et al. (2019) Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation. PeerJ 7:e7554 https://doi.org/10.7717/peerj.7554
Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle
The red-eared slider turtle (Trachemys scripta elegans; RES) is often considered one of the world’s most invasive species. Results from laboratory and mesocosm experiments suggest that introduced RES outcompete native turtles for key ecological resources, but such experiments can overestimate the strength of competition. We report on the first field experiment with a wild turtle community, involving introduced RES and a declining native species of conservation concern, the western pond turtle (Emys marmorata; WPT). Using a before/after experimental design, we show that after removing most of an introduced RES population, the remaining RES dramatically shifted their spatial basking distribution in a manner consistent with strong intraspecific competition. WPT also altered their spatial basking distribution after the RES removal, but in ways inconsistent with strong interspecific competition. However, we documented reduced levels of WPT basking post-removal, which may reflect a behavioral shift attributable to the lower density of the turtle community. WPT body condition also increased after we removed RES, consistent with either indirect or direct competition between WPT and RES and providing the first evidence that RES can compete with a native turtle in the wild. We conclude that the negative impacts on WPT basking by RES in natural contexts are more limited than suggested by experiments with captive turtles, although wild WPT do appear to compete for food with introduced RES. Our results highlight the importance of manipulative field experiments when studying biological invasions, and the potential value of RES removal as a management strategy for WPT.
Lambert et al. (2019) Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle. PeerJ 7:e7444 https://doi.org/10.7717/peerj.7444
Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study
Background Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a “healthy” cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants’ metadata. Methods The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants’ metadata were assessed using GraphPad Prism, R packages and an in-house script. Results The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6–17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2–1.9) versus 2.3 (0.6–2.3); p = 0.025) and beta (permutational multivariate analysis of variance (PERMANOVA) pseudo-F statistic =4.31, p = 0.019) diversity compared to non-users. There was no significant difference in the alpha (Shannon indices: 1.0 (0.3–2.2) versus 1.9 (0.3–2.2); p = 0.483) and beta (PERMANOVA pseudo-F statistic = 0.89, p = 0.373) diversity in women with versus without human papillomavirus infection. Conclusions The majority of Black women in our study had non-Lactobacillus-dominated cervical microbiota. Additional studies are needed to examine whether such microbiota represent abnormal, intermediate or variant states of health. Lastly, the association of hormonal contraception with L. iners dominance requires further in-depth research to confirm this association, determine its biological mechanism and whether it has a beneficial effect on the cervicovaginal health.
Onywera et al. (2019) Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study. PeerJ 7:e7488 https://doi.org/10.7717/peerj.7488
Assessment of the factors influencing primary care physicians’ approach to vaccination of adult risk groups in Istanbul, Turkey
Background We aimed to assess the factors influencing primary care physicians’ (PCPs) approach to adult vaccination in specific risk groups and evaluate the compliance to adult immunization guidelines. Methods This cross-sectional study performed between January 2016 and April 2016 in İstanbul, Turkey. A questionnaire designed to obtain physicians’ demographical data, experience, immunization status, and attitude on prescribing or recommending vaccines for adults in the risk group. Healthy individuals older than 65 and patients suffer from chronic diseases or had splenectomy before are considered as a risk group. The questionnaire was sent via email to a randomly selected group of 1,500 PCPs. The data of 221 physicians who responded emails were recorded for statistical analysis. Results Of the 221 participants (123 women, 98 men), the majority were aged 31–40 years. Their vaccination rates were 74.2% for hepatitis B, 54.3% for seasonal influenza, and 47.1% for tetanus. Among participants, the highest recommendation and prescription rate of adult vaccines was recorded in PCPs aged 31–40 years. In addition, PCPs with <10 years occupational experience were found to prescribe adult vaccines more frequently than PCPs with longer occupational experience. Conclusions Primary care physicians with lower age and relatively less experience are more intent to prescribe adult vaccines to patients that are in risk groups. This result may be due to increased awareness of adult immunization among PCPs who had more recent medical training. However, many other factors could have caused this difference, including physicians’ approach to primary medical care.
Yılmaz Karadağ et al. (2019) Assessment of the factors influencing primary care physicians’ approach to vaccination of adult risk groups in Istanbul, Turkey. PeerJ 7:e7516 https://doi.org/10.7717/peerj.7516
Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species
Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.
Santamaria (2019) Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species. PeerJ 7:e7531 https://doi.org/10.7717/peerj.7531
Modeling tree diversity, stand structure and productivity of northern temperate coniferous forests of Mexico
There is increasing evidence complex forest structure and tree diversity correlates positively with the productivity of forest ecosystems. However, there is little quantitative information regarding the effect of these factors on stand productivity of northern temperate coniferous forests of Mexico. This study aimed to test the hypothesis tree diversity and canopy structure positively associates with forest productivity. Parameterization of tree diversity, stand structure and productivity were carried out on dasometric data from 36 permanent sampling plots re-measured in 1982, 1993, and 2004. Statistical analysis of stand parameters tested the null hypothesis. Statistical relationships revealed well-balanced canopy strata and imbalanced diameter structures positively correlated with stand productivity. Tree diversity was also positively linked with stand productivity, but the effect appeared to be most important in the early to intermediate stages of succession. Further research is required to understand the long-term effects of tree diversity and canopy structure on stand productivity. These preliminary observations stress the importance of prescribing silvicultural practices that maintain the three-dimensional structure of stands and diversity of forest canopies that aim to preserve ecosystem function, diversity, and productivity.
Návar (2019) Modeling tree diversity, stand structure and productivity of northern temperate coniferous forests of Mexico. PeerJ 7:e7051 https://doi.org/10.7717/peerj.7051
Ontogenetic braincase development in Psittacosaurus lujiatunensis (Dinosauria: Ceratopsia) using micro-computed tomography
Ontogenetic sequences are relatively rare among dinosaurs, with Ceratopsia being one of the better represented clades, and especially among geologically earlier forms, such as Psittacosaurus. Psittacosaurus is a small, bipedal basal ceratopsian abundant in the Lower Cretaceous deposits of Asia, whose cranial and endocranial morphology has been well studied, but only cursory details have been published on the bones surrounding the brain. Using reconstructions created from micro-computed tomography scans of well-preserved skulls from the Barremian–Aptian Yixian Formation, China, we document morphological changes in the braincase of Psittacosaurus lujiatunensis through three growth stages, hatchling, juvenile, and adult, thus providing the first detailed study of ceratopsian braincase morphology through ontogeny. Notable ontogenetic changes in the braincase of P. lujiatunensis include a dramatic relative reduction in size of the supraoccipital, an increase in the lateral expansion of the paroccipital processes and a decrease in the angle between the lateral semicircular canal and the palatal plane. These ontogenetic morphological changes in the braincase relate to expansion of the cranium and brain through growth, as well as reflecting the switch from quadrupedal juveniles to bipedal adults as documented in the changing orientation of the horizontal semicircular canal through ontogeny. Recognition of these patterns in a basal ceratopsian has implications for understanding key events in later ceratopsian evolution, such as the development of the parieto-squamosal frill in derived neoceratopsians.
Bullar et al. (2019) Ontogenetic braincase development in Psittacosaurus lujiatunensis (Dinosauria: Ceratopsia) using micro-computed tomography. PeerJ 7:e7217 https://doi.org/10.7717/peerj.7217