PeerJ
Latest Publications


TOTAL DOCUMENTS

12056
(FIVE YEARS 10552)

H-INDEX

72
(FIVE YEARS 53)

Published By Peerj

2167-8359
Updated Wednesday, 22 September 2021

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11915
Author(s):  
André Boraks ◽  
Anthony S. Amend

Ecological processes that control fungal distribution are not well understood because many fungi can persist in a wide variety of dissimilar habitats which are seldom sampled simultaneously. Geographic range size is reflective of species’ resource usage, and for plants and animals, there is a robust positive correlation between niche-breadth and range-size. It remains unknown whether this pattern is true for fungi. To investigate the fungal niche breadth–range size relationship we identified habitat specialists and generalists from two habitats (plant leaves and soil) and asked whether habitat specialization influenced fungal biogeography. We sampled fungi from the soil and phylloplane of tropical forests in Vanuatu and used DNA metabarcoding of the fungal ITS1 region to examine rarity, range size, and habitat connectivity. Fungal communities from the soil and phylloplane are spatially autocorrelated and the spatial distribution of individual fungal OTU are coupled between habitats. Habitat breadth (generalist fungi) did not result in larger range sizes but did correlate positively with occurrence frequency. Fungi that were frequently found were also found in high abundance, a common observation in similar studies of plants and animals. Fungal abundance-occupancy relationships differed by habitat and habitat-specificity. Soil specialists were found to be locally abundant but restricted geographically. In contrast, phylloplane generalists were found to be abundant over a large range in multiple habitats. These results are discussed in the context of differences between habitat characteristics, stability and spatial distribution. Identifying factors that drive spatial variation is key to understanding the mechanisms that maintain biodiversity in forests.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11993
Author(s):  
Kate Mortimer ◽  
Kirk Fitzhugh ◽  
Ana Claudia dos Brasil ◽  
Paulo Lana

Known as shovel head worms, members of Magelonidae comprise a group of polychaetes readily recognised by the uniquely shaped, dorso-ventrally flattened prostomium and paired ventro-laterally inserted papillated palps. The present study is the first published account of inferences of phylogenetic hypotheses within Magelonidae. Members of 72 species of Magelona and two species of Octomagelona were included, with outgroups including members of one species of Chaetopteridae and four of Spionidae. The phylogenetic inferences were performed to causally account for 176 characters distributed among 79 subjects, and produced 2,417,600 cladograms, each with 404 steps. A formal definition of Magelonidae is provided, represented by a composite phylogenetic hypothesis explaining seven synapomorphies: shovel-shaped prostomium, prostomial ridges, absence of nuchal organs, ventral insertion of palps and their papillation, presence of a burrowing organ, and unique body regionation. Octomagelona is synonymised with Magelona due to the latter being paraphyletic relative to the former. The consequence is that Magelonidae is monotypic, such that Magelona cannot be formally defined as associated with any phylogenetic hypotheses. As such, the latter name is an empirically empty placeholder, but because of the binomial name requirement mandated by the International Code of Zoological Nomenclature, the definition is identical to that of Magelonidae. Several key features for future descriptions are suggested: prostomial dimensions, presence/absence of prostomial horns, morphology of anterior lamellae, presence/absence of specialised chaetae, and lateral abdominal pouches. Additionally, great care must be taken to fully describe and illustrate all thoracic chaetigers in descriptions.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12116
Author(s):  
Yong Song ◽  
Long Nie ◽  
Yu-Ting Zhang

Background Cervical cancer is the fourth most common gynecological tumor in terms of both the incidence and mortality of females worldwide. Cervical squamous cell carcinoma (CSCC) accounts for 70–80% of cervical cancers, and endocervical adenocarcinoma (EAC) accounts for 20–25%. Unlike CSCC, EAC has worse clinical outcomes and prognosis. In this study, we explored the relationship between various types of long noncoding RNAs (lncRNAs) and pathological types of cervical cancer. Methods RNA sequencing (RNA-Seq) and clinical data from The Cancer Genome Atlas (TCGA) were used in this study. A single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE package were used to assess lncRNA activity and immune responses, respectively. RT-qPCR was performed to verify our findings. Results We explored the relationship between various types of lncRNAs and pathological types of cervical cancer. A series of long intergenic noncoding RNAs (lincRNAs) and antisense RNAs, which are the major types of lncRNAs, were identified to be specifically expressed in EAC and associated with a poor recurrence prognosis in patients with cervical cancer, suggesting that they might serve as independent prognostic markers of recurrence in patients with cervical cancer. RT-qPCR was performed to verify the 10 EAC-specific lncRNAs in cervical cancer samples we collected. Furthermore, the overexpression of these lncRNAs was positively correlated with EAC pathology levels but negatively correlated with immune responses in the microenvironment of cervical cancer. Conclusions These lncRNAs potentially represent new biomarkers for the prediction of the recurrence prognosis and help obtain deeper insights into potential immunotherapeutic approaches for treating cervical cancer.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12022
Author(s):  
Chen Xu ◽  
Yuan Shi ◽  
Xiaoyue Yu ◽  
Ruijie Chang ◽  
Huwen Wang ◽  
...  

Background The prevalence of depression in sexually transmitted infections (STIs) patients is much higher than general public. However, studies focusing on comprehensive psychosocial effects on depression among STIs patients are limited. This study aimed to examine association of multiple psychosocial syndemic conditions with depression among STIs patients in Shanghai, China. Methods We conducted a cross-sectional study and recruited 910 STIs patients from Shanghai Skin Disease Hospital. Participants self-reported their demographics and themselves completed the scales of depression, self-esteem, loneliness, social support, entrapment, defeat and interpersonal needs. Logistic regressions were performed to detect the possible contributing psychosocial factors for depression and to verify the syndemic conditions of psychosocial problems. Results Of the STIs patient sample, the prevalence of depression was 17.9%. Multivariable analysis showed low-level self-esteem (odds ratio [ORm]: 2.18, 95% CI [1.19–4.00]) and social support (ORm: 2.18, 95% CI [1.37–3.46]), high-level entrapment (ORm: 6.31, 95% CI [3.75–10.62]) and defeat (ORm: 2.60, 95% CI [1.51–4.48]) increased the risk of depression. Psychosocial syndemic conditions magnified effect in fusing depression (adjusted odds ratio [AOR]: 11.94, 95% CI [7.70–18.53]). Participants with more than 4 psychosocial problems were about 22 times more likely to have depression (AOR: 22.12, 95% CI [13.19–37.09]). Conclusions The psychosocial problems syndemic magnifying the risk of depression was confirmed and psychosocial interventions to prevent depression is needed among STIs patients.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12030
Author(s):  
Sergey Bazhenov ◽  
Olga Melkina ◽  
Vadim Fomin ◽  
Ekaterina Scheglova ◽  
Pavel Krasnik ◽  
...  

LitR is a master-regulator of transcription in the ainS/R and luxS/PQ quorum sensing (QS) systems of bacteria from Vibrio and Aliivibrio genera. Here, we for the first time directly investigated the influence of LitR on gene expression in the luxI/R QS system of psychrophilic bacteria Aliivibrio logei. Investigated promoters were fused with Photorhabdus luminescens luxCDABE reporter genes cassette in a heterological system of Escherichia coli cells, litR A. logei was introduced into the cells under control of Plac promoter. LitR has been shown to upregulate genes of autoinducer synthase (luxI), luciferase and reductase (luxCDABE), and this effect doesn’t depend on presence of luxR gene. To a much lesser degree, LitR induces luxR1, but not the luxR2 — the main luxI/R regulator. Enhanced litR expression leads to an increase in a LuxI-autoinducer synthesis and a subsequent LuxR-mediated activation of the luxI/R QS system. Effect of LitR on luxI transcription depends on lux-box sequence in luxI promoter even in absence of luxR (lux-box is binding site of LuxR). The last finding indicates a direct interaction of LitR with the promoter in the lux-box region. Investigation of the effect of LitR A. logei on luxI/R QS systems of mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio salmonicida showed direct luxR-independent upregulation of luxI and luxCDABE genes. To a lesser degree, it induces luxR A. fischeri and luxR1 A. salmonicida. Therefore, we assume that the main role of LitR in cross-interaction of these three QS systems is stimulating the expression of luxI.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12191
Author(s):  
Marko Gómez-Hernández ◽  
Emily Avendaño-Villegas ◽  
María Toledo-Garibaldi ◽  
Etelvina Gándara

Macromycetes are a group of fungi characterized by the production of fruit bodies and are highly relevant in most terrestrial ecosystems as pathogens, mutualists, and organic matter decomposers. Habitat transformation can drastically alter macromycete communities and diminish the contribution of these organisms to ecosystem functioning; however, knowledge on the effect of urbanization on macrofungal communities is scarce. Diversity metrics based on functional traits of macromycete species have shown to be valuable tools to predict how species contribute to ecosystem functionality since traits determine the performance of species in ecosystems. The aim of this study was to assess patterns of species richness, functional diversity, and composition of macrofungi in an urban ecosystem in Southwest Mexico, and to identify microclimatic, environmental, and urban factors related to these patterns in order to infer the effect of urbanization on macromycete communities. We selected four oak forests along an urbanization gradient and established a permanent sampling area of 0.1 ha at each site. Macromycete sampling was carried out every week from June to October 2017. The indices used to measure functional diversity were functional richness (FRic), functional divergence (FDig), and functional evenness (FEve). The metric used to assess variation of macrofungal ecological function along the study area was the functional value. We recorded a total of 134 macromycete species and 223 individuals. Our results indicated a decline of species richness with increased urbanization level related mainly to microclimatic variables, and a high turnover of species composition among study sites, which appears to be related to microclimatic and urbanization variables. FRic decreased with urbanization level, indicating that some of the available resources in the niche space within the most urbanized sites are not being utilized. FDig increased with urbanization, which suggests a high degree of niche differentiation among macromycete species within communities in urbanized areas. FEve did not show notable differences along the urbanization gradient, indicating few variations in the distribution of abundances within the occupied sections of the niche space. Similarly, the functional value was markedly higher in the less urbanized site, suggesting greater performance of functional guilds in that area. Our findings suggest that urbanization has led to a loss of macromycete species and a decrease in functional diversity, causing some sections of the niche space to be hardly occupied and available resources to be under-utilized, which could, to a certain extent, affect ecosystem functioning and stability.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12180
Author(s):  
Tomomasa Matsuyama ◽  
Satoshi Miwa ◽  
Tohru Mekata ◽  
Yuta Matsuura ◽  
Tomokazu Takano ◽  
...  

Mass mortality of 0-year-old pearl oysters, Pinctada fucata (Gould), and anomalies in adults were observed in Japan’s major pearl farming areas in the summer of 2019 and 2020. Although adult oyster mortality was low, both adult and juvenile oysters underwent atrophy of the soft body, detachment of the mantle from nacre (the shiny inner surface of the valves), deposition of brownish material on the nacre, and loss of nacre luster. Infection trials were conducted to verify the involvement of pathogens in this phenomenon. Healthy adult pearl oysters were obtained from areas where this disease had not occurred to use as the recipients. The sources of infection were either affected adult oysters with atrophied soft bodies or batches of juveniles in which mortality had reached conspicuous levels. Transmission of the disease to the healthy oysters were tested either by cohabitation with affected oysters or by injections of the hemolymph of affected animals. The injection infection test examined the effects of filtration and chloroform exposure on the pathogen. Occurrence of the disease was confirmed by the appearance of brown deposits on the nacre and loss of nacre luster. The abnormalities of nacre were clearly reproduced in recipient shells in three out of four cohabitation trials with affected oysters. The disease was also reproduced in six out of six injection trails either with hemolymph filtered through 100 nm filter or with hemolymph treated with chloroform. In a serial passage with hemolymph injections, the disease was successfully transmitted through eight passages. These results suggest that the etiology of the disease is a non-enveloped virus with a diameter ≤100 nm.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12221
Author(s):  
Junchang Li ◽  
Yumei Jiang ◽  
Jing Zhang ◽  
Yongjing Ni ◽  
Zhixin Jiao ◽  
...  

Tillering ability is a key agronomy trait for wheat (Triticum aestivum L.) production. Studies on a dwarf monoculm wheat mutant (dmc) showed that ARF11 played an important role in tillering of wheat. In this study, a total of 67 ARF family members were identified and clustered to two main classes with four subgroups based on their protein structures. The promoter regions of T. aestivum ARF (TaARF) genes contain a large number of cis-acting elements closely related to plant growth and development, and hormone response. The segmental duplication events occurred commonly and played a major role in the expansion of TaARFs. The gene collinearity degrees of the ARFs between wheat and other grasses, rice and maize, were significantly high. The evolution distances among TaARFs determine their expression profiles, such as homoeologous genes have similar expression profiles, like TaARF4-3A-1, TaARF4-3A-2 and their homoeologous genes. The expression profiles of TaARFs in various tissues or organs indicated TaARF3, TaARF4, TaARF9 and TaARF22 and their homoeologous genes played basic roles during wheat development. TaARF4, TaARF9, TaARF12, TaARF15, TaARF17, TaARF21, TaARF25 and their homoeologous genes probably played basic roles in tiller development. qRT-PCR analyses of 20 representative TaARF genes revealed that the abnormal expressions of TaARF11 and TaARF14 were major causes constraining the tillering of dmc. Indole-3-acetic acid (IAA) contents in dmc were significantly less than that in Guomai 301 at key tillering stages. Exogenous IAA application significantly promoted wheat tillering, and affected the transcriptions of TaARFs. These data suggested that TaARFs as well as IAA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of ARFs in wheat.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12197
Author(s):  
Jinzhong Zhang ◽  
Xiuzhi Zhang ◽  
Lingxiao Wang ◽  
Chunyan Kang ◽  
Ningning Li ◽  
...  

Dysregulation and prognostic roles of Karyopherin α2 (KPNA2) were reported in many malignancies including hepatocellular carcinoma (HCC). A multi-omics analysis of KPNA2 is needed to gain a deeper understanding of its multilevel molecular characteristics and provide novel clues for HCC diagnosis, prognosis, and target therapy. Herein multi-omic alterations of KPNA2 were analyzed at genetic, epigenetic, transcript, and protein levels with evaluation of their relevance with clinicopathological features of HCC by integrative analyses. The significant correlations of KPNA2 expression with its gene copy number variation (CNV) and methylation status were shown through Spearman correlation analyses. With Cox regression, Kaplan-Meier survival, and receiver operating characteristic (ROC) analyses, based on the factors of KPNA2 CNV, methylation, expression, and tumor stage, risk models for HCC overall survival (OS) and disease-free survival (DFS) were constructed which could discriminate the 1-year, 3-year, and 5-year OS/DFS status effectively. With Microenvironment Cell Populations-counter (MCP-counter), the immune infiltrations of HCC samples were evaluated and their associations with KPNA2 were shown. KPNA2 expression in liver was found to be influenced by low fat diet and presented significant correlations with fatty acid metabolism and fatty acid synthase activity in HCC. KPNA2 was detected lowered in HCC patient’s plasma by enzyme linked immunosorbent assay (ELISA), consistent with its translocation to nuclei of HCC cells. In conclusion, KPNA2 multilevel dysregulation in HCC and its correlations with immune infiltration and the fatty acid metabolism pathway indicated its multiple roles in HCC. The clinicopathological significance of KPNA2 was highlighted through the in-depth analyses at multilevels.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12222
Author(s):  
Qian Lyu ◽  
Jiangli Liu ◽  
Junjie Liu ◽  
Yan Luo ◽  
Luman Chen ◽  
...  

As one means of close-to-nature management, forest gaps have an important impact on the ecological service function of plantations. To improve the current situation of P. massoniana plantations, three different sizes of forest gaps (large gaps, medium gaps and small gaps) were established to observe whether gap setting can improve the soil fertility and plant diversity of forest plantations. The results showed that compared with the control, the soil organic matter content of different soil layers increased significantly in the medium forest gap and large forest gap. The content of soil organic matter in the surface layer of the middle gap had the largest increase (80.64%). Compared with the control, the content of soil-available potassium between different soil layers decreased significantly by 15.93% to 25.80%. The soil hydrolysable nitrogen reached its maximum under the medium gap. Soil moisture showed significant changes among different gap treatments, different soil layers and their interaction, decreasing significantly in large gaps and small gaps but increasing significantly in medium gaps. The soil bulk density decreased significantly compared with the control, and the surface soil reached the minimum in the medium gap. There were different plant species in forest gaps of different sizes, and shrub layer plants were more sensitive to gap size differences than herb layer plants. The plant diversity indices of the shrub layer increased significantly and showed a maximum under the medium gap. The plant diversity of the herb layer showed the opposite trend, and the Shannon-Wiener index, Simpson index and Pielou index were significantly lower than those of the control. RDA showed that different gap treatments had significant effects on the distribution of plants under the forest. Soil available potassium, soil moisture and soil bulk density affected the distribution and diversity of plants under the forest, serving as the limiting factors of plant growth. In forest management, if we strictly consider the improvement of plant diversity and soil physicochemical properties, these results suggest that a medium gap should be established in a plantation for natural restoration.


Sign in / Sign up

Export Citation Format

Share Document