LitR directly upregulates autoinducer synthesis and luminescence in Aliivibrio logei
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.
Bazhenov et al. (2021) LitR directly upregulates autoinducer synthesis and luminescence in Aliivibrio logei. PeerJ 9:e12030 https://doi.org/10.7717/peerj.12030
LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response
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.
Song et al. (2021) LncRNAs specifically overexpressed in endocervical adenocarcinoma are associated with an unfavorable recurrence prognosis and the immune response. PeerJ 9:e12116 https://doi.org/10.7717/peerj.12116
Mass mortality of pearl oyster (Pinctada fucata (Gould)) in Japan in 2019 and 2020 is caused by an unidentified infectious agent
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.
Matsuyama et al. (2021) Mass mortality of pearl oyster (Pinctada fucata (Gould)) in Japan in 2019 and 2020 is caused by an unidentified infectious agent. PeerJ 9:e12180 https://doi.org/10.7717/peerj.12180
Graft survival of Pinus engelmannii Carr. in relation to two grafting techniques with dormant and sprouting buds
Developing methods for successfully grafting forest species will be helpful for establishing asexual seed orchards and increasing the success of forest genetic improvement programs in Mexico. In this study we investigated the effects of two grafting techniques (side veneer and top cleft) and two phenological stages of the scion buds (end of latency and beginning of sprouting), in combination with other seven grafting variables, on the sprouting and survival of 120 intraspecific grafts of Pinus engelmannii Carr. The scions used for grafting were taken from a 5.5-year-old commercial forest plantation. The first grafting was performed on January 18 (buds at the end of dormancy) and the second on February 21 (buds at the beginning of sprouting). The data were examined by analysis of variance and a test of means and were fitted to two survival models (the Weibull’s accelerated failure time and the Cox’s proportional hazards model) and the respective hazard ratios were calculated. Survival was higher in the top cleft grafts made with buds at the end of latency, with 80% sprouting and an estimated average survival time of between 164 and 457 days after the end of the 6-month evaluation period. Four variables (grafting technique, phenological stage of the scion buds, scion diameter and rootstock height) significantly affected the risk of graft death in both survival models. Use of top cleft grafts with buds at the end of the latency stage, combined with scion diameters smaller than 11.4 mm and rootstock heights greater than 58.5 cm, was associated with a lower risk of death.
Pérez-Luna et al. (2021) Graft survival of Pinus engelmannii Carr. in relation to two grafting techniques with dormant and sprouting buds. PeerJ 9:e12182 https://doi.org/10.7717/peerj.12182
Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico
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.
Gómez-Hernández et al. (2021) Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico. PeerJ 9:e12191 https://doi.org/10.7717/peerj.12191
Multiomics-based analyses of KPNA2 highlight its multiple potentials in hepatocellular carcinoma
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.
Zhang et al. (2021) Multiomics-based analyses of KPNA2 highlight its multiple potentials in hepatocellular carcinoma. PeerJ 9:e12197 https://doi.org/10.7717/peerj.12197
Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc
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.
Li et al. (2021) Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc. PeerJ 9:e12221 https://doi.org/10.7717/peerj.12221
Response of plant diversity and soil physicochemical properties to different gap sizes in a Pinus massoniana plantation
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.
Lyu et al. (2021) Response of plant diversity and soil physicochemical properties to different gap sizes in a Pinus massoniana plantation. PeerJ 9:e12222 https://doi.org/10.7717/peerj.12222
Cortinarius subsalor and C. tibeticisalor spp. nov., two new species from the section Delibuti from China
Cortinarius subsalor and C. tibeticisalor, belonging to the section Delibuti, are described from China as new to science. Cortinarius subsalor has been found to be associated with Lithocarpus trees in subtropical China and resembling C. salor, but it differs from the later by having slender basidiomata and the narrower basidiospores. Cortinarius tibeticisalor was collected from eastern Tibetan Plateau, associated with Abies. It differs from other species within sect. Delibuti by having olive tinge of mature or dried basidiomata and bigger basidiospores. The molecular data also support C. subsalor and C. tibeticisalor as new species. The phylogenetic analyses and biogeography of sect. Delibuti are discussed and a key to the species of this section currently known in the world is provided.
Xie et al. (2021) Cortinarius subsalor and C. tibeticisalor spp. nov., two new species from the section Delibuti from China. PeerJ 9:e11982 https://doi.org/10.7717/peerj.11982
The association between serum CD4 T lymphocyte counts and surgical outcomes in HIV/AIDS patients in Guangxi, China: a retrospective cohort study
Background HIV/AIDS is a chronic disease leading to complications in infected individuals that often require surgical intervention. These patients’ serum CD4 T lymphocyte (CD4) counts represent one of the most important indicators of their ability to tolerate surgical treatment. Previous studies have demonstrated that CD4 cell count (CD4-CC) < 200 cells/μl may increase the risk of surgical complications in these patients, limiting their ability to undergo surgery, which may negatively affect their quality of life. Further investigation into the surgical outcomes of patients with CD4-CC < 200 cells/μl should provide guidance in making appropriate clinical decisions for the optimal healthcare of this patient demographic. Methods All enrolled patients were selected from 14 prefecture-level general hospitals in Guangxi, China, and were referred to AIDS outpost hospitals for inpatient surgical therapy. A total cohort of 168 adult patients was retrospectively analyzed. Multifactorial and stratified analyses were performed to evaluate the in surgical outcome differences for patients with CD4-CC < 200 cells/μl (N = 43), using those with CD4-CC ≥ 200 cells/μl (N = 125) as controls. Results Poor incisional healing was used as the primary outcome indicator, and postoperative complications were used as the secondary outcome indicator. In the patient group with CD4-CC < 200 cells/μl, the risk of surgical complications was significantly increased (OR 2.379; 95% CI [1.049–5.394]) after adjustment. Adjusted stratified analysis of the CD4-CC < 200 cells/μl group revealed that individuals over 60 years (OR 27.504; 95% CI [2.297–329.317]) with erythrocyte counts below 4.00/ml for males or 3.50/ml for females (OR 3.353; 95% CI [1.079–10.419]) had a significantly higher risk of postoperative complications; this finding was statistically different from the control (CD4 ≥ 200 cells/μl) group. However, there was no significant difference between the two groups regarding the risk of poorly healed incision outcomes. Conclusions Preliminary findings suggest that a serum CD4-CC < 200 cells/μl is not a definitive contraindication for surgical therapy and that baseline and surgical characteristics may help predict surgical outcomes in these patients. Further studies are needed to confirm these findings.
Liu et al. (2021) The association between serum CD4 T lymphocyte counts and surgical outcomes in HIV/AIDS patients in Guangxi, China: a retrospective cohort study. PeerJ 9:e12023 https://doi.org/10.7717/peerj.12023