PAP3 Regulates Stamen but Not Petal Development in Capsicum annuum L.

AbstractPepper flowers are hermaphroditic; the plant's male sterility trait is characterized by its inability to produce pollen grains. In the ABC model of flower development, B-function genes play roles in petal and stamen development in the angiosperm. In this study, a B-class gene designated as PAP3 (GenBank accession no. HM104635) was isolated in pepper. The gene encoded 226 amino acids and shared high similarity with the MADS-box protein family, with a conservative MADS domain and semiconservative K domain. Furthermore, the expression of PAP3 was abundant only in petals and anthers but not in leaves. A functional study employing virus-induced gene silencing (VIGS) showed that knockdown of PAP3 led to the shriveling of pollen grains and male sterility; however, it did not affect petal development. These results suggest an essential role for PAP3 in the development of the pepper stamen and in contributing to the variation of floral traits

Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies

IntroductionPepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in pepper breeding.MethodsIn the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers.ResultsIn this study, a 45K pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits.DiscussionIn summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new pepper varieties

The Double Burdens of Mental Health Among AIDS Patients With Fully Successful Immune Restoration: A Cross-Sectional Study of Anxiety and Depression in China

Background: Anxiety and depression continue to be significant comorbidities for people with HIV infection. We investigated the prevalence of and factors associated with anxiety and depression among adult HIV-infected patients across China.Methods: In this cross-sectional study, we described clinical and psychosocial variables related to depression and anxiety in 4103 HIV-infected persons. Doctors assessed anxiety and depression by asking patients whether they had experienced anxiety or depression in the prior month. Patients also self-administered the Hospital Anxiety and Depression (HAD) scale; those with score ≥8 on HAD-A/D were considered to be at high risk of anxiety or depression.Results: Associations between socio-demographic, psychosocial, and ART-related clinical factors and risk of depression or anxiety were investigated using multivariable logistic regression. Among patients assessed between 9/2014 and 11/2015, 27.4% had symptoms of anxiety, 32.9% had symptoms of depression, and 19.0% had both. Recentness of HIV diagnoses (P = 0.046) was associated with elevated odds of anxiety. Older age (P = 0.004), higher educational attainment (P < 0.001), employment (P = 0.001), support from family / friends (P < 0.001), and sleep disturbance (P < 0.001), and number of ART regimen switches (P = 0.046) were associated with risk of depression, while neither sex nor transmission route showed any associations. There were no significant associations with HIV-specific clinical factors including current CD4+ T cell count and current viral load.Conclusions: Prevalence of symptoms of anxiety and depression is high in this cohort of treatment-experienced HIV patients. Psychological and social-demographic factors, rather than HIV disease status, were associated with risk of depression and anxiety. This finding highlights the need to deliver interventions to address the mental health issues affecting HIV-infected persons with fully successful immune restoration across China

Expression Pattern of Class B Gene PAP3 in Flower Development of Pepper

Class B gene APETALA3 (AP3) plays a key role in the development of petals and stamens. Here, we investigated the expression pattern of PAP3 gene (genbank accession number: HM104635) in the buds of cytoplasmic male sterility line 121A and its near-isogenic restorer line 121C at four developmental stages and analyzed the possible association between Class B genes and cytoplasmic male sterility of pepper. Semi-quantitative PCR and quantitative real-time RT-PCR (qRT-PCR) as well as RNA in situ hybridization showed increased expression of PAP3 at late phase of anther development and its higher expression in restorer line compared with sterility line indicating PAP3’s role at late developmental stage of anther and suppressed expression in sterility line. RNA in situ hybridization showed Class B gene features: high abundance in stamen and petal; lower expression in pistil; no expression in sepal. Results of transient expression in onion epidermal cells also showed PAP3 localized in the nucleus, which is consistent with the expression pattern of transcription factors of MADS-box gene family

A Coupled Model of Two-Phase Fluid Flow and Heat Transfer to Transient Temperature Distribution and Seepage Characteristics for Water-Flooding Production Well with Multiple Pay Zones

Temperature is one of the most prominent factors affecting production operations, predicting the accurate wellbore-formation temperature in a water-flooding production well is of great importance for multiple applications. In this paper, an improved coupled model of oil–water two-phase fluid flow and heat transfer was developed to investigate the transient temperature behavior for a producing well with multiple pay zones. Firstly, a novel method was derived to simulate the water saturation and the water breakthrough time (WBT) for tubing, which are key monitoring parameters in the process of water flooding. Then, we incorporated water saturation and an equation set for immiscible displacement to calculate the seepage velocity and the pressure of the two-phase fluid in the pay zones. Next, the upward seepage velocity of the tubing fluid change with depth was focused on, and the proper coupled initial and boundary conditions are presented at the interfaces, therewith the implicit finite difference method was used to compute the transient temperature with the input of the seepage characteristics for the reservoirs. Meanwhile, the validity of the proposed model has been verified by the typical model. Finally, a sensitivity analysis delineated that the production rate and the production time had a significant impact on the tubing fluid temperature. The overburden was hotter with a lower volumetric heat capacity or a higher thermal conductivity. In addition, the sensitivity of the porosity and the irreducible water saturation to formation temperature was significantly different before and after the WBT. The coupled model presented herein helps to advance the transient seepage characteristics analysis of pay zones, the precise temperature prediction is very useful for reservoir characterization and production analysis purposes and provides insight for designing the exploitation scheme in deep reservoirs and geothermal resources

Data-driven lithofacies prediction in complex tight sandstone reservoirs: a supervised workflow integrating clustering and classification models

Abstract Lithofacies identification plays a pivotal role in understanding reservoir heterogeneity and optimizing production in tight sandstone reservoirs. In this study, we propose a novel supervised workflow aimed at accurately predicting lithofacies in complex and heterogeneous reservoirs with intercalated facies. The objectives of this study are to utilize advanced clustering techniques for facies identification and to evaluate the performance of various classification models for lithofacies prediction. Our methodology involves a two-information criteria clustering approach, revealing six distinct lithofacies and offering an unbiased alternative to conventional manual methods. Subsequently, Gaussian Process Classification (GPC), Support Vector Machine (SVM), Artificial Neural Network (ANN), and Random Forest (RF) models are employed for lithofacies prediction. Results indicate that GPC outperforms other models in lithofacies identification, with SVM and ANN following suit, while RF exhibits comparatively lower performance. Validated against a testing dataset, the GPC model demonstrates accurate lithofacies prediction, supported by synchronization measures for synthetic log prediction. Furthermore, the integration of predicted lithofacies into acoustic impedance versus velocity ratio cross-plots enables the generation of 2D probability density functions. These functions, in conjunction with depth data, are then utilized to predict synthetic gamma-ray log responses using a neural network approach. The predicted gamma-ray logs exhibit strong agreement with measured data (R2 = 0.978) and closely match average log trends. Additionally, inverted impedance and velocity ratio volumes are employed for lithofacies classification, resulting in a facies prediction volume that correlates well with lithofacies classification at well sites, even in the absence of core data. This study provides a novel methodological framework for reservoir characterization in the petroleum industry

Lithology and mineralogy recognition from geochemical logging tool data using multivariate statistical analysis

The availability of a deep well that penetrates deep into the Ultra High Pressure (UHP) metamorphic rocks is unusual and consequently offers a unique chance to study the metamorphic rocks. One such borehole is located in the southern part of Donghai County in the Sulu UHP metamorphic belt of Eastern China, from the Chinese Continental Scientific Drilling Main hole. This study reports the results obtained from the analysis of oxide log data. A geochemical logging tool provides in situ, gamma ray spectroscopy measurements of major and trace elements in the borehole. Dry weight percent oxide concentration logs obtained for this study were SiO2, K2O, TiO2, H2O, CO2, Na2O, Fe2O3, FeO, CaO, MnO, MgO, P2O5 and Al2O3. Cross plot and Principal Component Analysis methods were applied for lithology characterization and mineralogy description respectively. Cross plot analysis allows lithological variations to be characterized. Principal Component Analysis shows that the oxide logs can be summarized by two components related to the feldspar and hydrous minerals. This study has shown that geochemical logging tool data is accurate and adequate to be tremendously useful in UHP metamorphic rocks analysis

Quantitative Characterization of Shallow Marine Sediments in Tight Gas Fields of Middle Indus Basin: A Rational Approach of Multiple Rock Physics Diagnostic Models

For the successful discovery and development of tight sand gas reserves, it is necessary to locate sand with certain features. These features must largely include a significant accumulation of hydrocarbons, rock physics models, and mechanical properties. However, the effective representation of such reservoir properties using applicable parameters is challenging due to the complicated heterogeneous structural characteristics of hydrocarbon sand. Rock physics modeling of sandstone reservoirs from the Lower Goru Basin gas fields represents the link between reservoir parameters and seismic properties. Rock physics diagnostic models have been utilized to describe the reservoir sands of two wells inside this Middle Indus Basin, including contact cement, constant cement, and friable sand. The results showed that sorting the grain and coating cement on the grain’s surface both affected the cementation process. According to the models, the cementation levels in the reservoir sands of the two wells ranged from 2% to more than 6%. The rock physics models established in the study would improve the understanding of characteristics for the relatively high Vp/Vs unconsolidated reservoir sands under study. Integrating rock physics models would improve the prediction of reservoir properties from the elastic properties estimated from seismic data. The velocity–porosity and elastic moduli-porosity patterns for the reservoir zones of the two wells are distinct. To generate a rock physics template (RPT) for the Lower Goru sand from the Early Cretaceous period, an approach based on fluid replacement modeling has been chosen. The ratio of P-wave velocity to S-wave velocity (Vp/Vs) and the P-impedance template can detect cap shale, brine sand, and gas-saturated sand with varying water saturation and porosity from wells in the Rehmat and Miano gas fields, both of which have the same shallow marine depositional characteristics. Conventional neutron-density cross-plot analysis matches up quite well with this RPT’s expected detection of water and gas sands

Quantitative Characterization of Shallow Marine Sediments in Tight Gas Fields of Middle Indus Basin: A Rational Approach of Multiple Rock Physics Diagnostic Models

For the successful discovery and development of tight sand gas reserves, it is necessary to locate sand with certain features. These features must largely include a significant accumulation of hydrocarbons, rock physics models, and mechanical properties. However, the effective representation of such reservoir properties using applicable parameters is challenging due to the complicated heterogeneous structural characteristics of hydrocarbon sand. Rock physics modeling of sandstone reservoirs from the Lower Goru Basin gas fields represents the link between reservoir parameters and seismic properties. Rock physics diagnostic models have been utilized to describe the reservoir sands of two wells inside this Middle Indus Basin, including contact cement, constant cement, and friable sand. The results showed that sorting the grain and coating cement on the grain’s surface both affected the cementation process. According to the models, the cementation levels in the reservoir sands of the two wells ranged from 2% to more than 6%. The rock physics models established in the study would improve the understanding of characteristics for the relatively high Vp/Vs unconsolidated reservoir sands under study. Integrating rock physics models would improve the prediction of reservoir properties from the elastic properties estimated from seismic data. The velocity–porosity and elastic moduli-porosity patterns for the reservoir zones of the two wells are distinct. To generate a rock physics template (RPT) for the Lower Goru sand from the Early Cretaceous period, an approach based on fluid replacement modeling has been chosen. The ratio of P-wave velocity to S-wave velocity (Vp/Vs) and the P-impedance template can detect cap shale, brine sand, and gas-saturated sand with varying water saturation and porosity from wells in the Rehmat and Miano gas fields, both of which have the same shallow marine depositional characteristics. Conventional neutron-density cross-plot analysis matches up quite well with this RPT’s expected detection of water and gas sands