-
Microbial Ecology Jun 2024Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined...
Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 μg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 μM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27-34%), root length (20-50%), shoot length (20-40%), vigor index (50-75%), carotenoid content (0.543-1.733), and lycopene content (2.333-2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.
Topics: Bacillus; Soil Microbiology; Biodiversity; India; Plant Roots; Cicer; Solanum lycopersicum; RNA, Ribosomal, 16S; Rhizosphere; Phylogeny; Antibiosis; Siderophores; Indoleacetic Acids
PubMed: 38888737
DOI: 10.1007/s00248-024-02397-w -
Frontiers in Microbiology 2024is an endangered traditional medicinal herb in China. In May 2020, the emergence of white root rot severely impacted the quality and yield of , affecting about 5% of...
is an endangered traditional medicinal herb in China. In May 2020, the emergence of white root rot severely impacted the quality and yield of , affecting about 5% of the plants at plant nurseries of the Chengdu Academy of Agricultural and Forestry Sciences. Through a series of experiments and evaluations, the pathogen was identified as . This is the first report of white root rot caused by in Sichuan, China. To better understand this disease and provide data support for its control, a combination of morphological, molecular characterisation and pathogenicity determination was used in this study for assessment. Meanwhile, the effects of different carbon and nitrogen sources, culture medium, temperature, photoperiod and pH on mycelial growth and spore production of were investigated. In addition, effective fungicides were screened and the concentration ratios of fungicides were optimized using response surface methodology (RSM). The experimental results showed that sucrose was the optimum carbon source for the pathogen, and the optimum temperature and pH were 25°C and pH 7, respectively, while light did no significant effect. Effective fungicides were screened, among which difenoconazole showed the strongest inhibition with EC of 142.773 µg/mL. The optimum fungicide concentration scheme (difenoconazole, pyraclostrobin, and thiophanate-methyl at 395.42, 781.03, and 561.11 µg/mL, respectively) was obtained using response surface methodology (RSM) to improve the inhibition rate of 92.24 ± 0.34%. This study provides basic data for the pathogen characterization of white root rot and its potential fungicides in Sichuan, China. In addition, the optimal fungicide concentration ratios were obtained through response surface methodology (RSM) optimization, which significantly enhanced the fungicidal effect and provided a scientific basis for the future control of white root rot.
PubMed: 38887710
DOI: 10.3389/fmicb.2024.1374137 -
Beilstein Journal of Nanotechnology 2024Photothermal conversion of light into heat energy is an intrinsic optical property of metal nanoparticles when irradiated using near-infrared radiation. However, the...
Photothermal conversion of light into heat energy is an intrinsic optical property of metal nanoparticles when irradiated using near-infrared radiation. However, the impact of size and shape on the photothermal behaviour of gold nanomakura particles possessing optical absorption within 600-700 nm as well as on incorporation in hydrogels is not well reported. In this study, nanomakura-shaped anisotropic gold nanoparticles (AuNMs) were synthesized via a surfactant-assisted seed-mediated protocol. Quaternary cationic surfactants having variable carbon tail length ( = 16, 14, 12) were used as capping for tuning the plasmon peak of gold nanomakura within a 600-700 nm wavelength. The aspect ratio as well as anisotropy of synthesized gold nanomakura can influence photothermal response upon near-infrared irradiation. The role of carbon tail length was evident via absorption peaks obtained from longitudinal surface plasmon resonance analysis at 670, 650, and 630 nm in CTAB-AuNM, MTAB-AuNM, and DTAB-AuNM, respectively. Furthermore, the impact of morphology and surrounding milieu of the synthesized nanomakuras on photothermal conversion is investigated owing to their retention of plasmonic stability. Interestingly, we found that photothermal conversion was exclusively assigned to morphological features (i.e., nanoparticles of higher aspect ratio showed higher temperature change and vice versa irrespective of the surfactant used). To enable biofunctionality and stability, we used kappa-carrageenan- (k-CG) based hydrogels for incorporating the nanomakuras and further assessed their photothermal response. Nanomakura particles in association with k-CG were also able to show photothermal conversion, depicting their ability to interact with light without hindrance. The CTAB-AuNM, MTAB-AuNM, and DTAB-AuNM after incorporation into hydrogel beads attained up to ≈17.2, ≈17.2, and ≈15.7 °C, respectively. On the other hand, gold nanorods after incorporation into k-CG did not yield much photothermal response as compared to that of AuNMs. The results showed a promising platform to utilize nanomakura particles along with kappa-carrageenan hydrogels for enabling usage on nanophotonic, photothermal, and bio-imaging applications.
PubMed: 38887524
DOI: 10.3762/bjnano.15.56 -
Cancer Imaging : the Official... Jun 2024The Response Evaluation Criteria in Solid Tumors (RECIST) are often inadequate for the early assessment of the response to cancer therapy, particularly bevacizumab-based...
Prognostic value of the tumor-to-liver density ratio in patients with metastatic colorectal cancer treated with bevacizumab-based chemotherapy. A post-hoc study of the STIC-AVASTIN trial.
BACKGROUND
The Response Evaluation Criteria in Solid Tumors (RECIST) are often inadequate for the early assessment of the response to cancer therapy, particularly bevacizumab-based chemotherapy. In a first cohort of patients with colorectal cancer liver metastases (CRLM), we showed that variations of the tumor-to-liver density (TTLD) ratio and modified size-based criteria determined using computed tomography (CT) data at the first restaging were better prognostic criteria than the RECIST. The aims of this study were to confirm the relevance of these radiological biomarkers as early predictors of the long-term clinical outcome and to assess their correlation with contrast-enhanced ultrasound (CEUS) parameters in a new patient cohort.
METHODS
In this post-hoc study of the multicenter STIC-AVASTIN trial, we retrospectively reviewed CT data of patients with CRLM treated with bevacizumab-based regimens. We determined the size, density and TTLD ratio of target liver lesions at baseline and at the first restaging and also performed a morphologic evaluation according to the MD Anderson criteria. We assessed the correlation of these parameters with progression-free survival (PFS) and overall survival (OS) using the log-rank test and a Cox proportional hazard model. We also examined the association between TTLD ratio and quantitative CEUS parameters.
RESULTS
This analysis concerned 79 of the 137 patients included in the STIC-AVASTIN trial. PFS and OS were significantly longer in patients with tumor size reduction > 15% at first restaging, but were not correlated with TTLD ratio variations. However, PFS was longer in patients with TTLD ratio > 0.6 at baseline and first restaging than in those who did not reach this threshold. In the multivariate analysis, only baseline TTLD ratio > 0.6 was a significant survival predictor. TTLD ratio > 0.6 was associated with improved perfusion parameters.
CONCLUSIONS
Although TTLD ratio variations did not correlate with the long-term clinical outcomes, TTLD absolute values remained a good predictor of survival at baseline and first restaging, and may reflect tumor microvascular features that might influence bevacizumab-based treatment efficiency.
TRIAL REGISTRATION
NCT00489697, registration number of the STIC-AVASTIN trial.
Topics: Humans; Bevacizumab; Colorectal Neoplasms; Liver Neoplasms; Male; Female; Middle Aged; Aged; Retrospective Studies; Prognosis; Tomography, X-Ray Computed; Antineoplastic Combined Chemotherapy Protocols; Adult; Ultrasonography; Liver
PubMed: 38886836
DOI: 10.1186/s40644-024-00722-7 -
Genome Biology Jun 2024Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola...
BACKGROUND
Lettuce (Lactuca sativa L.) is an economically important vegetable crop worldwide. Lettuce is believed to be domesticated from a single wild ancestor Lactuca serriola and subsequently diverged into two major morphologically distinct vegetable types: leafy lettuce and stem lettuce. However, the role of epigenetic variation in lettuce domestication and divergence remains largely unknown.
RESULTS
To understand the genetic and epigenetic basis underlying lettuce domestication and divergence, we generate single-base resolution DNA methylomes from 52 Lactuca accessions, including major lettuce cultivars and wild relatives. We find a significant increase of DNA methylation during lettuce domestication and uncover abundant epigenetic variations associated with lettuce domestication and divergence. Interestingly, DNA methylation variations specifically associated with leafy and stem lettuce are related to regulation and metabolic processes, respectively, while those associated with both types are enriched in stress responses. Moreover, we reveal that domestication-induced DNA methylation changes could influence expression levels of nearby and distal genes possibly through affecting chromatin accessibility and chromatin loop.
CONCLUSION
Our study provides population epigenomic insights into crop domestication and divergence and valuable resources for further domestication for diversity and epigenetic breeding to boost crop improvement.
Topics: Lactuca; DNA Methylation; Domestication; Epigenesis, Genetic; Genetic Variation; Crops, Agricultural; Gene Expression Regulation, Plant; Genome, Plant
PubMed: 38886807
DOI: 10.1186/s13059-024-03310-x -
BMC Plant Biology Jun 2024Changing climate is causing erratic rainfall and prolonged drought periods, thus posing serious threats to crop productivity. Owing to severity of drought events, it is...
BACKGROUND
Changing climate is causing erratic rainfall and prolonged drought periods, thus posing serious threats to crop productivity. Owing to severity of drought events, it is imperative to take proactive measures to enhance the resilience of drought sensitive crops like rice. Therefore, the present study was carried out to improve the drought stress tolerance in rice through gamma amino butyric acid (GABA) application.
METHODS
The experiment was included four GABA concentrations i.e., 0 mM as control, 1 mM, 1.5 mM, and 2 mM, two water levels i.e., 100% and 50% field capacity (referred as FC100 for well-watered and FC50 for drought conditions, respectively), and two fragrant rice cultivars i.e., Super Basmati and Basmati-515.
RESULTS
The findings unveiled a comprehensive improvement in various parameters with GABA application in fragrant rice under both well-watered (FC100) and water-limited (FC50) conditions, compared to the control. Specifically, GABA induced enhancements were observed in plant height, root length, fresh weight, dry weight, total soluble protein content, and total free amino acid content across both cultivars. Moreover, GABA application significantly improved peroxidase (POD) and catalase (CAT) enzyme activities, alongside elevating anthocyanin levels, while concurrently reducing HO contents in both FC100 and FC50 treatments. Furthermore, the positive impact of GABA extended to morphological traits, with notable increases in panicle length, total tillers and productive tillers per hill, branch and grain numbers per panicle, and 1000-grain weight for Super Basmati and Basmati 515 cultivars under both water regimes, compared to Ck. Similarly, the grain yield increased by 31.01% and 27.32% under FC100 and 36.85% and 27.71% under FC50 in Super Basmati and Basmati-515, respectively, in response to GABA application, compared to Ck. Additionally, principal component analysis (PCA) revealed significant variances attributed to Dim1 and Dim2, with 86.1% and 4.0% of the variance, respectively, across three bi-plots encompassing rice cultivars, water levels, and GABA treatments. Notably, all tested indices, except for HO and non-productive tillers per hill, exhibited positive correlations amongst themselves and with rice yield, further emphasizing the beneficial effects of GABA application on fragrant rice under well-watered and drought conditions.
CONCLUSIONS
GABA significantly improved fragrant rice performance under both well-watered (FC100) and water-limited (FC50) conditions. Moreover, integrating GABA application into rice cultivation practices could not only improve the crop resilience to drought stress but also potentially benefiting the future food and nutritional security globally. However, however; further research is needed to understand the cellular and molecular mechanisms of the functionality of GABA in fragrant rice, particularly under drought conditions.
Topics: Oryza; gamma-Aminobutyric Acid; Droughts; Water
PubMed: 38886652
DOI: 10.1186/s12870-024-05272-5 -
Briefings in Bioinformatics May 2024Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of... (Review)
Review
Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine learning and deep learning, especially in computer vision, have led to substantial improvements in analyzing large-scale high-content images at high throughput. These efforts have facilitated understanding of compound mechanism of action, drug repurposing, characterization of cell morphodynamics under perturbation, and ultimately contributing to the development of novel therapeutics. In this review, we provide a comprehensive overview of the recent advances in the field of morphological profiling. We summarize the image profiling analysis workflow, survey a broad spectrum of analysis strategies encompassing feature engineering- and deep learning-based approaches, and introduce publicly available benchmark datasets. We place a particular emphasis on the application of deep learning in this pipeline, covering cell segmentation, image representation learning, and multimodal learning. Additionally, we illuminate the application of morphological profiling in phenotypic drug discovery and highlight potential challenges and opportunities in this field.
Topics: Deep Learning; Drug Discovery; Humans; Image Processing, Computer-Assisted; Machine Learning
PubMed: 38886164
DOI: 10.1093/bib/bbae284 -
JMIR Public Health and Surveillance Jun 2024The biological characteristics of mosquito vectors vary, impacting their response to control measures. Thus, having up-to-date information on vector bionomics is...
BACKGROUND
The biological characteristics of mosquito vectors vary, impacting their response to control measures. Thus, having up-to-date information on vector bionomics is essential to maintain the effectiveness of existing control strategies and tools, particularly as India aims for malaria elimination by 2030.
OBJECTIVE
This study aims to assess the proportions of vector species resting indoors and outdoors, determine their preference for host biting/feeding, identify transmission sites, and evaluate the susceptibility of vectors to insecticides used in public health programs.
METHODS
Mosquito collections were conducted in 13 districts across 8 Indian states from 2017 to 2020 using various methods to estimate their densities. Following morphological identification in the field, sibling species of Anopheles mosquitoes were identified molecularly using polymerase chain reaction (PCR)-specific alleles. Plasmodium falciparum and Plasmodium vivax infections in the vectors were detected using enzyme-linked immunosorbent assay (ELISA) and PCR assays. In addition, we assessed the insecticide susceptibility status of primary malaria vectors following the World Health Organization (WHO) protocol.
RESULTS
Anopheles culicifacies, a primary malaria vector, was collected (with a man-hour density ranging from 3.1 to 15.9) from all states of India except those in the northeastern region. Anopheles fluviatilis, another primary vector, was collected from the states of Madhya Pradesh, Maharashtra, Karnataka, and Odisha. In Haryana and Karnataka, An. culicifacies sibling species A predominated, whereas species C and E were predominant in Madhya Pradesh and Maharashtra. An. culicifacies displayed mainly endophilic behavior across all states, except in Madhya Pradesh, where the proportion of semigravid and gravid mosquitoes was nearly half of that of unfed mosquitoes. The human blood index of An. culicifacies ranged from 0.001 to 0.220 across all study sites. The sporozoite rate of An. culicifacies ranged from 0.06 to 4.24, except in Madhya Pradesh, where none of the vector mosquitoes were found to be infected with the Plasmodium parasite. In the study area, An. culicifacies exhibited resistance to DDT (dichlorodiphenyltrichloroethane; with <39% mortality). Moreover, it showed resistance to malathion (with mortality rates ranging from 49% to 78%) in all districts except Angul in Odisha and Palwal in Haryana. In addition, resistance to deltamethrin was observed in districts of Maharashtra, Gujarat, Haryana, and Karnataka.
CONCLUSIONS
Our study offers vital insights into the prevalence, resting behavior, and sibling species composition of malaria vectors in India. It is evident from our findings that resistance development in An. culicifacies, the primary vector, to synthetic pyrethroids is on the rise in the country. Furthermore, the results of our study suggest a potential change in the resting behavior of An. culicifacies in Madhya Pradesh, although further studies are required to confirm this shift definitively. These findings are essential for the development of effective vector control strategies in India, aligning with the goal of malaria elimination by 2030.
Topics: India; Animals; Mosquito Vectors; Malaria; Anopheles; Humans; Disease Eradication; Insecticides; Insecticide Resistance; Ecology
PubMed: 38885497
DOI: 10.2196/42050 -
PloS One 2024Photodynamic venous occlusion is a commonly accepted method for establishing mouse models of retinal vein occlusion (RVO). However, existing model parameters do not...
Photodynamic venous occlusion is a commonly accepted method for establishing mouse models of retinal vein occlusion (RVO). However, existing model parameters do not distinguish between acute and chronic RVO subtypes. Large variations in laser energy seem to correlate with fluctuating retinopathy severity and high rates of venous recanalization during the acute phase, along with the variable levels of retinal perfusion during the chronic phase. After optimizing the modeling procedure and defining success and exclusion criteria, laser energy groups of 80mW, 100mW, and 120mW were established. Multimodal imaging confirmed that higher energy levels increased the incidence of retinal cystoid edema and intraretinal hemorrhage, exacerbated the severity of exudative retinal detachment, and reduced the venous recanalization rate. For the acute model, 100mW was considered an appropriate parameter for balancing moderate retinopathy and venous recanalization. Continuous imaging follow-up revealed that day 1 after RVO was the optimal observation point for peaking of retinal thickness and intensive occurrence of retinal cystic edema and intraretinal hemorrhage. After excluding the influence of venous recanalization on retinal thickness, acute retinal edema demonstrated a positive response to standard anti-vascular endothelial growth factor therapy, validating the clinical relevance of the acute RVO model for further study in pathogenic mechanisms and therapeutic efficacy. For the chronic model, the 120mW parameter with the lowest venous recanalization rate was applied, accompanied by an increase in both photocoagulation shots and range to ensure sustained vein occlusion. Imaging follow-up clarified non-ischemic retinopathy characterized by tortuosity and dilation of the distal end, branches, and adjacent veins of the occluded vein. These morphological changes are quantifiable and could be combined with electrophysiological functional assessment for treatment effectiveness evaluation. Moreover, the stable state of venous occlusion may facilitate investigations into response and compensation mechanisms under conditions of chronic retinal hypoperfusion.
Topics: Retinal Vein Occlusion; Animals; Disease Models, Animal; Mice; Acute Disease; Chronic Disease; Lasers; Mice, Inbred C57BL; Male; Tomography, Optical Coherence; Retina
PubMed: 38885229
DOI: 10.1371/journal.pone.0305741 -
Frontiers in Oncology 2024The study aimed to compare and correlate morphological and functional parameters in pancreatic neuroendocrine tumors (pNET) and their synchronous liver metastases...
BACKGROUND
The study aimed to compare and correlate morphological and functional parameters in pancreatic neuroendocrine tumors (pNET) and their synchronous liver metastases (NELM), while also assessing prognostic imaging parameters.
METHODS
Patients with G1/G2 pNET and synchronous NELM underwent pretherapeutic abdominal MRI with DWI and 68Ga-DOTATATE/TOC PET/CT were included. ADC (mean, min), SNR_art and SNT_T2 (SNR on arterial phase and on T2) and SUV (max, mean) for three target NELM and pNET, as well as tumor-free liver and spleen (only in PET/CT) were measured. Morphological parameters including size, location, arterial enhancement, cystic components, T2-hyperintensity, ductal dilatation, pancreatic atrophy, and vessel involvement were noted. Response evaluation used progression-free survival (PFS) with responders (R;PFS>24 months) and non-responders (NR;PFS ≤ 24 months).
RESULTS
33 patients with 33 pNETs and 95 target NELM were included. There were no significant differences in ADC and SUV values between NELM and pNET. 70% of NELM were categorized as hyperenhancing lesions, whereas the pNETs exhibited significantly lower rate (51%) of hyperenhancement (p<0.01) and significant lower SNR_art. NELM were qualitatively and quantitatively (SNR_T2) significantly more hyperintense on T2 compared to pNET (p=0.01 and p<0.001). NELM of R displayed significantly lower ADCmean value in comparison to the ADC mean value of pNET (0.898 versus 1.037x10mm²/s,p=0.036). In NR, T2-hyperintensity was notably higher in NELM compared to pNET (p=0.017). The hepatic tumor burden was significantly lower in the R compared to the NR (10% versus 30%).
CONCLUSIONS
Arterial hyperenhancement and T2-hyperintensity differ between synchronous NELM and pNET. These findings emphasize the importance of a multifaceted approach to imaging and treatment planning in patients with these tumors as well as in predicting treatment responses.
PubMed: 38884077
DOI: 10.3389/fonc.2024.1352538