Transcriptomic analysis reveals the molecular basis of photoperiod-regulated sex differentiation in tropical pumpkins (Cucurbita moschata Duch.).

BACKGROUND: Photoperiod, or the length of the day, has a significant impact on the flowering and sex differentiation of photoperiod-sensitive crops. The "miben" pumpkin (the main type of Cucurbita moschata Duch.) is well-known for its high yield and strong disease resistance. However, its cultivation has been limited due to its sensitivity to photoperiod. This sensitivity imposes challenges on its widespread cultivation and may result in suboptimal yields in regions with specific daylength conditions. As a consequence, efforts are being made to explore potential strategies or breeding techniques to enhance its adaptability to a broader range of photoperiods, thus unlocking its full cultivation potential and further promoting its valuable traits in agriculture. RESULTS: This study aimed to identify photoperiod-insensitive germplasm exhibiting no difference in sex differentiation under different day-length conditions. The investigation involved a phenotypic analysis of photoperiod-sensitive (PPS) and photoperiod-insensitive (PPIS) pumpkin materials exposed to different day lengths, including long days (LDs) and short days (SDs). The results revealed that female flower differentiation was significantly inhibited in PPS_LD, while no differences were observed in the other three groups (PPS_SD, PPIS_LD, and PPIS_SD). Transcriptome analysis was carried out for these four groups to explore the main-effect genes of sex differentiation responsive to photoperiod. The main-effect gene subclusters were identified based on the principal component and hierarchical cluster analyses. Further, functional annotations and enrichment analysis revealed significant upregulation of photoreceptors (CmCRY1, F-box/kelch-repeat protein), circadian rhythm-related genes (CmGI, CmPRR9, etc.), and CONSTANS (CO) in PPS_LD. Conversely, a significant downregulation was observed in most Nuclear Factor Y (NF-Y) transcription factors. Regarding the gibberellic acid (GA) signal transduction pathway, positive regulators of GA signaling (CmSCL3, CmSCL13, and so forth) displayed higher expression levels, while the negative regulators of GA signaling, CmGAI, exhibited lower expression levels in PPS_LD. Notably, this effect was not observed in the synthetic pathway genes. Furthermore, genes associated with ethylene synthesis and signal transduction (CmACO3, CmACO1, CmERF118, CmERF118-like1,2, CmWIN1-like, and CmRAP2-7-like) showed significant downregulation. CONCLUSIONS: This study offered a crucial theoretical and genetic basis for understanding how photoperiod influences the mechanism of female flower differentiation in pumpkins.

A highly porous animal bone-derived char with a superiority of promoting nZVI for Cr(VI) sequestration in agricultural soils.

Paddy soil and irrigation water are commonly contaminated with hexavalent chromium [Cr(VI)] near urban industrial areas, thereby threatening the safety of agricultural products and human health. In this study, we develop a porous and high specific area bone char (BC) to support nanoscale zero-valent iron (nZVI) and apply it to remediate Cr(VI) pollution in water and paddy soil under anaerobic conditions. The batch experiments reveal that BC/nZVI exhibits a higher removal capacity of 516.7 mg/(g•nZVI) for Cr(VI) than nZVI when normalized to the actual nZVI content, which is 2.8 times that of nZVI; moreover, the highest nZVI utilization is the nZVI loading of 15% (BC/nZVI15). The Cr(VI) removal efficiency of BC/nZVI15 decreases with increasing pH (4 - 10). Coexisting ions (phosphate and carbonate) and humic acid can inhibit the removal of Cr(VI) with BC/nZVI15. Additionally, BC exhibits a strong advantage in promoting Cr(VI) removal by nZVI compared to the widely used biochar and activated carbon. Our results demonstrate that reduction and coprecipitation are the dominant Cr(VI) removal mechanisms. Furthermore, BC/nZVI15 shows a significantly higher reduction and removal efficiency as well as a strong anti-interference ability for Cr(VI) in paddy soil, as compared to nZVI. These findings provide a new effective material for remediating Cr(VI) pollution from water and soil.

Synergetic performance of isothermal amplification techniques and lateral flow approach for nucleic acid diagnostics.

The advancement in developing sensitive, rapid, and specific sensing tools is crucial in diagnostics and biotechnological applications. Although various isothermal amplification approaches exist for the detection and identification of nucleic acids, post-amplicon analysis is still based on traditional methods such as gel electrophoresis, colorimetry, turbidity, which could be non-specific and inconvenient. Thus, this review will first elaborate various isothermal amplification techniques (principle, merits, and demerits) and their potentials when combined with lateral flow approach for point-of-care nucleic acid diagnostics. Different methods for monitoring carryover contamination resulting from amplification product contamination will be discussed. Then, we will present recent advances in diagnostics with both target pre-amplification and CRISPR-Cas systems, which exhibit collateral cleavage of target nucleic acid and a reporter single strand nucleic acid within the vicinity. When the reporter is fluorophore-labeled, it provides a detectable signal by fluorescence or lateral flow biosensors. Lastly, we will discuss how CRISPR-Cas system based diagnostics could be more effective, affordable and portable for on-site detection.

A rapid and sensitive CRISPR/Cas12a based lateral flow biosensor for the detection of Epstein-Barr virus.

Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in the world, and several studies have associated Epstein-Barr virus (EBV) with NPC occurrence and development. EBV-PCR (polymerase chain reaction), in situ hybridization and immunoassays are the most common methods for NPC identification. However, these approaches have drawbacks, which include tedious procedures and false results. Therefore, a rapid, accurate, and sensitive clinical diagnostic method for the prognosis of EBV-related diseases is needed. In this study, we developed a simple and sensitive approach for EBV detection based on the combination of CRISPR-Cas12a and a lateral flow biosensor (LFB). Cas12a exhibits collateral cleavage propensity of both target DNA and any single-stranded(ss) DNA in the vicinity (herein referred to as a reporter). The LFB test line contained an ssDNA probe complementary to the reporter. In the presence of the target, Cas12a trans-cleaved the ssDNA reporter, which resulted in the inability of cleaved sequences to bind the LFB test line. With a PCR pre-amplification of the target (45 min), the assay achieved a sensitivity of 7.1 × 10-14 M (∼42 000 copies per µl) both in plasmid and plasmid-spiked samples. The assay attained a high specificity in the presence of various bacteria and applicability in EBV Burkitt's lymphoma serum samples. This method could be applied for the detection of EBV and other infectious diseases.

Biocontrol potential of lipopeptides produced by the novel Bacillus subtilis strain Y17B against postharvest Alternaria fruit rot of cherry.

The use of synthetic fungicides against postharvest Alternaria rot adversely affects human health and the environment. In this study, as a safe alternative to fungicides, Bacillus subtilis strain Y17B isolated from soil exhibited significant antifungal activity against Alternaria alternata. Y17B was identified as B. subtilis based on phenotypic identification and 16S rRNA sequence analysis. To reveal the antimicrobial activity of this strain, a PCR-based study detected the presence of antifungal lipopeptide (LP) biosynthetic genes from genomic DNA. UPLC Q TOF mass spectrometry analysis detected the LPs surfactin (m/z 994.64, 1022.68, and 1026.62), iturin (m/z 1043.56), and fengycin (m/z 1491.85) in the extracted LP crude of B. subtilis Y17B. In vitro antagonistic study demonstrated the efficiency of LPs in inhibiting A. alternata growth. Microscopy (SEM and TEM) studies showed the alteration of the morphology of A. alternata in the interaction with LPs. In vivo test results revealed the efficiency of LPs in reducing the growth of the A. alternata pathogen. The overall results highlight the biocontrol potential of LPs produced by B. subtilis Y17B as an effective biological control agent against A. alternata fruit rot of cherry.

Phosphate Removal Mechanisms in Aqueous Solutions by Three Different Fe-Modified Biochars.

Iron-modified biochar can be used as an environmentally friendly adsorbent to remove the phosphate in wastewater because of its low cost. In this study, Fe-containing materials, such as zero-valent iron (ZVI), goethite, and magnetite, were successfully loaded on biochar. The phosphate adsorption mechanisms of the three Fe-modified biochars were studied and compared. Different characterization methods, including scanning electron microscopy/energy-dispersive spectrometry (SEM-EDS), Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS), were used to study the physicochemical properties of the biochars. The dosage, adsorption time, pH, ionic strength, solution concentration of phosphate, and regeneration evaluations were carried out. Among the three Fe-modified biochars, biochar modified by goethite (GBC) is more suitable for phosphate removal in acidic conditions, especially when the pH = 2, while biochar modified by ZVI (ZBC) exhibits the fastest adsorption rate. The maximum phosphate adsorption capacities, calculated by the Langmuir-Freundlich isothermal model, are 19.66 mg g-1, 12.33 mg g-1, and 2.88 mg g-1 for ZBC, GBC, and CSBC (biochar modified by magnetite), respectively. However, ZBC has a poor capacity for reuse. The dominant mechanism for ZBC is surface precipitation, while for GBC and CSBC, the major mechanisms are ligand exchange and electrostatic attraction. The results of our study can enhance the understanding of phosphate removal mechanisms by Fe-modified biochar and can contribute to the application of Fe-modified biochar for phosphate removal in water.

Distribution of Aspergillus Fungi and Recent Aflatoxin Reports, Health Risks, and Advances in Developments of Biological Mitigation Strategies in China.

Aflatoxins (AFs) are secondary metabolites that represent serious threats to human and animal health. They are mainly produced by strains of the saprophytic fungus Aspergillus flavus, which are abundantly distributed across agricultural commodities. AF contamination is receiving increasing attention by researchers, food producers, and policy makers in China, and several interesting review papers have been published, that mainly focused on occurrences of AFs in agricultural commodities in China. The goal of this review is to provide a wider scale and up-to-date overview of AF occurrences in different agricultural products and of the distribution of A. flavus across different food and feed categories and in Chinese traditional herbal medicines in China, for the period 2000-2020. We also highlight the health impacts of chronic dietary AF exposure, the recent advances in biological AF mitigation strategies in China, and recent Chinese AF standards.

The Regulatory Mechanism of Water Activities on Aflatoxins Biosynthesis and Conidia Development, and Transcription Factor AtfB Is Involved in This Regulation.

Peanuts are frequently infected by Aspergillus strains and then contaminated by aflatoxins (AF), which brings out economic losses and health risks. AF production is affected by diverse environmental factors, especially water activity (aw). In this study, A. flavus was inoculated into peanuts with different aw (0.90, 0.95, and 0.99). Both AFB1 yield and conidia production showed the highest level in aw 0.90 treatment. Transcriptional level analyses indicated that AF biosynthesis genes, especially the middle- and later-stage genes, were significantly up-regulated in aw 0.90 than aw 0.95 and 0.99. AtfB could be the pivotal regulator response to aw variations, and could further regulate downstream genes, especially AF biosynthesis genes. The expressions of conidia genes and relevant regulators were also more up-regulated at aw 0.90 than aw 0.95 and 0.99, suggesting that the relative lower aw could increase A. flavus conidia development. Furthermore, transcription factors involved in sexual development and nitrogen metabolism were also modulated by different aw. This research partly clarified the regulatory mechanism of aw on AF biosynthesis and A. flavus development and it would supply some advice for AF prevention in food storage.

Rational Programming of Cas12a for Early-Stage Detection of COVID-19 by Lateral Flow Assay and Portable Real-Time Fluorescence Readout Facilities.

Coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 virus has led to a global pandemic with a high spread rate and pathogenicity. Thus, with limited testing solutions, it is imperative to develop early-stage diagnostics for rapid and accurate detection of SARS-CoV-2 to contain the rapid transmission of the ongoing COVID-19 pandemic. In this regard, there remains little knowledge about the integration of the CRISPR collateral cleavage mechanism in the lateral flow assay and fluorophotometer. In the current study, we demonstrate a CRISPR/Cas12a-based collateral cleavage method for COVID-19 diagnosis using the Cas12a/crRNA complex for target recognition, reverse transcription loop-mediated isothermal amplification (RT-LAMP) for sensitivity enhancement, and a novel DNA capture probe-based lateral flow strip (LFS) or real-time fluorescence detector as the parallel system readout facility, termed CRICOLAP. Our novel approach uses a customized reporter that hybridizes an optimized complementary capture probe fixed at the test line for naked-eye result readout. The CRICOLAP system achieved ultra-sensitivity of 1 copy/µL in ~32 min by portable real-time fluorescence detection and ~60 min by LFS. Furthermore, CRICOLAP validation using 60 clinical nasopharyngeal samples previously verified with a commercial RT-PCR kit showed 97.5% and 100% sensitivity for S and N genes, respectively, and 100% specificity for both genes of SARS-CoV-2. CRICOLAP advances the CRISPR/Cas12a collateral cleavage result readout in the lateral flow assay and fluorophotometer, and it can be an alternative method for the decentralized field-deployable diagnosis of COVID-19 in remote and limited-resource locations.

Mycotoxins in Ethiopia: A Review on Prevalence, Economic and Health Impacts.

Mycotoxigenic fungi and their toxins are a global concern, causing huge economic and health impacts in developing countries such as Ethiopia, where the mycotoxin control system is inadequate. This work aimed to review the occurrences of agriculturally essential fungi such as Aspergillus, Fusarium, and Penicillium and their major mycotoxins in Ethiopian food/feedstuffs. The incidents of crucial toxins, including aflatoxins (B1, B2, G1, G2, M1), fumonisins (B1, B2), zearalenone, deoxynivalenol, and ochratoxin A, were studied. The impacts of chronic aflatoxin exposure on liver cancer risks, synergy with chronic hepatitis B infection, and possible links with Ethiopian childhood malnutrition were thoroughly examined. In addition, health risks of other potential mycotoxin exposure are also discussed, and the impacts of unsafe level of mycotoxin contaminations on economically essential export products and livestock productions were assessed. Feasible mycotoxin mitigation strategies such as biocontrol methods and binding agents (bentonite) were recommended because they are relatively cheap for low-income farmers and widely available in Ethiopia, respectively. Moreover, Ethiopian mycotoxin regulations, storage practice, adulteration practice, mycotoxin tests, and knowledge gaps among value chain actors were highlighted. Finally, sustained public awareness was suggested, along with technical and human capacity developments in the food control sector.

A CRISPR/Cas12a Based Universal Lateral Flow Biosensor for the Sensitive and Specific Detection of African Swine-Fever Viruses in Whole Blood.

Cross-border pathogens such as the African swine fever virus (ASFV) still pose a socio-economic threat. Cheaper, faster, and accurate diagnostics are imperative for healthcare and food safety applications. Currently, the discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) has paved the way for the diagnostics based on Cas13 and Cas12/14 that exhibit collateral cleavage of target and single-stranded DNA (ssDNA) reporter. The reporter is fluorescently labeled to report the presence of a target. These methods are powerful; however, fluorescence-based approaches require expensive apparatuses, complicate results readout, and exhibit high-fluorescence background. Here, we present a new CRISPR-Cas-based approach that combines polymerase chain reaction (PCR) amplification, Cas12a, and a probe-based lateral flow biosensor (LFB) for the simultaneous detection of seven types of ASFV. In the presence of ASFVs, the LFB responded to reporter trans-cleavage by naked eyes and achieved a sensitivity of 2.5 × 10-15 M within 2 h, and unambiguously identified ASFV from swine blood. This system uses less time for PCR pre-amplification and requires cheaper devices; thus, it can be applied to virus monitoring and food samples detection.

Impact of sugarcane bagasse-derived biochar on heavy metal availability and microbial activity: A field study.

In the current study, we conducted a field experiment using the test plant, Brassica chinesis L. (pak choi), to investigate the effect of sugarcane bagasse-derived biochar on the bioavailability of cadmium (Cd), copper (Cu) and lead (Pb), and the health of soil microbiota in a contaminated soil. Biochar application significantly (P < 0.05) increased pak choi yield. Bioavailability of heavy metals to plant shoots and roots decreased with increasing biochar application rates (at 0, 1.5, 2.25 and 3.0 t ha-1). Sequential extraction of the biochar-treated and -untreated soil revealed that exchangeable Cd reduced whereas organically-bound fraction increased with increasing biochar rate. The labile fractions of Cu and Pb decreased, but the residual fraction increased in biochar-treated soils compared to the control. Urease, catalase and invertase activities, and the populations of bacteria and actinomycetes were significantly enhanced, whereas fungi population declined in biochar-treated soils. This study highlights that sugarcane bagasse biochar has the potential to support the remediation of soils contaminated with heavy metals, and as such can improve the yield and quality of agricultural crops.

[Effect of transgenic plants on biodiversity of agroecosystem].

The effect of transgenic plants on the biodiversity of agroecosystem is an important environmental issue. There are many researches in this field at home and abroad recently. This paper reviewed the advances of the researches based on three levels of biodiversity as genetic diversity, species diversity and ecosystem diversity. They included following aspects: the effect of insect-resistant transgenic crops on target pest; the effect of herbicide-resistant transgenic crops on crops and wild weedy relatives; the effect of virus-resistant transgenic crops on virus; and the effect of transgenic crops on non-target organisms. This paper also discussed the effect of transgenic crops on soil ecosystem and crop genetic diversity. Their potential risks included uncontrolled flows of genes to wild relatives; development of herbicide, insect, and virus resistance in wild relatives; reduced crop genetic diversity; and adverse effects on organisms that were not pests, such as beneficial insects.

[Research advance in cyclic hydroxamic acids, main allelochemicals of Zea mays].

The research advance in cyclic hydroxamic acids was reviewed in this paper. Cyclic hydroxamic acids are the important natural products of cereal crops. They and their respective derivatives are the constitutive compounds of a wide variety of gramineous plants and few dicot plants. They have structural diversity and different natural occurrences. Because of their phytotoxic properties, cyclic hydroxamic acids show a great variety of biological activities. They are the defensive agents against plant diseases, pests, nematodes and other plants. The distribution of cyclic hydroxamic acids in Zea mays and their variation in relation to the age were focused on in the paper. In Zea mays, there are structural diversity of cyclic hydroxamic acids and related benzoxazolinones. DIMBOA (1,4-benzoxazin-3(4H)-ones) is the most abundant derivative in Zea mays. The content of cyclic hydroxamic acids is strongly cultivar-dependent in Zea mays. Hydroxamic acids are not present in seeds. After germination, the level of DIMBOA increases, and the maximum level occurs in young seedlings a few days after germination. DIMBOA exists in all parts of plants, and its concentration is generally higher in shoots than in roots. In all stages, the young leaves of Zea mays have relatively high content of DIMBOA. The concentrations of these hydroxamic acids are highly dependent on environmental growth conditions. Under UV-light and water deficiencies, the levels of hydroxamic acids in plant increase rapidly. Cyclic hydroxamic acids exuded by Zea mays root can be quantitatively analyzed by HPLC. Supplying iron can significantly increase the exudation of DIMBOA from Zea mays root.

[Chemical components of Vetiveria zizanioides volatiles].

The chemical components of the volatiles from Vetiveria zizanioides were analyzed by SPME and GC-MS. In the roots, the main component was valencene (30.36%), while in the shoots and leaves, they were 9-octadecenamide (33.50%), 2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene (27.46%), and 1,2-benzendicarboxylic acid, diisooctyl ester(18.29%). The results showed that there were many terpenoids in the volatils. In shoot volatiles, there existed 3 monoterpenes, 2 sequiterpenes and 1 triterpene. Most of the volatiles in roots were sesquiterpenes.