A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen.

Fusarium oxysporum is an asexual filamentous fungus that causes vascular wilt in hundreds of crop plants and poses a threat to public health through Fusariosis. F. oxysporum f. sp. conglutinans strain Fo5176, originally isolated from Brassica oleracea, is pathogenic to Arabidopsis, making it a model pathosystem for dissecting the molecular mechanisms underlying host-pathogen interactions. Assembling the F. oxysporum genome is notoriously challenging due to the presence of repeat-rich accessory chromosomes. Here, we report a gap-free genome assembly of Fo5176 using PacBio HiFi and Hi-C data. The 69.56 Mb assembly contained 18 complete chromosomes, including all centromeres and most telomeres (20/36), representing the first gap-free genome sequence of a pathogenic F. oxysporum strain. In total, 21,460 protein-coding genes were annotated, a 26.3% increase compared to the most recent assembly. This high-quality reference genome for F. oxysporum f. sp. conglutinans Fo5176 provides a valuable resource for further research into fungal pathobiology and evolution.

Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis.

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.

Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen's pangenomic landscape and aiding in the development of novel disease management strategies. Database URL: http://www.fopgdb.site.

De novo chromosome-level genome assembly of Chinese motherwort (Leonurus japonicus).

Chinese motherwort (Leonurus japonicus), a member of Lamiaceae family, is a commonly used medicinal herb for treating obstetrical and gynecological diseases, producing over 280 officinal natural products. Due to limited genomic resources, little progress has been made in deciphering the biosynthetic pathway of valuable natural products in L. japonicus. Here, we de novo assembled the L. japonicus genome using high-coverage ONT long reads and Hi-C reads. The chromosome-level genome assembly contained ten chromosomes representing 99.29% of 489.34 Mb genomic sequence with a contig and scaffold N50 of 7.27 Mb and 50.86 Mb, respectively. Genome validations revealed BUSCO and LAI score of 99.2% and 21.99, respectively, suggesting high quality of genome assembly. Using transcriptomic data from various tissues, 22,531 protein-coding genes were annotated. Phylogenomic analysis of 13 angiosperm plants suggested L. japonicus had 58 expanded gene families functionally enriched in specialized metabolism such as diterpenoid biosynthesis. The genome assembly, annotation, and sequencing data provide resources for the elucidation of biosynthetic pathways behind natural products of pharmaceutical applications in L. japonicus.

Green ultrasonication-assisted extraction of microalgae Chlorella sp. for polysaturated fatty acid (PUFA) rich lipid extract using alternative solvent mixture.

Conventionally, microalgal lipid extraction uses volatile organic compounds as an extraction solvent. However, these solvents are harmful to human and environmental health. Therefore, this study evaluated the feasibility of alternative green solvents, namely, ethanol, dimethyl carbonate (DMC), cyclopentyl methyl ether (CPME), and 2-methyltetrahydrofuran (2-MeTHF) in lipid extraction from Chlorella sp. via ultrasound-assisted extraction (UAE). This study indicated that extraction parameters, such as ethanol-to-2-MeTHF ratio, solvent-to-biomass ratio, temperature, and time, significantly affected the crude lipid yield (P < 0.05). The highest crude lipid yield of 25.05 ± 0.924% was achieved using ethanol-2-MeTHF mixture (2:1, v/v) with a solvent-to-biomass ratio of 20:1 (v/w) at 60 °C for 25 min accompanying 100 W and 40 kHz. Ethanol-2-MeTHF-extracted lipids showed dominance in linoleic acid, α-linolenic acid, and palmitic acid. Overall this findings supported UAE using ethanol and 2-MeTHF as extraction solvents is a promising green alternative to conventional solvent extraction of lipids from microalgae.

Gapless genome assembly of Fusarium verticillioides, a filamentous fungus threatening plant and human health.

Fusarium verticillioides is a filamentous fungus that causes plant diseases and harms human health through cancer-inducing mycotoxin and life-threatening Fusariosis. Given its threat to agriculture and public health, genome assembly of this fungus is critical to our understanding of its pathobiology and developing antifungal drugs. Here, we report a gap-free genome assembly of F. verticillioides using PacBio HiFi data and high-throughput chromosome capture (Hi-C) sequencing data. The assembled 42.0 Mb sequence contains eleven gapless chromosomes capturing all centromeres and 19 of all 22 telomeres. This assembly represents a significant improvement over previous version on contiguity (contig N50: 4.3 Mb), completeness (BUSCO score: 99.0%) and correctness (QV: 88.8). A total of 15,230 protein-coding genes were predicted, 6.2% of which are newly annotated genes. In addition, we identified three-dimension chromatin structures such as TADs-like structures and chromatin loops based on Hi-C data of ultra-high coverage. This gap-free genome of F. verticillioides is an excellent resource for further panoramic understanding mechanisms of fungal genome evolution, mycotoxin production and pathogenesis on plant and human host.

Degradation of geosmin and 2-methylisoborneol in UV-based AOPs for photoreactors with reflective inner surfaces: Kinetics and transformation products.

Geosmin (GSM) and 2-methylisoborneol (2-MIB) are representative musty/earthy odor compounds commonly present in surface water. In present study, the degradation of GSM and 2-MIB subject to different UV-based advanced oxidation processes (AOPs), including UV/H2O2, UV/S2O82-, UV/chlorine, and UV/chloramine, in a phosphate-buffered saline (PBS) was conducted in a photoreactor with reflective inner surfaces and compared with that in an environmental water sample. A dynamic model to predict the degradation of GSM and 2-MIB in the photoreactor with reflective inner surfaces in the four UV-based AOPs was developed applying the second-order rate constants for the GSM and 2-MIB with primary reactive species (i.e., •OH, •Cl, and •SO4-) determined in this study. The model was proven to successfully simulate the degradation of GSM and 2-MIB. In addition, 8, 7, 8, and 11 degradation intermediates were detected from UV/H2O2, UV/S2O82-, UV/chlorine, and UV/chloramine in this study, and possible degradation pathways were proposed. This study is the first to report the degradation kinetics and formation products of GSM and 2-MIB in UV/chloramine. Research based on photoreactors with reflective inner surfaces may provide some guidance for eliminating GSM and 2-MIB in UV-based AOPs for full-scale engineering applications.

Analysis of microalgal growth kinetic model and carbohydrate biosynthesis cultivated using agro-industrial waste residuals as carbon source.

Microalgal carbohydrate is considered one of the potential feedstock for biofuel produced via the bioconversion process. However, the current cultivation process using commercial medium exhibited low biomass production and its carbohydrate productivity which become a bottleneck for sustainable microalgal-carbohydrate-based biofuel production. Thus, the objective of this study is to assess the utilization of industrial waste including molasses and glycerol on the Halochlorella rubescens and Tetraselmis suecica growth as well as its carbohydrate content under different cultivation modes such as autotrophic, heterotrophic and photoheterotrophic conditions. From this study, the highest maximum biomass of H. rubenscens and T. suecica of 0.653 ± 0.009 and 0.669 ± 0.01gL-1 were obtained when the cultivation was performed under photoheterotrophic using molasses. High carbohydrate content of H. rubescens and T. seucica of 56.81 ± 0.39% and 71.52 ± 0.03% with glucose represent the dominant sugar was observed under this condition. The growth kinetic model of the analysis indicated that Huang and Gompertz Models described well the growth of H. rubescens and T. suecica under photoheteroptroph condition with a high significant R2 of 0.99. The information generated could be beneficial for the future development of low-cost microalgal cultivation media formulation for future microalgal carbohydrate-based products such as bioethanol.

The optimal dose of oxidants in UV-based advanced oxidation processes with respect to primary radical concentrations.

UV-based advanced oxidation processes (AOPs) via photolysis of precursor chemical oxidants have been of interest to numerous researchers over the past several decades due to their capacity to generate highly active radical species and interesting radical chemistry. However, applications of UV-based AOPs have been commonly optimized case by case, due to the lack of theoretical investigations on process optimization, especially on oxidant doses. In this study, a simple equation for UV/H2O2 (•OH as the sole primary reactive species (PRS)) to obtain the theoretical optimal concentration (Copt-theoretical) for H2O2 was derived (Copt-theoretical=Ab·Scε·k). The equation was then validated for its accuracy in the calculation of Copt-theoretical for H2O2 in the UV/H2O2 AOP using a well-established comprehensive kinetic model. A competition kinetics method for the measurement of scavenging capacity (Sc, the unknown parameter for the simple equation) was designed, for which nitrobenzene was employed as the probe compound and tert­butyl alcohol was introduced as the standard compound. Based on this simple equation, we calculated the Copt-theoretical of 77 environmental water samples and introduced the concept of a practical optimal oxidants dose for the UV/H2O2 AOP, while minimizing the operation costs in engineering applications. Moreover, this study mathematically proved that the simple equation obtained from UV/H2O2 could be successfully extended to other UV-based AOPs, including UV/chlorine, UV/NH2Cl, UV/S2O82-, and UV/peracetic acid. The simple equation of Copt-theoretical derived in this study may not only help to provide instructions for engineering applications, but also point out the ultimate treatment capability of each UV-based AOPs.

Maternal bone adaptation to mechanical loading during pregnancy, lactation, and post-weaning recovery.

The maternal skeleton undergoes dramatic bone loss during pregnancy and lactation, and substantial bone recovery post-weaning. The structural adaptations of maternal bone during reproduction and lactation exert a better protection of the mechanical integrity at the critical load-bearing sites, suggesting the importance of physiological load-bearing in regulating reproduction-induced skeletal alterations. Although it is suggested that physical exercise during pregnancy and breastfeeding improves women's physical and psychological well-being, its effects on maternal bone health remain unclear. Therefore, the objective of this study was to investigate the maternal bone adaptations to external mechanical loading during pregnancy, lactation, and post-weaning recovery. By utilizing an in vivo dynamic tibial loading protocol in a rat model, we demonstrated improved maternal cortical bone structure in response to dynamic loading at tibial midshaft, regardless of reproductive status. Notably, despite the minimal loading responses detected in the trabecular bone in virgins, rat bone during lactation experienced enhanced mechano-responsiveness in both trabecular and cortical bone compartments when compared to rats at other reproductive stages or age-matched virgins. Furthermore, our study showed that the lactation-induced elevation in osteocyte peri-lacunar/canalicular remodeling (PLR) activities led to enlarged osteocyte lacunae. This may result in alterations in interstitial fluid flow-mediated mechanical stimulation on osteocytes and an elevation in solute transport through the lacunar-canalicular system (LCS) during high-frequency dynamic loading, thus enhancing mechano-responsiveness of maternal bone during lactation. Taken together, findings from this study provide important insights into the relationship between reproduction- and lactation-induced skeletal changes and external mechanical loading, emphasizing the importance of weight-bearing exercise on maternal bone health during reproduction and postpartum.

Bacillus megaterium: a Potential and an Efficient Bio-Degrader of Polystyrene

Abstract This research has been conducted to investigate the biodegradation of polystyrene (PS) by isolated strain Bacillus megaterium from Zophobas morio's. The viability and metabolic activity of Bacillus megaterium utilizing emulsified PS in liquid carbon free basal medium as sole carbon source was confirmed using redox probe 2,3,5-triphenyltetrazolium chloride (TTC). Bacillus megaterium showed prominent result with TTC, which forms red colored insoluble TPF (triphenyl formazan) within four to seven days. The formation of TPF confirmed the metabolism activity of the cell using PS as source of carbon. The biodegradation activity of Bacillus megaterium on PS film was also confirmed by FTIR analysis, the result showed changes in functional groups due to microbial activities. FESEM analysis was carried out on the PS surface, revealing the formation of bacterial biofilm as well as occurrence of porosity and fragility of the bacterial deteriorate surface compared to control. Overall, the identification of plastic degrading bacteria (PDB) will become a fundamental platform promoting more in-depth research for optimal plastic waste management to switch from the conventional landfilling to enzymatic biodegradation. In the long run, it is to regulate the current global plastic waste accumulation on Earth which poses potent ecological threat.

Achieving GWAS with homomorphic encryption.

BACKGROUND: One way of investigating how genes affect human traits would be with a genome-wide association study (GWAS). Genetic markers, known as single-nucleotide polymorphism (SNP), are used in GWAS. This raises privacy and security concerns as these genetic markers can be used to identify individuals uniquely. This problem is further exacerbated by a large number of SNPs needed, which produce reliable results at a higher risk of compromising the privacy of participants. METHODS: We describe a method using homomorphic encryption (HE) to perform GWAS in a secure and private setting. This work is based on a proposed algorithm. Our solution mainly involves homomorphically encrypted matrix operations and suitable approximations that adapts the semi-parallel GWAS algorithm for HE. We leverage upon the complex space of the CKKS encryption scheme to increase the number of SNPs that can be packed within a ciphertext. We have also developed a cache module that manages ciphertexts, reducing the memory footprint. RESULTS: We have implemented our solution over two HE open source libraries, HEAAN and SEAL. Our best implementation took 24.70 minutes for a dataset with 245 samples, over 4 covariates and 10643 SNPs. CONCLUSIONS: We demonstrate that it is possible to achieve GWAS with homomorphic encryption with suitable approximations.

Reactive Nitrogen Species Mediated Degradation of Estrogenic Disrupting Chemicals by Biochar/Monochloramine in Buffered Water and Synthetic Hydrolyzed Urine.

There is increasing concern about the severe endocrine-related health problems because of the discharge of estrogenic disrupting chemicals (EDCs) into the natural environment. In this study, we investigated the activation of monochloramine (NH2Cl) by biochar [pyrolyzed by cotton straw at 350 °C (Cot350), wheat straw at 350 and 700 °C (WS350 and WS700), and corn straw at 350 and 700 °C (CS350 and CS700)] for the degradation of estradiol (E2) and ethinylestradiol (EE2). Approximately 95% of parent E2 and EE2 was removed by Cot350/NH2Cl in buffered solution, and 87% of E2 and 75% of EE2 were removed in urine within 24 h. Electronic paramagnetic resonance analysis and radical-quenching experiments showed that biochar activated NH2Cl and primarily generated •NO radicals for the degradation of the EDCs. The nitrogen and silicon elements of Cot350 served as primary catalytic sites for NH2Cl activation, whereas the sp2-hybridized carbon on WS700 and CS700 played a major role. The effect of major urine components (i.e., ammonia species, chloride, and bicarbonate) on the reaction pathways of biochar/NH2Cl was also elucidated. This study provides new insights into the reaction pathways of NH2Cl activation by biochar and suggests potential applications for other carbonaceous materials for NH2Cl activation.

Degradation of Organic Micropollutants in UV/NH2Cl Advanced Oxidation Process.

Monochloramine (NH2Cl) can be irradiated by UV to create an advanced oxidation condition (i.e., UV/NH2Cl) for the elimination of organic micropollutants (OMPs) from source water. However, information in retrospective studies was scarce on how UV/NH2Cl performance would be affected by the water matrix and OMP molecular structures. In this study, the degradation of five representative OMPs, including triclosan, carbamazepine, sulfamethoxazole, estradiol (E2), and ethinylestradiol (EE2), was examined in different water matrices. All OMPs were rapidly removed by UV/NH2Cl but exhibited different degradation mechanisms. Although •OH, •Cl, and direct photolysis mainly contributed to the overall degradation of OMPs in buffered nanopure water, the contribution of reactive nitrogen species (RNS) generated from the photolysis of NH2Cl was not negligible in the degradation of E2 and EE2. A phenolic group was identified as the moiety reactive toward RNS. Based on quantitative analysis of the impact on OMP degradation from cosolutes (including Cl-, HCO3-, NOM) as well as pH and NH2Cl doses, we developed a kinetic model for the prediction of OMP degradation in complex water matrices. In environmental water matrices, the performance and radical contributions in UV/NH2Cl and UV/H2O2 systems were taken into comparison, which showed faster degradation of OMPs and a more significant contribution of CO3•- in the UV/NH2Cl process.

Removal of sulfonamide antibiotics and human metabolite by biochar and biochar/H2O2 in synthetic urine.

Source-separated urine has been increasingly regarded as a promising alternative waste-stream for effectively removing pharmaceuticals and human metabolites. This study investigated the removal of sulfonamide antibiotics, one category among the most frequently detected antibiotics in the environment, by biochar and biochar/H2O2 in synthetic urine matrix. The adsorption and degradation of four parent sulfonamide antibiotics, including sulfamethoxazole, sulfadiazine, sulfamethazine, sulfadimethoxine, and one human metabolite, N4-acetyl-sulfamethoxazole (together referred as SAs) were investigated. Biochar derived from cotton straw was applied as adsorbent for SAs and catalyst for H2O2. Results showed that the adsorption of SAs was inhibited in urine compared with that in phosphate buffer solution. Bicarbonate in urine placed major influence. Langmuir isotherm model well described the adsorption process in both buffer and urine matrices. Adsorption and desorption rates were estimated by a kinetic model, which well fitted the removal of SAs from aqueous phase at various biochar doses. The adsorption of SAs on biochar was due to multiple forces, in which van der Waals forces and hydrophobicity played major roles in distinguishing the sorption behavior of different SAs. To destruct the SAs, H2O2 was added with biochar. Except for N4-acetyl-sulfamethoxazole, all the parent SAs can be degraded in urine matrix. Carbonate radical, produced from the activation of peroxymonocarbonate by biochar, was proposed to be the major contributing reactive species in biochar/H2O2 system in urine matrix.

Generalized polyspike train: An EEG biomarker of drug-resistant idiopathic generalized epilepsy.

OBJECTIVE: To identify clinical and EEG biomarkers of drug resistance in adults with idiopathic generalized epilepsy. METHODS: We conducted a case-control study consisting of a discovery cohort and a replication cohort independently assessed at 2 different centers. In each center, patients with the idiopathic generalized epilepsy phenotype and generalized spike-wave discharges on EEG were classified as drug-resistant or drug-responsive. EEG changes were classified into predefined patterns and compared between the 2 groups in the discovery cohort. Factors associated with drug resistance in multivariable analysis were tested in the replication cohort. RESULTS: The discovery cohort included 85 patients (29% drug-resistant and 71% drug-responsive). Their median age at assessment was 32 years and 50.6% were female. Multivariable analysis showed that higher number of seizure types ever experienced (3 vs 1: odds ratio [OR] = 31.1, 95% confidence interval [CI]: 4.5-214, p < 0.001; 3 vs 2: OR = 14.6, 95% CI: 2.3-93.1, p = 0.004) and generalized polyspike train (burst of generalized rhythmic spikes lasting less than 1 second) during sleep were associated with drug resistance (OR = 10.8, 95% CI: 2.4-49.4, p = 0.002). When these factors were tested in the replication cohort of 80 patients (27.5% drug-resistant and 72.5% drug-responsive; 71.3% female; median age 27.5 years), the proportion of patients with generalized polyspike train during sleep was also higher in the drug-resistant group (OR = 4.0, 95% CI: 1.35-11.8, p = 0.012). CONCLUSION: Generalized polyspike train during sleep may be an EEG biomarker for drug resistance in adults with idiopathic generalized epilepsy.

Gonadal differentiation and its sensitivity to androgens during development of Pelophylax nigromaculatus.

Our previous observations proposed Pelophylax nigromaculatus as a model species for studying the masculinizing effects of androgenic EDCs in amphibians. To better develop this model species, we studied the process of the gonadal differentiation/development and the sensitive stage to androgens. We found that the earliest sexual dimorphism in gonads at morphological and histological levels occurred at stages 38-40 and stage 36 respectively. Further examination of molecular markers for testicular and ovarian differentiation during development revealed that the cyp17 and cyp19 expressions were sexually dimorphic from stage 32 and stage 36 respectively. Further, we investigated the sex-reversal induced by 100 ng/L 5α-dihydrotestosterone (DHT) when exposures were initiated at stages 24, 26 and 28. We found that when exposed from stage 24, DHT resulted masculinization of all tadpoles with no typical ovaries, whereas exposures from stage 26 or 28 dramatically reduced the effect of DHT. Our findings show that gonads of P. nigromaculatus are bipotential at stage 24, in the process of differentiation at stage 26 and determined to become either testis or ovary at stage 28. Altogether, exposure of P. nigromaculatus should begin at stage 24 in order to sensitively detect masculinizing effects of EDCs. Present study provides useful information about the gonadal differentiation and development in P. nigromaculatus for effectively evaluating masculinizing effects of EDCs on gonads.

PPCP Degradation by Chlorine-UV Processes in Ammoniacal Water: New Reaction Insights, Kinetic Modeling, and DBP Formation.

The combination of chlorine and UV (i.e., chlorine-UV process) has been attracting more attention in recent years due to its ready incorporation into existing water treatment facilities to remove PPCPs. However, limited information is available on the impact of total ammonia nitrogen (TAN). This study investigated two model PPCPs, N,N-diethyl-3-toluamide (DEET) and caffeine (CAF), in the two stages of the chlorine-UV process (i.e., chlorination and UV/chlor(am)ine) to elucidate the impact of TAN. During chlorination, the degradation of DEET and CAF was positively correlated with the overall consumption of total chlorine by TAN. Reactive nitrogen intermediates, including HNO/NO- and ONOOH/ONOO-, along with •OH were identified as major contributors to the removal of DEET and CAF. During UV irradiation, DEET and CAF were degraded under UV/chlorine or UV/NH2Cl conditions. •OH and •Cl were the major reactive species to degrade DEET and CAF under UV/NH2Cl conditions, whereas •OCl played a major role for degrading CAF under UV/chlorine conditions. Numerical models were developed to predict the removal of DEET and CAF under chlorination-UV process. Chlorinated disinfection byproducts were detected. Overall, this study presented kinetic features and mechanistic insights on the degradation of PPCPs under the chlorine-UV process in ammoniacal water.