Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis.

Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise data quality and can damage the chromatography and MS instruments. However, researchers often discover contamination issues only after they acquire the data. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and cost-effective contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in the MS sample preparation workflow. Only 1 µL of the sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom-up proteomic methods regarding the effectiveness of removing detergent, peptide recovery, reproducibility, and proteome coverage. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers. ContamSPOT can also provide a unique readout of sample cleanliness for developing new MS-based sample preparation methods in the future.

A chromosome-level genome of Semiothisa cinerearia provides insights into its genome evolution and control.

BACKGROUND: Semiothisa cinerearia belongs to Geometridae, which is one of the most species-rich families of lepidopteran insects. It is also one of the most economically significant pests of the Chinese scholar tree (Sophora japonica L.), which is an important urban greenbelt trees in China due to its high ornamental value. A genome assembly of S. cinerearia would facilitate study of the control and evolution of this species. RESULTS: We present a reference genome for S. cinerearia; the size of the genome was ~ 580.89 Mb, and it contained 31 chromosomes. Approximately 43.52% of the sequences in the genome were repeat sequences, and 21,377 protein-coding genes were predicted. Some important gene families involved in the detoxification of pesticides (P450) have expanded in S. cinerearia. Cytochrome P450 gene family members play key roles in mediating relationships between plants and insects, and they are important in plant secondary metabolite detoxification and host-plant selection. Using comparative analysis methods, we find positively selected gene, Sox15 and TipE, which may play important roles during the larval-pupal metamorphosis development of S. cinerearia. CONCLUSION: This assembly provides a new genomic resource that will aid future comparative genomic studies of Geometridae species and facilitate future evolutionary studies on the S. cinerearia.

Headspace Gas Monitoring of Gut Microbiota Using Targeted and Globally Optimized Targeted Secondary Electrospray Ionization Mass Spectrometry.

This study aimed to develop and incorporate a secondary electrospray ionization (SESI) setup in combination with both targeted tandem mass spectrometry (MS/MS) and a hybrid metabolomics technique, globally optimized targeted mass spectrometry (GOT-MS), to sensitively detect volatile metabolites from the headspace of in vitro gut microbial culture in a human colonic model (HCM). Two SESI-tandem mass spectrometry panels with a comparable number of targeted metabolites/features (77 compounds in the targeted SESI-MS/MS panel and 75 features in the SESI-GOT-MS/MS panel) were established. The analytical performance of the SESI-GOT-MS/MS method, as well as its biological capability, were examined and compared with the targeted SESI-MS/MS method. As a result, the SESI-GOT-MS/MS method detected a similar number of metabolic features with good reproducibility (coefficient of variation <10%) compared to the targeted SESI-MS/MS method. Both methods showed a comparable ability to differentiate the gut microbial culture with or without the addition of green tea extract (GTE) to a HCM. The results from analysis of variance (ANOVA) showed that similar numbers of compounds from targeted SESI-MS/MS and metabolic features from SESI-GOT-MS/MS have significant differences when comparing samples collected from different HCM treatment stages. Partial least-squares discriminant analysis (PLS-DA) indicated that both methods could clearly differentiate the stages of GTE treatment. In summary, we demonstrated that SESI-MS/MS in combination with either targeted or GOT approaches can be a useful tool for monitoring gut microbial metabolism and their response to perturbations.

Genetically Encoding a Lipidated Amino Acid for Extension of Protein Half-Life in†vivo.

Protein therapeutics are increasingly used to treat various diseases, yet they often suffer from short serum half-lives. An emerging strategy to extend lifetime in vivo is to attach fatty acids onto proteins to increase their binding to human serum albumin (HSA). Herein, the genetic encoding of ϵ-N-heptanoyl-l-lysine (HepoK) is reported, which introduces a fatty-acid-containing amino acid into proteins with exquisite site-specificity and homogeneity, overcoming issues associated with existing chemical conjugation methods. The expression in E .coli and purification of HepoK-incorporated glucagon-like peptide-1 (GLP1) is demonstrated. GLP1(HepoK) showed stronger binding to HSA than GLP1(WT), without impairing the stimulation of the GLP1 receptor in cells. Moreover, GLP1(HepoK) decreased blood glucose level to the same level as GLP1(WT) in mice, showing longer-lasting effects than GLP1(WT). HepoK incorporation will also be useful for investigating the function of protein lipidation.

Differentiating Antibiotic-Resistant Staphylococcus aureus Using Secondary Electrospray Ionization Tandem Mass Spectrometry.

Secondary electrospray ionization mass spectrometry (SESI-MS) is an innovative metabolomics approach that primarily focuses on the gas-phase analyte detection. In this study, we developed a secondary electrospray ionization tandem mass spectrometry (SESI-MS/MS) method with a homemade SESI-MS front end, for sensitive, reproducible and selective detection of headspace volatile organic compounds (VOCs) emitted from bacterial culture. The optimized SESI-MS/MS was applied to examine the VOC metabolome of a pair of isogenic methicillin-susceptible and resistant Staphylococcus aureus (MSSA and MRSA) strains. From the headspace of bacterial culture, twelve organic acids, and eight amino acids with the mass range of 40-300 Da were specifically targeted with two selected reaction monitoring (SRM) transitions. Our results indicated that MSSA and MRSA strains can be clearly differentiated via partial least-squares discriminant analysis (PLS-DA) based on their headspace metabolic profiles. Furthermore, we studied the stress response of MSSA and MRSA to antibiotics treatment. Our result showed that MSSA and MRSA generated dramatically changed VOC metabolic profiles in response to ampicillin, which indicated that SESI-MS/MS could also be used for antibiotic treatment response monitoring in future studies. This study showed that SESI-MS/MS VOC analysis provides an additional approach to the bacterial metabolome detection complementary to traditional aqueous phase metabolite analysis. To the best of our knowledge, this was the first time that SESI-MS/MS was applied to investigate the bacterial metabolic perturbations caused by antibiotic treatment.

[Development of double-component rapid curing bioadhesive].

Mussel foot proteins (MFp) could cure rapidly under water and adhere to different substrates. It has broad application prospects as an biocompatible bioglue. The soluble recombinant SUMO-MFp fusion protein (SFp3) was efficiently expressed in E.coli, and about 5% of tyrosine of SFp3 were converted into DOPA by using mushroom tyrosinase. The adhesion strength of the mixture of DOPA-containing SFp3 (DSFp3) and hyaluronic acid (MW = 1 500 kD) was more than twice that of the cyanoacrylate-based tissue adhesives, Dermabond ®, and it reached 52% of its maximal strength within 5 minutes on cowhide. A layer-by-layer assembly of hyaluronic acid with DSFp3 was observed to form compact sheet structures through biofilm interferometry assay and scanning electron microscopy. This work provides a solution and theoretical basis for the low adhesion strength and slow curing of protein-based bioglue.

Targeted metabolic profiling rapidly differentiates Escherichia coli and Staphylococcus aureus at species and strain level.

RATIONALE: Pathogenic foodborne bacteria have been associated with severe infectious disease in humans and animals worldwide. Rapid detection and screening of these foodborne pathogens are critical for our food safety. This study aimed at detecting Escherichia coli and Staphylococcus aureus, two important foodborne bacteria, at the species and strain/serovar level using a mass spectrometry (MS)-based targeted metabolic profiling approach. METHODS: Ten E. coli strains (8 out of 10 were foodborne outbreak isolates) and four S. aureus strains were tested at two growth time points. A high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS)-based targeted metabolomics approach was applied for metabolic profile based bacteria detection. A total of 108 metabolites from multiple metabolic pathways were confidently detected from these bacteria. RESULTS: Our study demonstrated that with only 4 h of enrichment in the same medium, the metabolic profiles from E. coli and S. aureus showed significant difference. Furthermore, seven out of ten E. coli strains and all four tested S. aureus strains showed strain/serovar-level differentiation at the 4-h time point, which indicated great potential for strain level stratification in future food screening using our MS-based targeted metabolic profiling approach. CONCLUSIONS: A targeted metabolomics method was developed to demonstrate the utility of HPLC/MS/MS-based metabolic profiling in rapidly (4 h) differentiating E. coli and S. aureus bacteria, two of the most notorious foodborne bacteria, at both the species and strain/serovar levels. The results indicated that our approach has great potential in the future for fast and specific detection of foodborne pathogenic bacteria based on their metabolic diversity.

Effect of chlorogenic acid on melanogenesis of B16 melanoma cells.

Chlorogenic acid (CGA), the ester formed between caffeic acid and l-quinic acid, is a widespread phenolic compound. It is part of the human diet, found in foods such as coffee, apples, pears, etc. CGA is also was widely used in cosmetics, but the effects of CGA on melanogenesis are unknown. In this study, we analyzed the effects of CGA on cell proliferation, melanin content and tyrosinase of B16 murine melanoma cells. Additionally, the enzymatic reactions of CGA in B16 melanoma cells lytic solution were detected by UV spectrophotometry. Results showed CGA at 30 and 60 µM significantly suppresses cell proliferation. 8-MOP at 100 µM significantly promotes cell proliferation, but CGA can counter this. Incubated for 24 h, CGA (500 µM) improves melanogenesis while suppressing tyrosinase activity in B16 melanoma cells or 8-methoxypsoralen (8-MOP) co-incubated B16 melanoma cells. After 12 h, B16 melanoma cell treatment with CGA leads to an increase in melanin accumulation, however, after 48 h there is a decrease in melanin production which correlates broadly with a decrease in tyrosinase activity. CGA incubated with lytic solution 24 h turned brown at 37 °C. The formation of new products (with a maximum absorption at 295 nm) is associated with reduction of CGA (maximum absorption at 326 nm). Therefore, CGA has its two sidesroles in melanogenesis of B16 melanoma cells. CGA is a likely a substrate of melanin, but the metabolic product(s) of CGA may suppress melanogenesis in B16 melanoma cells by inhibiting tyrosinase activity.

A High-Proton Conductivity All-Biomass Proton Exchange Membrane Enabled by Adenine and Thymine Modified Cellulose Nanofibers.

Nanocellulose fiber materials were considered promising biomaterials due to their excellent biodegradability, biocompatibility, high hydrophilicity, and cost-effectiveness. However, their low proton conductivity significantly limited their application as proton exchange membranes. The methods previously reported to increase their proton conductivity often introduced non-biodegradable groups and compounds, which resulted in the loss of the basic advantages of this natural polymer in terms of biodegradability. In this work, a green and sustainable strategy was developed to prepare cellulose-based proton exchange membranes that could simultaneously meet sustainability and high-performance criteria. Adenine and thymine were introduced onto the surface of tempo-oxidized nanocellulose fibers (TOCNF) to provide many transition sites for proton conduction. Once modified, the proton conductivity of the TOCNF membrane increased by 31.2 times compared to the original membrane, with a specific surface area that had risen from 6.1 m²/g to 86.5 m²/g. The wet strength also increased. This study paved a new path for the preparation of environmentally friendly membrane materials that could replace the commonly used non-degradable ones, highlighting the potential of nanocellulose fiber membrane materials in sustainable applications such as fuel cells, supercapacitors, and solid-state batteries.

A Novel Nanofiber Hydrogel Adhesive Based on Carboxymethyl Cellulose Modified by Adenine and Thymine.

Natural polymer-based adhesive hydrogels have garnered significant interest for their outstanding strength and versatile applications, in addition to being eco-friendly. However, the adhesive capabilities of purely natural products are suboptimal, which hampers their practical use. To address this, we engineered carboxymethyl cellulose (CMC) surfaces with complementary bases, adenine (A) and thymine (T), to facilitate the self-assembly of adhesive hydrogels (CMC-AT) with a nanofiber configuration. Impressively, the shear adhesive strength reached up to 6.49 MPa with a mere 2% adhesive concentration. Building upon this innovation, we conducted a comparative analysis of the shear adhesion properties between CMC and CMC-AT hydrogel adhesives when applied to delignified and non-delignified wood chips. We examined the interplay between the adhesives and the substrate, as well as the role of mechanical interlocking in overall adhesion performance. Our findings offer a fresh perspective on the development of new biodegradable polymer hydrogel adhesives.

Hair Follicle-Targeted Delivery of Azelaic Acid Micro/Nanocrystals Promote the Treatment of Acne Vulgaris.

Purpose: Acne vulgaris is a chronic inflammatory skin disorder centered on hair follicles, making hair follicle-targeted delivery of anti-acne drugs a promising option for acne treatment. However, current researches have only focused on the delivering to healthy hair follicles, which are intrinsically different from pathologically clogged hair follicles in acne vulgaris. Patients and Methods: Azelaic acid (AZA) micro/nanocrystals with different particle sizes were prepared by wet media milling or high-pressure homogenization. An experiment on AZA micro/nanocrystals delivering to healthy hair follicles was carried out, with and without the use of physical enhancement techniques. More importantly, it innovatively designed an experiment, which could reveal the ability of AZA micro/nanocrystals to penetrate the constructed clogged hair follicles. The anti-inflammatory and antibacterial effects of AZA micro/nanocrystals were evaluated in vitro using a RAW264.7 cell model stimulated by lipopolysaccharide and a Cutibacterium acnes model. Finally, both the anti-acne effects and skin safety of AZA micro/nanocrystals and commercial products were compared in vivo. Results: In comparison to commercial products, 200 nm and 500 nm AZA micro/nanocrystals exhibited an increased capacity to target hair follicles. In the combination group of AZA micro/nanocrystals and ultrasound, the ability to penetrate hair follicles was further remarkably enhanced (ER value up to 9.6). However, toward the clogged hair follicles, AZA micro/nanocrystals cannot easily penetrate into by themselves. Only with the help of 1% salicylic acid, AZA micro/nanocrystals had a great potential to penetrate clogged hair follicle. It was also shown that AZA micro/nanocrystals had anti-inflammatory and antibacterial effects by inhibiting pro-inflammatory factors and Cutibacterium acnes. Compared with commercial products, the combination of AZA micro/nanocrystals and ultrasound exhibited an obvious advantage in both skin safety and in vivo anti-acne therapeutic efficacy. Conclusion: Hair follicle-targeted delivery of AZA micro/nanocrystals provided a satisfactory alternative in promoting the treatment of acne vulgaris.

Recyclable Polymer Composites with a Wrinkled Core-Shell Structure for Highly Efficient EMI Shielding and Low Reflection.

Green electromagnetic interference (EMI) shielding materials not only require high shielding effectiveness (SE) and low reflection but also need to be recyclable after damage; however, it is challenging to strike a balance in practice. Here, a polyacrylamide (PAM) composite composed of numerous chemically cross-linked PAM@carbon nanotube (cPAM@CNT) core-shell particles featuring rich wrinkled microstructures was prepared using an adsorption-drying-shrinking strategy. The wrinkled microstructures enable the incident electromagnetic waves (EMWs) to undergo attenuation within the composites, achieving an average EMI SE of 67.5 dB in the X band. Due to the hygroscopicity of hydrophobically associated PAM (hPAM, an adhesive for cPAM@CNTs core-shell particles), the average EMI SE of the composites further increased to 83.2 dB after exposure to 91% relative humidity for 24 h, with only a 2.7 dB low reflection. Additionally, the composites also demonstrated excellent Joule heating, photothermal performance, and recyclability, which exhibit substantial promise for advanced EMI shielding applications.

Pharmacogenomic analysis in adrenocortical carcinoma reveals genetic features associated with mitotane sensitivity and potential therapeutics.

Background: Adrenocortical carcinoma (ACC) is an aggressive endocrine malignancy with limited therapeutic options. Treating advanced ACC with mitotane, the cornerstone therapy, remains challenging, thus underscoring the significance to predict mitotane response prior to treatment and seek other effective therapeutic strategies. Objective: We aimed to determine the efficacy of mitotane via an in vitro assay using patient-derived ACC cells (PDCs), identify molecular biomarkers associated with mitotane response and preliminarily explore potential agents for ACC. Methods: In vitro mitotane sensitivity testing was performed in 17 PDCs and high-throughput screening against 40 compounds was conducted in 8 PDCs. Genetic features were evaluated in 9 samples using exomic and transcriptomic sequencing. Results: PDCs exhibited variable sensitivity to mitotane treatment. The median cell viability inhibition rate was 48.4% (IQR: 39.3-59.3%) and -1.2% (IQR: -26.4-22.1%) in responders (n=8) and non-responders (n=9), respectively. Median IC50 and AUC were remarkably lower in responders (IC50: 53.4 µM vs 74.7 µM, P<0.0001; AUC: 158.0 vs 213.5, P<0.0001). Genomic analysis revealed CTNNB1 somatic alterations were only found in responders (3/5) while ZNRF3 alterations only in non-responders (3/4). Transcriptomic profiling found pathways associated with lipid metabolism were upregulated in responder tumors whilst CYP27A1 and ABCA1 expression were positively correlated to in vitro mitotane sensitivity. Furthermore, pharmacologic analysis identified that compounds including disulfiram, niclosamide and bortezomib exhibited efficacy against PDCs. Conclusion: ACC PDCs could be useful for testing drug response, drug repurposing and guiding personalized therapies. Our results suggested response to mitotane might be associated with the dependency on lipid metabolism. CYP27A1 and ABCA1 expression could be predictive markers for mitotane response, and disulfiram, niclosamide and bortezomib could be potential therapeutics, both warranting further investigation.

A chromosome-level genome assembly of the Henosepilachna vigintioctomaculata provides insights into the evolution of ladybird beetles.

The ladybird beetle Henosepilachna vigintioctomaculata is an economically significant oligophagous pest that induces damage to many Solanaceae crops. An increasing number of studies have examined the population and phenotype diversity of ladybird beetles. However, few comparative genome analyses of ladybird beetle species have been conducted. Here, we obtained a high-quality chromosome-level genome assembly of H. vigintioctomaculata using various sequencing technologies, and the chromosome-level genome assembly was ~581.63 Mb, with 11 chromosomes successfully assembled. The phylogenetic analysis showed that H. vigintioctomaculata is a more ancient lineage than the other three sequenced ladybird beetles, Harmonia axyridis, Propylea japonica, and Coccinella septempunctata. We also compared positively selected genes (PSGs), transposable elements (TEs) ratios and insertion times, and key gene families associated with environmental adaptation among these ladybird beetles. The pattern of TEs evolution of H. vigintioctomaculata differs from the other three ladybird beetles. The PSGs were associated with ladybird beetles development. However, the key gene families associated with environmental adaptation in ladybird beetles varied. Overall, the high-quality draft genome sequence of H. vigintioctomaculata provides a useful resource for studies of beetle biology, especially for the invasive biology of ladybird beetles.

Multi-modal Proteomic Characterization of Lysosomal Function and Proteostasis in Progranulin-Deficient Neurons.

Progranulin (PGRN) is a lysosomal protein implicated in various neurodegenerative diseases. Over 70 mutations discovered in the GRN gene all result in reduced expression of PGRN protein. However, the detailed molecular function of PGRN within lysosomes and the impact of PGRN deficiency on lysosomal biology remain unclear. Here we leveraged multifaceted proteomic techniques to comprehensively characterize how PGRN deficiency changes the molecular and functional landscape of neuronal lysosomes. Using lysosome proximity labeling and immuno-purification of intact lysosomes, we characterized lysosome compositions and interactomes in both human induced pluripotent stem cell (iPSC)-derived glutamatergic neurons (i3Neurons) and mouse brains. Using dynamic stable isotope labeling by amino acids in cell culture (dSILAC) proteomics, we measured global protein half-lives in i3Neurons for the first time and characterized the impact of progranulin deficiency on neuronal proteostasis. Together, this study indicated that PGRN loss impairs the lysosome's degradative capacity with increased levels of v-ATPase subunits on the lysosome membrane, increased catabolic enzymes within the lysosome, elevated lysosomal pH, and pronounced alterations in neuron protein turnover. Collectively, these results suggested PGRN as a critical regulator of lysosomal pH and degradative capacity, which in turn influences global proteostasis in neurons. The multi-modal techniques developed here also provided useful data resources and tools to study the highly dynamic lysosome biology in neurons.

Nodal Metastases Associated With Fusion Oncogenes Are Age Dependent in Young Adult Patients With Thyroid Cancer.

CONTEXT: Fusion oncogenes, especially those involving RET or NTRK, are known drivers of papillary thyroid cancer (PTC). They are prevalent in pediatric patients and correlate with aggressive tumor behavior. OBJECTIVE: We explored the age dependence of fusion oncogenes and aggressive tumor behavior in young adult PTC patients. EXPERIMENTAL DESIGN: We examined 150 tumors from 142 PTC patients aged between 17∼35 years old with established tumor-node-metastasis stages. Oncogenic drivers and the thyroid differentiation score (TDS) were determined by DNA and RNA sequencing of a target panel. Transcriptome analysis was performed in PTCs with RET fusions. RESULTS: Among 150 PTCs, we detected BRAF V600E (n = 105), RET fusions (n = 15), NTRK3 fusions (n = 8), and BRAF fusions (n = 4). We found that fusion oncogenes were associated with nodal metastasis when age was tiered into 3 groups: <25 years, 25∼29 years, and 30∼35 years. Patients under 25 years old showed a marginal increase in tumor stage compared to those over 25 years (75.00% vs 21.74%, P = .0646). Risk of lateral lymph node metastasis increased with younger age (75.00% vs 27.27% vs 8.33%, P = .0369). As with advanced tumor and node stage, patients harboring fusion oncogenes and aged under 25 years showed the lowest TDS; genes associated with immunoglobulin production and production of molecular mediators of the immune response were significantly upregulated. CONCLUSIONS: Adult PTC patients under 25 years with fusion oncogenes showed a tendency toward advanced tumor stage and lower thyroid differentiation. Integrating onset age together with oncogenic alterations is worthwhile when managing adult PTC patients.

Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons.

BACKGROUND: Progranulin (PGRN) is a lysosomal glycoprotein implicated in various neurodegenerative diseases, including frontotemporal dementia and neuronal ceroid lipofuscinosis. Over 70 mutations discovered in the GRN gene all result in reduced expression of the PGRN protein. Genetic and functional studies point toward a regulatory role for PGRN in lysosome functions. However, the detailed molecular function of PGRN within lysosomes and the impact of PGRN deficiency on lysosomes remain unclear. METHODS: We developed multifaceted proteomic techniques to characterize the dynamic lysosomal biology in living human neurons and fixed mouse brain tissues. Using lysosome proximity labeling and immuno-purification of intact lysosomes, we characterized lysosome compositions and interactome in both human induced pluripotent stem cell (iPSC)-derived glutamatergic neurons (i3Neurons) and mouse brains. Using dynamic stable isotope labeling by amino acids in cell culture (dSILAC) proteomics, we measured global protein half-lives in human i3Neurons for the first time. RESULTS: Leveraging the multi-modal proteomics and live-cell imaging techniques, we comprehensively characterized how PGRN deficiency changes the molecular and functional landscape of neuronal lysosomes. We found that PGRN loss impairs the lysosome's degradative capacity with increased levels of v-ATPase subunits on the lysosome membrane, increased hydrolases within the lysosome, altered protein regulations related to lysosomal transport, and elevated lysosomal pH. Consistent with impairments in lysosomal function, GRN-null i3Neurons and frontotemporal dementia patient-derived i3Neurons carrying GRN mutation showed pronounced alterations in protein turnover, such as cathepsins and proteins related to supramolecular polymerization and inherited neurodegenerative diseases. CONCLUSION: This study suggested PGRN as a critical regulator of lysosomal pH and degradative capacity, which influences global proteostasis in neurons. Beyond the study of progranulin deficiency, these newly developed proteomic methods in neurons and brain tissues provided useful tools and data resources for the field to study the highly dynamic neuronal lysosome biology.

Chromosome-level genome assembly of the black widow spider Latrodectus elegans illuminates composition and evolution of venom and silk proteins.

BACKGROUND: The black widow spider has both extraordinarily neurotoxic venom and three-dimensional cobwebs composed of diverse types of silk. However, a high-quality reference genome for the black widow spider was still unavailable, which hindered deep understanding and application of the valuable biomass. FINDINGS: We assembled the Latrodectus elegans genome, including a genome size of 1.57 Gb with contig N50 of 4.34 Mb and scaffold N50 of 114.31 Mb. Hi-C scaffolding assigned 98.08% of the genome to 14 pseudo-chromosomes, and with BUSCO, completeness analysis revealed that 98.4% of the core eukaryotic genes were completely present in this genome. Annotation of this genome identified that repetitive sequences account for 506.09 Mb (32.30%) and 20,167 protein-coding genes, and specifically, we identified 55 toxin genes and 26 spidroins and provide preliminary analysis of their composition and evolution. CONCLUSIONS: We present the first chromosome-level genome assembly of a black widow spider and provide substantial toxin and spidroin gene resources. These high-qualified genomic data add valuable resources from a representative spider group and contribute to deep exploration of spider genome evolution, especially in terms of the important issues on the diversification of venom and web-weaving pattern. The sequence data are also firsthand templates for further application of the spider biomass.

A chromosome-level genome of Brachymystax tsinlingensis provides resources and insights into salmonids evolution.

Brachymystax tsinlingensis Li, 1966 is an endangered freshwater fish with economic, ecological, and scientific values. Study of the genome of B. tsinlingensis might be particularly insightful given that this is the only Brachymystax species with genome. We present a high-quality chromosome-level genome assembly and protein-coding gene annotation for B. tsinlingensis with Illumina short reads, Nanopore long reads, Hi-C sequencing reads, and RNA-seq reads from 5 tissues/organs. The final chromosome-level genome size is 2,031,709,341 bp with 40 chromosomes. We found that the salmonids have a unique GC content and codon usage, have a slower evolutionary rate, and possess specific positively selected genes. We also confirmed the salmonids have undergone a whole-genome duplication event and a burst of transposon-mediated repeat expansion, and lost HoxAbß Hox cluster, highly expressed genes in muscle may partially explain the migratory habits of B. tsinlingensis. The high-quality B. tsinlingensis assembled genome could provide a valuable reference for the study of other salmonids as well as aid the conservation of this endangered species.

Integrated proteomic and metabolomic analyses of the mitochondrial neurodegenerative disease MELAS.

MELAS (mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes) is a progressive neurodegenerative disease caused by pathogenic mitochondrial DNA variants. The pathogenic mechanism of MELAS remains enigmatic due to the exceptional clinical heterogeneity and the obscure genotype-phenotype correlation among MELAS patients. To gain insights into the pathogenic signature of MELAS, we designed a comprehensive strategy integrating proteomics and metabolomics in patient-derived dermal fibroblasts harboring the ultra-rare MELAS pathogenic variant m.14453G>A, specifically affecting the mitochondrial respiratory complex I. Global proteomics was achieved by data-dependent acquisition (DDA) and verified by data-independent acquisition (DIA) using both Spectronaut and the recently launched MaxDIA platforms. Comprehensive metabolite coverage was achieved for both polar and nonpolar metabolites in both reverse phase and HILIC LC-MS/MS analyses. Our proof-of-principle MELAS study with multi-omics integration revealed OXPHOS dysregulation with a predominant deficiency of complex I subunits, as well as alterations in key bioenergetic pathways, glycolysis, tricarboxylic acid cycle, and fatty acid ß-oxidation. The most clinically relevant discovery is the downregulation of the arginine biosynthesis pathway, likely due to blocked argininosuccinate synthase, which is congruent with the MELAS cardinal symptom of stroke-like episodes and its current treatment by arginine infusion. In conclusion, we demonstrated an integrated proteomic and metabolomic strategy for patient-derived fibroblasts, which has great clinical potential to discover therapeutic targets and design personalized interventions after validation with a larger patient cohort in the future.