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Horticulture Research Jul 2024Avocado ( Mill.) is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits. Its fatty acid content, especially the...
A telomere-to-telomere gap-free reference genome assembly of avocado provides useful resources for identifying genes related to fatty acid biosynthesis and disease resistance.
Avocado ( Mill.) is an economically valuable plant because of the high fatty acid content and unique flavor of its fruits. Its fatty acid content, especially the relatively high unsaturated fatty acid content, provides significant health benefits. We herein present a telomere-to-telomere gapless genome assembly (841.6 Mb) of West Indian avocado. The genome contains 40 629 predicted protein-coding genes. Repeat sequences account for 57.9% of the genome. Notably, all telomeres, centromeres, and a nucleolar organizing region are included in this genome. Fragments from these three regions were observed via fluorescence hybridization. We identified 376 potential disease resistance-related nucleotide-binding leucine-rich repeat genes. These genes, which are typically clustered on chromosomes, may be derived from gene duplication events. Five genes (, , , , and ) were highly expressed in leaves, stems, and fruits, indicating they may be involved in avocado disease responses in multiple tissues. We also identified 128 genes associated with fatty acid biosynthesis and analyzed their expression patterns in leaves, stems, and fruits. , which encodes one of 11 stearoyl-acyl carrier protein desaturases mediating C18 unsaturated fatty acid synthesis, was more highly expressed in the leaves than in the stems and fruits. These findings provide valuable insights that enhance our understanding of fatty acid biosynthesis in avocado.
PubMed: 38966866
DOI: 10.1093/hr/uhae119 -
Horticulture Research Jul 2024Centromeres in eukaryotes mediate the accurate segregation of chromosomes during cell division. They serve as essential functional units of chromosomes and play a core...
Centromeres in eukaryotes mediate the accurate segregation of chromosomes during cell division. They serve as essential functional units of chromosomes and play a core role in the process of genome evolution. Centromeres are composed of satellite repeats and highly repetitive centromeric retrotransposons (CRs), which vary greatly even among closely related species. Cucumber () is a globally cultivated and economically important vegetable and the only species in the genus with seven pairs of chromosomes. Therefore, studying the centromeres of the subgenus may yield valuable insights into its genome structure and evolution. Using chromatin immunoprecipitation (ChIP) techniques, we isolated centromeric DNA from cucumber reference line 9930. Our investigation into cucumber centromeres uncovered the centromeric satellite sequence, designated as CentCs, and the prevalence of Ty1/ long terminal repeat retrotransposons. In addition, active genes were identified in the CsCENH3 nucleosome regions with low transcription levels. To the best of our knowledge, this is the first time that characterization of centromeres has been achieved in cucumber. Meanwhile, our results on the distribution of CentCs and CsCRs in the subgenus indicate that the content of centromeric repeats in the wild variants was significantly reduced compared with the cultivated cucumber. The results provide evidence for centromeric DNA amplification that occurred during the domestication process from wild to cultivated cucumber. Furthermore, these findings may offer new information for enhancing our understanding of phylogenetic relationships in the genus.
PubMed: 38966863
DOI: 10.1093/hr/uhae127 -
Journal of Biomedical Optics Jul 2024Optical coherence tomography has great utility for capturing dynamic processes, but such applications are particularly data-intensive. Samples such as biological tissues...
SIGNIFICANCE
Optical coherence tomography has great utility for capturing dynamic processes, but such applications are particularly data-intensive. Samples such as biological tissues exhibit temporal features at varying time scales, which makes data reduction challenging.
AIM
We propose a method for capturing short- and long-term correlations of a sample in a compressed way using non-uniform temporal sampling to reduce scan time and memory overhead.
APPROACH
The proposed method separates the relative contributions of white noise, fluctuating features, and stationary features. The method is demonstrated on mammary epithelial cell spheroids in three-dimensional culture for capturing intracellular motility without loss of signal integrity.
RESULTS
Results show that the spatial patterns of motility are preserved and that hypothesis tests of spheroids treated with blebbistatin, a motor protein inhibitor, are unchanged with up to eightfold compression.
CONCLUSIONS
The ability to measure short- and long-term correlations compressively will enable new applications in (3+1)D imaging and high-throughput screening.
Topics: Tomography, Optical Coherence; Humans; Spheroids, Cellular; Cell Movement; Image Processing, Computer-Assisted; Epithelial Cells; Algorithms; Heterocyclic Compounds, 4 or More Rings
PubMed: 38966847
DOI: 10.1117/1.JBO.29.7.076002 -
RSC Advances Jun 2024The coronavirus disease 2019 (COVID-19) has spread worldwide with severe health, social, and economic repercussions. Although vaccines have significantly reduced the...
The coronavirus disease 2019 (COVID-19) has spread worldwide with severe health, social, and economic repercussions. Although vaccines have significantly reduced the severity of symptoms and deaths, alternative medications derived from natural products (NPs) are vital to further decrease fatalities, especially in regions with low vaccine uptake. When paired with the latest computational developments, NPs, which have been used to cure illnesses and infections for thousands of years, constitute a renewed resource for drug discovery. In the present report, a combination of computational and methods reveals the repositioning of NPs and identifies salvinorin A and deacetylgedunin (DCG) as having potential anti-SARS-CoV-2 activities. Salvinorin A was found both and to inhibit both SARS-CoV-2 spike/host ACE2 protein interactions, consistent with blocking viral cell entry, and well as live virus replication. Plant extracts from and , which contain high levels of DCG, inhibited viral cell replication by targeting the main protease (Mpro) and/or inhibited viral cell entry by blocking the interaction between spike RBD-ACE2 protein at concentrations lower than salvinorin A. Our findings suggest that salvinorin A represent promising chemical starting points where further optimization may result in effective natural product-derived and potent anti-SARS-CoV-2 inhibitors to supplement vaccine efforts.
PubMed: 38966817
DOI: 10.1039/d4ra02593h -
Frontiers in Aging Neuroscience 2024The molecular mechanisms underlying neuronal dysfunction in Alzheimer's disease (AD) remain uncharacterized. Here, we identify genes, molecular pathways and cellular...
The molecular mechanisms underlying neuronal dysfunction in Alzheimer's disease (AD) remain uncharacterized. Here, we identify genes, molecular pathways and cellular components associated with whole-brain dysregulation caused by amyloid-beta (Aβ) and tau deposits in the living human brain. We obtained resting-state functional MRI (rs-fMRI), Aβ- and tau-PET for 47 cognitively unimpaired and 16 AD participants from the Translational Biomarkers in Aging and Dementia cohort. Adverse neuronal activity impacts by Aβ and tau were quantified with personalized dynamical models by fitting pathology-mediated computational signals to the participant's real rs-fMRIs. Then, we detected robust brain-wide associations between the spatial profiles of Aβ-tau impacts and gene expression in the neurotypical transcriptome (Allen Human Brain Atlas). Within the obtained distinctive signature of neuronal dysfunction, several genes have prominent roles in microglial activation and in interactions with Aβ and tau. Moreover, cellular vulnerability estimations revealed strong association of microglial expression patterns with Aβ and tau's synergistic impact on neuronal activity ( < 0.001). These results further support the central role of the immune system and neuroinflammatory pathways in AD pathogenesis. Neuronal dysregulation by AD pathologies also associated with neurotypical synaptic and developmental processes. In addition, we identified drug candidates from the vast LINCS library to halt or reduce the observed Aβ-tau effects on neuronal activity. Top-ranked pharmacological interventions target inflammatory, cancer and cardiovascular pathways, including specific medications undergoing clinical evaluation in AD. Our findings, based on the examination of molecular-pathological-functional interactions in humans, may accelerate the process of bringing effective therapies into clinical practice.
PubMed: 38966801
DOI: 10.3389/fnagi.2024.1383163 -
Journal of Food Science and Technology Aug 2024The interest in algae-derived bioactive compounds has grown due to their potential therapeutic efficacy against a range of diseases. These compounds, derived from...
The interest in algae-derived bioactive compounds has grown due to their potential therapeutic efficacy against a range of diseases. These compounds, derived from proteins, exhibit diverse functions and profound pharmacological effects. Recent research has highlighted the extensive health benefits of algae-derived bioactive compounds, positioning them as potential natural antioxidants in the food, pharmaceutical, and cosmetic industries. This study focuses on extracting proteins from using innovative physical pre-treatment methods such as stirring, ball milling, and homogenization, under various acidic and alkaline conditions. Enzymatic hydrolysis, employing commercial enzymes at optimal temperature, pH, and enzyme-substrate ratios, produced distinct fractions according to molecular weight. Pepsin demonstrated the highest hydrolysis rate, with the fraction above 10 kDa identified as the most bioactive hydrolysate. Antioxidant activity was evaluated through DPPH, ABTS, ferrous ion chelation, and reducing power assays, demonstrating high antioxidant potential and the ability to mitigate oxidative stress. The 10 kDa fraction of pepsin hydrolysate exhibited 82.6% DPPH activity, 77.5% ABTS activity, 88.4% ferrous ion chelation activity, and higher reducing power potential (0.84 absorbance at 700 nm). Further exploration of mechanisms, amino acid profiles, and potential in vivo benefits is essential to fully exploit the medicinal potential of these algae-derived hydrolysates.
PubMed: 38966797
DOI: 10.1007/s13197-024-05935-z -
Journal of Food Science and Technology Aug 2024Aquafaba is the residual water from cooking chickpea in water. It has a high gelling ability, allowing it to create stable gels. However, those functional properties... (Review)
Review
UNLABELLED
Aquafaba is the residual water from cooking chickpea in water. It has a high gelling ability, allowing it to create stable gels. However, those functional properties depend on the legume composition, genotype, cooking time, pressure, and temperature. This study aimed to evaluate the different processes for obtaining aquafaba and compare their nutritional composition and technological characteristics using a systematic review. The authors performed the systematic review by performing specific search strategies for Scopus, Web of Science, Pubmed, Lilacs, Google Scholar, and ProQuest. A total of 17 studies were analyzed. Of them, 17.64% (n = 3) used the wastewater from canned chickpeas, 17.64% (n = 3) compared the wastewater of canned chickpeas and dry grains, and 58.82% (n = 10) used dry chickpeas. Studies used different methods to analyze the protein content. The most used (n = 5) was the Association of Official Analytical Chemists (AOAC). The aquafaba presented carbohydrates at 2.03-2.59 g/100ml; protein at 0.0.8-2.8 g/100ml; and fat at 0.07-0.1 g/100ml. In general, preparing aquafaba followed: soaking (8-10 h at 4 °C-1 chickpea: 4 water), pressure cooking (30 min-2 chickpea: 3 water), and refrigerating (24h/4 °C). In general, the results showed the following steps to prepare aquafaba: soaking for 8-10 h at 4 °C at the proportion of 1:4 (chickpea:water), pressure cooking for 30 min in the proportion of 2:3 (chickpea: water), and refrigerating 24 h/4 °C. These procedures in a homemade aquafaba presented the best results, considering foam development and higher stability. The aquafaba from canned chickpeas has a higher foam-ability and lower emulsion properties than homemade cooking aquafaba.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13197-023-05920-y.
PubMed: 38966796
DOI: 10.1007/s13197-023-05920-y -
Journal of Food Science and Technology Aug 2024Ora-pro-nobis (OPN) is an unconventional food plant with high nutritional value, and its nutritional composition can be altered according to cultivation. Cereal bars are...
Ora-pro-nobis (OPN) is an unconventional food plant with high nutritional value, and its nutritional composition can be altered according to cultivation. Cereal bars are a popular nutrient-poor foods, and OPN could be incorporated to improve the nutritional quality. This study aimed to evaluate the physicochemical characteristics and sensory acceptability of cereal bars enriched with OPN flour (OpnF) from different forms of cultivation. OpnF was obtained by dehydrating and grinding OPN leaves collected in rural (ROpnF) and urban (UOpnF) municipalities. Two formulations of cereal bars, peanut flavor (Bpn) and mango flavor (Bmg), each with 10% OpnF, were prepared. The macronutrients and mineral composition, oxalate content, water activity, texture, color profile, and acceptability were evaluated. ROpnF had the highest protein, iron, and manganese content, whereas UOpnF had the highest ash and magnesium content. The oxalic acid/calcium ratio was 1.43 and did not imply calcium bioavailability. In addition to nutritional and protein values, Bpn and Bmg presented a good sensory acceptability index of > 77.5% with market potential. Bmg has the highest mineral content and is a source of iron, manganese, and magnesium. OpnF can be used in cereal bars and potentially improve nutritional attributes and used in other foods in a similar way.
PubMed: 38966795
DOI: 10.1007/s13197-024-05924-2 -
Journal of Food Science and Technology Aug 2024In this present study, a three-factor Box-Behnken, response surface methodology (RSM) design was employed to optimize the skimmed milk powder (SMP)/whey protein...
In this present study, a three-factor Box-Behnken, response surface methodology (RSM) design was employed to optimize the skimmed milk powder (SMP)/whey protein concentrate (WPC) ratio (0.25-0.75%w/v) as a source of milk protein, inulin (1-2%w/v), and honey (4-6%w/v) for production of high-quality goat milk (GMY). The resulting ANOVA and response surface equations revealed the significant effect ( < 0.05) of these variables on the various attributes such as total solid (%), pH, titratable acidity [(LA) % by weight], syneresis (%), DPPH (% inhibition), viscosity (m.Pa⋅s), whiteness index (WI), and overall acceptability (OA). The coefficient of determination (R) for all response variables ranged from 0.88 to 0.99. Lack-of-fit tests resulted in non-significant F-values. The optimal conditions were determined as SMP/WPC at 0.36%w/v, inulin at 1.00%w/v, and honey at 6.00%w/v. The optimum values for total solid, pH, titratable acidity, syneresis, DPPH, viscosity, WI, and OA were 22.03, 4.46, 0.77, 6.34, 25.20, 182.30, 76.29 and 8.37, respectively with desirability value of 0.95.
PubMed: 38966794
DOI: 10.1007/s13197-024-05932-2 -
Journal of Food Science and Technology Aug 2024The majority of millets are produced in India, particularly pearl millet, which is more nutritious than both wheat and rice. Native to India, the "north-western...
The majority of millets are produced in India, particularly pearl millet, which is more nutritious than both wheat and rice. Native to India, the "north-western semi-arid region" produces rabadi, a natural dairy beverage made from cereal and fermented by lactic acid bacteria. The three components of rabadi viz. pearl millet, buttermilk and deionized water were optimized by using Design Expert software trial version13.0.12.0. Rabadi was processed by using the traditional technique i.e., the three components were mixed in sterile conditions and fermented for 4 h at 37 °C and then cooked for 7-8 min at high flame and finally boiled. Parameters such as pH, viscosity, ash, moisture, total solids, antioxidants, total phenols, tannins, suspension stability, titratable acidity, total sugars, and reducing sugars were analysed for all 16 runs predicted by the software. 6.83 g of pearl millet, 42.44 ml of buttermilk, and 50.72 ml of deionized water were predicted to be the best formulation of rabadi, when using the set goal of maximizing the antioxidants, total phenols and minimizing the tannins. FTIR analysis was also carried out, after the final concentration optimization, to confirm the presence of phenolic compounds, antioxidants, carbohydrates, proteins and fatty acids.
PubMed: 38966788
DOI: 10.1007/s13197-024-05926-0