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"Shi, Qing"
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الحجر السماوي : قصص قصيرة /
مجموعة مترادفات قصصية للأديب الصيني «ما تشونغ جينغ» ضمن سلسلة إبداعات أدب الأقليات الصينية، وتضم قصصا قصيرة لعادات الأقليات الصينية، وسلوكيات العائلات في المناسبات الدينية والاحتفالات الأخرى المختلفة، وتتباين فيها الشخصيات والزمان والمكان، لتضع القارئ أمام رسم أدبي يشرح حياة الأقليات الصينية المليئة بالتناص.
Book
Characterization of archaeal promoters using explainable and web-based CNN model
Background
Archaea, the third realm of life, shows unique genetic and metabolic adaptations that enable its survival in harsh environments. Despite its biotechnological and evolutionary importance, limited research has been done on archaeal promoter prediction compared to bacteria and eukaryotes. Current tools have shortcomings such as relying solely on DNA duplex stability feature encoding, high false-positive rates, low precision and lack of publicly accessible archaeal promoter prediction tool.
Results
To overcome these limitations, we present “iProm-Archaea”, a CNN-based tool for precise archaeal promoter prediction. Our method systematically assesses different feature encoding schemes and finds K-mer (K = 6) as the best representation to capture promoter motifs. For model training, we utilized experimentally validated archaeal promoters from
Sulfolobus solfataricus
,
Haloferax volcanii
, and
Thermococcus kodakarensis
. And
T. Kodakarensis KOD1
for independent testing. To enhance interpretability, we incorporated explainable artificial intelligence and performed shapley additive explanations to uncover the most influential motifs contributing to the model’s predictions. iProm-Archaea achieves 92% accuracy on training data and 89% on an independent test dataset, outperforming state-of-the-art models. Cross-organism analysis reveals limited generalizability to prokaryotic and eukaryotic promoters, underscoring the distinct regulatory architecture of archaea. To facilitate practical use, we have developed a user-friendly webserver. Moreover, we leverage iProm-Archaea and annotate 5,86,455 archaeal promoters from 478 unannotated archaea genomes.
Conclusions
This work advances archaeal genomics by offering a robust, domain-specific tool for archaeal promoter detection. The development of a user-friendly webserver enhances practical accessibility for researchers. Our work not only improves prediction performance but also enhances the understanding of archaeal gene regulation to facilitate future biotechnological and evolutionary studies in this underexplored domain of life.
Journal Article
تاريخ التبت : حكايات عن سقف العالم
يمثل تاريخ التبت جزءا مهما في تاريخ الصين، وتعد التبت التي توصف بأنها سقف العالم لكونها تضم أعلى نقطة من اليابسة على كوكب الأرض، وهي من المناطق تفردا وتميزا في الصين، جغرافيا وثقافيا واجتماعيا، وقد كونت التبت مع غيرها من مناطق القوميات الصينية الأخرى ظروفا مواتية للتبادلات الثقافية والاقتصادية داخل الصين نفسها، وقد اعتمد الكاتب على مؤلفات الكتاب القدامى مرجعا له أثناء تحرير هذا الكتاب.
BOOK
Ferruginous seawater facilitates the transformation of glauconite to chamosite; an example from the Mesoproterozoic Xiamaling Formation of north China
Berthierine and chamosite are iron-rich clay minerals that share similar chemical compositions. Berthierine forms at low temperature (25-45 °C) during early diagenesis and may transfer to chamosite at temperatures of ≥70 °C. Because the formation of berthierine and chamosite requires significant amount of Fe2+ supply, their presence in marine sediments is often used as a mineral proxy for ferruginous conditions in porewater. Recent studies reveal that the Precambrian oceans were characterized by pervasive ferruginous water-column conditions that may favor the formation of iron-rich clay minerals like berthierine and chamosite. To evaluate if ferruginous water-column conditions in the Precambrian ocean played a role on iron-rich clay mineral formation, we conducted an integrated petrographic, mineralogical, and geochemical study on the chamosite- and glauconite-bearing strata of the Mesoproterozoic Xiamaling Formation (∼1.40-1.35 Ga) in North China. Petrographic, XRD, SEM, and EDS analyses show that the chamosites of the Xiamaling Formation was transferred from glauconite, with berthierine as an intermediate mineral phase during early diagenesis. Geochemical analyses indicate that a complete transformation from glauconite-dominated to chamosite-dominated end-members (samples) requires an addition of a large amount of Fe (16.9 wt%), Mg (2.4 wt%), and a small amount of Al (1.4 wt%), but a simultaneous release of Si (11.8 wt%) and K (6.0 wt%). Considering that the glauconite- and chamosite-bearing strata are devoid of iron-rich detrital minerals (e.g., biotite and iron oxides) and lack evidence of hydrothermal alteration, the required Fe2+ for glauconite-berthierine-chamosite transformation was most likely from Fe2+-rich (ferruginous) seawater, which may have promoted glauconite-berthierine transformation at the very early diagenetic stage when Fe2+ exchange between porewater and seawater was still available. This interpretation is consistent with the high FeHR/FeT (but low Fepy/FeHR), Fe/Al, and V/Al ratios from the hosting strata that support ferruginous depositional environments. Because most Precambrian strata have passed the oil window temperature (>50-150 °C), the preservation of berthierine would be rare and chamosite should be the representative iron-rich clay mineral. Thus, the abundance of chamosite in fine-grained, marine siliciclastic sediments may be used as a mineral indicator of ferruginous water-column conditions.
Journal Article
حكايات الطائر الأزرق : عن المختبئين في زوايا التاريخ وعلاقتهم السرية
إنه ليس تاريخا فحسب، بل حياة أيضا تفاصيل التاريخ شكل الحاضر وتكونة سرا، أراها في ابتسامه في كأس من النبيذ رائحة العشب في منتصف الليل علامات المطر على النوافذ الزجاجية. إنها ندبة طويلة ورفيعة نغمة، ضوء يومض كعينين في الظلام كل هذه الأشياء لا تزال مفعمة وتجعل الحياة حقيقة ذات مغزى في هذا الكتاب ينتقي لي جينغ تزه بعضا من النصوص التاريخية ويجمع حولها القرائن، وينسخ صورة متعددة الطبقات للماضي يحاول العثور على هؤلاء المختئبين في زوايا التاريخ وعلاقاتهم السرية، ومن مروا بالحضارة بين الشرق والغرب وطبعت آثارهم في الظل والماء يلتقط طرفا واهنا من خيط بلون الزمن فيغزله بكلماته وينفخ فيه من أدبه فيدفعك للتفكيرعما وراء هذا الخيط تماما كما يضع عينك على ثقب في باب يفضلك عن عالم متكامل لم تره، أو كنت تحسبه غير موجود فالسمكة التي تخيلها المصريون تحمل أرض مصر ليست من المعنية بذاتها، بل براعة المصريين في الصمت وفى ثقل الكلمة ومسؤوليتها، وفي حق الكلمة وواجبها.
Book
The MYB family and their response to abiotic stress in ginger (Zingiber officinale Roscoe)
Background
Zingiber officinale
Roscoe, colloquially known as ginger, is a crop of significant medicinal and culinary value that frequently encounters adversity stemming from inhospitable environmental conditions. The MYB transcription factors have garnered recognition for their pivotal role in orchestrating a multitude of plant biological pathways. Nevertheless, the enumeration and characterization of the MYBs within
Z. officinale
Roscoe remains unknown. This study embarks on a genome-wide scrutiny of the MYB gene lineage in ginger, with the aim of cataloging all
ZoMYB
genes implicated in the biosynthesis of gingerols and curcuminoids, and elucidating their potential regulatory mechanisms in counteracting abiotic stress, thereby influencing ginger growth and development.
Results
In this study, we identified an MYB gene family comprising 231 members in ginger genome. This ensemble comprises 74 singular-repeat MYBs (1R-MYB), 156 double-repeat MYBs (R2R3-MYB), and a solitary triple-repeat MYB (R1R2R3-MYB). Moreover, a comprehensive analysis encompassing the sequence features, conserved protein motifs, phylogenetic relationships, chromosome location, and gene duplication events of the
ZoMYBs
was conducted. We classified ZoMYBs into 37 groups, congruent with the number of conserved domains and gene structure analysis. Additionally, the expression profiles of
ZoMYBs
during development and under various stresses, including ABA, cold, drought, heat, and salt, were investigated in ginger utilizing both RNA-seq data and qRT-PCR analysis.
Conclusion
This work provides a comprehensive understanding of the MYB family in ginger and lays the foundation for the future investigation of the potential functions of
ZoMYB
genes in ginger growth, development and abiotic stress tolerance of ginger.
Journal Article
Scutellarin ameliorates pulmonary fibrosis through inhibiting NF-κB/NLRP3-mediated epithelial–mesenchymal transition and inflammation
Idiopathic pulmonary fibrosis (IPF) is featured with inflammation and extensive lung remodeling caused by overloaded deposition of extracellular matrix. Scutellarin is the major effective ingredient of breviscapine and its anti-inflammation efficacy has been reported before. Nevertheless, the impact of scutellarin on IPF and the downstream molecular mechanism remain unclear. In this study, scutellarin suppressed BLM-induced inflammation via NF-κB/NLRP3 pathway both in vivo and in vitro. BLM significantly elevated p-p65/p65 ratio, IκBα degradation, and levels of NLRP3, caspase-1, caspase-11, ASC, GSDMD
Nterm
, IL-1β, and IL-18, while scutellarin reversed the above alterations except for that of caspase-11. Scutellarin inhibited BLM-induced epithelial–mesenchymal transition (EMT) process in vivo and in vitro. The expression levels of EMT-related markers, including fibronectin, vimentin, N-cadherin, matrix metalloproteinase 2 (MMP-2) and MMP-9, were increased in BLM group, and suppressed by scutellarin. The expression level of E-cadherin showed the opposite changes. However, overexpression of NLRP3 eliminated the anti-inflammation and anti-EMT functions of scutellarin in vitro. In conclusion, scutellarin suppressed inflammation and EMT in BLM-induced pulmonary fibrosis through NF-κB/NLRP3 signaling.
Journal Article
Expression profiling of genes coding for abundant proteins in the alkenone body of marine haptophyte alga Tisochrysis lutea
Background
Several abundant proteins have been identified in lipid body of an alkenone-producing marine haptophyte alga
Tisochrysis lutea.
The gene expression patterns of these proteins were investigated to better understand their roles in alkenone biosynthesis. For this purpose,
T. lutea
was first cultured in nitrogen-sufficient medium for biomass production and then shifted to nitrogen-deprived medium to induce lipid body formation.
Results
There were remarkable increases in the volume of alkenone body (AB) and alkenone content in the alga after they were exposed to nitrogen depletion medium. Relative mRNA levels of the genes coding for the identified proteins V-ATPase subunit V
A
, V-ATPase subunit V
d
, hypothetical protein EMIHUDRAFT_465,517, coccolith scale associated protein-1, cycloartenol-c-24-methyltransferase 1-like and SPFH domain-containing protein were investigated over the culture period. RT-PCR data showed that the expression of all these genes except the gene coding for SPFH domain-containing protein was up-regulated during the transition period from nitrogen-sufficient to nitrogen-deficient medium. Among them, the expression of the coccolith scale associated protein-1 gene was up-regulated 50–650 folds. These up-regulations were consistent with the increased alkenone production in nitrogen-deprived medium, suggesting that these proteins are involved in alkenone biosynthesis in
T. lutea.
Conclusions
Expression analysis of the lipoprotein genes suggests that five out of the six genes are up-regulated and are therefore likely to code for the identified lipoproteins associated with alkenone biosynthesis in
T. lutea
. These data would help better understand alkenone metabolism and engineer for improved biofuel production in
T. lutea.
Journal Article
The In Vitro Anti-Inflammatory Activities of Galangin and Quercetin towards the LPS-Injured Rat Intestinal Epithelial (IEC-6) Cells as Affected by Heat Treatment
Flavonols possess several beneficial bioactivities in vitro and in vivo. In this study, two flavonols galangin and quercetin with or without heat treatment (100 °C for 15–30 min) were assessed for their anti-inflammatory activities in lipopolysaccharide (LPS)-stimulated rat intestinal epithelial (IEC-6) cells and whether the heat treatment caused activity changes. The flavonol dosages of 2.5–20 μmol/L had no cytotoxicity on the cells but could enhance cell viability (especially using 5 μmol/L flavonol dosage). The flavonols could decrease the production of prostaglandin E2 and three pro-inflammatory cytokines interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α, and simultaneously promote the production of two anti-inflammatory cytokines IL-10 and transforming growth factor-β. The Western-blot results verified that the flavonols could suppress the LPS-induced expression of TLR4 and phosphorylated IκBα and p65, while the molecular docking results also illustrated that the flavonols could bind with TLR4 and NF-κB to yield energy decreases of −(21.9–28.6) kJ/mol. Furthermore, an inhibitor BAY 11-7082 blocked the NF-κB signaling pathway by inhibiting the expression of phosphorylated IκBα/p65 and thus mediated the production of IL-6/IL-10 as the flavonols did, which confirmed the assessed anti-inflammatory effect of the flavonols. Consistently, galangin had higher anti-inflammatory activity than quercetin, while the heated flavonols (especially those with longer heat time) were less active than the unheated counterparts to exert these target anti-inflammatory effects. It is highlighted that the flavonols could antagonize the LPS-caused IEC-6 cells inflammation via suppressing TLR4/NF-κB activation, but heat treatment of the flavonols led to reduced anti-inflammatory efficacy.
Journal Article