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Commercial resource potential of an invasive sea cucumber: nutritional analysis of Synaptula reciprocans. 入侵海参的商业资源潜力:海参的营养分析。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-04 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20466
Mulkibar Ciftcioglu, Osman Sabri Kesbiç, Halit Filiz, Sevan Ağdamar

Background: Synaptula reciprocans, originally native to the Indo-Pacific region, is widespread in the Red Sea. The species entered the Mediterranean during the 1970s and 1980s and has been reported along the Turkish coastline since 2003, where it has established invasive populations. European Union Regulation No. 1143/2014 encourages the investigation of alternative uses and the assessment of the economic potential of invasive species as part of management and control strategies. This study aims to evaluate the nutritional value and elemental composition of S. reciprocans, an invasive species in the Mediterranean, in order to assess its suitability for human consumption and potential alternative applications.

Methods: S. reciprocans were sampled from two different stations (L1: Gokova Bay and L2: Gulluk Bay) over two seasons, as winter (S1) and summer (S2), and transported to the laboratory under cold chain conditions (+4 °C). Moisture, ash, crude protein, crude fat, fatty acid, amino acid, and elemental content analyses were performed using standardized methods, including gravimetric, Kjeldahl, GC/MS, LC/MS-MS, and ICP-OES techniques.

Results: The findings indicate that both locality and season significantly influence the species' nutritional properties (p < 0.05). Dry matter content exhibited considerable variation across seasons, with the highest concentration observed in L2/S2 and L2/S1. Crude protein levels peaked in winter across both regions (L2S1, L1S1), while fat content was consistently higher in Bodrum samples compared to Gokova (p < 0.05). Ash content was highest in Gokova across both seasonal periods (p < 0.05). The fatty acid profile demonstrated notable seasonal and regional differences (p < 0.05), with linoleic acid (C 18:2) emerging as the predominant polyunsaturated ω-6 fatty acid. Additionally, amino acid analysis revealed significant variation (p < 0.05), identifying alanine, asparagine, glutamine, and proline as the dominant amino acids. Elemental analysis highlighted the absence of copper (Cu) in all sampled tissues, while sodium (Na) was consistently the most abundant mineral.

背景:原产于印度-太平洋地区的互生突触,广泛分布于红海。该物种在20世纪70年代和80年代进入地中海,自2003年以来一直沿着土耳其海岸线报道,并在那里建立了入侵种群。欧盟第1143/2014号法规鼓励调查入侵物种的替代用途和评估其经济潜力,作为管理和控制战略的一部分。本研究旨在评估地中海入侵物种往复式葡萄球菌的营养价值和元素组成,以评估其对人类食用的适宜性和潜在的替代应用。方法:在冬季(S1)和夏季(S2)两个季节,分别从两个不同的站点(L1: Gokova Bay和L2: Gulluk Bay)采集往复式沙门氏菌,并在冷链条件下(+4°C)运输到实验室。水分、灰分、粗蛋白质、粗脂肪、脂肪酸、氨基酸和元素含量分析采用标准化方法,包括重量法、凯氏定氮法、GC/MS、LC/MS-MS和ICP-OES技术。结果:产地和季节对鱼种的营养特性有显著影响(p < 0.05)。干物质含量在不同季节变化较大,L2/S2和L2/S1的含量最高。两个地区(L2S1和L1S1)的粗蛋白质含量在冬季均达到峰值,而Bodrum样品的脂肪含量始终高于Gokova (p < 0.05)。两个季节Gokova的灰分含量最高(p < 0.05)。脂肪酸分布具有显著的季节和地区差异(p < 0.05),亚油酸(C 18:2)是主要的多不饱和ω-6脂肪酸。此外,氨基酸分析显示显著差异(p < 0.05),丙氨酸、天冬酰胺、谷氨酰胺和脯氨酸是优势氨基酸。元素分析强调了所有样本组织中铜(Cu)的缺失,而钠(Na)一直是最丰富的矿物质。
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引用次数: 0
A quick and reliable menthol-induced bleaching protocol for the Caribbean staghorn coral, Acropora cervicornis. 一种快速可靠的薄荷醇诱导的加勒比海鹿角珊瑚白化方案。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-04 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20888
J Grace Klinges, Marina Villoch Diaz-Mauriño, Roger M Wilder, Maia C Erbes, Eleftherios C Karabelas, Erinn M Muller, Cory J Krediet

Corals and dinoflagellate algae form a unique mutualistic symbiosis that provides the energetic and structural foundation for shallow coral reef ecosystems. Despite the long success of this partnership in oligotrophic seas, coral reefs are in decline due to increasing threats from rising seawater temperatures and disease, both of which can lead to bleaching and mortality. In order to better understand the mechanisms that underpin this mutualism, it may be necessary to dismantle the coral-algal symbiosis. Previous studies have experimentally bleached corals using thermal stress, photosynthetic inhibitors (DCMU), and menthol. We compared lab-induced bleaching of staghorn coral Acropora cervicornis by menthol treatment to traditional thermal stress. The larger aim was to adapt existing bleaching protocols for this important coral species, providing a guide for future studies. Bleaching in corals treated with menthol or exposed to elevated temperature stress (31°C) was monitored by measuring photosynthetic activity determined by Fv/Fm using pulse-amplitude modulated (PAM) fluorescence and compared to untreated conspecifics. Corals were also monitored for symbiont density and overall health using the CoralWatch Coral Health Chart card throughout the experiment. We found that A. cervicornis bleached in response to both menthol treatment and thermal stress, but menthol treatment was more effective at reducing algal symbiont photosynthetic capacity (Fv/Fm) without negatively affecting the health of the coral. Our results indicate that menthol treatment at 0.38 mM rendered staghorn coral aposymbiotic within fourteen days without any visual or physiological damage to the coral. This study provides a simple and effective menthol-bleaching treatment protocol for future studies on staghorn coral.

珊瑚和鞭毛藻形成了一种独特的共生关系,为浅层珊瑚礁生态系统提供了能量和结构基础。尽管这种伙伴关系在少营养海洋中取得了长期的成功,但由于海水温度上升和疾病的威胁越来越大,珊瑚礁正在减少,这两者都可能导致白化和死亡。为了更好地理解支撑这种共生关系的机制,可能有必要拆除珊瑚-藻类共生关系。以前的研究已经用热应激、光合抑制剂(DCMU)和薄荷醇实验性地漂白了珊瑚。以鹿角珊瑚为研究对象,比较了薄荷醇对鹿角珊瑚和传统热胁迫对鹿角珊瑚的影响。更大的目标是为这种重要的珊瑚物种调整现有的漂白方案,为未来的研究提供指导。通过使用脉冲幅度调制(PAM)荧光测量Fv/Fm测定的光合活性来监测经薄荷醇处理或暴露于高温胁迫(31°C)下的珊瑚的白化情况,并将其与未处理的同种珊瑚进行比较。在整个实验过程中,还使用珊瑚观察珊瑚健康图表卡监测珊瑚的共生密度和整体健康状况。研究发现,薄荷醇处理和热胁迫均导致颈角藻白化,但薄荷醇处理更有效地降低了藻类共生光合能力(Fv/Fm),而不会对珊瑚的健康产生负面影响。我们的研究结果表明,0.38 mM的薄荷醇处理使鹿角珊瑚在14天内发生反共生,而不会对珊瑚造成任何视觉或生理损害。本研究为鹿角珊瑚的进一步研究提供了一种简单有效的薄荷醇漂白处理方案。
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引用次数: 0
Neuro-immune-related gene signatures define molecular subtypes and prognostic score in bladder cancer with SERPINE2 as a potential therapeutic target. 神经免疫相关基因特征定义了膀胱癌的分子亚型和预后评分,SERPINE2作为潜在的治疗靶点。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-04 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20917
Qiwei Nie, Minyao Jiang, Song Wan, Ming Xi, Wei Hua, Funeng Jiang, Weide Zhong

Neuro-immune interactions are critical in cancer, yet their molecular features in bladder cancer remain unclear. We analyzed transcriptomic data from TCGA and UCSC Xena to investigate the expression profiles and molecular subtypes of neuro-immune-related genes, and constructed a neuro-immune-related score (NAS) model. Single-cell transcriptomic data were integrated to explore the immune microenvironmental features, and functional validation was performed by knocking down SERPINE2 with shRNA in T24 cells. The results showed that six core genes (SERPINE2, NXPH4, SERPINB2, C2orf40, SERPINB12, SERPINB10) were identified to stratify patients into high- and low-risk groups, with robust predictive power across clinical subgroups and validation cohorts. Single-cell RNA-seq data revealed significant NAS heterogeneity among cell populations. The NAS-high state was enriched in TGFβ, EGF, and FGF signaling with activation of EZH2 and SMARCA4, while the NAS-low state showed immune-regulatory features. Functional assays confirmed that SERPINE2 knockdown suppressed proliferation, migration, invasion, while increasing apoptosis of T24 cells, highlighting its oncogenic role. Moreover, genome-wide association studies (GWAS) suggested that genetic variants in SERPINE2 and related genes may increase bladder cancer susceptibility. Collectively, our findings provide novel insights into neuro-immune-driven tumor heterogeneity and immune remodeling, establish the NAS model as an innovative prognostic tool, and identify SERPINE2 as a promising therapeutic target for precision management of bladder cancer.

神经免疫相互作用在癌症中至关重要,但其在膀胱癌中的分子特征尚不清楚。我们分析了TCGA和UCSC Xena的转录组学数据,研究了神经免疫相关基因的表达谱和分子亚型,并构建了神经免疫相关评分(NAS)模型。整合单细胞转录组学数据,探索免疫微环境特征,并通过shRNA在T24细胞中敲除SERPINE2进行功能验证。结果显示,6个核心基因(SERPINE2、NXPH4、SERPINB2、C2orf40、SERPINB12、SERPINB10)被鉴定出来,将患者分为高风险和低风险组,在临床亚组和验证队列中具有强大的预测能力。单细胞RNA-seq数据揭示了细胞群体中显著的NAS异质性。nas -高状态下,tgf - β、EGF和FGF信号富集,EZH2和SMARCA4被激活,而nas -低状态则表现出免疫调节特征。功能实验证实,SERPINE2敲低抑制了T24细胞的增殖、迁移、侵袭,同时增加了T24细胞的凋亡,突出了其致癌作用。此外,全基因组关联研究(GWAS)表明SERPINE2及相关基因的遗传变异可能增加膀胱癌的易感性。总的来说,我们的研究结果为神经免疫驱动的肿瘤异质性和免疫重塑提供了新的见解,建立了NAS模型作为一种创新的预后工具,并确定了SERPINE2作为精确治疗膀胱癌的有希望的治疗靶点。
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引用次数: 0
Potential of Vγ9Vδ2T cells in tuberculosis: integration of innate and adaptive immunity for vaccine development. v - γ - 9v - δ 2t细胞在结核病中的潜力:先天免疫和适应性免疫在疫苗开发中的整合
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-04 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20904
Dalin Di, Chun'e Gao, Yonggen Deng, Yuxia Li, Yanyan Zhang

Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis that poses major global health challenges. The Bacillus Calmette-Guérin (BCG) vaccine provides only limited protection against TB in adults and the current therapeutic regimens for TB are constrained by prolonged treatment cycles and the emergence of drug-resistant strains. Consequently, the role of Vγ9Vδ2 T cells in anti-TB immunity has increasingly garnered attention. These nonconventional T lymphocytes rapidly recognize Mtb-infected cells and exert effector functions through a unique T-cell receptor that directly recognizes phosphorylated antigens independent of the major histocompatibility complex. Vγ9Vδ2 T cells mediate direct cytotoxicity against infected cells and coordinate with other immune components to strengthen the host defense against TB. These distinctive attributes highlight the potential of Vγ9Vδ2 T cells as targets in novel TB vaccine strategies. The current understanding of Vγ9Vδ2 T cell-mediated immunity to Mtb, recent advances in TB vaccine research, and prospective directions for future investigation are synthesized in this review.

结核病是一种由结核分枝杆菌引起的慢性传染病,对全球健康构成重大挑战。卡介苗仅对成人结核病提供有限的保护,目前的结核病治疗方案受到治疗周期延长和耐药菌株出现的限制。因此,v - γ - 9v - δ2 T细胞在抗结核免疫中的作用越来越受到关注。这些非常规的T淋巴细胞迅速识别mtb感染的细胞,并通过一种独特的T细胞受体发挥效应功能,该受体直接识别独立于主要组织相容性复合体的磷酸化抗原。v - γ - 9v - δ2 T细胞介导对感染细胞的直接细胞毒性,并与其他免疫成分协同增强宿主对结核病的防御。这些独特的属性突出了Vγ9Vδ2 T细胞作为新型结核病疫苗策略靶点的潜力。本文综述了目前对v γ - 9v - δ2 T细胞介导的Mtb免疫的认识、TB疫苗研究的最新进展以及未来研究的展望方向。
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引用次数: 0
Identification and validation of biomarkers associated with lactic acid metabolism in diabetic nephropathy. 糖尿病肾病乳酸代谢相关生物标志物的鉴定和验证。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-03 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20761
Hua Guo, Xiaoman Lu, Guilin Fang, Yun Qi, Huili Cui, Xiaojuan Zhang

Background: Previous studies have demonstrated a close association between diabetic nephropathy (DN) and lactic acid metabolism; however, the underlying mechanisms remain unclear. This study aimed to investigate the role of lactic acid metabolism-related biomarkers in the pathogenesis of DN.

Methods: The DN training and validation datasets were obtained from public databases, while lactic acid metabolism-related genes (LRGs) were sourced from the literature. Using a comprehensive bioinformatics approach, we screened for potential biomarkers. Subsequent analyses included nomogram construction, functional enrichment, immune cell infiltration profiling, regulatory network mapping, drug target prediction, and molecular docking to elucidate the biomarkers' roles in DN pathogenesis. Finally, reverse transcription quantitative polymerase chain reaction (RT-qPCR) was performed to validate biomarker expression levels in clinical samples.

Results: Through a comprehensive analysis of bioinformatics methods, we identified two biomarkers-PTGS2 and NFE2L2-as significant candidates in DN. The nomogram demonstrated robust predictive efficacy, validating their utility. NFE2L2 and PTGS2 were positively correlated with the five signal pathways, such as hypoxia and IL2 STAT5 signaling. Both PTGS2 and NFE2L2 had the highest positive correlation with T follicular helper cells (correlation coefficient (cor) = 0.49, p < 0.01, and cor = 0.54, p < 0.01). Two biomarkers predicted multiple miRNAs and transcription factors (TFs), such as miR-144-3p, GATA2, and GATA3. Drug-target analysis highlighted high-affinity interactions for NFE2L2 -lagascatriol and PTGS2 -cimicoxib, further supported by molecular docking. Finally, RT-qPCR confirmed significantly elevated expression of PTGS2 and NFE2L2 in DN samples compared to controls (p < 0.05), aligning with bioinformatics predictions.

背景:既往研究表明糖尿病肾病(DN)与乳酸代谢密切相关;然而,潜在的机制仍不清楚。本研究旨在探讨乳酸代谢相关生物标志物在DN发病机制中的作用。方法:DN训练和验证数据集来源于公共数据库,乳酸代谢相关基因(LRGs)来源于文献。使用综合生物信息学方法,我们筛选潜在的生物标志物。随后的分析包括nomogram构建、功能富集、免疫细胞浸润谱、调控网络作图、药物靶点预测和分子对接等,以阐明生物标志物在DN发病机制中的作用。最后,通过逆转录定量聚合酶链反应(RT-qPCR)验证临床样本中生物标志物的表达水平。结果:通过生物信息学方法的综合分析,我们确定了两个生物标志物- ptgs2和nfe2l2 -作为DN的重要候选物。nomogram显示了稳健的预测效果,验证了它们的实用性。NFE2L2和PTGS2与缺氧、IL2 STAT5信号通路呈正相关。PTGS2和NFE2L2与T滤泡辅助细胞呈正相关(相关系数(cor) = 0.49, p p p p
{"title":"Identification and validation of biomarkers associated with lactic acid metabolism in diabetic nephropathy.","authors":"Hua Guo, Xiaoman Lu, Guilin Fang, Yun Qi, Huili Cui, Xiaojuan Zhang","doi":"10.7717/peerj.20761","DOIUrl":"10.7717/peerj.20761","url":null,"abstract":"<p><strong>Background: </strong>Previous studies have demonstrated a close association between diabetic nephropathy (DN) and lactic acid metabolism; however, the underlying mechanisms remain unclear. This study aimed to investigate the role of lactic acid metabolism-related biomarkers in the pathogenesis of DN.</p><p><strong>Methods: </strong>The DN training and validation datasets were obtained from public databases, while lactic acid metabolism-related genes (LRGs) were sourced from the literature. Using a comprehensive bioinformatics approach, we screened for potential biomarkers. Subsequent analyses included nomogram construction, functional enrichment, immune cell infiltration profiling, regulatory network mapping, drug target prediction, and molecular docking to elucidate the biomarkers' roles in DN pathogenesis. Finally, reverse transcription quantitative polymerase chain reaction (RT-qPCR) was performed to validate biomarker expression levels in clinical samples.</p><p><strong>Results: </strong>Through a comprehensive analysis of bioinformatics methods, we identified two biomarkers-PTGS2 and NFE2L2-as significant candidates in DN. The nomogram demonstrated robust predictive efficacy, validating their utility. NFE2L2 and PTGS2 were positively correlated with the five signal pathways, such as hypoxia and IL2 STAT5 signaling. Both PTGS2 and NFE2L2 had the highest positive correlation with T follicular helper cells (correlation coefficient (cor) = 0.49, <i>p</i> < 0.01, and cor = 0.54, <i>p</i> < 0.01). Two biomarkers predicted multiple miRNAs and transcription factors (TFs), such as miR-144-3p, GATA2, and GATA3. Drug-target analysis highlighted high-affinity interactions for NFE2L2 -lagascatriol and PTGS2 -cimicoxib, further supported by molecular docking. Finally, RT-qPCR confirmed significantly elevated expression of PTGS2 and NFE2L2 in DN samples compared to controls (<i>p</i> < 0.05), aligning with bioinformatics predictions.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e20761"},"PeriodicalIF":2.4,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12965171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147378102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Relationship between blood pressure level and activity of renin-aldosterone axis in patients with essential hypertension-a retrospective study. 原发性高血压患者血压水平与肾素-醛固酮轴活性关系的回顾性研究。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-03 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20883
Peijuan Li, Bo Liao, Zhaoquan Yang, Jiulin Zhang, Kun Chen, Zhipeng Li

Background: A study indicates that elevated aldosterone levels increase the risk of hypertension by 16%. This retrospective cohort study examines the relationship between blood pressure and renin-aldosterone levels in patients with essential hypertension (EH), aiming to elucidate the clinical features and risk factors of inappropriate hyperaldosteronism in Chinese individuals with essential hypertension.

Methods: Clinical data of 309 EH patients were analyzed. The participants were divided into three groups with a high (H)/medium (M)/low (L) blood pressure level: Group H (BP≥160 / (or) 100 mmHg, n = 151), Group M (BP 140-160/90-100 mmHg, n = 101), Group L (BP < 140/90 mmHg, n = 57). Since the data were all non-normal distributions, they were represented by the median and extreme values, and the Wilcoxon rank sum test was used. Categorical data were analyzed using the χ2 test. In the one-factor variance analysis, those with P < 0.05 were included in the multivariate analysis, and the multiple linear regression analysis method was used for the multivariate analysis. The study assessed the relationship between the plasma renin activity (PRA), plasma aldosterone concentration (PAC), and the aldosterone/renin activity ratio (ARR) in patients with EH and their blood pressure levels.

Results: Among the 309 EH patients, 65 cases (21.04%) had elevated aldosterone levels, and 94 cases (30.42%) had increased renin activity. The diastolic blood pressure of patients with elevated aldosterone levels was higher than that of patients with normal or decreased aldosterone levels (100 vs. 95, 87, p < 0.05), while there was no significant difference in systolic blood pressure between patients with elevated aldosterone levels and those with normal or decreased aldosterone levels (152 vs. 151.5, 142, p > 0.05). The proportion of patients with heightened aldosterone levels was greater in Group H compared to the others (23.8% vs. 20.8% and 14.0%, p < 0.05). Multiple linear stepwise regression indicated that higher aldosterone levels correlated with increased diastolic blood pressure. PAC increased by 3.66 ng/dL for every 10 mmHg of DBP.

Conclusion: The increase in aldosterone levels is relatively common among EH patients in China. The increase in aldosterone levels is correlated with the elevation of diastolic blood pressure. The elevated aldosterone levels are an independent risk factor for the increase in diastolic blood pressure in EH patients.

背景:一项研究表明,醛固酮水平升高可使高血压的风险增加16%。本回顾性队列研究探讨了原发性高血压(EH)患者血压与肾素醛固酮水平的关系,旨在阐明中国原发性高血压患者不适当高醛固酮血症的临床特征和危险因素。方法:对309例EH患者的临床资料进行分析。参与者按高(H)/中(M)/低(L)血压水平分为三组:H组(血压≥160 /(或)100 mmHg, n = 151), M组(血压140-160/90-100 mmHg, n = 101), L组(血压< 140/90 mmHg, n = 57)。由于数据均为非正态分布,故用中位数和极值表示,采用Wilcoxon秩和检验。分类资料采用χ2检验。结果:309例EH患者中,65例(21.04%)醛固酮水平升高,94例(30.42%)肾素活性升高。醛固酮水平升高的患者舒张压高于醛固酮水平正常或降低的患者(100比95,87,p比151.5,142,p < 0.05)。H组患者醛固酮水平升高的比例高于其他组(23.8% vs. 20.8%和14.0%),p结论:醛固酮水平升高在中国EH患者中较为普遍。醛固酮水平升高与舒张压升高相关。醛固酮水平升高是EH患者舒张压升高的独立危险因素。
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引用次数: 0
Differences in extinction selectivity and their relationship to functional traits in late Cenozoic mollusks. 晚新生代软体动物灭绝选择性的差异及其与功能性状的关系。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-03 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20715
Daniel Rojas-Ariza, Luke C Strotz, Bruce S Lieberman

Identifying generalizable patterns of extinction selectivity is crucial for understanding the mechanisms driving extinction processes. Differences in the trait composition of extinct surviving species may represent evidence of processes of extinction selectivity during the past. Here, we leverage the information from the late Cenozoic molluscan fossil record and extant biota from the western Atlantic coast of North America, to test for differences in the trait composition of extinct and surviving species of bivalves and gastropods. We found basal metabolic rate (BMR) is the trait most closely associated with the extinction patterns observed in our data. On average across all studied molluscan species, odds of survival decrease by ∼11% for every 1-milliwatt (mW) increase in BMR, but this pattern was consistent only for bivalves. BMR thus represents an organismal trait that scales up to predict species survival in bivalves. By contrast, a variety of other functional traits shown to be important in other taxonomic and temporal contexts, including shell composition in bivalves and shell structures such as varices and the callus in gastropods, were not found to be associated with survival. This could suggest some of these traits, sometimes posited to represent important organismic adaptations, may not have played a prominent role in long term species survival in Cenozoic bivalves and gastropods. A variety of biotic and abiotic factors may likely determine the extent to which particular organismal traits influence patterns of species survival.

识别灭绝选择性的可推广模式对于理解驱动灭绝过程的机制至关重要。灭绝幸存物种的性状组成差异可能是过去灭绝选择性过程的证据。在这里,我们利用来自晚新生代软体动物化石记录和北美大西洋西部海岸现存生物群的信息,来测试已灭绝和幸存的双壳类和腹足类物种的特征组成差异。我们发现基础代谢率(BMR)是与我们的数据中观察到的灭绝模式最密切相关的性状。平均而言,在所研究的所有软体动物物种中,BMR每增加1毫瓦(mW),生存几率就会下降~ 11%,但这种模式仅在双壳类动物中是一致的。因此,BMR代表了一种有机体特征,可以扩大到预测双壳类动物的物种生存。相比之下,在其他分类和时间背景下显示出重要的其他各种功能特征,包括双壳类动物的壳组成和腹足类动物的壳结构,如静脉曲张和愈伤组织,都没有发现与生存相关。这可能表明,这些特征中的一些,有时被认为是重要的有机体适应,可能在新生代双壳类和腹足类物种的长期生存中没有发挥重要作用。多种生物和非生物因素可能决定特定的生物特征对物种生存模式的影响程度。
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引用次数: 0
Identification of key circadian rhythm-associated genes as differentially expressed genes for cytomegalovirus infection in very-low-birth-weight infants. 极低出生体重儿巨细胞病毒感染中关键昼夜节律相关基因差异表达的鉴定
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-03 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20885
Qianqian Li, Ying Liu, Dongmei Chen, Wenjie Yuan, Liu Han, Ting Zu, Junmei Yan

Background: Human cytomegalovirus (HCMV) infection has adverse effects on very low-birth-weight infants (VLBW) and is complicated with liver dysfunction, thrombocytopenia, and hearing impairment. Therefore, we explored new potential intervention targets in VLBW infants with HCMV infection.

Methods: Enrichment analysis of adult HCMV infection and control groups was performed in the GSE81246 dataset. Peripheral blood mononuclear cells (PBMCs) from VLBW infants with HCMV and those without HCMV (n = 3 per group) (collection: 9-10 a.m.) were sent for RNA-seq to enrich the transcriptome of the obtained GSE290897 dataset. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways with the same enrichment results and significant changes in the two datasets were selected and analyzed. Then the screened genes were verified using reverse transcription polymerase chain reaction (RT-PCR) and quantitative PCR (qPCR).

Results: The key circadian rhythm genes PER1 and CRY1 were screened. RT-qPCR was used to detect PER1 and CRY1 mRNA levels in the PBMCs of VLBW infants with HCMV (n = 12) and the controls (n = 6) (collection: 9-10 a.m.). And results showed that PER1 and CRY1 mRNA was significantly decreased in HCMV infection than in the controls (P < 0.0001; P < 0.0001).

Conclusion: PER1 and CRY1 mRNA was significantly decreased in PBMCs from HCMV infected VLBW infants, providing new ideas for studying potential effective therapeutic targets for HCMV infection in VLBW infants.

背景:人巨细胞病毒(HCMV)感染对极低出生体重儿(VLBW)有不良影响,并发肝功能障碍、血小板减少症和听力障碍。因此,我们探索了VLBW婴儿HCMV感染的新的潜在干预靶点。方法:在GSE81246数据集中对成人HCMV感染组和对照组进行富集分析。从患有HCMV和未患有HCMV的VLBW婴儿(每组n = 3)(收集时间:上午9点至10点)的外周血单个核细胞(PBMCs)被送去进行rna测序,以丰富获得的GSE290897数据集的转录组。选择富集结果相同且变化显著的基因本体和京都基因与基因组百科全书路径进行分析。然后用逆转录聚合酶链反应(RT-PCR)和定量PCR (qPCR)对筛选的基因进行验证。结果:筛选到关键昼夜节律基因PER1和CRY1。采用RT-qPCR检测患有HCMV的VLBW婴儿(n = 12)和对照组(n = 6) PBMCs中PER1和CRY1 mRNA水平(采集时间:上午9-10点)。结果显示,与对照组相比,HCMV感染组PER1和CRY1 mRNA表达明显降低(P P)。结论:HCMV感染的VLBW婴儿外周血中PER1和CRY1 mRNA表达明显降低,为研究VLBW婴儿HCMV感染的潜在有效治疗靶点提供了新的思路。
{"title":"Identification of key circadian rhythm-associated genes as differentially expressed genes for cytomegalovirus infection in very-low-birth-weight infants.","authors":"Qianqian Li, Ying Liu, Dongmei Chen, Wenjie Yuan, Liu Han, Ting Zu, Junmei Yan","doi":"10.7717/peerj.20885","DOIUrl":"10.7717/peerj.20885","url":null,"abstract":"<p><strong>Background: </strong>Human cytomegalovirus (HCMV) infection has adverse effects on very low-birth-weight infants (VLBW) and is complicated with liver dysfunction, thrombocytopenia, and hearing impairment. Therefore, we explored new potential intervention targets in VLBW infants with HCMV infection.</p><p><strong>Methods: </strong>Enrichment analysis of adult HCMV infection and control groups was performed in the GSE81246 dataset. Peripheral blood mononuclear cells (PBMCs) from VLBW infants with HCMV and those without HCMV (<i>n</i> = 3 per group) (collection: 9-10 a.m.) were sent for RNA-seq to enrich the transcriptome of the obtained GSE290897 dataset. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways with the same enrichment results and significant changes in the two datasets were selected and analyzed. Then the screened genes were verified using reverse transcription polymerase chain reaction (RT-PCR) and quantitative PCR (qPCR).</p><p><strong>Results: </strong>The key circadian rhythm genes PER1 and CRY1 were screened. RT-qPCR was used to detect PER1 and CRY1 mRNA levels in the PBMCs of VLBW infants with HCMV (<i>n</i> = 12) and the controls (<i>n</i> = 6) (collection: 9-10 a.m.). And results showed that PER1 and CRY1 mRNA was significantly decreased in HCMV infection than in the controls (<i>P</i> < 0.0001; <i>P</i> < 0.0001).</p><p><strong>Conclusion: </strong>PER1 and CRY1 mRNA was significantly decreased in PBMCs from HCMV infected VLBW infants, providing new ideas for studying potential effective therapeutic targets for HCMV infection in VLBW infants.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e20885"},"PeriodicalIF":2.4,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12965172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147378138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic differentiation of morphologically similar polyploid wheat species. 形态相似多倍体小麦种的遗传分化。
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-03 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20723
Uzuk Kasymova, Asiye Ulug

Background: Wheat is a globally important polyploid crop, with hexaploid bread wheat (Triticum aestivum L.) and tetraploid durum wheat (T. turgidum subsp. durum (Desf.) Husn.) as its main cultivated forms. Despite distinct end-use properties, these species are morphologically similar, making their identification difficult. Traditional phenotypic approaches often fail to resolve closely related polyploid wheats, emphasizing the need for a reliable molecular diagnostic and wheat barcoding strategy.

Method: This study developed and validated a multilocus molecular diagnostic framework for the discrimination of polyploid wheat species. The approach integrates plastid (rbcL, matK), nuclear ribosomal (ITS2, IGS), and nuclear-coding markers (Glu-1 and XDuPw167), all amplified using the Polymerase Chain Reaction. Validation was performed using ten experimental samples and 203 reference sequences retrieved from the NCBI GenBank database. We developed and validated a multilocus molecular diagnostic method for the reliable discrimination of wheat species.

Results: Plastid loci showed limited variation, whereas the IGS region contained a diagnostic 71 bp insertion linked to the D genome, clearly distinguishing hexaploids from tetraploids. The Glu-1 and XDuPw167 loci exhibited genome-specific polymorphisms that further differentiated the two species. The multilocus diagnostic method achieved over 95% amplification success and consistent sequence profiles across replicates, confirming its accuracy and reproducibility.

Conclusions: The proposed molecular diagnostic method provides a reproducible, cost-effective, and high-resolution molecular diagnostic tool for reliable wheat species identification. By combining genome-specific nuclear and expressed sequence tag-simple sequence repeat (EST-SSR) markers, this approach establishes a robust and scalable system applicable to species authentication, seed purity testing, germplasm characterization, and genetic resource management.

背景:小麦是全球重要的多倍体作物,有六倍体面包小麦(Triticum aestivum L.)和四倍体硬粒小麦(T. turgidum subsp.)。硬质(Desf)。)作为其主要栽培形式。尽管这些物种的最终用途不同,但它们在形态上相似,这使得它们的识别变得困难。传统的表型方法往往不能解决密切相关的多倍体小麦,强调需要一个可靠的分子诊断和小麦条形码策略。方法:建立并验证了多倍体小麦品种的多位点分子诊断框架。该方法整合了质体(rbcL, matK),核糖体(ITS2, IGS)和核编码标记(glu1和XDuPw167),所有这些标记都使用聚合酶链反应扩增。使用NCBI GenBank数据库中检索的10个实验样本和203个参考序列进行验证。我们开发并验证了一种可靠的小麦品种多位点分子诊断方法。结果:质体位点显示有限的变异,而IGS区域包含一个与D基因组连接的71 bp的诊断插入,清楚地区分了六倍体和四倍体。Glu-1和XDuPw167位点表现出基因组特异性多态性,进一步区分了两个物种。多位点诊断方法扩增成功率超过95%,且序列分布在多个重复中一致,证实了其准确性和可重复性。结论:所建立的分子诊断方法为小麦品种鉴定提供了一种重复性高、成本低、高分辨率的分子诊断工具。该方法通过结合基因组特异性核标记和表达序列标记-简单序列重复(EST-SSR)标记,建立了一个健壮且可扩展的系统,适用于物种鉴定、种子纯度检测、种质鉴定和遗传资源管理。
{"title":"Genetic differentiation of morphologically similar polyploid wheat species.","authors":"Uzuk Kasymova, Asiye Ulug","doi":"10.7717/peerj.20723","DOIUrl":"10.7717/peerj.20723","url":null,"abstract":"<p><strong>Background: </strong>Wheat is a globally important polyploid crop, with hexaploid bread wheat (<i>Triticum aestivum</i> L.) and tetraploid durum wheat (<i>T. turgidum</i> subsp<i>. durum</i> (Desf.) Husn.) as its main cultivated forms. Despite distinct end-use properties, these species are morphologically similar, making their identification difficult. Traditional phenotypic approaches often fail to resolve closely related polyploid wheats, emphasizing the need for a reliable molecular diagnostic and wheat barcoding strategy.</p><p><strong>Method: </strong>This study developed and validated a multilocus molecular diagnostic framework for the discrimination of polyploid wheat species. The approach integrates plastid (<i>rbcL</i>, <i>matK</i>), nuclear ribosomal (<i>ITS2</i>, <i>IGS</i>), and nuclear-coding markers (<i>Glu-1</i> and <i>XDuPw167</i>), all amplified using the Polymerase Chain Reaction. Validation was performed using ten experimental samples and 203 reference sequences retrieved from the NCBI GenBank database. We developed and validated a multilocus molecular diagnostic method for the reliable discrimination of wheat species.</p><p><strong>Results: </strong>Plastid loci showed limited variation, whereas the <i>IGS</i> region contained a diagnostic 71 bp insertion linked to the D genome, clearly distinguishing hexaploids from tetraploids. The <i>Glu-1</i> and <i>XDuPw167</i> loci exhibited genome-specific polymorphisms that further differentiated the two species. The multilocus diagnostic method achieved over 95% amplification success and consistent sequence profiles across replicates, confirming its accuracy and reproducibility.</p><p><strong>Conclusions: </strong>The proposed molecular diagnostic method provides a reproducible, cost-effective, and high-resolution molecular diagnostic tool for reliable wheat species identification. By combining genome-specific nuclear and expressed sequence tag-simple sequence repeat (EST-SSR) markers, this approach establishes a robust and scalable system applicable to species authentication, seed purity testing, germplasm characterization, and genetic resource management.</p>","PeriodicalId":19799,"journal":{"name":"PeerJ","volume":"14 ","pages":"e20723"},"PeriodicalIF":2.4,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12965169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147378107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pathological features of BRCA-mutated breast cancer in Shenzhen, China: a single-center study. 中国深圳brca突变乳腺癌的病理特征:一项单中心研究
IF 2.4 3区 生物学 Q2 MULTIDISCIPLINARY SCIENCES Pub Date : 2026-03-03 eCollection Date: 2026-01-01 DOI: 10.7717/peerj.20813
Jiayu Guan, Sihang Lin, Yanjia Liu, Wenbin Zhou

Background: Most studies on breast cancer susceptibility gene (BRCA) mutations have focused on Caucasian populations in Europe and North America. Currently, there is a lack of literature and data research in related fields in Shenzhen, China, and even in Guangdong Province. This study aims to establish a registry of BRCA mutation carriers by analyzing and comparing the pathological features of breast cancer patients carrying and not carrying BRCA mutations in the Shenzhen area.

Methods: Blood samples were collected from 406 breast cancer patients who met the inclusion criteria (from July 2016 to November 2024) and genetic testing was performed using next-generation sequencing (NGS) technology. Patients were divided into two groups: BRCA mutation group with 54 cases and BRCA non-mutation group with 352 cases. A retrospective analysis was conducted on patient data collected from the health information system of Shenzhen People's Hospital, including demographic data, clinical pathological characteristics, and variables related to molecular typing. We used SPSS software for statistical analysis of the data.

Results: In 406 breast cancer patients, the average age of the BRCA mutation group was 39.3 ± 9.2 years, while the average age of the BRCA non-mutation group was 41.8 ± 8.8 years. The proportion of tumors ≤ 2 cm in the mutation group is 72.2%, higher than the 53.1% in the non-mutation group (P = 0.009, 95% confidence interval [1.220-4.313]). The proportion of grade III pathologic grading in the mutation group is 59.3%, higher than the 36.1% in the non-mutation group (P = 0.001, 95% confidence interval [1.436-4.625]). In the mutation group, there are seven cases of Luminal A (13.0%), zero cases of Luminal B (Her-2 positive) (0%), and 23 cases of triple-negative breast cancer (TNBC) (42.6%). In the non-mutation group, there are 93 cases of Luminal A (26.4%), 54 cases of Luminal B (Her-2 positive) (15.3%), and 67 cases of TNBC (19.0%). (Luminal A: P = 0.033, 95% confidence interval [0.181-0.950]; Luminal B (Her-2 positive): P = 0.002; TNBC: P < 0.001, 95% confidence interval [1.730-5.759]). The expression levels of estrogen receptor (ER) (P = 0.009), progesterone receptor (PR) (P < 0.001), and Ki-67 (P < 0.001) show significant differences between the BRCA mutation group and the BRCA non-mutation group.

Conclusions: Compared to BRCA non-mutated patients, BRCA mutated patients in Shenzhen have smaller tumor volumes, with pathological grades mainly at grade 3, and molecular subtypes predominantly being triple-negative breast cancer.

背景:大多数关于乳腺癌易感基因(BRCA)突变的研究都集中在欧洲和北美的高加索人群中。目前,在中国深圳,甚至广东省,相关领域的文献和数据研究都很缺乏。本研究旨在通过分析比较深圳地区携带和不携带BRCA突变的乳腺癌患者的病理特征,建立BRCA突变携带者名册。方法:采集2016年7月至2024年11月符合纳入标准的406例乳腺癌患者的血样,采用新一代测序(NGS)技术进行基因检测。将患者分为两组:BRCA突变组54例,BRCA非突变组352例。回顾性分析深圳市人民医院卫生信息系统收集的患者资料,包括人口学资料、临床病理特征和与分子分型相关的变量。我们使用SPSS软件对数据进行统计分析。结果:406例乳腺癌患者中,BRCA突变组的平均年龄为39.3±9.2岁,BRCA非突变组的平均年龄为41.8±8.8岁。突变组≤2 cm的肿瘤比例为72.2%,高于非突变组的53.1% (P = 0.009, 95%可信区间[1.220-4.313])。突变组III级病理分级比例为59.3%,高于非突变组的36.1% (P = 0.001, 95%可信区间[1.436-4.625])。突变组Luminal A 7例(13.0%),Luminal B 0例(Her-2阳性)(0%),三阴性乳腺癌(TNBC) 23例(42.6%)。非突变组Luminal A 93例(26.4%),Luminal B 54例(Her-2阳性)(15.3%),TNBC 67例(19.0%)。Luminal A: P = 0.033, 95%可信区间[0.181 ~ 0.950];Luminal B (Her-2阳性):P = 0.002;结论:深圳地区BRCA突变患者与未突变患者相比,肿瘤体积较小,病理分级以3级为主,分子亚型以三阴性乳腺癌为主。
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