bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self‐assembly of thiourea intercalated graphene oxide based dual IIP for the SPE coupled FAAS method development of Cu(II) and Pb(II) determination
Authors: Islam Aminul , Rais Saman 
Published: February 2024

AbstractA new dual‐template surface imprinted polymer for Cu(II) and Pb(II) was synthesized in one pot. Magnetic graphene oxide was self‐assembled with low cost and environmentally benign thiourea. Presence of sulfur and nitrogen donor atoms provide hooks for coordination and partial reduction of graphene oxide matrix. It was used as an solid‐phase extraction adsorbent for extraction, preconcentration, and coupled with flame atomic absorption spectrometry to manifest performance comparable with inductively coupled plasma atomic emission spectrometry (ICPAES) both in terms of quantification limit as well as interference. The critical experimental parameters such as pH; 4.6, contact time of 15 min and initial concentration of 777 (Qe; 227 mg g−1) and 800 μg L−1 (Qe; 273 mg g−1) for Cu(II) and Pb(II), respectively, were optimized using RSM‐CCD and artificial neural network. The adsorption process was kinetically faster (50% adsorption in 5 min), following fractal‐like‐pseudo‐second‐order (FLPSO) kinetics and Brouers–Sotolongo isotherm model owing to the heterogenous energy landscape. The imprinting factors were in the range of 4–7 in the presence of all coexisting ions. The proposed method was robust in the determination and removal of Cu(II) and Pb(II) from food, ground water, and industry effluents with low limit of detection (Cu(II); 1.03 μg L−1 & Pb(II); 1.79 μgL−1). Spiking and recovery tests were used to assess the method's accuracy. Cu(II)/Pb(II) loaded dual template IIP (DIIP) was utilized to remove anionic dyes with >95% efficiency. Thorough examination of the method and material selectivity (in binary, ternary, and multielement system), multi fold applications of determination, removal of Cu(II), Pb(II), and removal of anionic dyes makes DIIP a promising candidate for environmental remediation.
Marine protection enhances the resilience of biological communities on temperate rocky reefs
Authors: Sanabria‐Fernández José A. , Alday Josu G. 
Published: February 2024

Abstract
Conservation science faces the urgent challenge of halting the biodiversity loss caused by the biological crisis of the present era. To achieve this, conservation science requires cutting‐edge tools to focus on vital properties of ecosystems, such as the resilience. Resilience informs about the cost of recovering biological communities.
Here, we developed a metric to quantify the ecological assemblage recovery cost based on the dissimilarity between unprotected and partially protected communities compared with totally protected communities in Cabo de Gata Marine Reserve.
Our results show that the biological assemblage composed of fish, macroinvertebrates and cryptic fish, and macroalgae species in unprotected zones requires a higher ecological recovery cost than in partially protected zones when moving towards a fully protected community.
This research contributes to monitoring marine the effectiveness of marine protection from a resilience perspective, with the goal of promoting the use of the recovery cost metric for building resilient coastal ecosystems.
CRISPR/Cas system: A revolutionary tool for crop improvement
Authors: Mishra Ayushi , Pandey Veda P. 
Published: February 2024

AbstractWorld's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high‐yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator‐like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time‐consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target‐specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever‐growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.
Identification of critical process parameters for expansion of clinical grade human Wharton's jelly‐derived mesenchymal stromal cells in stirred‐tank bioreactors
Authors: López‐Fernández Alba , Garcia‐Gragera Víctor , Lecina Martí , Vives Joaquim 
Published: February 2024

AbstractCell therapies based on multipotent mesenchymal stromal cells (MSCs) are traditionally produced using 2D culture systems and platelet lysate‐ or serum‐containing media (SCM). Although cost‐effective for single‐dose autologous treatments, this approach is not suitable for larger scale manufacturing (e.g., multiple‐dose autologous or allogeneic therapies with banked MSCs); automated, scalable and Good Manufacturing Practices (GMP)‐compliant platforms are urgently needed. The feasibility of transitioning was evaluated from an established Wharton's jelly MSCs (WJ‐MSCs) 2D production strategy to a new one with stirred‐tank bioreactors (STRs). Experimental conditions included four GMP‐compliant xeno‐ and serum‐free media (XSFM) screened in 2D conditions and two GMP‐grade microcarriers assessed in 0.25 L‐STRs using SCM. From the screening, a XSFM was selected and compared against SCM using the best‐performing microcarrier. It was observed that SCM outperformed the 2D‐selected medium in STRs, reinforcing the importance of 2D‐to‐3D transition studies before translation into clinical production settings. It was also found that attachment efficiency and microcarrier colonization were essential to attain higher fold expansions, and were therefore defined as critical process parameters. Nevertheless, WJ‐MSCs were readily expanded in STRs with both media, preserving critical quality attributes in terms of identity, viability and differentiation potency, and yielding up to 1.47 × 109 cells in a real‐scale 2.4‐L batch.
Engineering and transcriptome study of Saccharomyces cerevisiae to produce ginsenoside compound K by glycerol
Authors: Zhang Chuanbo , Tian Jinping , Zhang Jiale , Liu Ruixia , Zhao Xiaomeng , Lu Wenyu 
Published: February 2024

AbstractSynthetic biology‐based engineering of Saccharomyces cerevisiae to produce terpenoid natural products is an effective strategy for their industrial application. Previously, we observed that glycerol addition was beneficial for ginsenoside compound K (CK) production in a S. cerevisiae when it was fermented using the YPD medium. Here, we reconstructed the CK synthesis and glycerol catabolic pathway in a high‐yield protopanaxadiol (PPD) S. cerevisiae strain. Remarkably, our engineered strain exhibited the ability to utilize glycerol as the sole carbon source, resulting in a significantly enhanced production of 433.1 ± 8.3 mg L−1 of CK, which was 2.4 times higher compared to that obtained in glucose medium. Transcriptomic analysis revealed that the transcript levels of several key genes involved in the mevalonate (MVA) pathway and the uridine diphosphate glucose (UDPG) synthesis pathway were up‐regulated in response to glycerol. The addition of glycerol enhanced CK titers by augmenting the flux of the terpene synthesis pathway and facilitating the production of glycosyl donors. These results suggest that glycerol is a promising carbon source in S. cerevisiae, especially for the production of triterpenoid saponins.
Secretory production and characterization of a highly effective chitosanase from Streptomyces coelicolor A3(2) M145 in Pichia pastoris
Authors: Liang Jiayu , He Shengbin , Sun Jian , Bao Haodong , Cui Lanyu 
Published: February 2024

AbstractIn this study, a glycoside hydrolase family 46 chitosanase from Streptomyces coelicolor A3(2) M145 was firstly cloned and expressed in Pichia pastoris GS115 (P. pastoris GS115). The recombinant enzyme (CsnA) showed maximal activity at pH 6.0 and 65°C. Both thermal stability and pH stability of CsnA expressed in P. pastoris GS115 were significantly increased compared with homologous expression in Streptomyces coelicolor A3(2). A stable chitosanase activity of 725.7 ± 9.58 U mL−1 was obtained in fed‐batch fermentation. It's the highest level of CsnA from Streptomyces coelicolor expressed in P. pastoris so far. The hydrolytic process of CsnA showed a time‐dependent manner. Chitosan oligosaccharides (COSs) generated by CsnA showed antifungal activity against Fusarium oxysporum sp. cucumerinum (F. oxysporum sp. cucumerinum). The secreted expression and hydrolytic performance make the enzyme a desirable biocatalyst for industrial controllable production of chitooligosaccharides with specific degree of polymerization, which have potential to control fungi that cause important crop diseases.
A highly sensitive and specific Homo1‐based real‐time qPCR method for quantification of human umbilical cord mesenchymal stem cells in rats
Authors: He Jing , Wang Zhangfan , Ao Chunchun , Tu Chengshu , Zhang Yaqi , Chang Cheng , Xiao Cuihong , Xiang E , Rao Wei , Li Changyong , Wu Dongcheng 
Published: February 2024

AbstractBackgroundOwing to the characteristics of easier access in vitro, low immunogenicity, and high plasticity, human umbilical cord‐derived mesenchymal stem cells (UC‐MSCs) are considered as a promising cell‐based drugs for clinical application. No internationally recognized technology exists to evaluate the pharmacokinetics and distribution of cell‐based drugs in vivo.MethodsWe determined the human‐specific gene sequence, Homo1, from differential fragments Homo sapiens mitochondrion and Rattus norvegicus mitochondrion. The expression of Homo1 was utilized to determine the distribution of UC‐MSCs in the normal and diabetic nephropathy (DN) rats.ResultsWe observed a significant correlation between the number of UC‐MSCs and the expression level of Homo1. Following intravenous transplantation, the blood levels of UC‐MSCs peaked at 30 min. A large amount of intravenously injected MSCs were trapped in the lungs, but the number of them decreased rapidly after 24 h. Additionally, the distribution of UC‐MSCs in the kidneys of DN rats was significantly higher than that of normal rats.ConclusionsIn this study, we establish a highly sensitive and specific Homo1‐based real‐time quantitative PCR method to quantify the distribution of human UC‐MSCs in rats. The method provides guidelines for the safety research of cells in preclinical stages.
In vitro evolution of diagnostic antibodies targeting native antigens in plasma by sandwich flow cytometry
Authors: Liang Mingxia , Ran Fanlei , Li Li , Hang Haiying , An Lili 
Published: February 2024

AbstractMonoclonal antibodies (mAbs) that recognize and bind to specific antigens (Ags) have a wide range of applications in research, therapy, and diagnostics. However, many of these antibodies cannot bind well to the native Ags. In this study, based on the Chinese hamster ovary (CHO) cell display platform developed previously in our lab, we reported a novel artificial evolution procedure to improve the affinity of mAb against the native Ag directly using the plasma samples without purification of the native Ag. In this procedure, a pair of antibodies able to bind the Ag in sandwich manner are first confirmed (Ab1/Ab2) and the antibody (Ab) to be affinity‐improved (Ab1) is displayed on CHO cells for Ab mutation. Then the cells were detected and sorted with flow cytometry in the form of Ab1‐Ag‐fluorescence labeled Ab2, which we named sandwich flow cytometry. Here, we used soluble isoform of suppression of tumorigenicity 2 (sST2) protein as model Ag, carried out “sandwich” maturation directly using the plasma samples containing the native sST2 protein and optimized a pair of antibodies with significantly improved sensitivity in the detection of the native sST2 in plasma. This method could be very useful in optimization of the diagnostic Ab pairs working in a “sandwich” manner if more antibodies were also successfully affinity‐matured with this method.
Exploring metabolic responses and pathway changes in CHO‐K1 cells under varied aeration conditions and copper supplementations using 1H NMR‐based metabolomics
Authors: Shi Yingting , Wan Yuxiang , Sun Yan , Yang Jiayu , Lu Yuting , Xie Xinyuan , Pan Jianyang , Wang Haibin , Qu Haibin 
Published: February 2024

AbstractThe optimization of bioprocess for CHO cell culture involves careful consideration of factors such as nutrient consumption, metabolic byproduct accumulation, cell growth, and monoclonal antibody (mAb) production. Valuable insights can be obtained by understanding cellular physiology to ensure robust and efficient bioprocess. This study aims to improve our understanding of the CHO‐K1 cell metabolism using 1H NMR‐based metabolomics. Initially, the variations in culture performance and metabolic profiles under varied aeration conditions and copper supplementations were thoroughly examined. Furthermore, a comprehensive metabolic pathway analysis was performed to assess the impact of these conditions on the implicated pathways. The results revealed substantial alterations in the pyruvate metabolism, histidine metabolism, as well as phenylalanine, tyrosine and tryptophan biosynthesis, which were especially evident in cultures subjected to copper deficiency conditions. Conclusively, significant metabolites governing cell growth and mAb titer were identified through orthogonal partial least square‐discriminant analysis (OPLS‐DA). Metabolites, including glycerol, alanine, formate, glutamate, phenylalanine, and valine, exhibited strong associations with distinct cell growth phases. Additionally, glycerol, acetate, lactate, formate, glycine, histidine, and aspartate emerged as metabolites influencing cell productivity. This study demonstrates the potential of employing 1H NMR‐based metabolomics technology in bioprocess research. It provides valuable guidance for feed medium development, feeding strategy design, bioprocess parameter adjustments, and ultimately the enhancement of cell proliferation and mAb yield.
Pipette‐free field‐deployable molecular diagnostic kit for bimodal visual detection of infectious RNA viruses
Authors: Park So Yeon , Trinh Kieu The Loan , Song Yoon‐Jae , Lee Nae Yoon 
Published: February 2024

AbstractHere, we developed a field‐deployable molecular diagnostic kit for the detection of RNA viruses that operates in a pipette‐free manner. The kit is composed of acrylic sticks, PCR tubes, and palm‐sized three‐dimensional(3D)‐printed heaters operated by batteries. The kit performs RNA extraction, reverse transcriptase loop‐mediated isothermal amplification (RT‐LAMP), and visual detection in one kit. An acrylic stick was engraved with one shallow and one deep cylindrical chamber at each end for the insertion of an FTA card and ethidium homodimer‐1 (EthD‐1), respectively, to perform RNA extraction/purification and bimodal visual detection of the target amplicons. First, an intercalation of EthD‐1 into the target DNA initially produces fluorescence upon UV illumination. Next, the addition of a strong oxidant, in this case sodium (meta) periodate (NaIO4), produces intense aggregates in the presence of EthD‐1‐intercalated DNA, realized by electrostatic interaction. In the absence of the target amplicon, no fluorescence or aggregates are observed. Using this kit, two major infectious viruses—severe fever with thrombocytopenia syndrome virus (SFTSV) and severe acute respiratory syndrome coronavirus (SARS‐CoV‐2)—were successfully detected in 1 h, and the limits of detection (LOD) were approximately 1 virus μL−1 for SFTSV and 103 copies μL−1 for SARS‐CoV‐2 RNA. The introduced kit is portable, end‐user‐friendly, and can be operated in a pipette‐free manner, paving the way for simple and convenient virus detection in resource‐limited settings.
Initial cyclic‐di‐GMP upregulation triggers sporadic cellular expansion leading to improved cellular survival
Authors: Yang Yongshuai , Guo Siyu , Hong Can‐Jian , Liang Zhao‐Xun , Ho Chun Loong 
Published: February 2024

AbstractBacterial second messenger c‐di‐GMP upregulation is associated with the transition from planktonic to sessile microbial lifestyle, inhibiting cellular motility, and virulence. However, in‐depth elucidation of the cellular processes resulting from c‐di‐GMP upregulation has not been fully explored. Here, we report the role of upregulated cellular c‐di‐GMP in promoting planktonic cell growth of Escherichia coli K12 and Pseudomonas aeruginosa PAO1. We found a rapid expansion of cellular growth during initial cellular c‐di‐GMP upregulation, resulting in a larger planktonic bacterial population. The initial increase in c‐di‐GMP levels promotes bacterial swarming motility during the growth phase, which is subsequently inhibited by the continuous increase of c‐di‐GMP, and ultimately facilitates the formation of biofilms. We demonstrated that c‐di‐GMP upregulation triggers key bacterial genes linked to bacterial growth, swarming motility, and biofilm formation. These genes are mainly controlled by the master regulatory genes csgD and csrA. This study provides us a glimpse of the bacterial behavior of evading potential threats through adapting lifestyle changes via c‐di‐GMP regulation.
Synergistic application of atmospheric and room temperature plasma mutagenesis and adaptive laboratory evolution improves the tolerance of Escherichia coli to L‐cysteine
Authors: Yang Hui , Zhang Bo , Wu Zidan , Pan Jiayuan , Chen Lifeng , Xiu Xiaoling , Cai Xue , Liu Zhiqiang , Zheng Yuguo 
Published: February 2024

AbstractL‐Cysteine production through fermentation stands as a promising technology. However, excessive accumulation of L‐cysteine poses a challenge due to the potential to inflict damage on cellular DNA. In this study, we employed a synergistic approach encompassing atmospheric and room temperature plasma mutagenesis (ARTP) and adaptive laboratory evolution (ALE) to improve L‐cysteine tolerance in Escherichia coli. ARTP‐treated populations obtained substantial enhancement in L‐cysteine tolerance by ALE. Whole‐genome sequencing, transcription analysis, and reverse engineering, revealed the pivotal role of an effective export mechanism mediated by gene eamB in augmenting L‐cysteine resistance. The isolated tolerant strain, 60AP03/pTrc‐cysEf, achieved a 2.2‐fold increase in L‐cysteine titer by overexpressing the critical gene cysEf during batch fermentation, underscoring its enormous potential for L‐cysteine production. The production evaluations, supplemented with L‐serine, further demonstrated the stability and superiority of tolerant strains in L‐cysteine production. Overall, our work highlighted the substantial impact of the combined ARTP and ALE strategy in increasing the tolerance of E. coli to L‐cysteine, providing valuable insights into improving L‐cysteine overproduction, and further emphasized the potential of biotechnology in industrial production.
NAT10‐mediated ac4C‐modified ANKZF1 promotes tumor progression and lymphangiogenesis in clear‐cell renal cell carcinoma by attenuating YWHAE‐driven cytoplasmic retention of YAP1
Authors: Miao Daojia , Shi Jian , Lv Qingyang , Tan Diaoyi , Zhao Chuanyi , Xiong Zhiyong , Zhang Xiaoping 
Published: February 2024

AbstractBackgroundLymphatic metastasis is one of the most common metastatic routes and indicates a poor prognosis in clear‐cell renal cell carcinoma (ccRCC). N‐acetyltransferase 10 (NAT10) is known to catalyze N4‐acetylcytidine (ac4C) modification of mRNA and participate in many cellular processes. However, its role in the lymphangiogenic process of ccRCC has not been reported. This study aimed to elucidate the role of NAT10 in ccRCC lymphangiogenesis, providing valuable insights into potential therapeutic targets for intervention.Methodsac4C modification and NAT10 expression levels in ccRCC were assessed using public databases and clinical samples. Functional investigations involved manipulating NAT10 expression in cellular and mouse models to study its role in ccRCC. Mechanistic insights were gained through a combination of RNA sequencing, mass spectrometry, co‐immunoprecipitation, RNA immunoprecipitation, immunofluorescence, and site‐specific mutation analyses.ResultsWe found that ac4C modification and NAT10 expression levels increased in ccRCC. NAT10 promoted tumor progression and lymphangiogenesis of ccRCC by enhancing the nuclear import of Yes1‐associated transcriptional regulator (YAP1). Subsequently, we identified ankyrin repeat and zinc finger peptidyl tRNA hydrolase 1 (ANKZF1) as the functional target of NAT10, and its upregulation in ccRCC was caused by NAT10‐mediated ac4C modification. Mechanistic analyses demonstrated that ANKZF1 interacted with tyrosine 3‐monooxygenase/tryptophan 5‐monooxygenase activation protein epsilon (YWHAE) to competitively inhibit cytoplasmic retention of YAP1, leading to transcriptional activation of pro‐lymphangiogenic factors.ConclusionsThese results suggested a pro‐cancer role of NAT10‐mediated acetylation in ccRCC and identified the NAT10/ANKZF1/YAP1 axis as an under‐reported pathway involving tumor progression and lymphangiogenesis in ccRCC.
Maxillary first molar with two distobuccal root canals and cervical deformity: A case report
Authors: Cai Xue , Tang Rentao 
Published: February 2024

Key Clinical MessageThe second distobuccal canal in the maxillary first molar is often missed because of the low prevalence rate (0%–4%). The article reports this kind of variation in one case. Promising outcomes have continued up to the present (2‐year follow‐up).
Distinct distribution of subplate neuron subtypes between the sensory cortices during the early postnatal period
Authors: Chang Minzi , Nehs Sophia , Xu Zheng , Kanold Patrick O 
Published: February 2024

AbstractSubplate neurons (SpNs) are a heterogeneous neuronal population actively involved in early cortical circuit formation. In rodents, many SpNs survive and form layer 6b. The molecular heterogeneity of SpNs raises the question of whether different subpopulations of SpNs survive through the early postnatal period similarly and whether such diverse SpN populations in the auditory cortex (ACtx) share a common distribution pattern with other sensory systems. To address that, we investigated the expression pattern of multiple specific SpN markers in the ACtx, as well as in the visual (VCtx) and somatosensory (SCtx) cortices as controls, using complexin 3 (Cplx3) antibodies and different SpN‐specific Cre‐driver mice, such as connective tissue growth factor (CTGF), dopamine receptor D1 (Drd1a), and neurexophilin 4 (Nxph4). We focused on two early time windows in auditory development: (1) during the second postnatal week (PNW) before ear‐canal opening and (2) during the third PNW after ear‐canal opening. We compared the expression pattern of different SpN markers in ACtx with VCtx and SCtx. At both examined timepoints, Cplx3 and Nxph4 expressing SpNs form the largest and smallest population in the ACtx, respectively. Similar distribution patterns are observable in the VCtx and SCtx during the second PNW but not during the third PNW, for a higher proportion of Drd1a expressing SpNs is detected in the VCtx and CTGF expressing SpNs in the SCtx. This study suggests that different populations of SpNs might contribute differently to the development of individual sensory circuits.