bluuebunny/crossref_metadata_2025 huggingface dataset:
Proliferation and Differentiation Potential of Bone Marrow–Derived Mesenchymal Stem Cells From Children With Polydactyly and Adults With Basal Joint Arthritis
Authors: Yeh Shih-Han , Yu Jin-Huei , Chou Po-Hsin , Wu Szu-Hsien , Liao Yu-Ting , Huang Yi-Chao , Chen Tung-Ming , Wang Jung-Pan
Published: January 2024

This study compared the proliferation and differentiation potential of bone marrow–derived mesenchymal stem cells (BMSCs) derived from infants with polydactyly and adults with basal joint arthritis. The proliferation rate of adult and infant BMSCs was determined by the cell number changes and doubling times. The γH2AX immunofluorescence staining, age-related gene expression, senescence-associated β-galactosidase (SA-β-gal) staining were analyzed to determine the senescence state of adult and infant BMSCs. The expression levels of superoxide dismutases (SODs) and genes associated with various types of differentiation were measured using Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR). Differentiation levels were evaluated through histochemical and immunohistochemical staining. The results showed that infant BMSCs had a significantly higher increase in cell numbers and faster doubling times compared with adult BMSCs. Infant BMSCs at late stages exhibited reduced γH2AX expression and SA-β-gal staining, indicating lower levels of senescence. The expression levels of senescence-related genes ( p16, p21, and p53) in infant BMSCs were also lower than in adult BMSCs. In addition, infant BMSCs demonstrated higher antioxidative ability with elevated expression of SOD1, SOD2, and SOD3 compared with adult BMSCs. In terms of differentiation potential, infant BMSCs outperformed adult BMSCs in chondrogenesis, as indicated by higher expression levels of chondrogenic genes ( SOX9, COL2, and COL10) and positive immunohistochemical staining. Moreover, differentiated cells derived from infant BMSCs exhibited significantly higher expression levels of osteogenic, tenogenic, hepatogenic, and neurogenic genes compared with those derived from adult BMSCs. Histochemical and immunofluorescence staining confirmed these findings. However, adult BMSCs showed lower adipogenic differentiation potential compared with infant BMSCs. Overall, infant BMSCs demonstrated superior characteristics, including higher proliferation rates, enhanced antioxidative activity, and greater differentiation potential into various lineages. They also exhibited reduced cellular senescence. These findings, within the context of cellular differentiation, suggest potential implications for the use of allogeneic BMSC transplantation, emphasizing the need for further in vivo investigation.
Geopolitical Issues and Trajectories of Water Security in South Asia
Authors: Fernando H. N.
Published: January 2024

In the current academic debate on non-traditional security, the issue of water security has come to the forefront of discussions. This is primarily due to the developing discourse on climate change as a threat multiplier linked with conflicts surrounding access, use, and the management of shared water resources. The Indian subcontinent is therefore an interesting case study where water security and inter-connected security issues have converged as both internal and external security threats. Using the case study of the Indian Subcontinent, this essay serves to enrich the debate on geopolitical challenges and the paths toward achieving water security. The essay provides a general review of the security environment, including the risks and vulnerabilities facing the Indian subcontinent and challenges to water governance arising from both internal and external security concerns, through examples of geopolitical tensions in the region. This includes India, Pakistan, Bangladesh, Afghanistan, Nepal, China, and Tibet (the latter which forms the Hindu Kush Himalaya region). The research leads to the conclusion that institutional structures may be able to reduce regional tensions.
Clozapine-related tachycardia: A conundrum to identify and treat
Authors: Brennan Dermot , Lal Sweta , Hugo Frans , Waters Flavie , Shymko Gordon
Published: January 2024

Objective

This study examined the rates and persistence of clozapine-induced tachycardia and heart-rate differences in patients treated with β-blockers in the largest sample of patients with a psychotic disorder to date.

Method

An audit of medical files for 101 patients who attended a clozapine community clinic and analysis of monthly measurements of resting heart rates.

Results

51% met the clinical criteria for tachycardia. Heart rates were stable over time. β-blockers were associated with small but significant reductions in heart rates.

Conclusion

The cardiovascular risks of clozapine are often overlooked. β-blockers are useful in lowering heart rates but they may be insufficient to reduce cardiac risk.
Salivary Diurnal Cortisol Predicts Post−Traumatic Stress Symptoms in Parents of Infants With Congenital Heart Disease
Authors: Lisanti Amy Jo , Dong Fanghong , Demianczyk Abigail , Vogiatzi Maria G. , Quinn Ryan , Chittams Jesse , Hoffman Rebecca , Medoff−Cooper Barbara
Published: January 2024

Background

Parents of infants born with congenital heart disease (CHD) who require open heart surgery after birth are at risk for prolonged psychological distress. Even after their infants are discharged, parents may experience anxiety, depressive, and post−traumatic stress (PTS) symptoms; yet, it is unclear which parents are at greater risk for ongoing symptoms. The purpose of this study was to explore whether measures of the biomarker cortisol in parents during their infants’ postoperative period were associated with subsequent psychological distress symptoms at three−month post discharge.

Methods

This was a prospective, longitudinal exploratory study of 40 parents of infants with CHD after open heart surgery using consecutive enrollment. Parents provided diurnal saliva samples for two consecutive days in the postoperative period. Six predictors were summarized and generated including waking cortisol, bedtime cortisol, cortisol awaking response, area under curve with respect to the ground (AUCg), cortisol index, and cortisol slope. Self−report outcome measures on anxiety, depressive, and PTS symptoms were collected three−months post−discharge. Linear mixed models examined the associations between each predictor and each outcome while accounting for within−dyad variance using an unstructured covariance matrix.

Results

Cortisol AUCg was a predictor of PTS at three−months post−discharge ( β = .34, p = .03, Cohen’s d = 2.05). No significant relationships were found with the other cortisol measures.

Conclusions & Implications

Findings suggest that cortisol area under curve may help to identify parents at risk for increased PTS in the months following their infants’ hospitalization for cardiac surgery, serving as a foundation for future study in this area.
NPS spillover in brand extensions: An empirical study
Authors: Cho Jihoon , Walker Doug , Nowlin Edward L.
Published: January 2024

This research proposes an empirical framework to help firms understand to what degree the transaction-specific Net Promoter Scores (NPS) spill over and affect customer spending across multiple product categories under the same parent brand. The proposed framework is applied to novel individual-level, cross-sectional, and time-series NPS ratings matched with transaction details from a leading lifestyle conglomerate in the Middle East. Findings provide strong support for the presence of the NPS spillover in brand extensions and show that the spillover is moderated by customer learning both within and across categories. The theoretical and managerial implications of these findings are discussed.
Comparison of Strengths of Mandibular Angle Fractures Following Different Plate Designs: A Human Cadaver Study
Authors: Squier Brendan R. , Kongsong Wichuda , Cofield Stacey S. , Bignault Samuel , Sittitavornwong Somsak
Published: January 2024

Study Design

This institutional cross-sectional study using cadaveric mandibles aimed to measure and compare the strengths of three plating designs utilized in osteosynthesis of mandibular angle fractures.

Objective

There have been prior studies on angle fracture fixation though few biomechanical studies on human cadaveric specimen. This study aims to directly compare the biomechanical strength of different plating designs to the mandibular angle fracture using a human cadaveric specimen substrate.

Methods

After receiving an angle osteotomy and either single plate, two plate, or 3D plate fixation, the specimens underwent biomechanical testing using the Instron 5565 mechanical testing unit. The primary outcomes measured were peak load at which permanent deformation started, displacement value at peak load, and load necessary for a specific amount of displacement at 1, 3, 5, and 7 mm.

Results

There were 15 hemi-mandibles in each group. Based on data analysis of all the specimens, there were no significant differences in the mandibular height, ramus width, mandibular thickness, angle height, and gonial angle between the hemimandibles.. This study demonstrated a statistically significant increased strength performance of the 3D plate over the single plate fixation and the 2-plate over the single plate fixation. The results between 2-plate and 3D plate were in similar values.

Conclusions

In terms of biomechanical strength, the 3D plate and two plate designs outperform the single plate design to mandibular angle fractures. There are various anatomical and patient specific situations that can aid in selection between them. In the absence of the favorable angle fracture and patient, biomechanical strength to the method of fixation selection needs to be considered.
Urban state venturism: On state-led venture capital investments in the urban process of capital accumulation
Authors: Su Xiaobo , Lim Kean Fan
Published: January 2024

Research on the urban process of capital accumulation has typically examined the state and capital as separate actors. This distinction is problematized by a long-standing, increasingly prominent but largely overlooked attempt by state institutions to drive urban development through venture capital (VC) investments. Conceptualized as urban state venturism in this paper, state-driven VC investments reflect at once a riskier extension of urban entrepreneurialism (through their speculative construction of place) and a transposition of state institutions into firm-level drivers of capitalist urbanization (through their roles as profit-oriented investors). To advance research on the urban process of capital accumulation through examining these imbricated state roles, this paper presents a new research agenda that comprises three dimensions, namely (i) the rationale of urban state venturism, (ii) the distribution of profits and risks, and (iii) the extent to which urban state venturism reflects state institutions’ intrinsic commitment to a ‘developmentalist’ ideology. In turn, the agenda foregrounds the value of assessing ‘new’ state capitalism through urban state venturism.
Transesophageal Echocardiography Utilization to Visualize Thrombi in the Pulmonary Vein Stump, Post Lung Lobectomy
Authors: Kobayashi Yuya , Kondo Yasufumi , Yamamoto Kanji , Sekijima Yoshiki
Published: January 2024

Lung lobectomy can cause a cerebral infarction due to thrombus formation in the pulmonary vein (PV). While contrast-enhanced computed tomography (CT) has commonly been used to detect thrombi, the utility of transesophageal echocardiography (TEE) for thrombus visualization, in the PV stump, is less known. Herein, a series of cases are provided, in which TEE was able to detect a thrombus in the PV stump, as an embolic source of a cerebral infarction. Transesophageal echocardiography is a powerful imaging technique for evaluating thrombi mobility and properties, which are impossible with enhanced CT. Thus, TEE can contribute to identifying the cause of stroke when the embolic source is unknown.
Study of changes in the aging process, microstructure, and mechanical properties of AA2024–AA1050 nanocomposites created by the accumulative roll bonding process, with the addition of 0.005 vol.% of alumina nanoparticles
Authors: Roghani Hamed , Borhani Ehsan , Ahmadi Ehsan , Jafarian Hamid Reza
Published: January 2024

We created AA2024–AA1050 and AA2024–AA1050/0.005 vol.% Al2O3 nanocomposites by six accumulative roll bonding (ARB) process cycles. We used AA2024 and AA1050 sheets with a thickness of 0.7 mm and plate-shaped alumina nanoparticles to create a composite. The two AA1050 and one AA2024 sheets (among the two AA1050 sheets) were ARB-ed up to six cycles with and without adding alumina nanoparticles. Also, a sample of the AA1050 without composite making was ARB-ed up to six cycles. We aged some composites after the ARB process in the furnace at 110, 150, and 190 °C. This project performed SEM, TEM, and EDS-MAP analyses, tensile strength, microhardness, and Pin-on-Disc tests to study the ARB-ed sheets. The results of the tensile tests showed that the tensile strength of AA2024–AA1050 created by the six cycles ARB process was two times more than primary AA1050. Also, the wear resistance of this composite was 74% more than six cycles ARB-ed the AA1050. Using 0.005 vol.% alumina nanoparticles in AA2024–AA1050 composite improved its wear resistance by 30%. In the following, the aging process caused an improvement in tensile strength and total elongation of AA2024–AA1050/Al2O3 nanocomposites.
Phenotype transition from wild mouflon to domestic sheep
Authors: Mereu Paolo , Pirastru Monica , Sanna Daria , Bassu Giovanni , Naitana Salvatore , Leoni Giovanni Giuseppe
Published: January 2024

The domestication of animals started around 12,000 years ago in the Near East region. This “endless process” is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today’s domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.
Graph embedding on mass spectrometry- and sequencing-based biomedical data
Authors: Alvarez-Mamani Edwin , Dechant Reinhard , Beltran-Castañón César A. , Ibáñez Alfredo J.
Published: January 2024

Graph embedding techniques are using deep learning algorithms in data analysis to solve problems of such as node classification, link prediction, community detection, and visualization. Although typically used in the context of guessing friendships in social media, several applications for graph embedding techniques in biomedical data analysis have emerged. While these approaches remain computationally demanding, several developments over the last years facilitate their application to study biomedical data and thus may help advance biological discoveries. Therefore, in this review, we discuss the principles of graph embedding techniques and explore the usefulness for understanding biological network data derived from mass spectrometry and sequencing experiments, the current workhorses of systems biology studies. In particular, we focus on recent examples for characterizing protein–protein interaction networks and predicting novel drug functions.
Prognostic value of oxidative stress-related genes in colorectal cancer and its correlation with tumor immunity
Authors: Yang Leilei , Fang Chengfeng , Zhang Ruili , Zhou Shenkang
Published: January 2024

Oxidative stress (OS) plays an essential role in chronic diseases such as colorectal cancer (CRC). In this study, we aimed to explore the relation between oxidative stress-related genes and CRC prognosis and their involvement in the immune microenvironment. Totally 101 OS-related genes were selected from the MsigDB database. Then, univariate Cox regression was used to explore the prognostic value of the selected genes correlated with the CRC patient survival in the TCGA database. A total of 9 prognostic OS-related genes in CRC were identified. Based on consensus clustering, CRC patients were then categorized into two molecular subtypes. A prognostic risk model containing 8 genes was established using Lasso regression, and CRC patients were divided into high or low-risk groups based on the median risk scores. The predictive value of the 8 genes in CRC prognosis was validated using ROC curves, which indicate that CTNNB1, STK25, RNF112, SFPQ, MMP3, and NOL3 were promising prognostic biomarkers in CRC. Furthermore, the immune cell infiltration levels in different risk groups or CRC subtypes were analyzed. We found that the high-risk or C1 subtype had immunosuppressive microenvironment, which might explain the unfavorable prognosis in the two groups of CRC patients. Additionally, functional experiments were conducted to investigate the effects of OS-related genes on CRC cell proliferation, stemness, and apoptosis. We found that CTNNB1, HSPB1, MMP3, and NOL3 were upregulated in CRC tissues and cells. Knockdown of CTNNB1, HSPB1, MMP3, and NOL3 significantly suppressed CRC cell proliferation, stemness and facilitated CRC cell apoptosis. In conclusion, we established prognostic CRC subtypes and an eight-gene risk model, which may provide novel prognostic indicators and benefit the design of individualized therapeutic strategies for CRC patients.
Ribosomal profiling of human endogenous retroviruses in healthy tissues
Authors: Dopkins Nicholas , Singh Bhavya , Michael Stephanie , Zhang Panpan , Marston Jez L. , Fei Tongyi , Singh Manvendra , Feschotte Cedric , Collins Nicholas , Bendall Matthew L. , Nixon Douglas F.
Published: January 2024

Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline “hervQuant” to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1–0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.
Genome-wide association study for stalk lodging resistance related traits in maize (Zea mays L.)
Authors: Wang Bangtai , Yang Meili , Guo Hua , Wang Jing , Wang Zhihong , Lu Hongwei , Qin Guiwen , Chen Jiafa
Published: January 2024

Background

The stalk traits stalk diameter, stalk length, rind penetrometer resistance and dry matter content are important indicators for measuring lodging resistance.

Results

In this study, 377 inbred lines were used as the basic materials, and four stalk-related traits including stalk diameter, stalk length, rind penetrometer resistance and dry matter content of the third segment of maize, were investigated at the tasseling, grain filling, and maturity stages. 461,053 high-quality SNPs which were obtained by whole genome resequencing were used for genome-wide association study. As a result of mixed linear model analysis (P < 9.77 × 10–6), 29 significant SNPs related to traits were detected, accounting for 7.19% -15.03% of phenotypic variation, among which 4, 1, 4 and 20 SNPs were found related to rind penetrometer resistance, stalk diameter, stalk length, and dry matter content respectively. Most candidate genes are related to plant element structure, signal transduction mechanisms, inorganic ion transport and metabolism, nucleotide transport and metabolism, and transporter enzyme families. Comparing mixed linear model with generalized linear model, a total of 12 candidate genes were detected repeatedly, during which the candidate gene Zm00001d014449 were detected 5 times, with a phenotypic variation interpretation rate of 9.95% -10.84%. This gene is mainly expressed in cells with active cell division and tissue differentiation, and is involved in the formation of stalk vascular bundles and the synthesis of cell walls. Another candidate gene, Zm00001d005300, encodes the transcription factor MYB44, which regulates the dependence of salt stress signal phosphorylation, can effectively inhibit the accumulation of destructive reactive oxygen species, and has a certain resistance to non-biotic stress. In addition, this study also found that 10 unknown functional genes can be further Functional verification.

Conclusions

This study helps to deepen the understanding of the genetic basis of traits related to maize stalk lodging resistance, and provides theoretical guidance for future maize lodging resistance breeding.
Molecular identification and functional characterization of a transcription factor GeRAV1 from Gelsemium elegans
Authors: Cui Tianzhen , Zang Shoujian , Sun Xinlu , Zhang Jing , Su Yachun , Wang Dongjiao , Wu Guran , Chen Ruiqi , Que Youxiong , Lin Qing , You Chuihuai
Published: January 2024

Background

Gelsemium elegans is a traditional Chinese medicinal plant and temperature is one of the key factors affecting its growth. RAV (related to ABI3/VP1) transcription factor plays multiple roles in higher plants, including the regulation of plant growth, development, and stress response. However, RAV transcription factor in G. elegans has not been reported.

Results

In this study, three novel GeRAV genes (GeRAV1-GeRAV3) were identified from the transcriptome of G. elegans under low temperature stress. Phylogenetic analysis showed that GeRAV1-GeRAV3 proteins were clustered into groups II, IV, and V, respectively. RNA-sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) analyses indicated that the expression of GeRAV1 and GeRAV2 was increased in response to cold stress. Furthermore, the GeRAV1 gene was successfully cloned from G. elegans leaf. It encoded a hydrophilic, unstable, and non-secretory protein that contained both AP2 and B3 domains. The amino acid sequence of GeRAV1 protein shared a high similarity of 81.97% with Camptotheca acuminata CaRAV. Subcellular localization and transcriptional self-activation experiments demonstrated that GeRAV1 was a nucleoprotein without self-activating activity. The GeRAV1 gene was constitutively expressed in the leaves, stems, and roots of the G. elegans, with the highest expression levels in roots. In addition, the expression of the GeRAV1 gene was rapidly up-regulated under abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA) stresses, suggesting that it may be involved in hormonal signaling pathways. Moreover, GeRAV1 conferred improved cold and sodium chloride tolerance in Escherichia coli Rosetta cells.

Conclusions

These findings provided a foundation for further understanding on the function and regulatory mechanism of the GeRAV1 gene in response to low-temperature stress in G. elegans.
Functional annotation of a divergent genome using sequence and structure-based similarity
Authors: Svedberg Dennis , Winiger Rahel R. , Berg Alexandra , Sharma Himanshu , Tellgren-Roth Christian , Debrunner-Vossbrinck Bettina A. , Vossbrinck Charles R. , Barandun Jonas
Published: January 2024

Background

Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes.

Results

In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome ofVairimorpha necatrix.First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of theV. necatrixgenome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterizedEncephalitozoon cuniculigenes.

Conclusion

We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
Genome-wide investigation of the TGF-β superfamily in scallops
Authors: Zhang Qian , Chen Jianming , Wang Wei , Lin Jingyu , Guo Jiabao
Published: January 2024

Background

Transforming growth factor β (TGF-β) superfamily genes can regulate various processes, especially in embryogenesis, adult development, and homeostasis. To understand the evolution and divergence patterns of the TGF-β superfamily in scallops, genome-wide data from the Bay scallop (Argopecten irradians), the Zhikong scallop (Chlamys farreri) and the Yesso scallop (Mizuhopecten yessoensis) were systematically analysed using bioinformatics methods.

Results

Twelve members of the TGF-β superfamily were identified for each scallop. The phylogenetic tree showed that these genes were grouped into 11 clusters, including BMPs, ADMP, NODAL, GDF, activin/inhibin and AMH. The number of exons and the conserved motif showed some differences between different clusters, while genes in the same cluster exhibited high similarity. Selective pressure analysis revealed that the TGF-β superfamily in scallops was evolutionarily conserved. The spatiotemporal expression profiles suggested that different TGF-β members have distinct functions. Several BMP-like and NODAL-like genes were highly expressed in early developmental stages, patterning the embryonic body plan. GDF8/11-like genes showed high expression in striated muscle and smooth muscle, suggesting that these genes may play a critical role in regulating muscle growth. Further analysis revealed a possible duplication of AMH, which played a key role in gonadal growth/maturation in scallops. In addition, this study found that several genes were involved in heat and hypoxia stress in scallops, providing new insights into the function of the TGF-β superfamily.

Conclusion

Characteristics of the TGF-β superfamily in scallops were identified, including sequence structure, phylogenetic relationships, and selection pressure. The expression profiles of these genes in different tissues, at different developmental stages and under different stresses were investigated. Generally, the current study lays a foundation for further study of their pleiotropic biological functions in scallops.
Sex differences in response to obesity and caloric restriction on cognition and hippocampal measures of autophagic-lysosomal transcripts and signaling pathways
Authors: Baer Sadie B. , Dorn Adrianah D. , Osborne Danielle M.
Published: January 2024

Background

Obesity rates in the U.S. continue to increase, with nearly 50% of the population being either obese or morbidly obese. Obesity, along with female sex, are leading risk factors for sporadic Alzheimer’s Disease (AD) necessitating the need to better understand how these variables impact cellular function independent of age or genetic mutations. Animal and clinical studies both indicate that autophagy-lysosomal pathway (ALP) dysfunction is among the earliest known cellular systems to become perturbed in AD, preceding cognitive decline, yet little is known about how obesity and sex affects these cellular functions in the hippocampus, a brain region uniquely susceptible to the negative effects of obesity. We hypothesized that obesity would negatively affect key markers of ALP in the hippocampus, effects would vary based on sex, and that caloric restriction would counteract obesity effects.

Methods

Female and male mice were placed on an obesogenic diet for 10 months, at which point half were switched to caloric restriction for three months, followed by cognitive testing in the Morris watermaze. Hippocampus was analyzed by western blot and qPCR.

Results

Cognitive function in female mice responded differently to caloric restriction based on whether they were on a normal or obesogenic diet; male cognition was only mildly affected by caloric restriction and not obesity. Significant male-specific changes occurred in cellular markers of autophagy, including obesity increasing pAkt, Slc38a9, and Atg12, while caloric restriction reduced pRPS6 and increased Atg7. In contrast females experienced changes due to diet/caloric restriction predominately in lysosomal markers including increased TFE3, FLCN, FNIP2, and pAMPK.

Conclusions

Results support that hippocampal ALP is a target of obesity and that sex shapes molecular responses, while providing insight into how dietary manipulations affect learning and memory based on sex.
Graph neural network and machine learning analysis of functional neuroimaging for understanding schizophrenia
Authors: Sunil Gayathri , Gowtham Smruthi , Bose Anurita , Harish Samhitha , Srinivasa Gowri
Published: January 2024

Background

Graph representational learning can detect topological patterns by leveraging both the network structure as well as nodal features. The basis of our exploration involves the application of graph neural network architectures and machine learning to resting-state functional Magnetic Resonance Imaging (rs-fMRI) data for the purpose of detecting schizophrenia. Our study uses single-site data to avoid the shortcomings in generalizability of neuroimaging data obtained from multiple sites.

Results

The performance of our graph neural network models is on par with that of our machine learning models, each of which is trained using 69 graph-theoretical measures computed from functional correlations between various regions of interest (ROI) in a brain graph. Our deep graph convolutional neural network (DGCNN) demonstrates a promising average accuracy score of 0.82 and a sensitivity score of 0.84.

Conclusions

This study provides insights into the role of advanced graph theoretical methods and machine learning on fMRI data to detect schizophrenia by harnessing changes in brain functional connectivity. The results of this study demonstrate the capabilities of using both traditional ML techniques as well as graph neural network-based methods to detect schizophrenia using features extracted from fMRI data. The study also proposes two methods to obtain potential biomarkers for the disease, many of which are corroborated by research in this area and can further help in the understanding of schizophrenia as a mental disorder.
PatWRKY71 transcription factor regulates patchoulol biosynthesis and plant defense response
Authors: Li Jian , Huang Huan-Chao , Zuo Yue-Qiu , Zhang Ming-Yong , He Meng-Ling , Xia Kuai-Fei
Published: January 2024

Patchoulol, a valuable compound belonging to the sesquiterpenoid family, is the primary component of patchouli oil produced by Pogostemon cablin (P. cablin). It has a variety of pharmacological and biological activities and is widely used in the medical and cosmetic industries. However, despite its significance, there is a lack of research on the transcriptional modulation of patchoulol biosynthesis.

Salicylic acid (SA), is a vital plant hormone that serves as a critical signal molecule and plays an essential role in plant growth and defense. However, to date, no studies have explored the modulation of patchoulol biosynthesis by SA. In our study, we discovered that the application of SA can enhance the production of patchoulol. Utilizing transcriptome analysis of SA-treated P. cablin, we identified a crucial downstream transcription factor, PatWRKY71. The transcription level of PatWRKY71 was significantly increased with the use of SA. Furthermore, our research has revealed that PatWRKY71 was capable of binding to the promoter of PatPTS, ultimately leading to an increase in its expression. When PatWRKY71 was silenced by a virus, the expression of both PatWRKY71 and PatPTS was reduced, resulting in the down-regulation of patchoulol production. Through our studies, we discovered that heterologous expression of PatWRKY71 leads to an increase in the sensitivity of Arabidopsis to salt and Cd, as well as an outbreak of reactive oxygen species (ROS). Additionally, we uncovered the regulatory role of PatWRKY71 in both patchoulol biosynthesis and plant defense response. This discovery provided a theoretical basis for the improvement of the content of patchoulol and the resistance of P. cablin through genetic engineering.
Reciprocal natural hybridization between Lycoris aurea and Lycoris radiata (Amaryllidaceae) identified by morphological, karyotypic and chloroplast genomic data
Authors: Quan Miaohua , Jiang Xianghui , Xiao Longqian , Li Jianglin , Liang Juan , Liu Guanghua
Published: January 2024

Background

Hybridization is considered as an important model of speciation, but the evolutionary process of natural hybridization is still poorly characterized in Lycoris. To reveal the phylogenetic relationship of two new putative natural hybrids in Lycoris, morphological, karyotypic and chloroplast genomic data of four Lycoris species were analyzed in this study.

Results

Two putative natural hybrids (2n = 18 = 4 m + 5t + 6st + 3 T) possessed obvious heterozygosity features of L. radiata (2n = 22 = 10t + 12st) and L. aurea (2n = 14 = 8 m + 6 T) in morphology (e.g. leaf shape and flower color), karyotype (e.g. chromosome numbers, CPD/DAPI bands, 45S rDNA-FISH signals etc.) and chloroplast genomes. Among four Lycoris species, the composition and structure features of chloroplast genomes between L. radiata and the putative natural hybrid 1 (L. hunanensis), while L. aurea and the hybrid 2, were completely the same or highly similar, respectively. However, the features of the cp genomes between L. radiata and the hybrid 2, while L. aurea and the hybrid 1, including IR-LSC/SSC boundaries, SSRs, SNPs, and SNVs etc., were significantly different, respectively. Combining the karyotypes and cp genomes analysis, we affirmed that the natural hybrid 1 originated from the natural hybridization of L. radiata (♀) × L. aurea (♂), while the natural hybrid 2 from the hybridization of L. radiata (♂) × L. aurea (♀).

Conclusion

The strong evidences for natural hybridization between L. radiata (2n = 22) and L. aurea (2n = 14) were found based on morphological, karyotypic and chloroplast genomic data. Their reciprocal hybridization gave rise to two new taxa (2n = 18) of Lycoris. This study revealed the origin of two new species of Lycoris and strongly supported the role of natural hybridization that facilitated lineage diversification in this genus.
Heterologous overexpression of heat shock protein 20 genes of different species of yellow Camellia in Arabidopsis thaliana reveals their roles in high calcium resistance
Authors: Zhong Lisha , Shi Yuxing , Xu Shaolei , Xie Sisi , Huang Xinhui , Li Yujie , Qu Chaofan , Liu Jianxiu , Liao Jialin , Huang Yang , Liang Yu
Published: January 2024

Yellow Camellia (Camellia sect. chrysantha) is a rare ornamental plant and an important germplasm resource globally. Camellia nitidissima thrives in normal acidic soils, while Camellia limonia can adapt to the calcareous soils found in karst areas. Our previous study on the karst adaptation of yellow camellias revealed that the expression levels of heat shock protein 20(HSP20) were higher in Camellia limonia than in Camellia nitidissima. However, the functions of the HSP20 gene of Camellia limonia remain unclear to data. In this study, the HSP20 genes of Camellia limonia (ClHSP20-OE lines) and Camellia. nitidissima (CnHSP20-OE lines) were cloned and overexpressed heterologously in Arabidopsis thaliana. Additionally, we overexpressed the HSP20 gene of Arabidopsis (AtHSP20-OE lines) was also overexpressed, and the T-DNA inserted mutants (athspmutant lines) were also used to determine the functions of HSP20 genes. Under high calcium stress, the chlorophyll, nitrogen, water content and humidity of leaves were increased in ClHSP20-OE lines, while those of other lines were declined. The size of the stomatal apertures, stomatal conductance, and the photosynthetic efficiency of ClHSP20-OE lines were higher than those of the other lines. However, the accumulation of H2O2 and O2− in the leaves of ClHSP20-OE lines was the lowest among all the lines. Energy spectrum scanning revealed that the percentage of calcium on the surfaces of the leaves of ClHSP20-OE lines was relatively low, while that of athspmutant lines was the highest. The ClHSP20 gene can also affected soil humidity and the contents of soil nitrogen, phosphorus, and potassium. Transcriptome analysis revealed that the expressions of FBA5 and AT5G10770 in ClHSP20-OE lines was significantly up-regulated compared to that of CnHSP20-OE lines. Compared to that of athspmutant lines, the expressions of DREB1A and AT3G30460 was significantly upregulated in AtHSP20-OE lines, and the expression of POL was down-regulated. Our findings suggest that the HSP20 gene plays a crucial role in maintained photosynthetic rate and normal metabolism by regulating the expression of key genes under high-calcium stress. This study elucidates the mechanisms underlying the karst adaptation in Camellia. limonia and provides novel insights for future research on karst plants.
Identification and characterization of yellow stripe-like genes in maize suggest their roles in the uptake and transport of zinc and iron
Authors: Song Zizhao , Li Suzhen , Li Yu , Zhou Xiaojin , Liu Xiaoqing , Yang Wenzhu , Chen Rumei
Published: January 2024

Background

Yellow Stripe-Like (YSL) proteins are involved in the uptake and transport of metal ions. They play important roles in maintaining the zinc and iron homeostasis in Arabidopsis, rice (Oryza sativa), and barley (Hordeum vulgare). However, proteins in this family have not been fully identified and comprehensively analyzed in maize (Zea mays L.).

Results

In this study, we identified 19 ZmYSLs in the maize genome and analyzed their structural features. The results of a phylogenetic analysis showed that ZmYSLs are homologous to YSLs of Arabidopsis and rice, and these proteins are divided into four independent branches. Although their exons and introns have structural differences, the motif structure is relatively conserved. Analysis of the cis-regulatory elements in the promoters indicated that ZmYSLs might play a role in response to hypoxia and light. The results of RNA sequencing and quantitative real-time PCR analysis revealed that ZmYSLs are expressed in various tissues and respond differently to zinc and iron deficiency. The subcellular localization of ZmYSLs in the protoplast of maize mesophyll cells showed that they may function in the membrane system.

Conclusions

This study provided important information for the further functional analysis of ZmYSL, especially in the spatio-temporal expression and adaptation to nutrient deficiency stress. Our findings provided important genes resources for the maize biofortification.
Genome-wide characterization of SDR gene family and its potential role in seed dormancy of Brassica napus L.
Authors: Zhang Fugui , Chen Tianhua , Liu Nian , Hou Xinzhe , Wang Ling , Cai Qingao , Li Rui , Qian Xingzhi , Xu Hong , Zhu Zonghe , Zheng Wenyin , Yu Yan , Zhou Kejin
Published: January 2024

Rapeseed (Brassica napus L.) with short or no dormancy period are easy to germinate before harvest (pre-harvest sprouting, PHS). PHS has seriously decreased seed weight and oil content in B. napus. Short-chain dehydrogenase/ reductase (SDR) genes have been found to related to seed dormancy by promoting ABA biosynthesis in rice and Arabidopsis. In order to clarify whether SDR genes are the key factor of seed dormancy in B. napus, homology sequence blast, protein physicochemical properties, conserved motif, gene structure, cis-acting element, gene expression and variation analysis were conducted in present study. Results shown that 142 BnaSDR genes, unevenly distributed on 19 chromosomes, have been identified in B. napus genome. Among them, four BnaSDR gene clusters present in chromosome A04、A05、C03、C04 were also identified. These 142 BnaSDR genes were divided into four subfamilies on phylogenetic tree. Members of the same subgroup have similar protein characters, conserved motifs, gene structure, cis-acting elements and tissue expression profiles. Specially, the expression levels of genes in subgroup A, B and C were gradually decreased, but increased in subgroup D with the development of seeds. Among seven higher expressed genes in group D, six BnaSDR genes were significantly higher expressed in weak dormancy line than that in nondormancy line. And the significant effects of BnaC01T0313900ZS and BnaC03T0300500ZS variation on seed dormancy were also demonstrated in present study. These findings provide a key information for investigating the function of BnaSDRs on seed dormancy in B. napus.
Genetic dissection of resistance to gray leaf spot by genome-wide association study in a multi-parent maize population
Authors: Hu Can , Kuang Tianhui , Shaw Ranjan K. , Zhang Yudong , Fan Jun , Bi Yaqi , Jiang Fuyan , Guo Ruijia , Fan Xingming
Published: January 2024

Background

Understanding the genetic mechanisms underlying gray leaf spot (GLS) resistance in maize is crucial for breeding GLS-resistant inbred lines and commercial hybrids. Genome-wide association studies (GWAS) and gene functional annotation are valuable methods for identifying potential SNPs (single nucleotide polymorphism) and candidate genes associated with GLS resistance in maize.

Results

In this study, a total of 757 lines from five recombinant inbred line (RIL) populations of maize at the F7 generation were used to construct an association mapping panel. SNPs obtained through genotyping-by-sequencing (GBS) were used to perform GWAS for GLS resistance using a linear mixture model in GEMMA. Candidate gene screening was performed by analyzing the 10 kb region upstream and downstream of the significantly associated SNPs linked to GLS resistance. Through GWAS analysis of multi-location phenotypic data, we identified ten candidate genes that were consistently detected in two locations or from one location along with best linear unbiased estimates (BLUE). One of these candidate genes, Zm00001d003257 that might impact GLS resistance by regulating gibberellin content, was further identified through haplotype-based association analysis, candidate gene expression analysis, and previous reports.

Conclusions

The discovery of the novel candidate gene provides valuable genomic resources for elucidating the genetic mechanisms underlying GLS resistance in maize. Additionally, these findings will contribute to the development of new genetic resources by utilizing molecular markers to facilitate the genetic improvement and breeding of maize for GLS resistance.
Dissecting the resilience of barley genotypes under multiple adverse environmental conditions
Authors: Abdelghany Ahmed M. , Lamlom Sobhi F. , Naser Mahmoud
Published: January 2024

As climate change increases abiotic stresses like drought and heat, evaluating barley performance under such conditions is critical for maintaining productivity. To assess how barley performs under normal conditions, drought, and heat stress, 29 different varieties were examined, considering agronomic, physiological, and disease-related characteristics. The research was conducted in five environments: two normal environments in 2020/2021 and 2021/2022, two drought stress environments in 2020/2021 and 2021/2022, and one heat stress environment in 2021/2022. The results demonstrated that genotype and environment significantly influenced all traits (p < 0.05), except canopy temperature, while genotype x environment interaction significantly influenced most traits, except total chlorophyll content and canopy temperature. Heat and drought stress environments often resulted in reduced performance for traits like plant height, spike length, grains per spike, and 100-grain weight compared to normal conditions. Based on individual traits, genotypes 07UT-44, 06WA-77, 08AB-09, and 07N6-57 exhibited the highest grain yield (4.1, 3.6, 3.6, and 3.6 t/ha, respectively). Also, these genotypes demonstrated enhanced stability in diverse drought and heat stress conditions, as assessed by the mean performance vs. stability index (Weighted Average of Absolute Scores, WAASB). The multi-trait stability index (MTSI) identified 07UT-44, 07UT-55, 07UT-71, and 08AB-09 as the most stable genotypes in terms of the performance of all traits. The imported lines demonstrated superior performance and stability, highlighting their potential as valuable genetic resources for developing climate-resilient barley.