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Article ; Online: Comparative Analyses of Complete Chloroplast Genomes of

Gao, Yunqing / Chen, Zhenjiang / Li, Xiuzhang / Malik, Kamran / Li, Chunjie

2024 Volume 15, Issue 2

Abstract: The present study provides a detailed analysis of the chloroplast genome ... ...

Abstract	The present study provides a detailed analysis of the chloroplast genome of
MeSH term(s)	Phylogeny ; Genome, Chloroplast ; Boraginaceae/genetics
Language	English
Publishing date	2024-02-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes15020226
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Article ; Online: Neurons as stromal drivers of nervous system cancer formation and progression.

Anastasaki, Corina / Gao, Yunqing / Gutmann, David H

Developmental cell

2023 Volume 58, Issue 2, Page(s) 81–93

Abstract: Similar to their pivotal roles in nervous system development, neurons have emerged as critical regulators of cancer initiation, maintenance, and progression. Focusing on nervous system tumors, we describe the normal relationships between neurons and ... ...

Abstract	Similar to their pivotal roles in nervous system development, neurons have emerged as critical regulators of cancer initiation, maintenance, and progression. Focusing on nervous system tumors, we describe the normal relationships between neurons and other cell types relevant to normal nerve function, and discuss how disruptions of these interactions promote tumor evolution, focusing on electrical (gap junctions) and chemical (synaptic) coupling, as well as the establishment of new paracrine relationships. We also review how neuron-tumor communication contributes to some of the complications of cancer, including neuropathy, chemobrain, seizures, and pain. Finally, we consider the implications of cancer neuroscience in establishing risk for tumor penetrance and in the design of future anti-tumoral treatments.
MeSH term(s)	Humans ; Neurons/metabolism ; Gap Junctions/metabolism ; Nervous System Neoplasms/metabolism
Language	English
Publishing date	2023-01-21
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2022.12.011
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Zs.A 5742: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Association Between Iron Metabolism and Acute Kidney Injury in Critically Ill Patients With Diabetes.

Mo, Manqiu / Gao, Yunqing / Deng, Ling / Liang, Yuzhen / Xia, Ning / Pan, Ling

Frontiers in endocrinology

2022 Volume 13, Page(s) 892811

Abstract: Objective: Iron overload plays an important role in the pathogenesis of diabetes and acute kidney injury (AKI). The aim of this present study was to explore the relationship between iron metabolism and AKI in patients with diabetes.: Methods: The ... ...

Abstract	Objective: Iron overload plays an important role in the pathogenesis of diabetes and acute kidney injury (AKI). The aim of this present study was to explore the relationship between iron metabolism and AKI in patients with diabetes. Methods: The clinical data of diabetes patients from MIMIC-III database in intensive care unit (ICU) were retrospectively analyzed. Regression analyses were used to explore the risk factors of AKI and all-cause death in critical patients with diabetes. Area under the receiver operating characteristic curves (AUROCs) were used to analyze serum ferritin (SF), and regression model to predict AKI in critical patients with diabetes. All diabetes patients were followed up for survival at 6 months, and Kaplan-Meier curves were used to compare the survival rate in patients with different SF levels. Results: A total of 4,997 diabetic patients in ICU were enrolled, with a male-to-female ratio of 1.37:1 and a mean age of 66.87 ± 12.74 years. There were 1,637 patients in the AKI group (32.8%) and 3,360 patients in the non-AKI group. Multivariate logistic regression showed that congestive heart failure (OR = 2.111, 95% CI = 1.320-3.376), serum creatinine (OR = 1.342, 95% CI = 1.192-1.512), Oxford Acute Severity of Illness Score (OR = 1.075, 95% CI = 1.045-1.106), increased SF (OR = 1.002, 95% CI = 1.001-1.003), and decreased transferrin (OR = 0.993, 95% CI = 0.989-0.998) were independent risk factors for AKI in critical patients with diabetes. Multivariate Cox regression showed that advanced age (OR = 1.031, 95% CI = 1.025-1.037), AKI (OR = 1.197, 95% CI = 1.011-1.417), increased Sequential Organ Failure Assessment score (OR = 1.055, 95% CI = 1.032-1.078), and increased SF (OR = 1.380, 95% CI = 1.038-1.835) were independent risk factors for 6-month all-cause death in critical diabetic patients. The AUROCs of SF and the regression model to predict AKI in critical patients with diabetes were 0.782 and 0.851, respectively. The Kaplan-Meier curve showed that the 6-month survival rate in SF-increased group was lower than that in SF-normal group (log-rank Conclusion: Critically ill diabetic patients with AKI were easily complicated with abnormal iron metabolism. Increase of SF is an important risk factor for AKI and all-cause death in critically ill patients with diabetes.
MeSH term(s)	Acute Kidney Injury/epidemiology ; Acute Kidney Injury/etiology ; Aged ; Critical Illness ; Diabetes Mellitus/epidemiology ; Female ; Humans ; Iron ; Male ; Middle Aged ; Prognosis ; Retrospective Studies
Chemical Substances	Iron (E1UOL152H7)
Language	English
Publishing date	2022-04-29
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2022.892811
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Article ; Online: NF1 mutation-driven neuronal hyperexcitability sets a threshold for tumorigenesis and therapeutic targeting of murine optic glioma.

Anastasaki, Corina / Chatterjee, Jit / Koleske, Joshua P / Gao, Yunqing / Bozeman, Stephanie L / Kernan, Chloe M / Marco Y Marquez, Lara I / Chen, Ji-Kang / Kelly, Caitlin E / Blair, Connor J / Dietzen, Dennis J / Kesterson, Robert A / Gutmann, David H

Neuro-oncology

2024

Abstract: Background: With the recognition that noncancerous cells function as critical regulators of brain tumor growth, we recently demonstrated that neurons drive low-grade glioma initiation and progression. Using mouse models of neurofibromatosis type 1 (NF1)- ...

Abstract	Background: With the recognition that noncancerous cells function as critical regulators of brain tumor growth, we recently demonstrated that neurons drive low-grade glioma initiation and progression. Using mouse models of neurofibromatosis type 1 (NF1)-associated optic pathway glioma (OPG), we showed that Nf1 mutation induces neuronal hyperexcitability and midkine expression, which activates an immune axis to support tumor growth, such that high-dose lamotrigine treatment reduces Nf1-OPG proliferation. Herein, we execute a series of complementary experiments to address several key knowledge gaps relevant to future clinical translation. Methods: We leverage a collection of Nf1-mutant mice that spontaneously develop OPGs to alter both germline and retinal neuron-specific midkine expression. Nf1-mutant mice harboring several different NF1 patient-derived germline mutations were employed to evaluate neuronal excitability and midkine expression. Two distinct Nf1-OPG preclinical mouse models were used to assess lamotrigine effects on tumor progression and growth in vivo. Results: We establish that neuronal midkine is both necessary and sufficient for Nf1-OPG growth, demonstrating an obligate relationship between germline Nf1 mutation, neuronal excitability, midkine production, and Nf1-OPG proliferation. We show anti-epileptic drug (lamotrigine) specificity in suppressing neuronal midkine production. Relevant to clinical translation, lamotrigine prevents Nf1-OPG progression and suppresses the growth of existing tumors for months following drug cessation. Importantly, lamotrigine abrogates tumor growth in two Nf1-OPG strains using pediatric epilepsy clinical dosing. Conclusions: Together, these findings establish midkine and neuronal hyperexcitability as targetable drivers of Nf1-OPG growth and support the use of lamotrigine as a potential chemoprevention or chemotherapy agent for children with NF1-OPG.
Language	English
Publishing date	2024-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2028601-6
ISSN	1523-5866 ; 1522-8517
ISSN (online)	1523-5866
ISSN	1522-8517
DOI	10.1093/neuonc/noae054
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Zs.A 5307: Show issues

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Article ; Online: Recombinant human brain natriuretic peptide attenuates ischemic brain injury in mice by inhibiting oxidative stress and cell apoptosis via activation of PI3K/AKT/Nrf2/HO-1 pathway.

Li, Tong / Su, DaJing / Lu, HuaWen / Gao, YunQing / Liu, YongGang / Wang, ShaoHua / Hou, YuTing / Qin, KeMin / Que, XianTing / Chen, XiaoPing / Qin, BaiLing / Wang, ZiJun / Deng, Yan

Experimental brain research

2023 Volume 241, Issue 11-12, Page(s) 2751–2763

Abstract: Ischemic stroke followed by cerebral artery occlusion is a main cause of chronic disability worldwide. Recombinant human brain natriuretic peptide (rhBNP) has been reported to alleviate sepsis-induced cognitive dysfunction and brain I/R injury. However, ... ...

Abstract	Ischemic stroke followed by cerebral artery occlusion is a main cause of chronic disability worldwide. Recombinant human brain natriuretic peptide (rhBNP) has been reported to alleviate sepsis-induced cognitive dysfunction and brain I/R injury. However, the function and molecular mechanisms of rhBNP in ischemic brain injury have not been clarified. For establishment of an animal model of ischemic brain injury, C57BL/6 mice were treated with middle cerebral artery occlusion (MCAO) surgery for 1 h and reperfusion for 24 h. After subcutaneous injection of rhBNP into model mice, neurologic deficits were assessed by evaluating behavior of mice according to Longa scoring system, and TTC staining was utilized to determine the brain infarct size of mice. The levels of oxidative stress markers, superoxide dismutase (SOD), catalase (CAT), glutathione (GSH) and malondialdehyde (MDA), were detected in hippocampal tissues of mice by corresponding kits. Cell apoptosis in hippocampus tissues was examined by TUNEL staining. Protein levels of antioxidant enzymes (HO-1 and NQO1) in cerebral cortex, apoptotic markers (Bax, Bcl-2, and cleaved caspase), and PI3K/AKT pathway-associated factors in hippocampus were tested by western blot analysis. The results revealed that injection of rhBNP decreased neurologic deficit scores, the percent of brain water content, and infarct volume. Additionally, rhBNP downregulated MDA level, upregulated the levels of SOD, CAT, and GSH in hippocampus of mice, and increased protein levels of HO-1 and NQO1 in the cortex. Cell apoptosis in hippocampus tissues of model mice was inhibited by rhBNP which was shown as the reduced TUNEL-positive cells, the decreased Bax, cleaved caspase-3, and cleaved caspase-9 protein levels, and the enhanced Bcl-2 protein level. In addition, rhBNP treatment activated the PI3K/AKT signaling pathway and upregulated the protein levels of HO-1 and NRF2. Overall, rhBNP activates the PI3K/AKT/HO-1/NRF2 pathway to attenuate ischemic brain injury in mice after MCAO by suppression of cell apoptosis and oxidative stress.
MeSH term(s)	Mice ; Humans ; Animals ; Natriuretic Peptide, Brain/pharmacology ; Natriuretic Peptide, Brain/therapeutic use ; Natriuretic Peptide, Brain/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; NF-E2-Related Factor 2/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; bcl-2-Associated X Protein/metabolism ; Mice, Inbred C57BL ; Oxidative Stress ; Infarction, Middle Cerebral Artery/complications ; Infarction, Middle Cerebral Artery/drug therapy ; Brain Ischemia/complications ; Brain Ischemia/drug therapy ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Apoptosis ; Brain Injuries ; Superoxide Dismutase/metabolism ; Reperfusion Injury
Chemical Substances	Natriuretic Peptide, Brain (114471-18-0) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; NF-E2-Related Factor 2 ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; bcl-2-Associated X Protein ; Proto-Oncogene Proteins c-bcl-2 ; Superoxide Dismutase (EC 1.15.1.1)
Language	English
Publishing date	2023-10-17
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1201-4
ISSN	1432-1106 ; 0014-4819
ISSN (online)	1432-1106
ISSN	0014-4819
DOI	10.1007/s00221-023-06716-4
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Zs.A 278: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: A common single nucleotide variant in the cytokine receptor-like factor-3 (CRLF3) gene causes neuronal deficits in human and mouse cells.

Wilson, Anna F / Barakat, Rasha / Mu, Rui / Karush, Leah L / Gao, Yunqing / Hartigan, Kelly A / Chen, Ji-Kang / Shu, Hongjin / Turner, Tychele N / Maloney, Susan E / Mennerick, Steven J / Gutmann, David H / Anastasaki, Corina

Human molecular genetics

2023 Volume 32, Issue 24, Page(s) 3342–3352

Abstract: Single nucleotide variants in the general population are common genomic alterations, where the majority are presumed to be silent polymorphisms without known clinical significance. Using human induced pluripotent stem cell (hiPSC) cerebral organoid ... ...

Abstract	Single nucleotide variants in the general population are common genomic alterations, where the majority are presumed to be silent polymorphisms without known clinical significance. Using human induced pluripotent stem cell (hiPSC) cerebral organoid modeling of the 1.4 megabase Neurofibromatosis type 1 (NF1) deletion syndrome, we previously discovered that the cytokine receptor-like factor-3 (CRLF3) gene, which is co-deleted with the NF1 gene, functions as a major regulator of neuronal maturation. Moreover, children with NF1 and the CRLF3L389P variant have greater autism burden, suggesting that this gene might be important for neurologic function. To explore the functional consequences of this variant, we generated CRLF3L389P-mutant hiPSC lines and Crlf3L389P-mutant genetically engineered mice. While this variant does not impair protein expression, brain structure, or mouse behavior, CRLF3L389P-mutant human cerebral organoids and mouse brains exhibit impaired neuronal maturation and dendrite formation. In addition, Crlf3L389P-mutant mouse neurons have reduced dendrite lengths and branching, without any axonal deficits. Moreover, Crlf3L389P-mutant mouse hippocampal neurons have decreased firing rates and synaptic current amplitudes relative to wild type controls. Taken together, these findings establish the CRLF3L389P variant as functionally deleterious and suggest that it may be a neurodevelopmental disease modifier.
MeSH term(s)	Child ; Humans ; Animals ; Mice ; Induced Pluripotent Stem Cells/metabolism ; Neurons/metabolism ; Brain/metabolism ; Receptors, Cytokine/metabolism ; Nucleotides/metabolism
Chemical Substances	Receptors, Cytokine ; Nucleotides ; CRLF3 protein, human
Language	English
Publishing date	2023-09-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddad155
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Article: High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement

Liu, Changyou / Wang, Yan / Peng, Jianxiang / Fan, Baojie / Xu, Dongxu / Wu, Jing / Cao, Zhimin / Gao, Yunqing / Wang, Xueqing / Li, Shutong / Su, Qiuzhu / Zhang, Zhixiao / Wang, Shen / Wu, Xingbo / Shang, Qibing / Shi, Huiying / Shen, Yingchao / Wang, Bingbing / Tian, Jing

Plant communications. 2022 June 22,

2022

Abstract: Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome ( ... ...

Abstract	Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a contig N50 length of 10.34 Mb. A total of 40,125 protein-coding genes were annotated, representing ∼96.9% of the genetic region. We also sequenced 217 accessions, mainly landraces and cultivars from China, and identified 2,229,343 high-quality single-nucleotide polymorphisms (SNPs). Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines. Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road. We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences. Among the genes, 83.1% were core genes and 16.9% were variable. Presence/absence variation (PAV) events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring. Genome-wide association studies (GWASs) revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits, including a SNP in the coding region of the SWEET10 homolog (jg24043) involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits. This high-quality reference genome and pan-genome will provide insights into mung bean breeding.
Keywords	crops ; cultivars ; genes ; genetic variation ; genome assembly ; genomics ; germplasm ; ingredients ; landraces ; medicine ; mung beans ; population structure ; spring ; starch ; vegetables ; China ; South Asia
Language	English
Dates of publication	2022-0622
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ISSN	2590-3462
DOI	10.1016/j.xplc.2022.100352
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Article ; Online: High-quality genome assembly and pan-genome studies facilitate genetic discovery in mung bean and its improvement.

Plant communications

2022 Volume 3, Issue 6, Page(s) 100352

Abstract	Mung bean is an economically important legume crop species that is used as a food, consumed as a vegetable, and used as an ingredient and even as a medicine. To explore the genomic diversity of mung bean, we assembled a high-quality reference genome (Vrad_JL7) that was ∼479.35 Mb in size, with a contig N50 length of 10.34 Mb. A total of 40,125 protein-coding genes were annotated, representing ∼96.9% of the genetic region. We also sequenced 217 accessions, mainly landraces and cultivars from China, and identified 2,229,343 high-quality single-nucleotide polymorphisms (SNPs). Population structure revealed that the Chinese accessions diverged into two groups and were distinct from non-Chinese lines. Genetic diversity analysis based on genomic data from 750 accessions in 23 countries supported the hypothesis that mung bean was first domesticated in south Asia and introduced to east Asia probably through the Silk Road. We constructed the first pan-genome of mung bean germplasm and assembled 287.73 Mb of non-reference sequences. Among the genes, 83.1% were core genes and 16.9% were variable. Presence/absence variation (PAV) events of nine genes involved in the regulation of the photoperiodic flowering pathway were identified as being under selection during the adaptation process to promote early flowering in the spring. Genome-wide association studies (GWASs) revealed 2,912 SNPs and 259 gene PAV events associated with 33 agronomic traits, including a SNP in the coding region of the SWEET10 homolog (jg24043) involved in crude starch content and a PAV event in a large fragment containing 11 genes for color-related traits. This high-quality reference genome and pan-genome will provide insights into mung bean breeding.
MeSH term(s)	Vigna/genetics ; Genome-Wide Association Study ; Plant Breeding ; Fabaceae/genetics ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2022-06-26
Publishing country	China
Document type	Journal Article
ISSN	2590-3462
ISSN (online)	2590-3462
DOI	10.1016/j.xplc.2022.100352
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