Article
Multidisciplinary Sciences
Huili Xue, Aili Yu, Na Lin, Xuemei Chen, Min Lin, Yan Wang, Hailong Huang, Liangpu Xu
Summary: The etiopathogenesis of fetal ventriculomegaly is not well understood. This study investigated the correlations between fetal ventriculomegaly and chromosome abnormalities, finding higher detection rates of clinically significant CNVs in non-isolated ventriculomegaly compared to isolated cases. Additionally, SNP arrays were found to effectively identify CNVs and increase the abnormal chromosomal detection rate, particularly in cases of ventriculomegaly accompanied by CNS anomalies.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Joseph T. Glessner, Xiao Chang, Yichuan Liu, Jin Li, Munir Khan, Zhi Wei, Patrick M. A. Sleiman, Hakon Hakonarson
Summary: The study developed a tool called Montage to enhance the accuracy of detecting mosaic copy number variants, identified numerous mosaic CNVs associated with phenotypes, and presented a novel algorithm for efficient detection of mosaic CNVs.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li
Summary: The recent advance of single-cell copy number variation (CNV) analysis is important in addressing intratumor heterogeneity and restoring tumor-evolving trajectories. However, existing tools lack real-time interaction and are hard to reproduce. We present an online platform for real-time interactive visualization of single-cell genomics data to accelerate the understanding of cancer clonal evolution.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Robin Nicole Bosman, Jessica Anne-Marie Vervalle, Danielle Lisa November, Phyllis Burger, Justin Graham Lashbrooke
Summary: Volatile organic compounds, such as terpenes, play a vital role in influencing the quality parameters of grapevine through their contribution to the flavor and aroma profile of grapes. The biosynthesis of these compounds is complex and controlled by multiple genes, many of which are unidentified. By analyzing volatile metabolic data from a grapevine mapping population, researchers identified several significant genomic regions associated with terpene modulation in grape berries. These findings provide insights into the molecular mechanisms of terpene accumulation and offer potential applications in developing grape cultivars with desired terpene profiles.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yu Zhao, Camila Coelho, Stephanie Lauer, Milosz Majewski, Jon M. Laurent, Ran Brosh, Jef D. Boeke
Summary: The use of synthetic genomics has revolutionized our ability to answer fundamental biological questions by designing and building "big" DNA constructs. Saccharomyces cerevisiae, or budding yeast, is a powerful platform for assembling large synthetic constructs, but introducing designer variations to episomal assemblies remains challenging. The CRISPR Engineering of EPisomes in Yeast (CREEPY) method provides a rapid and efficient way to edit large synthetic episomal DNA constructs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Biochemistry & Molecular Biology
Yiguan Wang, Paul McNeil, Rashidatu Abdulazeez, Marta Pascual, Susan E. Johnston, Peter D. Keightley, Darren J. Obbard
Summary: Mutation, recombination, and transposition rates are important parameters in models of evolution, but little is known about their variation between individuals, sexes, or populations. This study provides direct estimates of these rates in different populations of Drosophila melanogaster and Drosophila simulans. The results show variation in mutation, recombination, and transposition rates among populations and sexes, with paternal-derived mutations being more frequent. These findings will benefit future studies in population and evolutionary genetics.
Article
Neurosciences
Nam-Shik Kim, Francisca Rojas Ringeling, Ying Zhou, Ha Nam Nguyen, Stephanie J. Temme, Yu-Ting Lin, Stephen Eacker, Valina L. Dawson, Ted M. Dawson, Bo Xiao, Kuei-sen Hsu, Stefan Canzar, Weidong Li, Paul Worley, Kimberly M. Christian, Ki-Jun Yoon, Hongjun Song, Guo-li Ming
Summary: This study investigates the impact of gene dosage imbalance on neuropsychiatric disorders using mouse models. The results suggest that the Cyfip1 gene regulates protein translation of NMDAR and associated complex components at synapses, maintaining normal synaptic functions and behaviors. The findings provide insights into how gene dosage imbalance caused by CNVs may contribute to divergent neuropsychiatric disorders.
BIOLOGICAL PSYCHIATRY
(2022)
Article
Clinical Neurology
Dongfang Zou, Lin Wang, Jianxiang Liao, Hongdou Xiao, Jing Duan, Tongda Zhang, Jianbiao Li, Zhenzhen Yin, Jing Zhou, Haisheng Yan, Yushan Huang, Nianji Zhan, Ying Yang, Jingyu Ye, Fang Chen, Shida Zhu, Feiqiu Wen, Jian Guo
Summary: This study evaluated the diagnostic value of genome sequencing in children with epilepsy, identifying pathogenic/likely pathogenic variants in a proportion of patients and common single-nucleotide variants and copy number variants. Additionally, it found that some patients had specific treatable genetic causes identified by genome sequencing.
Article
Genetics & Heredity
Qixin Guo, Lan Huang, Hao Bai, Zhixiu Wang, Yulin Bi, Guohong Chen, Yong Jiang, Guobin Chang
Summary: In this study, a genome-wide association study was conducted to identify genetic variants associated with meat quality in ducks. Several genes were found to be associated with fat, water, collagen, and protein content. These findings can serve as markers for meat quality and help improve breeding plans and selection strategies.
Article
Genetics & Heredity
Ruixue Zhang, Lu Cao, Weiwei Chen, Huiyao Ge, Xia Hu, Zhuo Li, Yirui Wang, Wencheng Fan, Liang Yong, Yafen Yu, Yiwen Mao, Qi Zhen, Hong Liu, Furen Zhang, Liangdan Sun
Summary: This study assessed the association between HLA CNV and leprosy susceptibility in a Northern Han Chinese population for the first time, identifying four independent variants related to leprosy risk. Fine mapping of the MHC region in this population provided evidence for the contribution of HLA to leprosy susceptibility.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Shiwei Liu, Adam C. Huckaby, Audrey C. Brown, Christopher C. Moore, Ian Burbulis, Michael J. McConnell, Jennifer L. Guler
Summary: This study presents a single-cell sequencing pipeline for the intracellular parasite Plasmodium falciparum and provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes. The work enables detection of parasite heterogeneity contributing to P. falciparum adaptation.
Article
Clinical Neurology
Nadia Deflorin, Ulrike Ehlert, Rita T. Amiel Castro
Summary: Changes in the gut microbiome of infants have been associated with maternal psychological symptoms during pregnancy. This study found that maternal prenatal depressive symptoms are associated with lower diversity of the infant's microbiome, while maternal saliva cortisol levels are linked to increased diversity and changes in specific bacterial groups. Further research is needed to understand the implications of these microbiota alterations for child health.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Zheng Ma, Hui-Xia Zhou, Da-Chun Chen, Dong-Mei Wang, Xiang-Yang Zhang
Summary: The impaired glucose metabolism in drug-na & iuml;ve schizophrenia patients is strongly associated with suicidal behavior, suggesting that glucose metabolism abnormalities may be potential biomarkers of suicide in schizophrenia patients. Regular monitoring of glucose metabolism variables is essential for suicide prevention.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Katie M. Lavigne, Jiaxuan Deng, Delphine Raucher-Chene, Adele Hotte-Meunier, Chloe Voyer, Lisa Sarraf, Martin Lepage, Genevieve Sauve
Summary: Psychiatric disorders are characterized by cognitive deficits and cognitive biases, which are associated with specific symptoms. While cognitive biases are present across diagnoses, their severity varies.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Yong-Yu Yin, Jiao-Zhao Yan, Shi-Xin Lai, Qian-Qian Wei, Si-Rui Sun, Li-Ming Zhang, Yun-Feng Li
Summary: This study found that gamma oscillations are closely associated with depression and may serve as predictive biomarkers of depression. Chronic restraint stress and lipopolysaccharide induced significant depression-like behaviors in mice and reduced gamma oscillations in the medial prefrontal cortex. Administration of ketamine, scopolamine, or fluoxetine increased gamma oscillations and exhibited rapid-acting antidepressant effects.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Veronica Begni, Moira Marizzoni, Kerstin Camile Creutzberg, Diana Morena Silipo, Mariusz Papp, Annamaria Cattaneo, Marco Andrea Riva
Summary: Exposure to stressful experiences is a significant risk factor for mental disorders, and pharmacological interventions targeting stress-induced alterations can help restore brain function. Lurasidone, an antipsychotic drug, has been shown to normalize the impairments caused by stress exposure and could be a valuable treatment for stress-induced mental illnesses. However, the mechanisms underlying the therapeutic effects of lurasidone are not well understood. This study found that chronic lurasidone treatment counteracted some of the transcriptional changes induced by chronic mild stress exposure, providing new insights into the potential therapeutic effects of lurasidone.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Esther E. Palacios-Barrios, Kunal Patel, Jamie L. Hanson
Summary: This review examines the association between early life interpersonal stress (ELIS) and depression, as well as the underlying mechanisms. The research shows that ELIS affects how youth respond to social rewards, and similar impairments in social reward processing are observed in youth with depression. The authors propose a preliminary model that suggests neurobehavioral disruptions in social reward processing as a mediating factor in the connection between ELIS and depression.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Rui Li, Jiaming Tang, Yizhuo Wang, Ying Wang, Hua Yang, Hongen Wei
Summary: Restricted and repetitive behaviors (RRBs) are characteristic features of neuropsychiatric disorders. This study focused on repetitive self-grooming behavior and investigated the involvement of the Pax2 gene in its control. Through the use of Pax2 neuron-specific deletion mice, the study found that the deletion of Pax2 gene affects the expression of the Arc gene in the prefrontal cortex, leading to impaired synaptic plasticity and excitatory/inhibitory imbalance, thereby contributing to the occurrence of repetitive self-grooming behavior.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Sara Derosa, Paulina Misztak, Jessica Mingardi, Giulia Mazzini, Heidi Kaastrup Muller, Laura Musazzi
Summary: This study investigated the involvement of neurotrophic signaling pathways in stress vulnerability/resilience and fast antidepressant response/non-response to ketamine in a rat model of depression. The findings showed that stress and ketamine induced specific changes in these pathways in different brain areas and subcellular fractions.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Review
Clinical Neurology
Georgia F. Caruana, Sean P. Carruthers, Michael Berk, Susan L. Rossell, Tamsyn E. Van Rheenen
Summary: Cognitive impairment is related to both white matter macrostructure and microstructure in bipolar disorder patients. However, there is inconsistency in the results of the studies examining this relationship. Some studies have found an association between higher fractional anisotropy in white matter and better complex attention skills and executive functioning in bipolar disorder patients, while others have found no associations. Further research with increased statistical power and standardized methods is needed.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Review
Clinical Neurology
Alberto Galimberti, Martin Tik, Giovanni Pellegrino, Anna-Lisa Schuler
Summary: This study provides a systematic review and meta-analysis on the effectiveness of repetitive transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS) for post-traumatic brain injury (TBI) symptoms. The results show that non-invasive brain stimulation techniques have a small overall effect on TBI sequelae, with significant effects observed for anxiety and headache. However, larger randomized controlled trials with longer follow-ups, optimized stimulation parameters, and standardized methodology are needed to establish the efficacy of these techniques in addressing TBI sequelae.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Amanda J. Sales, Pedro H. Gobira, Joa F. C. Pedrazzi, Joao R. Silveia, Elaine Del Bel, Felipe V. Gomes, Francisco S. Guimaraes
Summary: The study found that doxycycline can inhibit metalloproteinase in the brain and attenuate the rewarding effects and locomotor sensitization of drug abuse. This suggests that doxycycline could be repurposed for the treatment of substance use disorders.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Alejandro Borrego-Ruiz, Juan J. Borrego
Summary: There is substantial evidence that the development of the nervous system is related to the composition and functions of the gut microbiome. The communication between the central nervous system (CNS) and the gut microbiota is bidirectional, with various routes such as immune, endocrine, and neural circuits. Dysbiosis of the gut microbiota has been associated with neuropsychiatric diseases and psychological disorders. Fecal microbiota transplantation (FMT) therapy has shown a causal-effect relationship between the gut microbiota and behavioral features. Interventions based on prebiotics, probiotics, or synbiotics have demonstrated their influence on neurological disorders through the synthesis of neuroactive compounds and regulation of inflammatory and endocrine processes. Further research is needed to explore the impact of gut microbiota dysbiosis on psychiatric and psychological disorders and the potential therapeutic role of microbiota-based interventions.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Zhinan Li, Zhuang Kang, Xiaowei Xia, Leijun Li, Junyan Wu, Jiamin Dai, Tong Liu, Cai Chen, Yong Qiu, Ming Chen, Yanxi Liu, Ziyi Zhang, Zili Han, Zhengjia Dai, Qinling Wei
Summary: This study found that patients with schizophrenia showed lower levels of resilience and cognitive functions compared to healthy controls, as well as abnormal global properties and nodal metrics in brain networks. Furthermore, characteristic path length might moderate the relationship between resilience and working memory in these patients.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
David H. Adamowicz, Tsung-Chin Wu, Rebecca Daly, Michael R. Irwin, Dilip Jeste, Xin M. Tu, Lisa T. Eyler, Ellen E. Lee
Summary: This study aimed to explore the relationship between executive functioning and inflammatory biomarkers in people with schizophrenia. The results showed that systemic inflammation did not predict long-term declines in executive functioning. This suggests the need for further research to better understand the relationship and mechanisms between inflammation and cognition in schizophrenia.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Clinical Neurology
Nina Walter, Julian Wenzel, Shalaila S. Haas, Letizia Squarcina, Carolina Bonivento, Anne Ruef, Dominic Dwyer, Theresa Lichtenstein, Oeznur Bastruek, Alexandra Stainton, Linda A. Antonucci, Paolo Brambilla, Stephen J. Wood, Rachel Upthegrove, Stefan Borgwardt, Rebekka Lencer, Eva Meisenzahl, Raimo K. R. Salokangas, Christos Pantelis, Alessandro Bertolino, Nikolaos Koutsouleris, Joseph Kambeitz, Lana Kambeitz-Ilankovic
Summary: Clinical and neuroimaging data can be used to predict the potential of cognitive training to improve social functioning in recent onset psychosis patients. The use of multivariate pattern analysis and support vector machine classifier allows for the prediction of social functioning improvement based on baseline cognitive data. The findings suggest that cognitive data can provide a robust individual estimate of future social functioning for patients with recent onset psychosis.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)