Negative / Null Result ReportBiochemistry, Genetics and Molecular Biology
Weitao Zhou, Xiaoyong Li, Daochao Huang et al. · 2015 · Current Alzheimer Research
It is reported that 7,8-dihydroxyflavone (DHF), a TrkB agonist, has beneficial effects on neuronal excitotoxicity, stroke, and Parkinson disease in animal models by enhancing axon regeneration, muscle reinnervation and neuromuscular…
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Luiz Carlos Vieira, Morgan L. Handojo, Claus O. Wilke · 2025 · Scientific Reports
Protein language models (pLMs) can offer deep insights into evolutionary and structural properties of proteins. While larger models, such as the 15 billion parameter model ESM-2, promise to capture more complex patterns in sequence space, they also present practical challenges due to their high dimensionality and high computational cost. We systematically evaluated the performance of various ESM-style models across multiple biological datasets to assess the impact of model size on transfer learning via feature extraction. Surprisingly, we found that larger models do not necessarily outperform
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Cheng Peng, Martijn den Dekker, Andrés Cárdenas et al. · 2018 · Environmental Health Perspectives
BACKGROUND: Epigenetic variability is hypothesized as a regulatory pathway through which prenatal exposures may influence child development and health. OBJECTIVE: We sought to examine the associations of residential proximity to roadways at birth and epigenome-wide DNA methylation. We also assessed associations of differential methylation with child cognitive outcomes. METHODS: We estimated residential proximity to roadways at birth using a geographic information system (GIS) and cord blood methylation using Illumina's HumanMethylation450-array in 482 mother-child pairs in Project Viva. We ide
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Satoru Taniguchi, Kohei Ninomiya, Itaru Kushima et al. · 2019 · Psychiatry and Clinical Neurosciences
AIMS: Recent studies have revealed that the interplay between polygenic risk scores (PRS) and large copy number variants (CNV; >500kb) is essential for the etiology of schizophrenia (SCZ). To replicate previous findings, including those for smaller CNV (>10kb), the PRS between SCZ patients with and without CNV were compared. METHODS: The PRS were calculated for 724 patients with SCZ and 1178 healthy controls (HC), genotyped using array-based comparative genomic hybridization and single nucleotide polymorphisms chips, and comparisons were made between cases and HC, or between subjects with and
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Beau J. Fenner, Jonathan F. Russell, Arlene V. Drack et al. · 2023 · Frontiers in Medicine
Introduction X-linked retinoschisis (XLRS) is an inherited retinal disease (IRD) caused by pathogenic mutations in the retinoschisin gene, RS1 . Affected individuals develop retinal layer separation, leading to loss of visual acuity (VA). Several XLRS gene therapy trials have been attempted but none have met their primary endpoints. An improved understanding of XLRS natural history and clinical outcomes may better inform future trials. Here, we report the long-term functional and structural outcomes of XLRS and the relevance of RS1 genotypes to the visual prognosis of affected individuals. Met
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Caroline R. Amendola, William T. Cordell, Colin M. Kneucker et al. · 2023 · Metabolic Engineering
Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome…
View details →Negative / Null Result ReportOpen accessBiochemistry, Genetics and Molecular Biology
Liza C. Villaruz, Grace Huang, Marjorie Romkes et al. · 2015 · Clinical Epigenetics
BACKGROUND: Carboplatin/paclitaxel (CP), with or without sorafenib, result in objective response rates of 18-20 % in unselected chemotherapy-naïve patients. Molecular predictors of survival and response to CP-based chemotherapy in metastatic melanoma (MM) are critical to improving the therapeutic index. Intergroup trial E2603 randomized MM patients to CP with or without sorafenib. Expression data were collected from pre-treatment formalin-fixed paraffin-embedded (FFPE) tumor tissues from 115 of 823 patients enrolled on E2603. The selected patients were balanced across treatment arms, BRAF stat
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Mboneye Anselme, Huafeng He, Chengyang Lai et al. · 2025 · Journal of Translational Medicine
In the realm of cellular biochemistry, mitochondria have been increasingly recognized for their critical role in both cellular metabolism and the etiology of various diseases. Mitochondrial transporters (MTs) are essential for maintaining…
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Josef Biber, Catharina Gandor, Elvir Bećirović et al. · 2025 · Pharmacology & Therapeutics
Gene therapy is an innovative medical approach that offers new treatment options for congenital and acquired diseases by transferring, correcting, inactivating or regulating genes to supplement, replace or modify a gene function. The approval of voretigene neparvovec (Luxturna), a gene therapy for RPE65-associated retinopathy, has marked a milestone for the field of retinal gene therapy, but has also helped to accelerate the development of gene therapies for genetic diseases affecting other organs. Voretigene neparvovec is a vector based on adeno-associated virus (AAV) that delivers a function
View details →Negative / Null Result ReportBiochemistry, Genetics and Molecular Biology
Da‐Tian Bau · 2011 · The Chinese Journal of Physiology
Many articles have reported the caveolin-1 gene to be down-regulated thus suggesting that it might be a candidate tumor suppressor gene in many tumors. However, its involvement in bladder cancer is not clear and may be depending on…
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Qiyao Zhang, Zhen Cao, Shangcheng Yan et al. · 2025 · Journal of Translational Medicine
Pancreatic cancer, specifically pancreatic ductal adenocarcinoma (PDAC), is notorious for its aggressive nature and dismal prognosis, ranking as a leading cause of cancer-related mortality worldwide. Despite advancements in surgical…
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José M. Eltit, Clara Franzini‐Armstrong, Claudio F. Pérez · 2014 · Journal of Biological Chemistry
The β1a subunit is a cytoplasmic component of the dihydropyridine receptor (DHPR) complex that plays an essential role in skeletal muscle excitation-contraction (EC) coupling. Here we investigate the role of the C-terminal end of this auxiliary subunit in the functional and structural communication between the DHPR and the Ca2+ release channel (RyR1). Progressive truncation of the β1a C terminus showed that deletion of amino acid residues Gln489 to Trp503 resulted in a loss of depolarization-induced Ca2+ release, a severe reduction of L-type Ca2+ currents, and a lack of tetrad formation as eva
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Andrea J. Savio, Mathieu Lemire, Miralem Mrkonjic et al. · 2012 · PLoS ONE
Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation. We previously demonstrated that SNPs (rs1800734, rs749072, and rs13098279) in the MLH1 gene region are associated with MLH1 promoter island methylation, loss of MLH1 protein expression, and microsatellite instability (MSI) in colorectal cancer (CRC) patients. Recent studies have identified less CpG-dense "shore" regions flanking many CpG islands. These shores often exhibit distinct methylation profiles between different tissues and matched normal versus tumor cells of patients. To date, most epigenetic studie
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Diego Chemello, Luís Eduardo Paim Rohde, Kátia Gonçalves dos Santos et al. · 2010 · EP Europace
AIMS: We investigated whether the combination of beta(1)-Gly389Arg and GNB3 C825T, two genetic polymorphisms strictly related to adrenergic system modulation, could act as predictors of appropriate therapies in patients with heart failure…
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Jialin Fan, Yunpeng Xu · 2026 · Frontiers in Genetics
Dietary restriction (DR), defined as reduced caloric intake or selective limitation of specific nutrients without malnutrition, is one of the most robust interventions known to extend lifespan and healthspan across species. Studies from yeast to mammals demonstrate that DR elicits conserved genetic, transcriptional, and epigenetic programs that promote cellular maintenance and stress resistance. At the molecular level, DR engages evolutionarily conserved nutrient-sensing pathways, including insulin/IGF-1 signaling (IIS), the mechanistic target of rapamycin (mTOR), AMP-activated protein kinase
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Hieab H.H. Adams, Vincentius J.A. Verlinden, Michele L. Callisaya et al. · 2015 · The Journals of Gerontology Series A
Human gait is a complex neurological and musculoskeletal function, of which the genetic basis remains largely unknown. To determine the influence of common genetic variants on gait parameters, we studied 2,946 participants of the Rotterdam…
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Marlee R. Labroo, Jeffrey B. Endelman, Dorcus C. Gemenet et al. · 2023 · Theoretical and Applied Genetics
KEY MESSAGE: Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have re
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Hui Shi, Christopher Medway, James M. Bullock et al. · 2010 · PubMed
We have performed cross-platform comparisons of output from 4 GWAS in late-onset Alzheimer's disease (LOAD) - Reiman et al., 2007; Li et al., 2008; Beecham et al., 2008 and Carrasquillo et al., 2009 to search for new association signals.…
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Michael Rabbia, Maitea Guridi Ormazabal, Hannah Staunton et al. · 2024 · Journal of Neuromuscular Diseases
Background: Stride Velocity 95th Centile (SV95C) is the first wearable device-derived clinical outcome assessment (COA) to receive European Medicines Agency (EMA) qualification as a primary endpoint in ambulant patients with Duchenne muscular dystrophy (DMD) aged ≥4 years. Objective: To compare SV95C-in its first-ever clinical trial application as a secondary endpoint-with established motor function COAs used in the trial (Four-Stair Climb [4SC] velocity, North Star Ambulatory Assessment [NSAA], and Six-Minute Walk Distance [6MWD]). Methods: SV95C was a secondary endpoint in a subset (n = 47)
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Enrique Rozengurt, G. Eibl · 2026 · Signal Transduction and Targeted Therapy
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease for which there is no effective treatment. A deep understanding of the mechanisms underlying the molecular pathogenesis, signaling pathways and risk factors leading to PDAC is of paramount importance for identifying novel targets, prognostic markers, preventive strategies, and signature markers for use in specific and personalized therapeutic procedures. Activating somatic mutations in the KRAS oncogene play a critical role in PDAC initiation and maintenance. Here, we highlight the complex interplay between KRAS signaling, the tr
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Burney, Saira, Muhammad Wasif Saif, Saif, Muhammad Wasif et al. · 2013 · PubMed
CONTEXT: Pancreatic cancer is the fourth leading cause of cancer mortality in the United States. Most of the patients are diagnosed in the metastatic staging. Consolidated risk factors include chronic pancreatitis, smoking and family…
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Ivan Antonov, Andrey V. Marakhonov, Maria A. Zamkova et al. · 2018 · Journal of Bioinformatics and Computational Biology
The discovery of thousands of long noncoding RNAs (lncRNAs) in mammals raises a question about their functionality. It has been shown that some of them are involved in post-transcriptional regulation of other RNAs and form inter-molecular…
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Taylor Yiu, Bin Chen, Haoyu Wang et al. · 2025 · Journal of Translational Medicine
Recent advances in single-cell multi-omics technologies have revolutionized cellular analysis, enabling comprehensive exploration of cellular heterogeneity, developmental trajectories, and disease mechanisms at unprecedented resolution.…
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Olayemi O. Adeoye, Vincent Bouthors, Margaret C. Hubbell et al. · 2014 · Journal of Applied Physiology
Recent studies suggest that VEGF contributes to hypoxic remodeling of arterial smooth muscle, although hypoxia produces only transient increases in VEGF that return to normoxic levels despite sustained changes in arterial structure and…
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Roberta Ottria, Susan Mirmajidi, Pierangela Ciuffreda · 2026 · International Journal of Molecular Sciences
This review delves into the complex relationship between short-chain fatty acids (SCFAs) produced by the gut microbiota and inflammatory bowel disease (IBD). IBD, which includes Crohn's disease and ulcerative colitis, is a group of chronic gastrointestinal disorders with an increasing global incidence. Despite extensive research, the exact etiopathogenesis remains elusive, although a complex interplay involving genetic predisposition, environmental influences, and abnormal immune responses against commensal gut microbes is widely recognized. SCFAs, primarily acetate and butyrate, emerge as key
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Marja-Liisa Nuotio, Heini Sánez Tähtisalo, Alexandra Lahtinen et al. · 2022 · Epigenetics
Essential hypertension remains the leading risk factor of global disease burden, but its treatment goals are often not met. We investigated whether DNA methylation is associated with antihypertensive responses to a diuretic, a beta-blocker, a calcium channel blocker or an angiotensin receptor antagonist. In addition, since we previously showed an SNP at the transcription start site (TSS) of the catecholamine biosynthesis-related ACY3 gene to associate with blood pressure (BP) response to beta-blockers, we specifically analysed the association of methylation sites close to the ACY3 TSS with BP
View details →Negative / Null Result ReportBiochemistry, Genetics and Molecular Biology
Bożena Nejman-Faleńczyk, Beata Nadratowska-Wesołowska, Agnieszka Szalewska-Pałasz et al. · 2010 · Microbiology
The pathogenicity of Shiga toxin-producing Escherichia coli (STEC) depends on the expression of stx genes that are located on lambdoid prophages. Effective toxin production occurs only after prophage induction, and one may presume that…
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Roohi Chaudhary, Ralf Weiskirchen, Marcelo Ehrlich et al. · 2025 · Frontiers in Pharmacology
The transforming growth factor-β (TGF-β) superfamily (TGF-β-SF) comprises over 30 cytokines, including TGF-β, activins/inhibins, bone morphogenetic proteins (BMPs), and growth differentiation factors (GDFs). These cytokines play critical roles in liver function and disease progression. Here, we discuss Smad-dependent (canonical) and non-Smad pathways activated by these cytokines in a hepatocellular context. We highlight the connection between the deregulation of these pathways or the balance between them and key hepatocellular processes (e.g., proliferation, apoptosis, and epithelial-mesenchym
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Aris Katzourakis, Stéphane Hué, Paul Kellam et al. · 2011 · Journal of Virology
Xenotropic murine leukemia virus (MLV)-related virus (XMRV) has been amplified from human prostate cancer and chronic fatigue syndrome (CFS) patient samples. Other studies failed to replicate these findings and suggested PCR contamination…
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Kevin J. Mitchell, Darren Dahly, Dorothy Bishop · 2025 · Neuron
The idea that the gut microbiome causally contributes to autism has gained currency in the scientific literature and popular press. Support for this hypothesis comes from three lines of evidence: human observational studies, preclinical experiments in mice, and human clinical trials. We critically assessed this literature and found that it is beset by conceptual and methodological flaws and limitations that undermine claims that the gut microbiome is causally involved in the etiology or pathophysiology of autism.
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