A combination of conserved and stage-specific lncRNA biomarkers to detect lung adenocarcinoma progression.

Lung adenocarcinoma is highly heterogeneous at the molecular level between different stages; therefore, understanding molecular mechanisms contributing to such heterogeneity is needed. In addition, multiple stages of progression are critical factors for lung adenocarcinoma treatment. However, previous studies showed that cancer progression is associated with altered lncRNA expression, highlighting the tissue-specific and developmental stage-specific nature of lncRNAs in various diseases.

Integrated systems pharmacology, molecular docking, and MD simulations investigation elucidating the therapeutic mechanisms of BHD in Alzheimer's disease treatment.

Alzheimer's disease (AD) poses a longstanding health challenge, prompting a century-long exploration into its etiology and progression. Despite significant advancements in medical science, current AD treatments provide only symptomatic relief, urging a shift towards innovative paradigms. This study, departing from the amyloid hypothesis, integrates Systems Pharmacology, Molecular Docking and Molecular Dynamic Simulations to investigate a polyherbal phytoformulation (US 7,273,626 B2) rooted in Ayurveda for AD, consisting of Bacopa monnieri, Hippophae rhamnoides, and Dioscorea bulbifera (BHD).

A positive selection at binding site 501 in the B.1 lineage might have triggered the highly infectious sub-lineages of SARS-CoV-2.

The descendants of the B lineage are the most predominant variants among the SARS-CoV-2 virus due to the incorporation of new mutations augmenting the infectivity of the virus. There is a substantial increase in the transition transversion bias, nucleotide diversity and purifying selection on the spike protein in the descendants of the B lineage of the SARS-CoV-2 virus on a temporal scale. A strong bias for C-to-U substitutions is found in the genes encoding spike protein in this lineage.

piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress.

Long considered active only in the germline, the PIWI/piRNA pathway is now known to play a significant role in somatic cells, especially neurons. In this study, piRNAs were profiled in the human retina and retinal pigment epithelium (RPE). Furthermore, RNA immunoprecipitation with HIWI2 (PIWIL4) in ARPE19 cells yielded 261 piRNAs, and the expression of selective piRNAs in donor eyes was assessed by qRT-PCR.

Genomic coevolution of papillomavirus and immune system in placental mammals indicates the role of IFN-γ in the emergence of new variants.

Papillomaviruses (PVs) are causative agents for warts and cancers in different parts of the body in the mammalian lineage. Therefore, these viruses are proposed as model organisms to study host immune responses to pathogens causing chronic infections. The virus-associated cancer progression depends on two integral processes namely angiogenesis and immune response (AIR).

Integrated network-based multiple computational analyses for identification of co-expressed candidate genes associated with neurological manifestations of COVID-19.

'Tripartite network' (TN) and 'combined gene network' (CGN) were constructed and their hub-bottleneck and driver nodes (44 genes) were evaluated as 'target genes' (TG) to identify 21 'candidate genes' (CG) and their relationship with neurological manifestations of COVID-19. TN was developed using neurological symptoms of COVID-19 found in literature. Under query genes (TG of TN), co-expressed genes were identified using pair-wise mutual information to genes available in RNA-Seq autopsy data of frontal cortex of COVID-19 victims.

CarcinoHPVPred: An ensemble of machine learning models for HPV carcinogenicity prediction using genomic data.

Human papillomavirus (HPV) infections often show no symptoms but sometimes lead to either warts or carcinoma based on the HPV genotype. The relationship between HPV infections and cervical cancer have been well studied in the past two decades. However, distinguishing carcinogenic HPV variants from non-carcinogenic ones remains a major challenge in clinical genetic testing of HPV-induced cancer samples.

Matrix metallopeptidase 9 as a host protein target of chloroquine and melatonin for immunoregulation in COVID-19: A network-based meta-analysis.

Aims: The molecular pathogenesis of COVID-19 is similar to other coronavirus (CoV) infections viz. severe acute respiratory syndrome (SARS) in human. Due to scarcity of the suitable treatment strategy, the present study was undertaken to explore host protein(s) targeted by potent repurposed drug(s) in COVID-19.

The cognitive and speech genes are jointly shaped by both positive and relaxed selection in the human lineage.

The emergence of a coordinated network of cognitive and speech genes in the human lineage performing overlapping functions is a great evolutionary puzzle. Prior studies on the speech gene FOXP2 are inconclusive on the nature of selection operating on this gene in the human lineage. Here, I show that the evolution of FOXP2 is accelerated in the human lineage due to relaxation of purifying selection (relaxed selection).

Identification of molecular biomarkers for ovarian cancer using computational approaches.

Ovarian cancer is one of the major causes of mortality among women. This is partly because of highly asymptomatic nature, lack of reliable screening techniques and non-availability of effective biomarkers of ovarian cancer. The recent availability of high-throughput data and consequently the development of network medicine approach may play a key role in deciphering the underlying global mechanism involved in a complex disease.

Computational medicine: quantitative modeling of complex diseases.

Biological complex systems are composed of numerous components that interact within and across different scales. The ever-increasing generation of high-throughput biomedical data has given us an opportunity to develop a quantitative model of nonlinear biological systems having implications in health and diseases. Multidimensional molecular data can be modeled using various statistical methods at different scales of biological organization, such as genome, transcriptome and proteome.

Increased Plasma Nitrite and von Willebrand Factor Indicates Early Diagnosis of Vascular Diseases in Chemotherapy Treated Cancer Patients.

Chemotherapy induced cardiotoxicity leads to development of hypertension, conduction abnormalities, and congestive heart failure. However, there is no simple test to detect and assess cardiovascular risk in a chemotherapy treated cancer patient. The aim of the present study on cancer patients treated with (n = 66) and without (n = 66) chemotherapy is to identify indicators from plasma for vascular injury.

Inhibition of the MurA enzyme in Fusobacterium nucleatum by potential inhibitors identified through computational and in vitro approaches.

Fusobacterium nucleatum plays a key role in several diseases such as periodontitis, gingivitis, appendicitis, and inflammatory bowel disease (IBD). The development of antibiotic resistance by this bacterium demands novel therapeutic intervention. Our recent study has reported UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA) as one of the potential target proteins in F.

Target identification in Fusobacterium nucleatum by subtractive genomics approach and enrichment analysis of host-pathogen protein-protein interactions.

Background: Fusobacterium nucleatum, a well studied bacterium in periodontal diseases, appendicitis, gingivitis, osteomyelitis and pregnancy complications has recently gained attention due to its association with colorectal cancer (CRC) progression. Treatment with berberine was shown to reverse F. nucleatum-induced CRC progression in mice by balancing the growth of opportunistic pathogens in tumor microenvironment.

Evolution of the Gene Is Linked to Intelligence in Mammals.

Background/aims: A recent duplication of the gene encoding SLIT-ROBO Rho GTPase-activating protein 2 in the primate lineage has been proposed to be associated with the human-specific extraordinary development of intelligence. There is no report regarding the role of the gene in the expression of neural traits indicating intelligence in mammals.

Methods: A phylogenetic tree of the gene from 11 mammals was reconstructed using MrBayes.

MRI characterization of temporal lobe epilepsy using rapidly measurable spatial indices with hemisphere asymmetries and gender features.

Introduction: The paucity of morphometric markers for hemispheric asymmetries and gender variations in hippocampi and amygdalae in temporal lobe epilepsy (TLE) calls for better characterization of TLE by finding more useful prognostic MRI parameter(s).

Methods: T1-weighted MRI (3 T) morphometry using multiple parameters of hippocampus-parahippocampus (angular and linear measures, volumetry) and amygdalae (volumetry) including their hemispheric asymmetry indices (AI) were evaluated in both genders. The cutoff values of parameters were statistically estimated from measurements of healthy subjects to characterize TLE (57 patients, 55% male) alterations.

Insights on the functional impact of microRNAs present in autism-associated copy number variants.

Autism spectrum disorder is a complex neurodevelopmental disorder that appears during the first three years of infancy and lasts throughout a person's life. Recently a large category of genomic structural variants, denoted as copy number variants (CNVs), were established to be a major contributor of the pathophysiology of autism. To date almost all studies have focussed only on the genes present in the CNV loci, but the impact of non-coding regulatory microRNAs (miRNAs) present in these regions remain largely unexplored.

The coordinated expression, interaction and evolution of the neuroendocrine genes.

The neuroendocrine system is a complex biological system controlled by various neuropeptides and hormones. The evolution and network properties of neuroendocrine genes are analyzed along with their expression profiles. The neuroendocrine genes show very similar expression profiles and local network properties across a wide range of tissues consistent with the physiological roles of their proteins.

Correlated evolution of gonadotropin-releasing hormone and gonadotropin-inhibitory hormone and their receptors in mammals.

Background: Evolutionary rate variation in genes (proteins) is manifested both within the species (genome) and between the species (genomes). However, the interdependent components of a biological system in form of a gene or a protein are expected to evolve in a correlated manner under a common functional constraint.

Methods: The phylogenetic analysis and correlation analysis of gonadotropin-releasing hormone (GnRH) and gonadotropin-inhibitory hormone (GnIH) and their receptors (GnRHR and GnIHR) was conducted along with other control neuropeptides.

The severity of mental disorders is linked to interaction among candidate genes.

There is a considerable overlap in the manifestation of symptoms in three mental disorders namely unipolar disorder, bipolar disorder and schizophrenia. A gene coexpression network was developed based on a mutual information approach including four candidate genes (NRG1, DISC1, BDNF and COMT) along with other coexpressing genes in unipolar disorder, bipolar disorder and schizophrenia. There is a significant difference in the degree distribution of nodes between normal and bipolar disorder network and bipolar disorder network and schizophrenia network.

Maintaining optimal state probabilities in biological systems.

A biological problem is usually studied experimentally by reducing it into a number of modules. In contrast, the systems biology approach seeks to address the collective behavior of interacting molecules vis-a-vis the corresponding higher level behavior. Various attributes of a biological system are conditionally dependent on each other, and these conditionalities are usually represented through Bayesian networks for computing easily the joint probability for a state of an attribute.

Gonadotropin releasing hormone (GnRH) neurones of triploid catfish, Heteropneustes fossilis (Bloch): an immunocytochemical study.

Gonadotropin-releasing hormone (GnRH), a regulator of gonadal maturation in vertebrates, is primarily secreted by neurosecretory cells of the pre-optic area (POA) in the forebrain of teleosts. GnRH-immunoreactive (GnRH-ir) cells of this area demonstrate positive correlation in number and size of soma with gonadal maturity and directly innervate the pituitary in most teleosts. Gonadal development in triploid fish remains impaired due to genetic sterility.

Testosterone triggers the brain-pituitary-gonad axis of juvenile female catfish (Heteropneustes fossilis Bloch) for precocious ovarian maturation.

The brain-pituitary-gonad axis of precociously matured females (PMFs) of Indian catfish (Heteropneustes fossilis), produced by testosterone treatment during juvenile stages, was analyzed by studies on immunoreactive gonadotropin-releasing hormone (ir-GnRH) secreting cells of the preoptic area of brain, plasma levels of gonadotropin (GtH-II), testosterone (T), and estradiol-17 beta (E(2)). GnRH cells of PMFs were large and strongly immunoreactive in comparison to control females. PMFs showed higher plasma levels of GtH-II, T, and E(2) than did control females.