deep sequencing

Visceral Leishmaniasis (VL), the second neglected tropical disease caused by various Leishmania species, presents a significant public health challenge due to limited treatment options and the absence of vaccines. The agent responsible for visceral leishmaniasis, also referred to as "black fever" in India, is Leishmania donovani. This study focuses on L. donovani Minichromosome maintenance 10 (LdMcm10), a crucial protein in the DNA replication machinery, as a potential therapeutic target in Leishmania therapy using in silico and in vitro approaches...

Pleomorphic rhabdomyosarcoma (PRMS) is a rare and highly aggressive sarcoma, occurring mostly in the deep soft tissues of middle-aged adults and showing a variable degree of skeletal muscle differentiation. The diagnosis is challenging as pathologic features overlap with embryonal rhabdomyosarcoma (ERMS), malignant Triton tumor, and other pleomorphic sarcomas. As recurrent genetic alterations underlying PRMS have not been described to date, ancillary molecular diagnostic testing is not useful in subclassification...

The deepest recorded depth for trematodes currently stands at approximately 6200 m. This depth record was achieved solely through sequence datasets of Lepidapedon sp. obtained from a gastropod. Given that trematodes of this genus typically use fish as definitive hosts, the origin of the trematode sequence was thought to be larval stages. However, the specific species remained unclear owing to the absence of reported adult-stage sequences. In the present study, we definitively identified the deepest trematode as Lepidapedon oregonense by comparing 28S ribosomal DNA sequences from adult worms from the macrourid fish Coelorinchus gilberti with data from the gastropod in the previous study...

Translational regulation plays the most critical role in gene expression. Ribosome profiling sequencing (Ribo-Seq) is one of the methods to study translation and its regulation. It is a high throughput technology based on deep sequencing, which targets ribosome protected mRNA fragments to produce a 'global snapshot' of translatome. There has been an annual increase in the number of publications incorporating Ribo-seq technology. Because of its importance, we used PubMed database to conduct a comprehensive bibliometric analysis on Ribo-seq...

Recent advances in single-cell omics technology have transformed the landscape of cellular and molecular research, enriching the scope and intricacy of cellular characterisation. Perturbation modelling seeks to comprehensively grasp the effects of external influences like disease onset or molecular knock-outs or external stimulants on cellular physiology, specifically on transcription factors, signal transducers, biological pathways, and dynamic cell states. Machine and deep learning tools transform complex perturbational phenomena in algorithmically tractable tasks to formulate predictions based on various types of single-cell datasets...

Transient receptor potential vanilloid 4 channel ( TRPV4 ) gene mutations have been described in skeletal system and peripheral nervous system pathology. The case described here is a 9-year-old male child patient, born to a nonconsanguineous marriage with normal birth history who had difficulty in walking and stiffness of joints for the last 7 years, and progressive weakness of all four limbs and urine incontinence for 1 year following falls. Physical examination showed below-average weight and height and short trunk...

A 3-year-old boy, firstborn to nonconsanguineous parents, presented with motor development delay and floppiness of bilateral lower limbs since birth. No significant family history presented at time of check-up. He could stand with support, eat with a spoon without spillage, and speak in two-word sentences. There was no history suggestive of cranial nerve impairment. Examination revealed normal head circumference, dry, scaly skin lesions on the trunk, distal weakness with sluggish deep tendon reflexes in bilateral lower limbs, and a high stepping gait...

BACKGROUND: Deep-learning-based reconstruction (DLR) improves the quality of magnetic resonance (MR) images which allows faster acquisitions. The aim of this study was to compare the image quality of standard and accelerated T2 weighted turbo-spin-echo (TSE) images of the prostate reconstructed with and without DLR and to find associations between perceived image quality and calculated image characteristics. METHODS: In a cohort of 47 prospectively enrolled consecutive patients referred for bi-parametric prostate magnetic resonance imaging (MRI), two T2-TSE acquisitions in the transverse plane were acquired on a 3T scanner-a standard T2-TSE sequence and a short sequence accelerated by a factor of two using compressed sensing (CS)...

BACKGROUND: Accurate preoperative diagnosis of endometrial cancer (EC) with deep myometrial invasion (DMI) is critical to deciding whether to perform lymphadenectomy. However, the presence of adenomyosis makes distinguishing DMI from superficial myometrial invasion (SMI) on magnetic resonance imaging (MRI) challenging. We aimed to evaluate the accuracy of multiparametric MRI (mpMRI) in diagnosing DMI in EC coexisting with adenomyosis (EC-A) compared with EC without coexisting adenomyosis and to evaluate the effect of different adenomyosis subtypes on myometrial invasion (MI) depth in EC...

BACKGROUND: Anterior cruciate ligament (ACL) injuries are closely associated with knee osteoarthritis (OA). However, diagnosing ACL injuries based on knee magnetic resonance imaging (MRI) has been subjective and time-consuming for clinical doctors. Therefore, we aimed to devise a deep learning (DL) model leveraging MRI to enable a comprehensive and automated approach for the detection of ACL injuries. METHODS: A retrospective study was performed extracting data from the Osteoarthritis Initiative (OAI)...

BACKGROUND: Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0...

BACKGROUND: High-throughput sequencing (HTS) has become the gold standard approach for variant analysis in cancer research. However, somatic variants may occur at low fractions due to contamination from normal cells or tumor heterogeneity; this poses a significant challenge for standard HTS analysis pipelines. The problem is exacerbated in scenarios with minimal tumor DNA, such as circulating tumor DNA in plasma. Assessing sensitivity and detection of HTS approaches in such cases is paramount, but time-consuming and expensive: specialized experimental protocols and a sufficient quantity of samples are required for processing and analysis...

A plant parasite associated with the white haze disease in apples, the Basidiomycota Gjaerumia minor, has been found in most samples of the global bathypelagic ocean. An analysis of environmental 18S rDNA sequences on 12 vertical profiles of the Malaspina 2010 expedition shows that the relative abundance of this cultured species increases with depth while its distribution is remarkably different between the deep waters of the Pacific and Atlantic oceans, being present in higher concentrations in the former...

BACKGROUND AND PURPOSE: Intracranial hemorrhage (ICH) has emerged as a notable concern in Chiari II malformation (CM II), yet its origins and clinical implications remain elusive. This study aims to validate the in-utero prevalence of ICH in CM II and investigate contributing factors, and visualize the findings in a network format. MATERIALS AND METHODS: A single-center retrospective review of fetal MRI scans obtained in fetuses with CM II presenting (January 2007 to December 2022) was performed for ICH utilizing EPI-T2* blood-sensitive sequence...

MOTIVATION: Protein-protein interactions (PPIs) underpin many cellular processes and their disruption due to mutations can lead to diseases. With the evolution of protein structure prediction methods like AlphaFold2 and the availability of extensive experimental affinity data, there is a pressing need for updated computational tools that can efficiently predict changes in binding affinity caused by mutations in protein-protein complexes. RESULTS: We developed a deep ensemble model that leverages protein sequences, predicted structure-based features, and protein functional classes to accurately predict the change in binding affinity due to mutations...

Shading is an important practical method to improve the quality of green tea. Previous research of our group found that because the biosynthesis and distribution of theanine in tea plants were affected by down regulation of gene encoding amino acid permeases, theanine content in tea leaves which grown under shading condition was significantly higher than those under natural light. In this study, our group analyzed the changes of tea leaf area, free amino acid content and photosynthetic parameters under natural light and shading conditions, to ensure that moderate shading did not reduce but improve the quality of tea...

α-zeins are amphiphilic maize seed storage proteins with material properties suitable for a multitude of applications e.g., in renewable plastics, foods, therapeutics and additive manufacturing (3D-printing). To exploit their full potential, molecular-level insights are essential. The difficulties in experimental atomic-resolution characterization of α-zeins have resulted in a diversity of published molecular models. However, deep-learning α-zein models are largely unexplored. Therefore, this work studies an AlphaFold2 (AF2) model of a highly expressed α-zein using molecular dynamics (MD) simulations...

Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity. However, relatively little is known about how prokaryotes successfully transition and persist across environments, and how these processes might vary between biomes and lineages. Here, we investigate biome transitions and specialisation in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK)...

Deep learning models have achieved remarkable success in medical image classification. These models are typically trained once on the available annotated images and thus lack the ability of continually learning new tasks (i.e., new classes or data distributions) due to the problem of catastrophic forgetting. Recently, there has been more interest in designing continual learning methods to learn different tasks presented sequentially over time while preserving previously acquired knowledge. However, these methods focus mainly on preventing catastrophic forgetting and are tested under a closed-world assumption; i...

A wide diversity of mycoviruses has been reported from Botrytis species, some with the potential to suppress the pathogenic abilities of this fungus. Considering their importance, this study was devised to find potential hypovirulence-associated mycoviruses found in Botrytis cinerea strains isolated from Pakistani strawberry fields. Here we report the complete genome characterization of two fusariviruses co-infecting a single isolate of phytopathogenic fungus B. cinerea (Kst14a). The viral genomes were sequenced by deep sequencing using total RNA fractions of the Kst14a isolate...