ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species.

The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst ( www.expressanalyst.

Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data.

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform ( www.

Native Microbiome Members of Act Synergistically in Biosynthesis of Pyridoxal 5'-Phosphate.

The roles of the healthy microbiome on the host and the relationships between members of the microbiome remain to be fully characterized. Due to the complexity of the interactions between the mammalian microbiome and its host, the use of model organisms such as the nematode worm is a promising strategy to study host-microbiome interactions in vivo, as well as bacterial crosstalk within the host. Previously it was found that native bacterial isolates of the worm, sp.

Oxidative stress suppression in . by peptides from dogfish skin regulation of transcription factors DAF-16 and HSF-1.

Functional peptides were obtained enzymatic hydrolysis of smooth dogfish () skin. The enzyme-assisted process was optimized to achieve high yield of smooth dogfish skin peptides (SDSP). Fractions of SDSP (MW < 2 kDa, 2-5 kDa, 5-10 kDa and >10 kDa) showed antioxidant activities.

The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension.

Background: A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome is highly complex and attributing host phenotypes to a specific member of the microbiome can be difficult. The model organism Caenorhabditis elegans and its native microbiome, discovered recently, can serve as a more tractable, experimental model system to study host-microbiome interactions.

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity in .

Engineered nanoparticles are used at an increasing rate in both industry and medicine without fully understanding their impact on health and environment. The nematode is a suitable model to study the toxic effects of nanoparticles as it is amenable to comprehensive phenotyping, such as locomotion, growth, neurotoxicity and reproduction. In this study, we systematically evaluated the effects of silver (Ag) and five metal oxide nanoparticles: SiO, CeO, CuO, AlO and TiO.

Genererating a core cluster of Fasciola hepatica virulence and immunomodulation-related genes using a comparative in silico approach.

A total of 71 virulence and immunomodulation-related transcripts (VIRs) of Fasciola hepatica have been previously proposed (Haçarız et al., 2015). In an attempt to further refine this cohort, an in silico meta analysis approach was carried out using publicly available sequence data of related liver flukes, Clonorchis sinensis and Opisthorchis viverrini.

The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years.

The evolution of technologies to explore parasite biology at a detailed level has made significant advances in recent years, particularly with the development of omic-based strategies. Whilst extensive efforts have been made in the past to develop therapeutic and prophylactic control strategies for trematode parasites, only the therapeutic anthelmintic approach can be regarded as usable in clinical practice. Currently, there is no commercialised prophylactic strategy (such as vaccination) for protection of the definitive host against any trematode parasite.

Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica.

Background: Fasciola hepatica causes chronic liver disease, fasciolosis, leading to significant losses in the livestock economy and concerns for human health in many countries. The identification of F. hepatica genes involved in the parasite's virulence through modulation of host immune system is utmost important to comprehend evasion mechanisms of the parasite and develop more effective strategies against fasciolosis.

[Investigation of the abundance of proteins secreted by Fasciola hepatica, which is exposed to environmental change in experimental studies, with an advanced proteomic approach].

Objective: Investigation of the abundance of proteins secreted by Fasciola hepatica, which is exposed to environmental change after it is removed from the main host, with an advanced proteomic approach.

Methods: Adult Fasciola hepatica parasites, obtained from the main host, were directly placed in phosphate-buffered saline (PBS, at room temperature) and incubated at 37°C for 2 hours (after arrival at the Institute within 1 hour). After this, without applying extra procedures, such as washing the parasites, secreted parasite proteins in PBS were investigated using an advanced proteomic method [a mass spectrometry system with electrospray ionization and quadrupole time-of-flight source coupled to ultra performance liquid chromatography, nano UPLC-ESI-QTOF-MS] with a reviewed F.

Generating a detailed protein profile of Fasciola hepatica during the chronic stage of infection in cattle.

Fasciola hepatica is a trematode helminth causing a damaging disease, fasciolosis, in ruminants and humans. Comprehensive proteomic studies broaden our knowledge of the parasite's protein profile, and provide new insights into the development of more effective strategies to deal with fasciolosis. The objective of this study was to generate a comprehensive profile of F.

TMCO1 deficiency causes autosomal recessive cerebrofaciothoracic dysplasia.

Cerebrofaciothoracic dysplasia (CFT) (OMIM #213980) is a multiple congenital anomaly and intellectual disability syndrome involving the cranium, face, and thorax. The characteristic features are cranial involvement with macrocrania at birth, brachycephaly, various CT/MRI findings including hypoplasia of corpus callosum, enlargement of septum pellicidum, and diffuse hypodensity of the grey matter, flat face, hypertelorism, cleft lip and cleft palate, low-set, posteriorly rotated ears, short neck, and multiple costal and vertebral anomalies. The underlying genetic defect remains unknown.

Fasciola hepatica - where is 28S ribosomal RNA?

Advanced molecular biology techniques are currently used to develop new effective strategies against fasciolosis. Assessment of the quality of extracted total RNA is an important step prior to commencing many molecular biology methods such as transcriptomics. However, RNA quality assessment is complicated for some organisms, including Fasciola hepatica, by the absence of a 28S rRNA peak/band, when assessed with modern protocols.

A proteomic approach to investigate the distribution and abundance of surface and internal Fasciola hepatica proteins during the chronic stage of natural liver fluke infection in cattle.

Fasciola hepatica, a trematode helminth, causes an economically important disease (fasciolosis) in ruminants worldwide. Proteomic analysis of the parasite provides valuable information to understand the relationship between the parasite and its host. Previous studies have identified various parasite proteins, some of which are considered as vaccine candidates or important drug targets.

Experimental Fasciola hepatica infection alters responses to tests used for diagnosis of bovine tuberculosis.

Fasciola hepatica is a prevalent helminth parasite of livestock. Infection results in polarization of the host's immune response and generation of type 2 helper (Th2) immune responses, which are known to be inhibitory to Th1 responses. Bovine tuberculosis (BTB) is a bacterial disease of economic and zoonotic importance.