Jan Lochman

• Masaryk University

The ABCB1 gene, encoding the ATP-dependent translocase ABCB1, plays a crucial role in the clearance of amyloid-beta (Aβ) peptides and the transport of cholesterol, implicating it in the pathogenesis of Alzheimer's disease. The study aims to investigate the association between polymorphisms in the ABCB1 gene and cognitive decline in individuals with...

Astrocytes are specialized glial cell types of the central nervous system (CNS) with remarkably high abundance, morphological and functional diversity. Astrocytes maintain neural metabolic support, synapse regulation, blood-brain barrier integrity and immunological homeostasis through intricate interactions with other cells, including neurons, micr...

Background Astrocytes have recently gained attention as key players in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease. Numerous differentiation protocols have been developed to study human astrocytes in vitro. However, the properties of the resulting glia are inconsistent, making it difficult to select an appropriate...

This research represents the first attempt to study the structure and diversity of the archaeal and methanogenic archaeal community in selected lakes around the Czech polar station J.G. Mendel on James Ross Island (JRI), Antarctica. Sediment samples from a total of 19 of JRI and the nearby Vega Island and Long Island, were analyzed using 16S rRNA a...

In recent years, there has been a growing interest in extending the potential of underground gas storage (UGS) facilities to hydrogen and carbon dioxide storage. However, this transition to hydrogen storage raises concerns regarding potential microbial reactions, which could convert hydrogen into methane. It is crucial to gain a comprehensive under...

16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficien...

Background Insulin‐degrading enzyme (IDE) is an important gene in studies of the pathophysiology of type 2 diabetes mellitus (T2DM). Recent studies have suggested a possible link between type 2 diabetes mellitus (T2DM) and the pathophysiology of schizophrenia (SZ). At the same time, significant changes in insulin‐degrading enzyme (IDE) gene express...

Recent RNA sequencing studies have given us a deeper insight into the cariogenic impact of carbohydrate sources in the bacterium Streptococcus mutans, the principal microbial agent in dental caries etiopathogenesis. The process of dental caries development is facilitated by the ability of this bacterium to ferment some carbohydrates into organic ac...

Prior exposure to microbial-associated molecular patterns or specific chemical compounds can promote plants into a primed state with stronger defence responses. β-aminobutyric acid (BABA) is an endogenous stress metabolite that induces resistance protecting various plants towards diverse stresses. In this study, by integrating BABA-induced changes...

Research of new input raw materials for biogas plants is a very actual topic. There are only a very few studies dealing with the possibility of using silage prepared from the above-ground parts of the Jerusalem artichoke (Helianthus tuberosus L.) and maize (Zea mayse L.) for methane production. This study deals with the determination of methane pro...

Plant diseases caused by pathogens lead to economic and agricultural losses, while plant resistance is defined by robustness and timing of defence response. Exposure to microbial-associated molecular patterns or specific chemical compounds can promote plants into a primed state with more robust defence responses. β-aminobutyric acid (BABA) is an en...

Background This pilot study aimed to investigate how fixed orthodontic appliances simultaneously applied on the upper and lower arches affect the oral environment in the medium term. Methods The oral status of 30 orthodontic patients was evaluated using the number of decay-missing-filled teeth (DMFT), plaque (PI), and gingival indices (GI) before...

In the past, several animal disease models were developed to study the molecular mechanism of neurological diseases and discover new therapies, but the lack of equivalent animal models has minimized the success rate. A number of critical issues remain unresolved, such as high costs for developing animal models, ethical issues, and lack of resemblan...

Objectives The aim of this study was the analysis of WNT10A variants in seven families of probands with various forms of tooth agenesis and self-reported family history of cancer.Materials and methodsWe enrolled 60 young subjects (aged 13 to 17) from the Czech Republic with various forms of tooth agenesis. Dental phenotypes were assessed using Plan...

This research is the first study focusing to explore the diversity of Archaea and methanogens in sediments of 19 selected lakes nearby the Czech polar station on James Ross Island (JRI), Antarctica. The 16S rRNA gene sequencing provided a general view of a diversity of archaeal members and the mcrA gene sequencing has offered deeper insight into th...

The risk of Alzheimer’s disease (AD) has a strong genetic component, also in the case of late-onset AD (LOAD). Attempts to sequence whole genome in large populations of subjects have identified only a few mutations common to most of the patients with AD. Targeting smaller well-characterized groups of subjects where specific genetic variations in se...

Securing new sources of renewable energy and achieving national self-sufficiency in natural gas have become increasingly important in recent times. The study described in this paper focuses on three geologically diverse underground gas reservoirs (UGS) that are the natural habitat of methane-producing archaea, as well as other microorganisms with w...

Background: Insulin-degrading enzyme (IDE) is a widely distributed Zn2+-binding metalloprotease that cleaves multiple short and medium-sized peptides prone to form β-structures. These include insulin and amyloid-β peptides. Accumulation and fibrillation of amyloid-β peptides leading to the formation of amyloid plaques is a characteristic sign of A...

Elicitins are proteinaceous elicitors that induce the hypersensitive response and plant resistance against diverse phytopathogens. Elicitin recognition by membrane receptors or high-affinity sites activates a variety of fast responses including the production of reactive oxygen species (ROS) and nitric oxide (NO), leading to induction of plant defe...

Regulation of protein function by reversible S-nitrosation, a post-translational modification based on the attachment of nitroso group to cysteine thiols, has emerged among key mechanisms of NO signalling in plant development and stress responses. S-nitrosoglutathione is regarded as the most abundant low-molecular-weight S-nitrosothiol in plants, w...

In this study, the taxonomic and functional diversity of methanogenic archaea in two parallel 120 l fermenters operated at different temperatures and fed with maize silage was estimated by mcrA metabarcoding analysis using two typical primer pairs (ML and MLA) amplifying part of the functional methyl coenzyme M reductase (mcrA) gene. The alpha dive...

Antibiotic resistance has become a global threat in which the anthropogenically influenced aquatic environment represents not only a reservoir for the spread of antibiotic resistant bacteria (ARB) among humans and animals but also an environment where resistance genes are introduced into natural microbial ecosystems. Wastewater is one of the source...

Background: Acromegaly is a disorder associated with hypersecretion of growth hormone, most usually caused by a pituitary adenoma. Dysmotility of the gastrointestinal tract has been reported in acromegalic patients. Achalasia is a disorder characterized by aperistalsis of the oesophagus with incomplete lower oesophageal sphincter relaxation and wh...

Several single-nucleotide polymorphisms (SNPs) and rare variants of non-receptor tyrosine kinase 1 gene (TNK1) have been associated with Alzheimer’s disease (AD). To date, none of the associations have proven to be of practical importance in predicting the risk of AD either because the evidence is not conclusive, or the risk alleles occur at very l...

Mannose-binding lectin (MBL) deficiency caused by the variability in the MBL2 gene is responsible for the susceptibility to and severity of various infectious and autoimmune diseases. A combination of six single nucleotide polymorphisms (SNPs) has a major impact on MBL levels in circulation. The aim of this study is to design and validate a sensiti...

Clusterin (CLU; also known as apolipoprotein J, ApoJ) is a protein of inconstant structure known to be involved in diverse processes inside and outside of brain cells. CLU can act as a protein chaperon or protein solubilizer, lipid transporter as well as redox sensor and be anti- or proapoptotic, depending on context. Primary structure of CLU is en...

Successful plant defence against microbial pathogens is based on early recognition and fast activation of inducible responses. Key mechanisms include detection of microbe-associated molecular patterns by membrane-localized Pattern Recognition Receptors that induce a basal resistance response. A well-described model of such responses to pathogens in...

Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respirat...

Phenolics play an essential role in the defense reaction of crop plants against pathogens. However, the intensity of their production induced by infection may differ during the life of a plant. Here, we identified age-related differences in phenolic biosynthesis in the pathosystem Solanum lycopersicum cv. Amateur and Pseudomonas syringae pv. tomato...

The first layer of plant immunity against pathogens is mediated by cell surface pattern recognition receptors (PRRs) that recognize pathogen molecules in the apoplast. Several pairs of PRRs and their matching extracellular ligands have been described but, in many cases, actual evidence for ligand binding by the PRR is lacking. The receptor-like pro...

Cerebrovascular abnormalities have been discussed as pathological mechanisms involved in schizophrenia, particularly in the context of the genetic–inflammatory–vascular hypothesis.1 The cerebral and retinal microcirculation have similarities with respect to morphology and physiology. It can therefore be tested if retinal vessel changes occur in pat...

Anaerobic sludge stabilization is a commonly used technology. Most fermenters are operated at a mesophilic temperature regime. Modern trends in waste management aim to minimize waste generation. One of the strategies can be achieved by anaerobically stabilizing the sludge by raising the temperature. Higher temperatures will allow faster decompositi...

The degradation of red clover isoflavones was studied in vitro using a rumen fluid buffer system. Various amounts of red clover extract (5–75 mg) together with hay or concentrate‐rich diet were added to 40 ml of rumen fluid obtained from non‐lactating and lactating dairy cows, respectively, and incubated for 0, 3, 6, 12 or 24 hr. Following incubati...

Successful plant defence responses to pathogen challenges are based on fast and specific pathogen recognition and plant reaction mechanisms. Elicitins, proteinaceous elicitors secreted by the Phytophthora and Pythium species, were first described in Phytophthora culture filtrates as proteins able to induce a hypersensitive response (HR) and resista...

Dental caries and periodontal diseases are associated with a shift from symbiotic microbiota to dysbiosis. The aim of our study was to develop a rapid, sensitive, and economical method for the identification and quantification of selected cariogenic and periodontal oral bacteria. Original protocols were designed for three real-time multiplex PCR as...

In the last decades, methanogenic archaea have been increasingly investigated with regard to their impact on the environment, technological applications or role in human health. Today, high-throughput sequencing of the functional mcrA gene is routinely used to assess methanogenic archaea diversity in environmental samples. Compared to the 16S rRNA...

Unfortunately, the complete conflict of interest statement was missed out in the original publication. The same is given below.

Purpose The presence of Propionibacterium acnes in a substantial component of resected disc specimens obtained from patients undergoing discectomy or microdiscectomy has led to the suggestion that this prominent human skin and oral commensal may exacerbate the pathology of degenerative disc disease. This hypothesis, therefore, raises the exciting p...

Main conclusion The level of resistance induced in different tomato genotypes after β-CRY treatment correlated with the upregulation of defence genes, but not sterol binding and involved ethylene and jasmonic acid signalling. Elicitins, a family of small proteins secreted by Phytophthora and Pythium spp., are the most well-known microbe-associated...

The aim of this study was to determine the degradation of dietary isoflavones in rumen fluid under 2 feeding regimens. The experiments were performed in vitro using a rumen fluid buffer system. The rumen fluid was taken from cows fed either a hay diet or a concentrate-rich diet (the diet consisted of 34.6% maize silage, 17.6% haylage, 12.8% alfalfa...

The genus Armillaria belongs to basidiomycetes and has been known to induce root rot disease and to cause extensive economic losses to a forest crop. We analysed about 40 isolates of Armillaria collected in Czech Republic by PCR and restriction analysis using gel electrophoresis and ion-exchange HPLC. Restrictase Hinf I was able to discriminate all...

Nitric oxide (NO) is considered as a signalling molecule involved in a variety of important physiological and pathological processes in plant and animal systems. The major pathway of NO reactions in vivo represents S-nitrosation of thiols to form S-nitrosothiols. S-nitrosoglutathione reductase (GSNOR) is the key enzyme in the degradation pathway of...

CD36 gene encodes a membrane glycoprotein (type B scavenger receptor) present on the surface of many types of cells and having multiple cellular functions ranging from angiogenesis to gustatory perception of fatty acids. Using a case control genetic association approach we have analyzed selected single nucleotide polymorphisms (SNP’s) in a total of...

The effect of supplementing a basal diet for dairy cows with “Soybean extract 40” (Biomedica, Prague, Czech Republic), containing 40% soybean isoflavones, on the contents of daidzein, glycitein, genistein, and equol in milk as well as fresh and mature yogurts was estimated. To determine the contents of these isoflavonoids, an efficient analytical L...

Plant plasma membrane associated proteins play significant roles in Microbe-Associated Molecular Pattern (MAMP) mediated defence responses including signal transduction, membrane transport or energetic metabolism. To elucidate the dynamics of proteins associated with plasma membrane in response to cryptogein, a well-known MAMP of defence reaction s...

Background and Aims Current strategies for increased crop protection of susceptible tomato plants against pathogen infections include treatment with synthetic chemicals, application of natural pathogen-derived compounds or transfer of resistance genes from wild tomato species within breeding programmes. In this study, a series of 45 genes potential...

Although plants are exposed to a great number of pathogens, they usually defend themselves by triggering mechanisms able to limit disease development. Alongside signalling events common to most such incompatible interactions, modifications of plasma membrane (PM) physical properties could be new players in the cell transduction cascade. Different p...

To study the various processes in the rumen the in vitro techniques are widely used to realize more controlled and reproducible conditions compared to in vivo experiments. Mostly, only the parameters like pH changes, volatile fatty acids content or metabolite production are monitored. In this study we examine the bacterial community dynamics of rum...

In this study, we compared the effects of two diets containing different isoflavone concentrations on the isoflavone transfer from feed into milk and on the rumen microbiota in lactating dairy cows. The on-farm experiment was conducted on twelve lactating Czech Fleckvieh x Holstein cows divided into two groups, each with similar mean milk yield. Tw...

Effect of supplementation of basal diet (CTRL) with 40% isoflavone extract (EXP) on characteristics of the rumen milieu of dairy cows. (PDF)

Average daily intake of nutrients and isoflavones of dairy cows fed basal diet either unsupplemented (CTRL) or supplemented with 40% isoflavone extract (EXP). (PDF)

OTU table of all microbiota detected in rumen of control and experimental cows classified down to genus level. (XLSX)

Composition of supplemental mixture. (PDF)

Effects of supplementation of basal diet (CTRL) with 40% isoflavone extract (EXP) on average milk yield, milk contents, yield of milk components and isoflavones, and isoflavone carry-over rate from feed to milk. (PDF)

Workflow of sequence analysis. (PDF)

Soybean-derived isoflavones belong to the family of biologically active phytoestrogens. The purpose of this study was to develop a sensitive method, which permits quantification of the soybean isoflavonoids and equol in bovine rumen fluid and milk using LC–MS-(TOF). The samples of rumen fluid and milk were obtained from 12 lactating dairy cows inge...

Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6–7 lysine residues) are generally 50- to 100-fold more active...

To clarify the pathway of anaerobic sulfur oxidation coupled with dissimilatory ferric iron reduction in Acidithiobacillus ferrooxidans strain CCM 4253 cells, we monitored their energy metabolism gene transcript profiles. Several genes encoding electron transporters involved in aerobic iron and sulfur respiration were induced during anaerobic growt...

Objectives: Tooth agenesis is one of the most common developmental anomalies in humans. Genetic and environmental factors may be of etiological importance in this condition. Among genes involved in tooth morphogenesis, mutations in PAX9, MSX1, AXIN2, WNT10a, and EDA genes have been associated with tooth agenesis. The aim of our study was to invest...

Cryptogein, a protein from oomycete Phytophthora cryptogea, induces a hypersensitive cell death in Nicotiana tabacum. We prepared a new series of cryptogein mutant proteins with altered abilities to bind sterols and with altered charge distribution in the proteins. The effect of the mutations on the cryptogein ability to induce plant defence mechan...

The objective of the study was to examine several polymorphisms in DISC1 and CTNX3 genes as possible risk factors in schizophrenia. DISC1 (disrupted-in-schizophrenia 1) has been studied extensively in relation to mental disease while CTXN3, has only recently emerged as a potential “candidate” gene in schizophrenia. CTXN3 resides in a genomic region...

Grey mould caused by Botrytis cinerea is one of the most important diseases of grapevine resulting in significant reductions in yield and fruit quality. In order to examine the molecular mechanisms that characterize the interaction between B. cinerea and the host plant, the grapevine cytoplasmic proteome was analyzed by two-dimensional polyacrylami...

Elicitors, endogenous compounds produced by microbial pathogens, induce defence responses in plants. They rank among chemically nonuniform groups including proteins, glycoproteins, oligo-and polysaccharides and lipids. By multiple mechanisms, elicitors are capable of triggering various modes of plant defence like oxidative burst, hypersensitive res...

Objectives Objectives: Increasing evidences support the importance of epigenetic control in schizophrenia pathogenesis. One of the enzymes involved in DNA methylation process through homocysteine metabolism is methylenetetrahydrofolate reductase (MTHFR). The most extensively studied variant in the MTHFR gene is the C677T polymorphism, resulting in...

Ergosterol, a principal compound of the fungal plasma membrane, is regarded as a pathogen-associated molecular pattern. In the present study, the role of salicylic acid (SA), jasmonic acid (JA) and spermine signaling pathways after ergosterol elicitation were evaluated. SA, JA and spermine production, as well as accumulation of transcripts for a li...

In contrast to iron-oxidizing Acidithiobacillus ferrooxidans, A. ferrooxidans from a stationary phase elemental sulfur-oxidizing culture exhibited a lag phase in pyrite oxidation, which is similar to its behaviour during ferrous iron oxidation. The ability of elemental sulfur-oxidizing A. ferrooxidans to immediately oxidize ferrous iron or pyrite w...

Objectives: The methylenetetrahydrofolate reductase (MTHFR) enzyme activity plays an important role in the metabolism of folate within methionine-homocysteine pathway and, consequently, in the development of vascular diseases. The C677T polymorphism (rs1801133) of the MTHFR gene affects the MTHFR activity, modifies the homocysteine plasma concentr...

The results of linkage and candidate gene association studies have led to a range of hypotheses about the pathogenesis of schizophrenia. We limited our study to polymorphisms in candidate genes involved in dopaminergic and noradrenergic systems, and in the 25KDa synaptosomal-associated protein (SNAP-25) gene that is related to neurotransmitter exoc...

Cryptogein is a proteinaceous elicitor secreted by Phytophthora cryptogea that can induce resistance to P. parasitica in tobacco plants. On the basis of previous computer modelling experiments, by site-directed mutagenesis a series of cryptogein variants was prepared with altered abilities to bind sterols, phospholipids or both. The sterol binding...

Impulsive and hyperactive behavior is related to a central serotonin dysfunction and the results of recent studies indicate the possible relationship between polymorphisms of the serotonin transporter gene (SLC6A4) and hyperkinetic disorder/ADHD. Sample: The sample included 90 boys with ADHD and the control group consisted of 82 boys. Method: The d...

Elicitins are family of small proteins secreted by species of the pathogenic fungus Phytophthora inducing a defence reaction in plants. They contain a hydrophobic cavity capable of binding sterols and fatty acids, and on the basis of their pI they are classified as either α-elicitins or more necrotising β-elicitins. The residue Lys13 was previously...

Capsidiol is a bicyclic sesquiterpene, which accumulates extracellularly in plants, and has been isolated from many types of Solanaceae. It acts as a phytoalexin produced by Nicotiana tabacum in response to pathogens. Capsidiol has antifungal activity and is formed first in tobacco and pepper plants after infestation. The amount of capsidiol in tob...

There is accumulating evidence that disturbances in N-methyl-D: -aspartate receptor (NMDA-R) functioning are associated with the pathogenesis of schizophrenia. To assess actual changes in the expression of the GluN1 subunit and its isoforms, we measured absolute differences in the levels of mRNA/protein for panGluN1 (eight isoforms altogether) as w...

Impulsive and hyperactive behavior is related to a central serotonin dysfunction and the results of recent studies indicate the possible relationship between polymorphisms of the serotonin transporter gene and hyperkinetic disorder/ADHD. The sample included 90 boys with ADHD and the control group consisted of 82 boys. The diagnosis was based on the...

An abnormality in neurodevelopment is one of the most accepted etiologic hypotheses in schizophrenia. There is strong evidence that genetic factors may influence abnormal neurodevelopment in this disease. Our study was focused on the relationship between functional A118G polymorphism of OPRM1 gene and schizophrenia on the group of 227 males. In our...

Elicitins are low-molecular-weight proteins representing the elicitor family secreted by many species of the oomycete Phytophthora. Elicitins induce a hypersensitive reaction in tobacco, a process that is triggered by binding of elicitin to the high-affinity site on the plasma membrane. Specific interaction of cryptogein with the binding sites on t...

Predisposition to alcohol dependence is affected by multiple environmental and genetic factors. Modern molecular genetic techniques allow examining specific genes involved in the pathophysiology of complex diseases such as alcohol dependence. Between strategies for susceptibility gene identification are association studies. We carried out the assoc...

Erectile dysfunction (ED) is a common problem of middle-aged and elderly men. The etiology of erectile dysfunction is 80% organic and the most frequent cause of ED is cardiovascular disease. Erectile dysfunction and coronary artery disease have the same base and hence the same risk factors. Therefore, coronary artery disease appears in patients wit...

Autosomal dominant early-onset Alzheimer disease is a heterogeneous condition that has been associated with mutations in 3 different genes: the amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2) genes. Hypothyroidism and subclinical hyperthyroidism have both been associated with cognitive impairment and dementia. In our...

Alcoholism induces the brain damage but it may also cause the color vision deficiency. In our association study of genetic dispositions to the alcoholism in 167 alcoholics and 289 non-alcoholic controls, we studied a relationship between candidate genes and alcoholism. In all subjects involved in this study many factors, e.g. color vision deficienc...

Armillaria socialis belongs to subgen. Desarmillaria . Its correct specific name (in comparison with the frequently used name A. tabescens ) is discussed, and its detailed macro– and microscopic description and distribution in the Czech Republic and Europe are given. It is a thermophilic species occurring in Europe, USA, Japan and China. The northe...

Ergosterol is the main sterol of most fungi. Production of reactive oxygen species after the treatment of tobacco and tomato cells by nano-molar concentrations of ergosterol was previously observed as well as the activation of some stress activated mitogen-activated protein kinases on alfalfa cells. In this paper, the expression of some defence-rel...