Analysis of Phage Regulatory RNAs: Sequencing Library Construction from the Fraction of Small Prokaryotic RNAs Less Than 50 Nucleotides in Length.

So far, bacterial regulatory sRNAs of length less than 50 nucleotides have been poorly understood, and a low number of such molecules has been identified. The first microRNA-size functional ribonucleic acid occurring in a bacterial cell has been described only recently, and it was found to be encoded by a bacteriophage. One of the reasons for such a scarcity in this field is the lack of procedures intended for the isolation and selection of molecules of this size from bacterial cells. To meet these difficulties, we describe here the few-step procedure of isolation, purification, selection, and sequencing library preparation that is dedicated to the fraction of very small, bacterial RNA molecules.

Neuropeptide Y and its receptors in prostate cancer: associations with cancer invasiveness and perineural spread.

PURPOSE: Neuropeptide Y (NPY) is a pleiotropic peptide, which is involved in many biological mechanisms important in regulation of cell growth and survival. The aim of this study was a comprehensive analysis of the NPY system in prostate pathology. METHODS: The study was based on immunohistochemical analysis of NPY and its receptors, Y1R, Y2R and Y5R, in tissue samples from benign prostate (BP), primary prostate cancer (PCa) and PCa bone metastases. Tissue microarray (TMA) technique was employed, with analysis of multiple cores from each specimen. Intensity of the immunoreactivity and expression index (EI), as well as distribution of the immunostaining in neoplastic cells and stromal elements were evaluated. Perineural invasion (PNI) and extraprostatic extension (EPE) were areas of special interests. Moreover, a transwell migration assay on the LNCaP PCa cell line was used to assess the chemotactic properties of NPY. RESULTS: Morphological analysis revealed homogeneous membrane and cytoplasmic pattern of NPY staining in cancer cells and its membrane localization with apical accentuation in BP glands. All elements of the NPY system were upregulated in pre-invasive prostate intraepithelial neoplasia, PCa and metastases. EI and staining intensity of NPY receptors were significantly higher in PCa then in BP with correlation between Y2R and Y5R. The strength of expression of the NPY system was further increased in the PNI and EPE areas. In bone metastases, Y1R and Y5R presented high expression scores. CONCLUSION: The results of our study suggest that the NPY system is involved in PCa, starting from early stages of its development to disseminated states of the disease, and participates in the invasion of PCa into the auto and paracrine matter.

Proteomic Studies of Roots in Hypoxia-Sensitive and -Tolerant Tomato Accessions Reveal Candidate Proteins Associated with Stress Priming.

Tomato (Solanum lycopersicum L.) is a vegetable frequently exposed to hypoxia stress induced either by being submerged, flooded or provided with limited oxygen in hydroponic cultivation systems. The purpose of the study was to establish the metabolic mechanisms responsible for overcoming hypoxia in two tomato accessions with different tolerance to this stress, selected based on morphological and physiological parameters. For this purpose, 3-week-old plants (plants at the juvenile stage) of waterlogging-tolerant (WL-T), i.e., POL 7/15, and waterlogging-sensitive (WL-S), i.e., PZ 215, accessions were exposed to hypoxia stress (waterlogging) for 7 days, then the plants were allowed to recover for 14 days, after which another 7 days of hypoxia treatment was applied. Root samples were collected at the end of each time-point and 2D-DIGE with MALDI TOF/TOF, and expression analyses of gene and protein-encoded alcohol dehydrogenase (ADH2) and immunolabelling of ADH were conducted. After collating the obtained results, the different responses to hypoxia stress in the selected tomato accessions were observed. Both the WL-S and WL-T tomato accessions revealed a high amount of ADH2, which indicates an intensive alcohol fermentation pathway during the first exposure to hypoxia. In comparison to the tolerant one, the expression of the adh2 gene was about two times higher for the sensitive tomato. Immunohistochemical analysis confirmed the presence of ADH in the parenchyma cells of the cortex and vascular tissue. During the second hypoxia stress, the sensitive accession showed a decreased accumulation of ADH protein and similar expression of the adh2 gene in comparison to the tolerant accession. Additionally, the proteome showed a greater protein abundance of glyceraldehyde-3-phosphate dehydrogenase in primed WL-S tomato. This could suggest that the sensitive tomato overcomes the oxygen limitation and adapts by reducing alcohol fermentation, which is toxic to plants because of the production of ethanol, and by enhancing glycolysis. Proteins detected in abundance in the sensitive accession are proposed as crucial factors for hypoxia stress priming and their function in hypoxia tolerance is discussed.

VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset.

Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS-a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters-selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software-VCF2CAPS-fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services.

The potential role of fatty acids in prostate cancer determined by GC-MS analysis of formalin-fixed paraffin-embedded tissue samples.

Prostate cancer (PCa) is one of the leading types of cancer in men. Although the diagnosis of this disease is currently quite effective, there is still a need to search for noninvasive diagnostic and monitoring methods. Consequently, identifying the mechanisms underlying the development and progression of PCa is crucial. It has been confirmed that the hallmarks of PCa include changes in metabolism, particularly that of fatty acids. Therefore, the application of lipidomics with an accurate histopathological assessment can provide the necessary information and reveal the metabolites that are characteristic of the disease. The use of formalin-fixed, paraffin-embedded (FFPE) tissue samples as an alternative matrix in retrospective research makes this approach highly innovative. The main goal of this study was to perform an untargeted lipidomic analysis of FFPE PCa tissue samples (n = 52) using gas chromatography coupled with mass spectrometry (GC-MS), in comparison to controls (n = 50). To our knowledge, this study is the first to simultaneously conduct a metabolic analysis and histopathological assessment. In the latter, the samples were evaluated based on Gleason grading score and pTNM stage. The obtained results were evaluated by univariate (Student's t-test or Mann-Whitney U-test) as well as multivariate statistical analysis (principal component analysis, partial least squares-discriminant analysis, variable importance into projection, and selectivity ratio) in order to select the metabolites with the most discriminative power. Additionally, the correlation between the level of metabolites and pathological characteristics was determined. The results of the analyses confirmed the changes in the lipid metabolism pathway in PCa. It can be assumed that PCa is linked with elevated de novo biosynthesis of steroid hormone-related fatty acids and beta-oxidation of fatty acids. An increased level of three fatty acids, namely 9-octadecanoic acid, 9,12-octadecadienoic acid, and 5, 8, 1,14-eicosatetraenoic acid, was observed in the PCa samples. These fatty acids were assigned as metabolites with the best discriminative power for the two tested groups. In practice, these compounds could be considered as specific biochemical factors that may be implemented in the diagnosis of PCa, but their significance should be validated on a more extensive set of samples. Undoubtedly, these results are valuable as they provide important information on prostate cancerogenesis in the context of a metabolic switch.

Stem Photosynthesis-A Key Element of Grass Pea (Lathyrus sativus L.) Acclimatisation to Salinity.

Grass pea (Lathyrus sativus) is a leguminous plant of outstanding tolerance to abiotic stress. The aim of the presented study was to describe the mechanism of grass pea (Lathyrus sativus L.) photosynthetic apparatus acclimatisation strategies to salinity stress. The seedlings were cultivated in a hydroponic system in media containing various concentrations of NaCl (0, 50, and 100 mM), imitating none, moderate, and severe salinity, respectively, for three weeks. In order to characterise the function and structure of the photosynthetic apparatus, Chl a fluorescence, gas exchange measurements, proteome analysis, and Fourier-transform infrared spectroscopy (FT-IR) analysis were done inter alia. Significant differences in the response of the leaf and stem photosynthetic apparatus to severe salt stress were observed. Leaves became the place of harmful ion (Na+) accumulation, and the efficiency of their carboxylation decreased sharply. In turn, in stems, the reconstruction of the photosynthetic apparatus (antenna and photosystem complexes) activated alternative electron transport pathways, leading to effective ATP synthesis, which is required for the efficient translocation of Na+ to leaves. These changes enabled efficient stem carboxylation and made them the main source of assimilates. The observed changes indicate the high plasticity of grass pea photosynthetic apparatus, providing an effective mechanism of tolerance to salinity stress.

Complexity of Neural Component of Tumor Microenvironment in Prostate Cancer.

The tumor microenvironment (TME) plays an essential role in the development and progression of neoplasms. TME consists of the extracellular matrix and numerous specialized cells interacting with cancer cells by paracrine and autocrine mechanisms. Tumor axonogenesis and neoneurogenesis constitute a developing area of investigation. Prostate cancer (PC) is one of the most common malignancies in men worldwide. During the past years, more and more studies have shown that mechanisms leading to the development of PC are not confined only to the epithelial cancer cell, but also involve the tumor stroma. Different nerve types and neurotransmitters present within the TME are thought to be important factors in PC biology. Moreover, perineural invasion, which is a common way of PC spreading, in parallel creates the neural niche for malignant cells. Cancer neurobiology seems to have become a new discipline to explore the contribution of neoplastic cell interactions with the nervous system and the neural TME component, also to search for potential therapeutic targets in malignant tumors such as PC.

Colonic Adenocarcinomas Harboring NTRK Fusion Genes: A Clinicopathologic and Molecular Genetic Study of 16 Cases and Review of the Literature.

This study was undertaken to determine the frequency, and the clinicopathologic and genetic features, of colon cancers driven by neurotrophic receptor tyrosine kinase (NTRK) gene fusions. Of the 7008 tumors screened for NTRK expression using a pan-Trk antibody, 16 (0.23%) had Trk immunoreactivity. ArcherDx assay detected TPM3-NTRK1 (n=9), LMNA-NTRK1 (n=3), TPR-NTRK1 (n=2) and EML4-NTRK3 (n=1) fusion transcripts in 15 cases with sufficient RNA quality. Patients were predominantly women (median age: 63 y). The tumors involved the right (n=12) and left colon unequally and were either stage T3 (n=12) or T4. Local lymph node and distant metastases were seen at presentation in 6 and 1 patients, respectively. Lymphovascular invasion was present in all cases. Histologically, tumors showed moderate to poor (n=11) differentiation with a partly or entirely solid pattern (n=5) and mucinous component (n=10), including 1 case with sheets of signet ring cells. DNA mismatch repair-deficient phenotype was seen in 13 cases. Tumor-infiltrating CD4/CD8 lymphocytes were prominent in 9 cases. Programmed death-ligand 1 positive tumor-infiltrating immune cells and focal tumor cell positivity were seen in the majority of cases. CDX2 expression and loss of CK20 and MUC2 expression were frequent. CK7 was expressed in 5 cases. No mutations in BRAF, RAS, and PIK3CA were identified. However, other genes of the PI3K-AKT/MTOR pathway were mutated. In several cases, components of Wnt/ß-catenin (APC, AMER1, CTNNB1), p53, and TGFß (ACVR2A, TGFBR2) pathways were mutated. However, no SMAD4 mutations were found. Two tumors harbored FBXW7 tumor suppressor gene mutations. NTRK fusion tumors constitute a distinct but rare subgroup of colorectal carcinomas.

Callitriche cophocarpa (water starwort) proteome under chromate stress: evidence for induction of a quinone reductase.

Chromate-induced physiological stress in a water-submerged macrophyte Callitriche cophocarpa Sendtn. (water starwort) was tested at the proteomic level. The oxidative stress status of the plant treated with 1 mM Cr(VI) for 3 days revealed stimulation of peroxidases whereas catalase and superoxide dismutase activities were similar to the control levels. Employing two-dimensional electrophoresis, comparative proteomics enabled to detect five differentiating proteins subjected to identification with mass spectrometry followed by an NCBI database search. Cr(VI) incubation led to induction of light harvesting chlorophyll a/b binding protein with a concomitant decrease of accumulation of ribulose bisphosphate carboxylase (RuBisCO). The main finding was, however, the identification of an NAD(P)H-dependent dehydrogenase FQR1, detectable only in Cr(VI)-treated plants. The FQR1 flavoenzyme is known to be responsive to oxidative stress and to act as a detoxification protein by protecting the cells against oxidative damage. It exhibits the in vitro quinone reductase activity and is capable of catalyzing two-electron transfer from NAD(P)H to several substrates, presumably including Cr(VI). The enhanced accumulation of FQR1 was chromate-specific since other stressful conditions, such as salt, temperature, and oxidative stresses, all failed to induce the protein. Zymographic analysis of chromate-treated Callitriche shoots showed a novel enzymatic protein band whose activity was attributed to the newly identified enzyme. We suggest that Cr(VI) phytoremediation with C. cophocarpa can be promoted by chromate reductase activity produced by the induced quinone oxidoreductase which might take part in Cr(VI) â†’ Cr(III) bioreduction process and thus enable the plant to cope with the chromate-generated oxidative stress.

Primary Spinal Intradural Mesenchymal Chondrosarcoma with Several Local Regrowths Treated with Osteoplastic Laminotomies: A Case Report.

Mesenchymal chondrosarcomas (MCSs) are rare malignant tumors of the bone and soft tissues. Only a few cases of such tumors originating from the spinal canal meninges have been described in the literature. The authors report on a case of a 22-year-old woman with MCS of the arachnoid at the T12-L1 level with a 14-year-long observation. The tumor was totally resected using osteoplastic laminotomy with reconstruction of laminar roof. This small spindle cell tumor was initially microscopically suspected of synovial sarcoma, but correctly verified with widened immunophenotyping and molecular studies as MCS. At its first recurrence, the neoplasm showed microscopically a typical bimorphic pattern of small round cell component with foci of hyaline cartilage. The patient experienced three local recurrences: 4, 6, and 10 years after the initial resection, respectively. The techniques of laminotomy and relaminotomy were also used during three following operations. The repeated surgical removal, radiotherapy, and chemotherapy were the methods of complex oncological treatment. The patient remains now in complete remission, fully self-dependent with slight motor disturbance, and mild sensory deficits. Current views on the clinicopathological characteristics and treatment modalities of the chondrosarcomas of the spinal canal are discussed.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) - literature review apropos an autopsy case.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a non-atherosclerotic, non-amyloid cerebral angiopathy involving small arteries and arterioles. This entity presents vascular changes in the form of smooth muscle degeneration with swollen myocytes and PAS-positive granular deposits, together with vascular fibrosis and hyalinization. In parallel, diffuse white matter destruction with infarcts, tissue rarefaction, spongiosis, lacunes and demyelination are characteristic. Ultrastructurally, vascular granular osmiophilic material (GOM) is pathognomonic for this hereditary disease caused by NOTCH3 mutation. We diagnosed CADASIL in the autopsy examination of a 53-year-old woman with a 9-year history of a progressive neurological disease with complex motor and cognitive deficits, accompanied by non-specific diffuse white matter changes on neuroimaging. Despite several multicentre hospitalizations, the precise diagnosis was not established until the post-mortem examination of the brain was made. CADASIL is a rare entity, but it should be considered by a pathologist in a differential diagnosis of vascular diseases of the brain, especially in cases with atypical clinical presentation and familial history. The prompt diagnosis depends on the quality of the brain autopsy and proper sampling. The post mortem examination, where "Morituri vivos docent", is still significant.

Extracardiac rhabdomyomas--presentation of two cases with analysis of AKT/mTOR and ERK1/2 signaling.

Extracardiac rhabdomyomas (RM) are very rare benign tumors with a poorly understood pathogenesis. In this report we describe two RM cases--a sublingual adult type tumor and a genital type tumor involving the uterine cervix. The patho-clinical characteristics, as well as the pioneer immunohistochemical analysis of ERK1/2 and AKT/mTOR pathway status is included. The expression of key proteins involved in above signaling gives new insight into the biology of extracardiac RM.

Analysis of the mitochondrial proteome in cytoplasmic male-sterile and male-fertile beets.

The reported analyses were aimed at identification of the mitochondrial proteome features which were associated with cytoplasmic male sterility (CMS) in beets. The set of analyzed accessions included CMS, maintainer and restored lines. Mitochondrial preparations were subjected to blue-native electrophoresis followed either by in-gel activity assays or separation in denaturing conditions. The CMS condition was associated with decreased activity of complex V and enhancement of additional complexes with the ATPase activity. This was accompanied by accumulation of heptamer HSP60, preSATP6 and an increase in the fraction of the free ATP9 oligomer (not bound to complex V). The ATP9 effect was reversed upon fertility restoration. BIOLOGICAL SIGNIFICANCE: The reported work provides one of very few comprehensive comparisons of the mitochondrial proteomes from cytoplasmic male-sterile (CMS) and male-fertile plants. It shows that in beets the CMS trait is associated with altered functioning of the mitochondrial ATP synthase complex. The presence of CMS-specific ATP synthase subcomplexes resembles deficiencies of this enzyme reported for mammalian cells.

Cancer metastases to meningioma: apropos two cases.

Tumour-to-tumour metastasis (TTTM) is the uncommon phenomenon in the systemic and central nervous system neoplasia. We report on two new cases of metastases to meningioma. The first case concerned a patient with renal cancer and synchronous asymptomatic meningioma followed up radiologically. In the fifth year of observation, he developed acute neurological symptoms. Neuroimaging showed meningioma enlargement with irregular surrounding oedema. On gross exam, the tumour had two different components, which histopathologically comprised atypical meningioma and renal cancer deposits. The patient's postoperative course was complicated with a subdural hematoma. The second TTTM case concerned a patient with a two-year history of colorectal cancer treatment with recent severe headaches. Radiologically the temporal lobe metastatic focus was detected. During cerebral metastasectomy, small meningeal incidentaloma was resected, histologically being meningioma with adenocarcinoma metastasis. Tumour metastasis to meningioma can be the only one or one of the places of cancer dissemination. TTTM can cause postoperative complications. Our cases prove the importance of the careful sampling of tumours and necessity of immunohistochemistry in differential diagnosis between meningioma subtypes and metastatic focus.

Comparison of tissue distribution and metabolism of 1,2- and 1,4-dibromobenzenes in female rats.

The distribution, excretion and metabolism of 1,4-dibromobenzene (1,4-DBB) and 1,2-dibromobenzene (1,2-DBB), following a single intraperitoneal administration to female Wistar rats, were investigated using radiotracer 3H and GC-MS technique. The maximum level of 3H after 1,4-DBB administration was detected in all examined rat tissues between 4 and 24 h foltowing the injection. The highest concentrations of 3H were found in fat tissue, muscles, adrenal glands and sciatic nerve. About 50% of administered dose was still retained in the rat 72 h after injection. For 1,2-DBB, the highest level of 3H was in the liver, kidneys and fat tissue 4 and 8 h after administration. Three days after injection, less than 2% of the given dose was retained in the rat body. Urine turned out to be the main route of 3H excretion following the injection of both compounds (30% and 82%, after 1,4-DBB and 1,2-DBB, respectively), and about 4% of the given dose was excreted in feces. In urine of rats the following substances were identified (in sequence 1,4-dBB and 1,2-dBB): (1) unchanged parent compounds (5 and 11%); (2) dibromophenols (84 and 73%); (3) dibromothiophenols (5 and 10%) and (4) monobromophenols (1.9 and 0.7%). This study suggests that 1,2-DBB is characterized by a relatively high turnover rate, whereas 1,4-DBB shows a tendency for long-term retention in the body.