Next-Generation Sequencing for Evaluating the Soil Nematode Diversity and Its Role in Composting Processes.

Biodiversity within composting systems involves a variety of microorganisms including nematodes. In the research, nematode populations were monitored within six simultaneously operating composting processes. These processes involved varying proportions of feedstock materials.

First molecular identification of Suillia gigantea (Meigen, 1830) (Diptera: Heleomyzidae).

In 2017, the presence of the fly Suillia gigantea (Meigen, 1830) was noted in Poland, after many years of research related to the ecology of insects associated with the fruiting bodies of hypogeous fungi. Finally, in 2020, after further studies, the distribution of the truffle fly in Poland was confirmed. Six adults were reared from larvae inhabiting the fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.

Tuber wenchuanense, a holarctic truffle with a wide range of host plants and description of its ectomycorrhiza with spruce.

Tuber wenchuanense ascomata (Ascomycota, Pezizales), a species originally described from Sichuan (China), were found in the Tatra Mountains in southern Poland. The purpose of this work was to (i) report and assess the first case of the holarctic natural distribution of a Tuber species, (ii) amend the original description of the species, (iii) summarize data on its host plants and (iv) describe its ectomycorrhiza. Specimens of Tuber wenchuanense from the Tatra Mountains were studied morphologically and molecularly.

Hybridization hotspots at bat swarming sites.

During late summer and early autumn in temperate zones of the Northern Hemisphere, thousands of bats gather at caves, mainly for the purpose of mating. We demonstrated that this swarming behavior most probably leads not only to breeding among bats of the same species but also interbreeding between different species. Using 14 nuclear microsatellites and three different methods (the Bayesian assignment approaches of STRUCTURE and NEWHYBRIDS and a principal coordinate analysis of pairwise genetic distances), we analyzed 375 individuals belonging to three species of whiskered bats (genus Myotis) at swarming sites across their sympatric range in southern Poland.

Validation of a 16-locus fluorescent multiplex system.

STR multiplexes have been indispensable for the efficient genotyping of forensic samples. The PowerPlex 16 System contains the coreCODIS loci, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, THOI, TPOX, vWA, the sex determinant locus, amelogenin, and two pentanucleotide STR loci, Penta D and Penta E. This multiplex satisfies the locus requirements for most national databases and is the most efficient currently available system due to its single PCR amplification.

Development of a human DNA quantitation system.

The AluQuant Human DNA Quantitation System has been developed for human-specific quantitation of forensic samples. This system uses probes specific to repetitive genetic elements allowing quantitation without target amplification. Target immobilization is unnecessary with employment of solution hybridization.

Reuse of denaturing polyacrylamide gels for short tandem repeat analysis.

Denaturing polyacrylamide gel electrophoretic analysis of amplified polymorphic short tandem repeat (STR) loci using fluorescent markers is a mainstay of forensic and paternity testing. To reduce the drawback of preparing gels or using expensive precast gels, we have developed a simple and rapid method to reuse gels between 2 and 8 times over a period of several days. Following the initial electrophoresis and scan, the original samples are removed from the gel by a 1-1.

A novel and simple method to assay the activity of individual protein kinases in a crude tissue extract.

Protein kinases and phosphatases play an important role in a variety of cellular functions. Thus, it is of interest to develop an assay system that can be used to quantify the activity of individual enzymes specifically in a crude cellular extract, is simple to perform, and is amenable to automation. Here we report on the development of a protein kinase assay that addresses these points and circumvents the pitfalls of existing methodologies.

Chromosomal sublocalization of the 2;13 translocation breakpoint in alveolar rhabdomyosarcoma.

A characteristic balanced reciprocal chromosomal translocation [t(2;13)(q35;q14)] has been identified in more than 50% of alveolar rhabdomyosarcomas. As the first step in characterization of the genes involved in this translocation, we constructed somatic cell hybrids that retained either the derivative chromosome 2 or the derivative chromosome 13 without a normal chromosome 13 homologue. Ten linked DNA probes known to be located within bands 13q13-q14 were mapped relative to the breakpoint on chromosome 13, allowing localization of the breakpoint region between two loci separated by 5.

The gene for aromatase (P450arom) in the chicken is located on the long arm of chromosome 1.

An 125I-labeled partial cDNA for the chicken aromatase P450 was used for in situ hybridization to chromosomes from primary chicken embryo fibroblast cultures. The results indicate that the gene that encodes aromatase is located on the long arm of chromosome 1 at approximately position 0.16.

Molecular evaluation of abnormalities of the short arm of chromosome 1 in neuroblastoma.

Cytogenetic analyses have documented the consistent deletion of part of the short arm of chromosome 1 in neuroblastoma cells suggesting the presence of a suppressor gene in this chromosomal region. To determine, the smallest region of deletion overlap at the molecular level on independently derived tumors and to define the location of the breakpoints more precisely, Southern analyses were performed on a somatic cell hybrid panel containing the normal and altered chromosomes 1 from seven neuroblastoma lines. By this method we were able to analyze a panel of 20 cloned sequences and two isozymes to determine the location of the breakpoints.

Excision of N-myc from chromosome 2 in human neuroblastoma cells containing amplified N-myc sequences.

Amplification of one of three growth-stimulating myc genes is a common method by which many tumor types gain a proliferative advantage. In metastatic human neuroblastoma, the amplification of the N-myc locus, located on chromosome 2, is a dominant feature of this usually fatal pediatric cancer. Of the many models proposed to explain this amplification, all incorporate as the initial step either disproportionate overreplication of the chromosomal site or recombination across a loop structure.

Agarose gel electrophoresis in isozyme separation and visualization.

Isozyme analysis of rodent-human somatic cell hybrids has been used frequently to detect specific human chromosomes. The majority of these isozyme systems employs starch gels, the use of which can be laborious when screening large numbers of cell lines. We describe the development of two procedures to detect the long arms of human chromosomes 1 and 2 in Chinese hamster-human cell hybrids by a rapid and reproducible method using 1-mm-thick agarose gels.

Molecular analysis of chromosome 1 abnormalities in neuroblastoma.

Tumor cells from 70% of neuroblastoma patients contain a deletion of part of the short arm of chromosome 1, indicating that this chromosomal region includes a gene involved in tumor formation. To more precisely evaluate the boundaries and mechanisms involved in generating these deletions, we have examined four neuroblastoma cell lines using a combination of somatic cell hybridization, isozyme analysis, and nucleic acid hybridization employing both standard and restriction fragment length polymorphic probes. The data suggest that the truncation of chromosome 1 in these neuroblastomas was most likely due to a complex translocation and deletion mechanism rather than a simple unbalanced translocation or terminal or interstitial deletion.

Use of somatic cell hybrids to analyze role of specific enzymes in daunorubicin cytotoxicity.

Through the use of drug-adapted tissue culture cells, correlations have been observed between the level of specific enzymes and drug resistance. Drug resistance, however, may be due to multiple factors. To test whether the activity of daunorubicin reductase or NADPH diaphorase independently influences in vitro daunorubicin-induced cytotoxicity, we developed somatic cell hybrid clones to partially isolate these factors.

Analysis of JHM central nervous system infections in rats.

Intracerebral inoculation of murine coronavirus JHM into 2- to 3-day-old Wistar Furth rats causes an acute encephalomyelitis, while inoculations at 10 days of age usually result in hind leg paralysis. To examine the distribution of viral antigens within this infected central nervous system (CNS) tissue, we used the avidin-biotin-peroxidase method to detect monoclonal and polyclonal antibodies bound to JHM structural proteins; in addition we used the Western blot technique to detect viral proteins. Our study demonstrated the following characteristics: Infected neuronal and glial cells produced viral nucleocapsid and E2 glycoprotein.

Transformation of mouse bone marrow cells by transfection with a human oncogene related to c-myc is associated with the endogenous production of macrophage colony stimulating factor 1.

We recently derived a series of transformed cell lines by transfecting mouse bone marrow cells highly enriched for macrophage progenitors with a newly described human gene, R-myc, which has homology to the c-myc oncogene. In this report, we show that these lines share some features characteristic of cells of the mononuclear phagocyte lineage. Specifically, all cell lines had macrophage- or monocytelike morphology, contained nonspecific esterase, were phagocytic for latex beads, secreted lysozyme, bore the Mac-1 antigen, and contained a minority of cells with Fc receptors.

Transcription of hematopoietic-associated oncogenes in childhood leukemia.

We have examined the transcriptional expression of the cellular homologues of several retrovirus-associated oncogenes, myc, rel, rasH, myb, src, and erb, in uncultured childhood leukemia and normal hematopoietic cells, as a first step in determining their normal function and possible association with human neoplasia. Cellular myc-specific RNA was detected in all 30 samples of hematopoietic tissue examined, including 18 leukemias of both the lymphoid and myeloid series, three lymphomas, five normal leukocytes, and four cell lines. Although the level of expression varied over a 25-fold range, no general pattern based on cell type or disease state was evident.

Chromosomal clustering of five defined endogenous retrovirus loci in White Leghorn chickens.

By using in situ hybridization, we localized three endogenous chicken retrovirus loci associated with the gs- chf- phenotype to distinct regions on chromosome 1. These three loci, ev4, ev5, and ev8, along with the two other known gs- chf--associated loci in White Leghorn chickens, ev1 and ev13, appear to be evenly distributed along chromosome 1, occurring approximately every 1.8 X 10(7) base pairs.

5'-terminal deletions are a common feature of endogenous retrovirus loci located on chromosome 1 of White Leghorn chickens.

My previous studies demonstrated that chromosome 1 has all five of the endogenous retrovirus loci associated with nonexpression of viral proteins (gs- chf-) in White Leghorn chickens. The current study was done to localize the two defective endogenous retrovirus loci, ev3 and ev6, to determine whether nonexpression of the viral loci on chromosome 1 is a transcriptional prerequisite or a result of an underlying structural defect. The structure of ev6 is every similar to that of two other gs- chf- -associated loci, ev4 and ev5; all three contain a 5'-terminal deletion that eliminates the viral transcriptional promoter.

Chromosomal localization of three endogenous retrovirus loci associated with virus production in White Leghorn chickens.

Proposed mechanisms for the generation of endogenous retrovirus loci have been examined by determining the chromosomal distribution of these loci by means of in situ hybridization. Unlike the clustering on chromosome 1 of five endogenous retrovirus loci associated with the gs- chf- phenotype A. Tereba and S.