The direct relationship between hydrogenase gene conformation and its function in green alga Chlamydomonas reinhardtii has been investigated. We have analyzed the conformation in the 29 kilobase (kb) ...chromosome region containing FeFe-hydrogenase gene (hydA1) of C. reinhardtii in aerobic and anaerobic conditions using chromosome conformation capture technique (3C). The results showed a loop organization in the FeFe-hydrogenase gene region under aerobic conditions when the hydrogenase gene is silenced. In contrast, under anaerobic conditions, when the hydrogenase gene is active, no loop conformation in the gene region is present.
► Relationship between hydrogenase gene conformation and its function in algae was established. ► Loop organization of Fe-hydrogenase gene region under aerobic conditions was found. ► No any loops exist in Fe-hydrogenase gene region under anaerobiosis when gene is expressed.
Gene expression and silencing in eukaryotic systems can be controlled by regulatory elements acting over a distance. Here, we analyze chromatin conformation of the 24-kb region of the Ifng gene ...during CD4+T helper (Th) cell differentiation. We find that chromatin within this region is a highly flexible structure that undergoes dynamic changes during the course of transcriptional activation and silencing of the Ifng gene. Each Th subset displays a common core conformation in this gene region and unique features that distinguish neutral and effector Th1 and Th2 lineages. This chromatin configuration brings distal regions into close proximity to the gene. Th1 cells that produce high levels of IFN-γ, display the most open conformation. In contrast, IFN-γ silent Th2 cells have a tightly closed conformation. Therefore, we postulate that there is a direct structure-function relationship between the spatial organization of the chromatin around the Ifng gene and its transcriptional potential.
An inorganic culture medium contaminated with ammonium was used to generate molecular hydrogen by cyanobacteria. First, ammonium ion uptake by immobilized on hollow fibers cells of cyanobacterium ...Anabaena variabilis was studied in flasks and in a photobioreactor. Next, after the ammonium was removed from water, H2 production by hollow fibers-immobilized cyanobacterial cells was investigated in flasks and in a photobioreactor. The photobioreactor was designed so that the growth medium with ammonium from a medium reservoir (where ammonium ion concentration was measured) was cycled through a photobioreactor column with hollow fiber-attached cells. The ammonium ion uptake efficiency by attached cells in the photobioreactor was found to be 90% after 25 days. The depletion of the ammonium in water inside a photobioreactor stimulated H2 production by cyanobacteria which was observed at an average rate of 18 mL·g dw−1·h−1 for three months.
•Inorganic culture medium with ammonium was used to generate H2 by cyanobacteria.•Ammonium ion uptake efficiency by attached cells in the photobioreactor was 90%.•Ammonium ion removal from water stimulated H2 production at rate of 18 mL·g−1·h−1.
Compartmentalization and compaction of DNA in the nucleus is the characteristic feature of eukaryotic cells. A fully extended DNA molecule has to be compacted 100,000 times to fit within the nucleus. ...At the same time it is critical that various DNA regions remain accessible for interaction with regulatory factors and transcription/replication factories. This puzzle is solved at the level of DNA packaging in chromatin that occurs in several steps: rolling of DNA onto nucleosomes, compaction of nucleosome fiber with formation of the so-called 30 nm fiber, and folding of the latter into the giant (50–200 kbp) loops, fixed onto the protein skeleton, the nuclear matrix. The general assumption is that DNA folding in the cell nucleus cannot be uniform. It has been known for a long time that a transcriptionally active chromatin fraction is more sensitive to nucleases; this was interpreted as evidence for the less tight compaction of this fraction. In this review we summarize the latest results on structure of transcriptionally active chromatin and the mechanisms of transcriptional regulation in the context of chromatin dynamics. In particular the significance of histone modifications and the mechanisms controlling dynamics of chromatin domains are discussed as well as the significance of spatial organization of the genome for functioning of distant regulatory elements.
In interphase nuclei as in metaphase chromosomes, the genome is organized into topologically closed loop domains. Here, we have mapped the ends of the loop domain that contains the
Ifng ...(interferon-γ) gene in primary and cultured murine T-lymphocytes. To determine whether the ends of the loop are located in close proximity to each other in the nuclear space, the 3C (chromosome conformation capture) technique, which detects protein-mediated DNA–DNA interactions, was utilized. A strong interaction was demonstrated between the two ends of the loop, which were close enough to become cross-linked
in vivo in the presence of paraformaldehyde. Chromatin immunoprecipitation combined with the 3C technique demonstrated that topoisomerase IIα and MeCP2, but not topoisomerase IIβ, heterochromatin-associated protein HP1 or CTCF, were involved in this interaction. The present findings have important implications in terms of mechanisms of illegitimate recombination that can result in chromosomal translocations and deletions.
Recruitment of the RNA polymerase II transcription complex to the promoter of the
Ifng gene has been studied by chromatin immunoprecipitation (ChIP) in activated functionally different CD4+ T helper ...(Th) cell subsets. In parallel, analysis of association of the nuclear scaffold/matrix with the
Ifng gene promoter has been carried out. The RNA polymerase II (RNA pol II) interacted with the
Ifng gene promoter in analyzed activated neutral Th cells, IFN-γ producing Th1 cells and IFN-γ silent Th2 cells. However, the interaction of the
Ifng gene promoter with the nuclear matrix occurred differentially in a lineage-specific manner. The pattern of the nuclear matrix interaction correlated directly with the gene expression. Strong association of the promoter with the nuclear matrix was observed only in the Th1 cell subset where the
Ifng gene was actively transcribed. We propose that it is the interaction of the
Ifng gene promoter with the nuclear matrix that may set off transcription in activated Th cells by promoter-associated RNA pol II.
The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article ...reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: (1) being a scientist and generating data; (2) teaching procedural knowledge; and (3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.
Objective
To assess the functional relationship between antibodies reactive with DNA and antibodies reactive with the idiotypes (idiopeptides) of anti‐DNA antibodies that are associated with systemic ...lupus erythematosus (SLE) in mice.
Methods
Antiidiotypic antibodies that appeared spontaneously in lupus mice, and others that were induced by immunization of normal, non‐lupus mice, were analyzed for their reactivity by a range of direct binding, competition enzyme‐linked immunosorbent assay (ELISA), and surface plasmon resonance (SPR) methods. Their reactions were assessed against synthetic peptides representing sequences of the VH region of anti‐DNA monoclonal antibody (mAb) V‐88, against the native mAb itself, and against mammalian DNA.
Results
In lupus mice, only sera with the highest reactivity against double‐stranded DNA (dsDNA) also reacted with idiopeptides in ELISA, and this showed a strong statistical correlation. However, there was no significant relationship between antiidiotypic antibodies and anti–single‐stranded DNA antibodies. Immunization of (BALB/c × NZW)F1 mice with idiopeptides p64 (VH residues 64–80) or p92 (VH residues 92–105) induced antibodies that reacted not only against the respective peptides, but also against the native parent anti‐DNA mAb V‐88. Furthermore, the immune antiidiopeptide antibodies cross‐reacted with dsDNA. Competition SPR experiments with the BIAcore system supported this observation. The binding reaction of VH peptide p64 (representing the CDR‐H2/FR‐H3 region of V‐88) with antiidiopeptide antibodies was inhibited by dsDNA.
Conclusion
This study identified a unique set of autoantibodies in SLE. They react with both autoantibody idiotopes and with dsDNA, thus having a dual specificity for 2 autoantigens. Because these antiidiotope antibodies arise naturally during the development of lupus disease, and because they bind also to dsDNA, this provides a mechanism whereby the production of anti‐dsDNA antibodies is stimulated. These idiotopes on autoantibodies in lupus act as natural mimotopes for inducing anti‐dsDNA antibodies, which, due to their dual specificity, may significantly contribute to the pathology of nephritis in SLE.
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