The chemokine CXCL13 in acute neuroborreliosis

Objective Recent studies have suggested an important role of the B cell chemoattractant CXCL13 in acute neuroborreliosis (NB). Our aim was to confirm the diagnostic role of CXCL13 and to evaluate its relevance as a therapy response and disease activity marker in NB. Methods CXCL13 was measured in cerebrospinal fluid (CSF) and serum of patients with NB (n = 28), systemic borreliosis (SB, n = 9), Guillaine-Barre syndrome (GBS, n = 11), Bell's palsy (BP, n = 19), other cranial nerve palsies (CNP, n = 5), cephalgia (C, n = 20), bacterial CNS infections (B-CNS-I, n = 16) and viral CNS infections (V-CNS-I, n = 18). For follow-up studies, serial sample pairs were evaluated from 25 patients with NB (n = 56), 11 with B-CNS-I (n = 25) and 14 with V-CNS-I (n = 36). Results CSF-CXCL13 was significantly elevated in NB compared with other neurological diseases (p<0.001). Using receiver operating characteristic analysis, 337 ng/g was determined as a cut-off with a sensitivity of 96.4% and a specificity of 96.9%. Of all the parameters investigated, CSF CXCL13 showed the fastest response to antibiotic therapy, decreasing significantly (p = 0.008) within 1 week. In untreated patients, CSF CXCL13 was elevated in patients with a short duration of disease. Borrelia burgdorferi antibody index showed no significant (p = 0.356) change over follow-up. Conclusions The study confirms the relevance of CXCL13 as a diagnostic biomarker of NB and suggests that CSF CXCL13 in NB is linked to duration of disease and could be a marker of disease activity and response to antibiotic therapy

DNA is a co-factor for its own replication in Xenopus egg extracts

Soluble Xenopus egg extracts efficiently replicate added plasmids using a physiological mechanism, and thus represent a powerful system to understand vertebrate DNA replication. Surprisingly, DNA replication in this system is highly sensitive to plasmid concentration, being undetectable below ∼10 pM and highly efficient above ∼75 pM. DNA replication at the high plasmid concentration does not require plasmid–plasmid contacts, since replication is not inhibited when plasmids are immobilized in agarose prior to addition of egg extract. The absence of replication at low plasmid concentration is due to a defect in the assembly of pre-replication complexes (pre-RCs). pre-RC assembly requires contact-independent communication between plasmids. Our results show that in Xenopus egg extracts, aggregation of multiple replication forks is not required for efficient replication of plasmid DNA, and they suggest that DNA functions as a co-factor for its own duplication

ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Replication-Dependent Unhooking of DNA Interstrand Cross-Links by the NEIL3 Glycosylase

During eukaryotic DNA interstrand cross-link (ICL) repair, cross-links are resolved (“unhooked”) by nucleolytic incisions surrounding the lesion. In vertebrates, ICL repair is triggered when replication forks collide with the lesion, leading to FANCI-FANCD2-dependent unhooking and formation of a double-strand break (DSB) intermediate. Using Xenopus egg extracts, we describe here a replication-coupled ICL repair pathway that does not require incisions or FANCI-FANCD2. Instead, the ICL is unhooked when one of the two N-glycosyl bonds forming the cross-link is cleaved by the DNA glycosylase NEIL3. Cleavage by NEIL3 is the primary unhooking mechanism for psoralen and abasic site ICLs. When N-glycosyl bond cleavage is prevented, unhooking occurs via FANCI-FANCD2-dependent incisions. In summary, we identify an incision-independent unhooking mechanism that avoids DSB formation and represents the preferred pathway of ICL repair in a vertebrate cell-free system

Replication-Dependent Unhooking of DNA Interstrand Cross-Links by the NEIL3 Glycosylase

During eukaryotic DNA interstrand cross-link (ICL) repair, cross-links are resolved (“unhooked”) by nucleolytic incisions surrounding the lesion. In vertebrates, ICL repair is triggered when replication forks collide with the lesion, leading to FANCI-FANCD2-dependent unhooking and formation of a double-strand break (DSB) intermediate. Using Xenopus egg extracts, we describe here a replication-coupled ICL repair pathway that does not require incisions or FANCI-FANCD2. Instead, the ICL is unhooked when one of the two N-glycosyl bonds forming the cross-link is cleaved by the DNA glycosylase NEIL3. Cleavage by NEIL3 is the primary unhooking mechanism for psoralen and abasic site ICLs. When N-glycosyl bond cleavage is prevented, unhooking occurs via FANCI-FANCD2-dependent incisions. In summary, we identify an incision-independent unhooking mechanism that avoids DSB formation and represents the preferred pathway of ICL repair in a vertebrate cell-free system

Calcium sulfate ameliorates the effect of aluminum toxicity differentially in genotypes of highbush blueberry (Vaccinium corymbosum L.)

The effect of gypsum (CaSO 4) amendment in the reduction of Al phytotoxicity of blueberry cultivars differing in Al resistance (Legacy and Brigitta, Al-resistant and Bluegold, Al-sensitive) was studied in a Hoagland's nutrient solution under acidic conditions for 2 weeks. Treatments were: Control (Hoagland solution), 2.5 mM CaSO 4, 5 mM CaSO 4, 100 μM Al (AlCl 3), 100 μM Al + 2.5 μM CaSO 4, 100 M Al + 5 mM CaSO 4. Physiological, biochemical and chemical features of leaves and roots were determined to establish the amendment efficiency in the reduction of Al toxicity in these cultivars. Results showed that under Al toxicity the three investigated cultivars accumulated high Al concentrations in leaves and roots. These concentrations decreased with CaSO 4 application. Statistically significant interactions among Al in leaves but not in roots (p=0.719) and cultivars (p&lt;0.001), were found. The lowest Ca concentration was found in the most Al-sensitive cultivar (Bluegold) and the highest in the more Al-resistant cultivars (Legacy and Brigitta). Among the underlying processes affected by Al stress in these blueberry cultivars the most evident changes were exhibited by the Al-sensitive cultivar Bluegold, where the photosynthetic performance decreased showing a slight recovery in presence of gypsum amendment at the end of experiment. Instead, the more Al-resistant cultivar (Legacy) did not change its photosynthetic parameters in presence of the gypsum amendments during the treatment, whereas in Brigitta, only a slight recovery at the end of treatment was evidenced by the gypsum application. Thus, in relation to these parameters the gypsum amendment was efficient in complete recovery from the toxic Al effect in the Al-resistant cultivar Brigitta and a slight recovery of the toxic Al effect in the Al-sensitive cultivar Bluegold. Nonetheless, this amendment is a good alternative to ameliorate Al toxicity in Al-sensitive cultivars and additionally provides a good source of Ca and S

The mechanism of DNA replication termination in vertebrates

Eukaryotic DNA replication terminates when replisomes from adjacent replication origins converge. Termination involves local completion of DNA synthesis, decatenation of daughter molecules, and replisome disassembly. Termination has been difficult to study because termination events are generally asynchronous and sequence non-specific. To overcome these challenges, we paused converging replisomes with a site-specific barrier in Xenopus egg extracts. Upon removal of the barrier, forks underwent synchronous and site-specific termination, allowing mechanistic dissection of this process. We show that DNA synthesis does not slow detectably as forks approach each other and that leading strands pass each other unhindered before undergoing ligation to downstream lagging strands. Dissociation of CMG helicases occurs only after the final ligation step, and is not required for completion of DNA synthesis, strongly suggesting that converging CMGs pass one another and dissociate from double-stranded DNA. This termination mechanism allows rapid completion of DNA synthesis while avoiding premature replisome disassembl

Mitotic CDK Promotes Replisome Disassembly, Fork Breakage, and Complex DNA Rearrangements

DNA replication errors generate complex chromosomal rearrangements and thereby contribute to tumorigenesis and other human diseases. One mechanism that triggers these errors is mitotic entry before the completion of DNA replication. To address how mitosis might affect DNA replication, we used Xenopus egg extracts. When mitotic CDK (Cyclin B1-CDK1) is used to drive interphase egg extracts into a mitotic state, the replicative CMG (CDC45/MCM2-7/GINS) helicase undergoes ubiquitylation on its MCM7 subunit, dependent on the E3 ubiquitin ligase TRAIP. Whether replisomes have stalled or undergone termination, CMG ubiquitylation is followed by its extraction from chromatin by the CDC48/p97 ATPase. TRAIP-dependent CMG unloading during mitosis is also seen in C. elegans early embryos. At stalled forks, CMG removal results in fork breakage and end joining events involving deletions and templated insertions. Our results identify a mitotic pathway of global replisome disassembly that can trigger replication fork collapse and DNA rearrangements. Mitotic entry before completion of DNA replication causes genome instability via an unknown mechanism. Using Xenopus egg extracts, Deng et al. find that mitotic cyclin-dependent kinase triggers replication fork breakage and DNA rearrangements. The mechanism requires TRAIP-dependent ubiquitylation of the replicative helicase followed by p97 ATPase-dependent helicase removal from chromatin.</p

Bypass of a protein roadblock by a replicative DNA helicase

Replicative DNA helicases generally unwind DNA as a single hexamer that encircles and translocates along one strand of the duplex while excluding the complementary strand (“steric exclusion”). In contrast, large T antigen (T-ag), the replicative DNA helicase of the Simian Virus 40 (SV40), is reported to function as a pair of stacked hexamers that pumps double-stranded DNA through its central channel while laterally extruding single-stranded DNA. Here, we use single-molecule and ensemble assays to show that T-ag assembled on the SV40 origin unwinds DNA efficiently as a single hexamer that translocates on single-stranded DNA in the 3′ to 5′ direction. Unexpectedly, T-ag unwinds DNA past a DNA-protein crosslink on the translocation strand, suggesting that the T-ag ring can open to bypass bulky adducts. Together, our data underscore the profound conservation among replicative helicase mechanisms while revealing a new level of plasticity in their interactions with DNA damage