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Article ; Online: DNA-dependent phase separation by human SSB2 (NABP1/OBFC2A) protein points to adaptations to eukaryotic genome repair processes.

Kovács, Zoltán J / Harami, Gábor M / Pálinkás, János / Kuljanishvili, Natalie / Hegedüs, József / Harami-Papp, Hajnalka / Mahmudova, Lamiya / Khamisi, Lana / Szakács, Gergely / Kovács, Mihály

Protein science : a publication of the Protein Society

2024 Volume 33, Issue 4, Page(s) e4959

Abstract: Single-stranded DNA binding proteins (SSBs) are ubiquitous across all domains of life and play essential roles via stabilizing and protecting single-stranded (ss) DNA as well as organizing multiprotein complexes during DNA replication, recombination, and ...

Abstract	Single-stranded DNA binding proteins (SSBs) are ubiquitous across all domains of life and play essential roles via stabilizing and protecting single-stranded (ss) DNA as well as organizing multiprotein complexes during DNA replication, recombination, and repair. Two mammalian SSB paralogs (hSSB1 and hSSB2 in humans) were recently identified and shown to be involved in various genome maintenance processes. Following our recent discovery of the liquid-liquid phase separation (LLPS) propensity of Escherichia coli (Ec) SSB, here we show that hSSB2 also forms LLPS condensates under physiologically relevant ionic conditions. Similar to that seen for EcSSB, we demonstrate the essential contribution of hSSB2's C-terminal intrinsically disordered region (IDR) to condensate formation, and the selective enrichment of various genome metabolic proteins in hSSB2 condensates. However, in contrast to EcSSB-driven LLPS that is inhibited by ssDNA binding, hSSB2 phase separation requires single-stranded nucleic acid binding, and is especially facilitated by ssDNA. Our results reveal an evolutionarily conserved role for SSB-mediated LLPS in the spatiotemporal organization of genome maintenance complexes. At the same time, differential LLPS features of EcSSB and hSSB2 point to functional adaptations to prokaryotic versus eukaryotic genome metabolic contexts.
MeSH term(s)	Animals ; Humans ; Phase Separation ; DNA ; DNA-Binding Proteins/chemistry ; DNA Repair ; DNA Replication ; DNA, Single-Stranded/genetics ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Mammals/genetics
Chemical Substances	DNA (9007-49-2) ; DNA-Binding Proteins ; DNA, Single-Stranded
Language	English
Publishing date	2024-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4959
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Article ; Online: Fast camera studies at an electron cyclotron resonance table plasma generator.

Rácz, R / Biri, S / Hajdu, P / Pálinkás, J

The Review of scientific instruments

2014 Volume 85, Issue 2, Page(s) 02A507

Abstract: A simple table-size ECR plasma generator operates in the ATOMKI without axial magnetic trap and without any particle extraction tool. Radial plasma confinement is ensured by a NdFeB hexapole. The table-top ECR is a simplified version of the 14 GHz ATOMKI- ...

Abstract	A simple table-size ECR plasma generator operates in the ATOMKI without axial magnetic trap and without any particle extraction tool. Radial plasma confinement is ensured by a NdFeB hexapole. The table-top ECR is a simplified version of the 14 GHz ATOMKI-ECRIS. Plasma diagnostics experiments are planned to be performed at this device before installing the measurement setting at the "big" ECRIS. Recently, the plasma generator has been operated in pulsed RF mode in order to investigate the time evolution of the ECR plasma in two different ways. (1) The visible light radiation emitted by the plasma was investigated by the frames of a fast camera images with 1 ms temporal resolution. Since the visible light photographs are in strong correlation with the two-dimensional spatial distribution of the cold electron components of the plasma it can be important to understand better the transient processes just after the breakdown and just after the glow. (2) The time-resolved ion current on a specially shaped electrode was measured simultaneously in order to compare it with the visible light photographs. The response of the plasma was detected by changing some external setting parameters (gas pressure and microwave power) and was described in this paper.
Language	English
Publishing date	2014-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/1.4847215
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Article ; Online: The toposiomerase IIIalpha-RMI1-RMI2 complex orients human Bloom's syndrome helicase for efficient disruption of D-loops.

Harami, Gábor M / Pálinkás, János / Seol, Yeonee / Kovács, Zoltán J / Gyimesi, Máté / Harami-Papp, Hajnalka / Neuman, Keir C / Kovács, Mihály

Nature communications

2022 Volume 13, Issue 1, Page(s) 654

Abstract: Homologous recombination (HR) is a ubiquitous and efficient process that serves the repair of severe forms of DNA damage and the generation of genetic diversity during meiosis. HR can proceed via multiple pathways with different outcomes that may aid or ... ...

Abstract	Homologous recombination (HR) is a ubiquitous and efficient process that serves the repair of severe forms of DNA damage and the generation of genetic diversity during meiosis. HR can proceed via multiple pathways with different outcomes that may aid or impair genome stability and faithful inheritance, underscoring the importance of HR quality control. Human Bloom's syndrome (BLM, RecQ family) helicase plays central roles in HR pathway selection and quality control via unexplored molecular mechanisms. Here we show that BLM's multi-domain structural architecture supports a balance between stabilization and disruption of displacement loops (D-loops), early HR intermediates that are key targets for HR regulation. We find that this balance is markedly shifted toward efficient D-loop disruption by the presence of BLM's interaction partners Topoisomerase IIIα-RMI1-RMI2, which have been shown to be involved in multiple steps of HR-based DNA repair. Our results point to a mechanism whereby BLM can differentially process D-loops and support HR control depending on cellular regulatory mechanisms.
MeSH term(s)	DNA Topoisomerases, Type I/genetics ; DNA Topoisomerases, Type I/metabolism ; DNA, Cruciform/chemistry ; DNA, Cruciform/genetics ; DNA, Cruciform/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Kinetics ; Models, Genetic ; Multiprotein Complexes/genetics ; Multiprotein Complexes/metabolism ; Protein Binding ; RecQ Helicases/genetics ; RecQ Helicases/metabolism ; Recombinational DNA Repair/genetics
Chemical Substances	DNA, Cruciform ; DNA-Binding Proteins ; Multiprotein Complexes ; RMI1 protein, human ; RMI2 protein, human ; Bloom syndrome protein (EC 3.6.1.-) ; RecQ Helicases (EC 3.6.4.12) ; DNA Topoisomerases, Type I (EC 5.99.1.2)
Language	English
Publishing date	2022-02-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28208-9
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Article ; Online: Status and special features of the Atomki ECR ion source.

Biri, S / Rácz, R / Pálinkás, J

The Review of scientific instruments

2012 Volume 83, Issue 2, Page(s) 02A341

Abstract: The ECR ion source has been operating in ATOMKI (Debrecen) since 1996. During the past 15 years lots of minor and numerous major technical modifications have been carried out on the ECRIS. Many of these changes aimed the increasing of beams charge, ... ...

Abstract	The ECR ion source has been operating in ATOMKI (Debrecen) since 1996. During the past 15 years lots of minor and numerous major technical modifications have been carried out on the ECRIS. Many of these changes aimed the increasing of beams charge, intensity, and the widening of the ion choice. Another group of the modifications were performed to develop special, non-standard operation modes or to produce peculiar plasmas and beams.
Language	English
Publishing date	2012-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/1.3673006
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Article: Vestibular Stimulation May Drive Multisensory Processing: Principles for Targeted Sensorimotor Therapy (TSMT).

Tele-Heri, Brigitta / Dobos, Karoly / Harsanyi, Szilvia / Palinkas, Judit / Fenyosi, Fanni / Gesztelyi, Rudolf / More, Csaba E / Zsuga, Judit

Brain sciences

2021 Volume 11, Issue 8

Abstract: At birth, the vestibular system is fully mature, whilst higher order sensory processing is yet to develop in the full-term neonate. The current paper lays out a theoretical framework to account for the role vestibular stimulation may have driving ... ...

Abstract	At birth, the vestibular system is fully mature, whilst higher order sensory processing is yet to develop in the full-term neonate. The current paper lays out a theoretical framework to account for the role vestibular stimulation may have driving multisensory and sensorimotor integration. Accordingly, vestibular stimulation, by activating the parieto-insular vestibular cortex, and/or the posterior parietal cortex may provide the cortical input for multisensory neurons in the superior colliculus that is needed for multisensory processing. Furthermore, we propose that motor development, by inducing change of reference frames, may shape the receptive field of multisensory neurons. This, by leading to lack of spatial contingency between formally contingent stimuli, may cause degradation of prior motor responses. Additionally, we offer a testable hypothesis explaining the beneficial effect of sensory integration therapies regarding attentional processes. Key concepts of a sensorimotor integration therapy (e.g., targeted sensorimotor therapy (TSMT)) are also put into a neurological context. TSMT utilizes specific tools and instruments. It is administered in 8-weeks long successive treatment regimens, each gradually increasing vestibular and postural stimulation, so sensory-motor integration is facilitated, and muscle strength is increased. Empirically TSMT is indicated for various diseases. Theoretical foundations of this sensorimotor therapy are discussed.
Language	English
Publishing date	2021-08-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2651993-8
ISSN	2076-3425
ISSN	2076-3425
DOI	10.3390/brainsci11081111
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Article ; Online: Electron cyclotron resonance plasma photos.

Rácz, R / Biri, S / Pálinkás, J

The Review of scientific instruments

2010 Volume 81, Issue 2, Page(s) 02B708

Abstract: In order to observe and study systematically the plasma of electron cyclotron resonance (ECR) ion sources (ECRIS) we made a high number of high-resolution visible light plasma photos and movies in the ATOMKI ECRIS Laboratory. This required building the ... ...

Abstract	In order to observe and study systematically the plasma of electron cyclotron resonance (ECR) ion sources (ECRIS) we made a high number of high-resolution visible light plasma photos and movies in the ATOMKI ECRIS Laboratory. This required building the ECR ion source into an open ECR plasma device, temporarily. An 8MP digital camera was used to record photos of plasmas made from Ne, Ar, and Kr gases and from their mixtures. We studied and recorded the effect of ion source setting parameters (gas pressure, gas composition, magnetic field, and microwave power) to the shape, color, and structure of the plasma. The analysis of the photo series gave us many qualitative and numerous valuable physical information on the nature of ECR plasmas.
Language	English
Publishing date	2010-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/1.3267289
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Article ; Online: Molecular and negative ion production by a standard electron cyclotron resonance ion source.

Rácz, R / Biri, S / Juhász, Z / Sulik, B / Pálinkás, J

The Review of scientific instruments

2012 Volume 83, Issue 2, Page(s) 02A313

Abstract: Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas ... ...

Abstract	Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H(-), O(-), OH(-), O(2)(-), C(-), C(60)(-) negative ions and H(2)(+), H(3)(+), OH(+), H(2)O(+), H(3)O(+), O(2)(+) positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several μA and positive molecular ion beams in the mA range were successfully obtained.
Language	English
Publishing date	2012-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/1.3662960
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Article ; Online: Phase separation by ssDNA binding protein controlled via protein-protein and protein-DNA interactions.

Harami, Gábor M / Kovács, Zoltán J / Pancsa, Rita / Pálinkás, János / Baráth, Veronika / Tárnok, Krisztián / Málnási-Csizmadia, András / Kovács, Mihály

Proceedings of the National Academy of Sciences of the United States of America

2020 Volume 117, Issue 42, Page(s) 26206–26217

Abstract: Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C- ... ...

Abstract	Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein-protein interactions with DNA-metabolizing proteins. Here we show that the
MeSH term(s)	DNA Damage ; DNA Repair ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism ; DNA, Single-Stranded/genetics ; DNA, Single-Stranded/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/isolation & purification ; DNA-Binding Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/growth & development ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/isolation & purification ; Escherichia coli Proteins/metabolism ; Liquid-Liquid Extraction/methods ; Protein Binding
Chemical Substances	DNA, Single-Stranded ; DNA-Binding Proteins ; Escherichia coli Proteins ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2020-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2000761117
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Article ; Online: X-ray pinhole camera setups used in the Atomki ECR Laboratory for plasma diagnostics.

Rácz, R / Biri, S / Pálinkás, J / Mascali, D / Castro, G / Caliri, C / Romano, F P / Gammino, S

The Review of scientific instruments

2016 Volume 87, Issue 2, Page(s) 02A741

Abstract: Imaging of the electron cyclotron resonance (ECR) plasmas by using CCD camera in combination with a pinhole is a non-destructive diagnostics method to record the strongly inhomogeneous spatial density distribution of the X-ray emitted by the plasma and ... ...

Abstract	Imaging of the electron cyclotron resonance (ECR) plasmas by using CCD camera in combination with a pinhole is a non-destructive diagnostics method to record the strongly inhomogeneous spatial density distribution of the X-ray emitted by the plasma and by the chamber walls. This method can provide information on the location of the collisions between warm electrons and multiple charged ions/atoms, opening the possibility to investigate the direct effect of the ion source tuning parameters to the plasma structure. The first successful experiment with a pinhole X-ray camera was carried out in the Atomki ECR Laboratory more than 10 years ago. The goal of that experiment was to make the first ECR X-ray photos and to carry out simple studies on the effect of some setting parameters (magnetic field, extraction, disc voltage, gas mixing, etc.). Recently, intensive efforts were taken to investigate now the effect of different RF resonant modes to the plasma structure. Comparing to the 2002 experiment, this campaign used wider instrumental stock: CCD camera with a lead pinhole was placed at the injection side allowing X-ray imaging and beam extraction simultaneously. Additionally, Silicon Drift Detector (SDD) and High Purity Germanium (HPGe) detectors were installed to characterize the volumetric X-ray emission rate caused by the warm and hot electron domains. In this paper, detailed comparison study on the two X-ray camera and detector setups and also on the technical and scientific goals of the experiments is presented.
Language	English
Publishing date	2016-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/1.4933085
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Article: Application of a vibrating device for the prevention of flexion contracture after total knee arthroplasty.

Manó, Sándor / Pálinkás, Judit / Szabó, János / Nagy, Judit T / Bakó, Katalin / Csernátony, Zoltán

European journal of orthopaedic surgery & traumatology : orthopedie traumatologie

2014 Volume 25, Issue 1, Page(s) 167–172

Abstract: Our research team developed a new, heel support-based static and vibrating complementary treatment method for the prevention of flexion contractures often arising after total knee arthroplasty. We examined the efficiency of the method performing a ... ...

Abstract	Our research team developed a new, heel support-based static and vibrating complementary treatment method for the prevention of flexion contractures often arising after total knee arthroplasty. We examined the efficiency of the method performing a randomized clinical trial with 144 patients undergoing total knee replacement. Seventy-nine patients were treated for 1 week with a generally used continuous passive motion (CPM) device complemented with our new method, which was based on the application of a static and an alternating heel support. The 65 patients in the control group were treated with only a CPM device as in usual clinical practice. The femoro-tibial angle was measured immediately following surgery, and after 1 week of treatment. At the end of the 1 week treatment, the target extension angle (0° ± 5°) was achieved by significantly more patients with the new combined method. This way the elevated heel rest and the vibrating device proved to be a good adjunct treatment along with the CPM used in routine clinical practice in the first place for the prevention of flexion contractures.
MeSH term(s)	Arthroplasty, Replacement, Knee/adverse effects ; Arthroplasty, Replacement, Knee/rehabilitation ; Combined Modality Therapy/instrumentation ; Combined Modality Therapy/methods ; Contracture/prevention & control ; Humans ; Knee Joint/physiopathology ; Motion Therapy, Continuous Passive ; Range of Motion, Articular ; Vibration/therapeutic use
Language	English
Publishing date	2014-04-29
Publishing country	France
Document type	Journal Article ; Randomized Controlled Trial
ZDB-ID	1231084-0
ISSN	1432-1068 ; 1633-8065 ; 0948-4817 ; 0940-3264
ISSN (online)	1432-1068
ISSN	1633-8065 ; 0948-4817 ; 0940-3264
DOI	10.1007/s00590-014-1466-4
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