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The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in vitro single-molecule fluorescence imaging, we show that ParB from Bacillus subtilis can load onto DNA distantly of parS, as loaded ParB molecules themselves are found to be able to recruit additional ParB proteins from bulk. Notably, this recruitment can occur in cis but also in trans, where, at low tensions within the DNA, newly recruited ParB can bypass roadblocks as it gets loaded to spatially proximal but genomically distant DNA regions. The data are supported by molecular dynamics simulations, which show that cooperative ParB-ParB recruitment can enhance spreading. ParS-independent recruitment explains how ParB can cover substantial genomic distance during chromosome segregation, which is vital for the bacterial cell cycle.

This project contains all the required material for the reproducibility of the results presented in the paper Tubini et. al 2020, "A method for solving heat transfer with phase change in ice or soil that allows for large time steps while guaranteeing energy conservation".

Proton MRS (1 H MRS) provides noninvasive, quantitative metabolite profiles of tissue and has been shown to aid the clinical management of several brain diseases. Although most modern clinical MR scanners support MRS capabilities, routine use is largely restricted to specialized centers with good access to MR research support. Widespread adoption has been slow for several reasons, and technical challenges toward obtaining reliable good-quality results have been identified as a contributing factor. Considerable progress has been made by the research community to address many of these challenges, and in this paper a consensus is presented on deficiencies in widely available MRS methodology and validated improvements that are currently in routine use at several clinical research institutions. In particular, the localization error for the PRESS localization sequence was found to be unacceptably high at 3 T, and use of the semi-adiabatic localization by adiabatic selective refocusing sequence is a recommended solution. Incorporation of simulated metabolite basis sets into analysis routines is recommended for reliably capturing the full spectral detail available from short TE acquisitions. In addition, the importance of achieving a highly homogenous static magnetic field (B0 ) in the acquisition region is emphasized, and the limitations of current methods and hardware are discussed. Most recommendations require only software improvements, greatly enhancing the capabilities of clinical MRS on existing hardware. Implementation of these recommendations should strengthen current clinical applications and advance progress toward developing and validating new MRS biomarkers for clinical use.

Figure S1. Illustration of the influence of logistic model parameters on curve, and the model fitted to a CKC. From left to right: Îą defines the asymmetry of the logistic model, Ď the steepness of the curve and k influences the terminal slope. The regression curve fitted to a given CKC for a malignant (blue) and a benign lesion (green). Figure S2. Boxplot of automatic segmentation performance in terms of Dice similarity coefficient (DSC). DWI, diffusion-weighted imaging; GI, Gini Importance; mRMR, minimum-Redundancy-Maximum-Relevance; PET, positron emission tomography; w/o, without. (DOCX 219 kb)

The cryosphere is defined by the presence of frozen water in its many forms: glaciers, ice caps, ice sheets, snow, permafrost, and river and lake ice. In the extended Hindu Kush Himalaya (HKH) region, including the Pamirs, Tien Shan and Alatua, the cryosphere is a key freshwater resource, playing a vital and significant role in local and regional hydrology and ecology. Industry, agriculture, and hydroelectric power generation rely on timely and sufficient delivery of water in major river systems; changes in the cryospheric system may thus pose challenges for disaster risk reduction in the extended HKH region.

Long echo time (TE) MR spectroscopy (MRS) sequences are sensitive only to metabolites of low molecular weight. At shorter TE, significantly more metabolite signals are detectable, including broad signals of high-molecular-weight macromolecules (MMs). Although the presence of MM resonances can bias metabolite quantification at short TE, proper quantification of MMs is important since MMs themselves may serve as potentially valuable biomarkers for many pathologies.We have therefore developed an FID-based 2D-MR Spectroscopic Imaging (2D-MRSI) sequence to map MMs in healthy brain tissue at 7T within a scan time of ~17min and a repetition time of 879ms. This 2D-MRSI technique provides MM maps over a whole slice (i.e., including cortical gray matter) at an ultra-short acquisition delay of 1.3ms, using double inversion for efficient nulling of low-molecular-weight metabolites.The optimal sequence parameters were estimated using Bloch simulations, phantom testing, and in vivo validation. The acquired in vivo MM spectra (n=6) included nine distinct MM peaks in the range of ~0.9–3.7ppm. The measured average MM spectrum was incorporated into the LCModel basis set and utilized for further quantification of MRSI data sets without metabolite nulling, which were acquired in five additional volunteers. The quantification results for two basis sets, one including the MMs and one without MM spectrum, were compared.Due to the high spectral resolution and full signal detection provided by the FID-MRSI sequence, we could successfully map five important brain metabolites. Most quantified metabolite signal amplitudes were significantly lower since the inclusion of MMs into the basis set corrected the overestimation of metabolite signals. The precision of fit (i.e., Cramér Rao lower bounds) remained unchanged. Our MM maps show that the overall MM contribution was higher in gray matter than in white matter.In conclusion, the acquired MM spectrum improved the accuracy of metabolite quantification and allowed the acquisition of high spatial resolution maps of five major brain metabolites and also MMs.

Figure S1. Sequencing and assembly strategy of the A. salmonicida subsp. pectinolytica strain 34mel genome. Figure S2. Gene similarity and Mummer alignments to other Aeromonas genomes. Figure S3. Transposon conglomerates from A. salmonicida subsp. pectinolytica strain 34mel. Figure S4. Transposon family content in analyzed Aeromonas strains. Figure S5. Comparison of the A. salmonicida subsp. pectinolytica strain 34mel genome, plasmid pFBAOT6 from Aeromonas caviae, and transposon Tn1721. Table S1. Pathogenic as well as temperature-dependent growth features of analyzed Aeromonas strains. Table S2. General genome features of A. salmonicida subsp. pectinolytica strain 34mel. Table S3. Polymorphic sites in rRNAs from A. salmonicida subsp. pectinolytica strain 34mel. Table S4. Genes disrupted by transposons in A. salmonicida subsp. pectinolytica strain 34mel. Table S5. Transposon details from analyzed Aeromonas strains. Table S6. Genes retained in transposon TnAs1 from the environmental IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Text S1. Annotation details for RNA genes in the A. salmonicida subsp. pectinolytica strain 34mel genome. Text S2. Short unassigned contigs from the A. salmonicida subsp. pectinolytica strain 34mel draft genome. Text S3. Transposons: nomenclature and completeness. Text S4. On transposon counting and the meaning of â ISAs11â . Text S5. Insertions on pFBAOT6 in transposon Tn1721 and details of the regions shared with the A. salmonicida subsp. pectinolytica strain 34mel genome. Text S6. Details of PacBio library preparation, sequencing, and assembly of the genome from A. salmonicida subsp. pectinolytica strain 34mel. (PDF 1171 kb)

Item does not contain fulltext A large body of published work shows that proton (hydrogen 1 [(1)H]) magnetic resonance (MR) spectroscopy has evolved from a research tool into a clinical neuroimaging modality. Herein, the authors present a summary of brain disorders in which MR spectroscopy has an impact on patient management, together with a critical consideration of common data acquisition and processing procedures. The article documents the impact of (1)H MR spectroscopy in the clinical evaluation of disorders of the central nervous system. The clinical usefulness of (1)H MR spectroscopy has been established for brain neoplasms, neonatal and pediatric disorders (hypoxia-ischemia, inherited metabolic diseases, and traumatic brain injury), demyelinating disorders, and infectious brain lesions. The growing list of disorders for which (1)H MR spectroscopy may contribute to patient management extends to neurodegenerative diseases, epilepsy, and stroke. To facilitate expanded clinical acceptance and standardization of MR spectroscopy methodology, guidelines are provided for data acquisition and analysis, quality assessment, and interpretation. Finally, the authors offer recommendations to expedite the use of robust MR spectroscopy methodology in the clinical setting, including incorporation of technical advances on clinical units. © RSNA, 2014 Online supplemental material is available for this article.

SummaryCondensin—an SMC-kleisin complex—is essential for efficient segregation of sister chromatids in eukaryotes [1–4]. In Escherichia coli and Bacillus subtilis, deletion of condensin subunits results in severe growth phenotypes and the accumulation of cells lacking nucleoids [5, 6]. In many other bacteria and under slow growth conditions, however, the reported phenotypes are much milder or virtually absent [7–10]. This raises the question of what role prokaryotic condensin might play during chromosome segregation under various growth conditions. In B. subtilis and Streptococcus pneumoniae, condensin complexes are enriched on the circular chromosome near the single origin of replication by ParB proteins bound to parS sequences [11, 12]. Using conditional alleles of condensin in B. subtilis, we demonstrate that depletion of its activity results in an immediate and severe defect in the partitioning of replication origins. Multiple copies of the chromosome remain unsegregated at or near the origin of replication. Surprisingly, the growth and chromosome segregation defects in rich medium are suppressed by a reduction of replication fork velocity but not by partial inhibition of translation or transcription. Prokaryotic condensin likely prevents the formation of sister DNA interconnections at the replication fork or promotes their resolution behind the fork.

Summary Smc/ScpAB promotes chromosome segregation in prokaryotes, presumably by compacting and resolving nascent sister chromosomes. The underlying mechanisms, however, are poorly understood. Here, we investigate the role of the Smc ATPase activity in the recruitment of Smc/ScpAB to the Bacillus subtilis chromosome. We demonstrate that targeting of Smc/ScpAB to ParB/parS loading sites is strictly dependent on engagement of Smc head domains and relies on an open organization of the Smc coiled coils. We find that dimerization of the Smc hinge domain stabilizes closed Smc rods and hinders head engagement as well as chromosomal targeting. Conversely, the ScpAB sub-complex promotes head engagement and Smc rod opening and thereby facilitates recruitment of Smc to parS sites. Upon ATP hydrolysis, Smc/ScpAB is released from loading sites and relocates within the chromosome—presumably through translocation along DNA double helices. Our findings define an intermediate state in the process of chromosome organization by Smc., Graphical Abstract, Highlights • ATP-dependent head engagement is required for chromosomal targeting of Smc/ScpAB • ATP-dependent head engagement drives coiled-coil opening of Smc in vivo • Targeting of Smc/ScpAB to parS/ParB requires the head-proximal coiled coil of Smc • Hinge dimerization antagonizes head engagement, coiled-coil opening, and targeting, Smc/ScpAB is an important chromosome-organizing machine in bacteria. Minnen et al. show that targeting of Smc/ScpAB to chromosomal parS/ParB sites requires ATP-dependent engagement of Smc heads, which promotes disengagement of the Smc coiled coils and drives the complex into a targeting-competent open conformation.

In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2-Mnd1 reveals that it forms a curved rod-like structure consisting of three leucine zippers and two kinked junctions. One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra alpha-helices to form a helical bundle-like structure. Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament. Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations. These findings allow us to propose a model explaining how Hop2-Mnd1 juxtaposes Dmc1-bound ssDNA with distorted recipient double-stranded DNA and thus facilitates strand invasion.

Description, CTP binding and hydrolysis concentrate ParB at parS centromeres to mediate faithful chromosome segregation in bacteria., Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB acts as adaptor protein between the 16–base pair centromeric parS DNA sequences and the DNA segregation proteins ParA and Smc (structural maintenance of chromosomes). Upon cytidine triphosphate (CTP) and parS DNA binding, ParB dimers form DNA clamps that spread onto parS-flanking DNA by sliding, thus assembling the so-called partition complex. We show here that CTP hydrolysis is essential for efficient chromosome segregation by ParABS but largely dispensable for Smc recruitment. Our results suggest that CTP hydrolysis contributes to partition complex assembly via two mechanisms. It promotes ParB unloading from DNA to limit the extent of ParB spreading, and it recycles off-target ParB clamps to allow for parS retargeting, together superconcentrating ParB near parS. We also propose a model for clamp closure involving a steric clash when binding ParB protomers to opposing parS half sites.

A new interpretation modeling of freezing soils starting from Dall'Amico's Ph.D dissertation.

Rock fracturing due to ice formation and the formation of ice-bonded fracture zones at depth are hypothesized to be relevant preconditioning factors of rock falls in steep permafrost rock-walls as a response to climate change. Most knowledge about the processes associated with the ice-induced rock damage stems from theoretical studies or laboratory experiments. The transfer of corresponding insights to outdoor conditions is nontrivial because there are big spatial variations and temporal fluctuations of surface conditions in high mountain environments. The monitoring of acoustic emissions (AE) is a powerful technique to track the evolution of damage. The investigation of rock damage by AE measurements provides insights into the physical processes. This Master’s thesis describes the design of an AE measurement assembly for reliable acquisition of a multi-year time series in steep alpine rockwalls. Because measurements in steep rock slopes are challenging, this study investigates technical options suitable to capture AE signals from different depths while incurring minimal signal loss between the rock and the sensor. The requirements for the measurement assembly are outlined and different generic solutions are designed and presented. To evaluate and refine them, the coupling of the sensor with the measurement assembly as well as the contact between rock and measurement assembly were explored by determination of the wave attenuation. The determination of speed of sound, acoustic impedance, transmission and attenuation coefficients for different material candidates enabled to choose ideal components of the measurement assembly. Based on argumentation and testing outcomes, the final measurement assembly, called AE-rod, is designed. The AE sensor is inserted directly in the borehole whereby a thin metal plate glued on the rock provides a good contact. A hollow rod as casing protect the AE sensor against external influences and the sealing of the space between rod and rock prevents water flow in the hole. Four prototypes of the AE-rod are installed and tested in a field deployment at 3500 m a.s.l. on Jungfraujoch, Switzerland. The results of first measurements are promising and point to a successful design and construction of the AE-rod., Master's thesis, Faculty of Science, University of Zurich

Permafrost degradation in high mountain environments is one of the effects of climate change in the Alpine region (IPCC, 2007). The consequences may be manyfold, ranging from rock falls and debris flows, to structural damages in infrastructures located on high mountains. The exceptional rock-fall activity during the summer 2003 is likely an indication of this rapid destabilization that takes place as an almost immediate reaction to extreme warming (Gruber et al., 2004a). The understanding and prediction of such phenomena requires first the localization of permafrost affected areas, and then the monitoring of permafrost sites through proper measurement and modeling techniques. However, the modeling of alpine permafrost is not an easy task because of a variety of causes that contribute to increase the complexity. In particular, the crucial factors dominating alpine permafrost are (1) topography and soil type heterogeneity, (2) snow insulating effect, (3) presence of ice in the ground and (4) high thermal inertia for temperature change at depth. These disturbances could be dealt with through a physically based approach that accounts for the topographical characteristics of the basin, allows heterogeneous parameterization of thermal and hydraulic properties of the ground, solves snow accumulation and melting, and calculates temperature, water and ice content in the ground. GEOtop (Rigon et al., 2006) is a distributed physically-based hydrological model that appears suitable to deal with the above outlined requirements, as it solves coupled water and energy budgets, allows heterogeneous input parameters in the form of maps and includes a snow module that calculates accumulation-melting of snow through a multilayer discretization of the snowpack (Endrizzi, 2007). The model, at the beginning of this work, was lacking of a freezing-soil module capable to account for phase change and heat advection in the soils, extremely important in permafrost affected areas (Roth and Boike, 2001). The inclusion of this part, however, needs a deep thermodynamical analysis of the system, in order to derive the relations between pressure and temperature in a ground subject to freezing conditions. Furthermore, the solution of the energy equation requires a robust numerical scheme, which has to cope with the high non-linearities present in the apparent heat capacity formulation for phase change (Hansson et al., 2004). Finally, the snow-soil thermal interactions require a special attention, as they command the energy flux in input to the ground when the snow is present. The objectives of this thesis are to develop a new freezing soil module inside GEOtop, to test the model against analytical solutions, experimental data and field observations, and to apply the model to investigate the influence of coupled heat and water flow in arctic and alpine permafrost areas.