ALBERT

Description: The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.

Description: The main sources of magnetic minerals in soils unaffected by anthropogenic pollution are iron oxides and hydroxides derived from parent materials through soil formation processes. Soil magnetic minerals can be used as indicators of environmental factors including soil forming processes, degree of pedogenesis, weathering processes and biological activities. In this study measurements of magnetic susceptibility are used to detect the presence and the concentration of soil magnetic minerals in topsoil and bulk samples in a small cultivated field, which forms a hydrological unit that can be considered to be representative of the rainfed agroecosystems of Mediterranean mountain environments. Additional magnetic studies such as isothermal remanent magnetization (IRM), anhysteretic remanent magnetization (ARM) and thermomagnetic measurements are used to identify and characterize the magnetic mineralogy of soil minerals. The objectives were to analyse the spatial variability of the magnetic parameters to assess whether topographic factors, soil redistribution processes, and soil properties such as soil texture, organic matter and carbonate contents analysed in this study, are related to the spatial distribution pattern of magnetic properties. The medians of mass specific magnetic susceptibility at low frequency ( lf ) were 36.0 and 31.1 10 –8 m 3 kg –1 in bulk and topsoil samples respectively. High correlation coefficients were found between the lf in topsoil and bulk core samples ( r  = 0.951, p  〈 0.01). In addition, volumetric magnetic susceptibility was measured in situ in the field ( is ) and values varied from 13.3 to 64.0 10 –5 SI. High correlation coefficients were found between lf in topsoil measured in the laboratory and volumetric magnetic susceptibility field measurements ( r  = 0.894, p  〈 0.01). The results obtained from magnetic studies such as IRM, ARM and thermomagnetic measurements show the presence of magnetite, which is the predominant magnetic carrier, and hematite. The predominance of superparamagnetic minerals in upper soil layers suggests enrichment in pedogenic minerals. The finer soil particles, the organic matter content and the magnetic susceptibility values are statistically correlated and their spatial variability is related to similar physical processes. Runoff redistributes soil components including magnetic minerals and exports fine particles out the field. This research contributed to further knowledge on the application of soil magnetic properties to derive useful information on soil processes in Mediterranean cultivated soils.

Description: The Rogaland Igneous Complex (RIC) in southern Norway intruded into post-Sveconorwegian granulite facies crust ~930 Ma. It includes three massif anorthosites, several small leuconorite bodies and the ~7 km thick norite-quartz mangerite layered Bjerkreim-Sokndal (BKS) intrusion. The intrusion consists of five rhythmic megaunits created by repeated magma influxes topped by a transition zone and more evolved mangerites and quartz mangerites. Over 70 palaeomagnetic sites have been collected in the BKS, sampling all the megacyclic subunits and overlying mangerites. Remanence within the BKS is held in hemo-ilmenite-only rocks (lower parts of the megacyclic units), mixed hemo-ilmenite and magnetite rocks (upper parts of the lower megacyclic units) and magnetite only rocks in the upper highest megacyclic unit and overlying mangerites. Due to the different oxides present magnetic susceptibility varies over four orders of magnitude with a bimodal distribution (mean susceptibility of 6.4 x 10 –3 SI for hemo-ilmenite rocks, and 8.7 x 10 –2 SI for magnetite rocks). NRM values do not show a strong bimodal distribution as many of the rocks lacking magnetite have hemo-ilmenite with strong lamellar magnetism; average NRM for the entire suite is 8.83 A m –1 . All sites within the cyclic part of the intrusion have stable remanence and produce well-clustered site means. Samples from the upper mangerite rocks, dominated by MD magnetite, are commonly unstable and not all sites provide acceptable data. Mean directions for 66 sites spanning the entire intrusion are I = –73.5°, D = 303.4°, with α 95 = 3.7° and k = 24. The resulting pole position is at 35.9°S and 217.9°E, with a palaeolatitude for this part of Baltica of –59.4°. Examination of the magnetic mineralogy combined with geochronology for RIC rocks and cooling rates for the region yields an age of magnetization of 916 Ma. Metamorphic country rocks yield similar directions at least 10 km from the contact, confirming the presence of a contact aureole around the intrusion. Comparison to other early Neoproterozoic palaeomagnetic poles from southern Scandinavia confirms the high southern latitude position of Baltica at this time, and combined with the few other ~900 Ma poles from Baltica affirm the presence of the Rodinia supercontinent at this time.

Description: Post-depositional reductive diagenesis usually results in partial or entire cleansing of the pristine palaeomagnetic signal, therefore, its intensity is important to be assessed for sediments that are in the purpose of retrieving palaeomagnetic information. Grain size, rock magnetic and geochemical studies on the entire core, along with scanning electron microscope observations and X-ray diffraction analyses for representative samples were carried out on a Holocene sediment core retrieved from the deep water part of Huguangyan maar lake (HGY), southeast China. The pristine magnetic mineral assemblage of the studied core is domianted by superparamagnetic (SP) and stable single domain titanomagnetite, and high coercivity minerals are not detectable. Based on down-core variations of the average grain size ( M Z ), total organic carbon (TOC), detrital elements (Al, Ti, Fe and Mn) and the concentration and mineralogy of magnetic minerals, the studied core could be divided into three subsections. The uppermost subsection is the least affected by diagenesis, with detrital titanomagnetite as the dominant magnetic mineral. This is owing to low TOC contents, but high detrital input generated by weak Asian summer monsoon intensity during the late Holocene. The intermediate subsection shows down-core progressively enhanced dissolution of detrital titanomagnetite, and concomitant formation of authigenic pyrite and siderite, which indicates down-core progressively enhanced diagenesis generated by down-core progressive increasing TOC content, but decreasing detrital input as the result of down-core progressively strengthened Asian summer monsoon intensity. The pristine magnetic mineral assemblage has been profoundly modified in the lowermost subsection. At certain positions of the lowermost subsection, detrital titanomagnetite has been even completely dissolved via diagenesis, giving place to authigenic pyrite and siderite. High TOC content, but low detrital input generated from strong Asian summer monsoon intensity during the early Holocene are accountable for intensive diagenesis in the lowermost subsection. Complete erasing of detrital magnetic input signal at certain positions of the lowermost subsection, and considerable formation of authigenic siderite indicate that palaeomagnetic records of the studied core have been significantly compromised. The studied core has relatively higher TOC content, lower detrital matter content, calmer sedimentary environments, and less DO available at its water–sediment interface than the cores retrieved at relatively shallower water depths, which all contribute to its relatively stronger diagenesis. Progressive thickening of the upper two subsections with increasing water depth is owing to progressive increase in sedimentation rate with increasing water depth, which is the key factor in determining the thickness of each diagenetic subsection of cores from HGY. It would be better that lake sediments for palaeomagnetic investigations collected at a water depth shallower than the depth of its thermocline.

Description: The rocks in the crust and the upper mantle of the Earth are believed to exhibit electrical anisotropy to some extent. It is beneficial to further understand and recognize the propagation of the electromagnetic waves in the Earth by investigating the magnetotelluric (which is one of the main geophysical techniques to probe the deep structures in the Earth) responses of the media with anisotropic conductivity structures. In this study, we examine the magnetotelluric fields over an idealized 2-D model consisting of two segments with axially anisotropic conductivity structures overlying a perfect conductor basement by a quasi-static analytic approach. The resulting analytic solution could not only contribute to the electromagnetic induction theory in the anisotropic Earth but also serve as at least an initial standard solution which could be used to validate the reliability and accuracy of the numerical algorithms developed for modelling the magnetotelluric responses of the 2-D media with much more general anisotropic conductivity.

Description: It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense–antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan. CNCI software is available at http://www.bioinfo.org/software/cnci .

Description: Existing methods for interpreting protein variation focus on annotating mutation pathogenicity rather than detailed interpretation of variant deleteriousness and frequently use only sequence-based or structure-based information. We present VIPUR, a computational framework that seamlessly integrates sequence analysis and structural modelling (using the Rosetta protein modelling suite) to identify and interpret deleterious protein variants. To train VIPUR, we collected 9477 protein variants with known effects on protein function from multiple organisms and curated structural models for each variant from crystal structures and homology models. VIPUR can be applied to mutations in any organism's proteome with improved generalized accuracy (AUROC .83) and interpretability (AUPR .87) compared to other methods. We demonstrate that VIPUR's predictions of deleteriousness match the biological phenotypes in ClinVar and provide a clear ranking of prediction confidence. We use VIPUR to interpret known mutations associated with inflammation and diabetes, demonstrating the structural diversity of disrupted functional sites and improved interpretation of mutations associated with human diseases. Lastly, we demonstrate VIPUR's ability to highlight candidate variants associated with human diseases by applying VIPUR to de novo variants associated with autism spectrum disorders.

Description: Red Clay underlying the loess-palaeosol sequences on the Chinese Loess Plateau is an eolian deposit. There is a controversy over whether magnetic susceptibility ( ) variations in Red Clay sequence can be used as an indicator of summer palaeomonsoon intensity. This study investigates the magnetic mineralogy, magnetic concentration and magnetic grain size distribution of Jiaxian Red Clay with multimagnetic methods. Our results indicate that the magnetic properties of Jiaxian Red Clay are similar to those of the Quaternary loess-palaeosol sequences, and ultrafine ferrimagnetic grains produced during pedogenesis are responsible for an increase in susceptibility, therefore the enhancement mechanism of Red Clay is similar to that of the overlying loess-palaeosol sequences. This paper explores variations in the Red Clay sequence through spatial and temporal analysis. The susceptibility variation of six sites along a NNE to SSW transect correlate to palaeoclimatic cycles, so can be used to trace the summer palaeomonsoon intensity from a spatial perspective. However, a simple loess-derived calibration function cannot be used to quantitative reconstruct the palaeomonsoon intensity variations thought time. An adjusted calibration function for palaeosols from Red Clay sequence needs to be developed, so that can be used to quantitative reconstruct palaeomonsoon intensity. Further study is necessary to develop such a transfer function.

Description: The sedimentary sequence deposited during the deglaciation phase following the last glacial maximum in the Storfjorden trough, on the northwestern Barents Sea south of Svalbard, was sampled with 10 piston and gravity cores during the SVAIS and EGLACOM cruises. Three cores (SV-02, SV-03 and SV-05) collected on the upper continental slope are characterized by a thin (20–40 cm) Holocene interval and a thick (up to 4.5 m in core SV-03) late Pleistocene sequence of finely laminated fine-grained sediments that have been interpreted as plumites deposited during the Melt Water Pulse 1a (MWP-1a). Radiocarbon ages obtained at the top and bottom of this stratigraphic interval revealed that deposition occurred during less than two centuries at around 15 ka ago, with a very high sedimentary rate exceeding 3 cm a –1 . We studied the palaeomagnetic and rock magnetic properties of this interval, by taking magnetic measurements at 1 cm spacing on u-channel samples collected from the three cores. The data show that this sequence is characterized by good palaeomagnetic properties and the palaeomagnetic and rock magnetic trends may be correlated at high resolution from core to core. The obtained palaeomagnetic data therefore offer the unique opportunity to investigate in detail the rate of geomagnetic palaeosecular variation (PSV) in the high northern latitudes at a decadal scale. Notwithstanding the palaeomagnetic trends of the three cores may be closely matched, the amplitude of directional PSV and the consequent virtual geomagnetic pole (VGP) scatter (S) is distinctly higher in one core (SV-05) than in the other two cores (SV-02 and SV-03). This might result from a variable proportion of two distinct populations of magnetic minerals in core SV-05, as suggested by the variable tendency to acquire a gyromagnetic remanent magnetization at high fields during the AF demagnetization treatment. For the plumite interval of cores SV-02 and SV-03, where the magnetic mineralogy is uniform and magnetite is the main magnetic carrier, a S value of about 9° is obtained. We consider this value as a reliable approximation of palaeomagnetic secular variation at a latitude of 75°N over a time interval spanning a couple of centuries around 15 ka ago.

Description: A recent study of the Matuyama–Brunhes (M-B) geomagnetic field reversal recorded in exposed lacustrine sediments from the Sulmona Basin (Italy) provided a continuous, high-resolution record indicating that the reversal of the field direction at the terminus of the M-B boundary (MBB) occurred in less than a century, about 786 ka ago. In the sediment, thin (4–6 cm) remagnetized horizons were recognized above two distinct tephra layers—SUL2-19 and SUL2-20—that occur ~25 and ~35 cm below the MBB, respectively. Also, a faint, millimetre-thick tephra (SUL2-18) occurs 2–3 cm above the MBB. With the aim of improving the temporal resolution of the previous Sulmona MBB record and understanding the possible influence of cryptotephra on the M-B record in the Sulmona Basin, we performed more detailed sampling and analyses of overlapping standard and smaller samples from a 50 cm-long block that spans the MBB. The new data indicate that (i) the MBB is even sharper than previously reported and occurs ~2.5 cm below tephra SUL2-18, in agreement with the previous study; (ii) the MBB coincides with the rise of an intensity peak of the natural remanent magnetization (NRM) intensity, which extends across SUL2-18; (iii) except for a 2-cm-thick interval just above tephra SUL2-18, the rock magnetic parameters ( k , ARM, M r , M s , B c , B cr ) indicate exactly the same magnetic mineralogy throughout the sampled sequence. We conclude that either SUL2-18 resulted in the remagnetization of an interval of about 6 cm (i.e. during the NRM intensity peak spanning ~260 ± 110 yr, according to the estimated local sedimentation rate), and thus the detailed MBB record is lost because it is overprinted, or the MBB is well recorded, occurred abruptly about 2.5 cm below SUL2-18 and lasted less than 13 ± 6 yr. Both hypotheses challenge our understanding of the geomagnetic field behaviour during a polarity transition and/or of the NRM acquisition process in the Sulmona lacustrine sediment.