Parallel Profiles Research Articles

OAB-054: Single-cell RNA-sequencing identifies immune biomarkers of response to immunotherapy in patients with high-risk Smoldering Myeloma

<h3>Background</h3> Patients with Smoldering Multiple Myeloma (SMM) are typically observed until progression, but early treatment of high-risk patients may improve outcomes. Clinical and genomic biomarkers can be used to identify SMM patients at high risk of progression, however parallel profiling of the tumor immune microenvironment (TIME) may further improve prediction models. <h3>Methods</h3> Here, we performed single-cell RNA-sequencing on CD138- immune cells from 40 samples of 14 patients enrolled in a Phase II trial of Elotuzumab, Lenalidomide, and Dexamethasone, in patients with high-risk SMM (E-PRISM) to develop biomarkers for optimal patient selection and monitoring of response to treatment. Specifically, we profiled 33 bone marrow (BM) samples collected at baseline (n=11), cycle 9, Day 1 (C9D1, n=13) and EOT (n=9), and 7 peripheral blood mononuclear cell (PBMC) samples collected at baseline (n=4) and C9D1 (n=3). <h3>Results</h3> We found that higher abundance of mature B-cells, Th17 cells and GZMK+ T and NK cells and lower abundance of hematopoietic progenitor cells and plasmacytoid dendritic cells are associated with significantly longer progression-free survival (PFS) in SMM patients under treatment. This signal can be summarized by how normal-like the patients' immune composition is at baseline, whereby patients whose immune composition is normal-like have significantly shorter PFS (p=0.031). This model suggests that at least some of the compositional changes observed in disease reflect the immune system's capacity to react successfully to the immune challenge posed by the tumor, which we termed immune reactivity. Baseline immune reactivity may help to identify patients who will benefit the most from early treatment. Furthermore, we found that the expansion of tissue-resident NK cells and exhausted GZMK+ CD8+ T-cells at C9D1 of treatment is associated with significantly shorter PFS (p=0.039), suggesting that these immune biomarkers may help to monitor response to immunotherapy. Lastly, we found that patients would be classified the same way in terms of our immune biomarkers, had we assayed their peripheral blood instead of their bone marrow, suggesting that minimally invasive immune profiling for prognostication and monitoring may be feasible. <h3>Conclusion</h3> We used single-cell RNA-sequencing to profile the immune microenvironment of patients with high-risk SMM in a Phase II trial of Elotuzumab, Lenalidomide and Dexamethasone and developed immune biomarkers of response to treatment. Our study may usher in a next generation of clinical assays that assess both tumor biology and immune state, as well as common clinical biomarkers, in the marrow or blood, to accurately predict who may benefit from early treatment, monitor response and improve patient outcomes.

Synthesizing dual-track road elevation data

The ability to synthesize dual, parallel track road elevation profiles is essential for studying the multi-axial motion of vehicles. It is important that the profiles retain the random and variable character of real roads. This research introduces a novel method for synthesizing dual-track longitudinal pavement elevation profiles. Using measured data from asphalted roads, probability density functions were produced to describe the variations in roughness and correlation between the tracks. The correlation between the tracks was analysed using the coherence function and roughness ratio between the measured kerb-side and driver-side tracks. The results showed that variations in the roughness of the tracks were well described by the Weibull probability distribution function defined by the shape, scale and location parameters. The location and shape parameters were shown to be independent to road roughness, leaving the scale parameter as the main index to define the roughness distribution. This finding led to the creation of a new roughness classification scheme for asphalt roads which was used to select appropriate roughness levels for simulation. Variations in the coherence functions and roughness ratios were found to be independent of road roughness and were also able to be described using the Weibull distribution. Using the results from a detailed statistical survey, a novel method was developed to enable the synthesis of parallel track elevation profiles that emulate real roads.

Genomic and Molecular Analyses Identify Molecular Subtypes of Pancreatic Cancer Recurrence

Genomic and Molecular Analyses Identify Molecular Subtypes of Pancreatic Cancer Recurrence

Effects of mathematical models and algorithms on quantitative characterization of areal step height with optical and stylus profilometers

Step height characterization is essential for the quality control of various functional components, such as graphene and the step features of semiconductor devices. Two methods are proposed to characterize the areal step heights. The first method extends the two-dimensional characterization in the ISO specification into a three-dimensional one by extracting multiple parallel profiles. The second method calculates the step heights by projecting from the measurement points to the normal vector at the surface centroid. Mathematical models and algorithms of the two methods are introduced and validated by synthetic data. Experiments are conducted by comparing the assessment results of the two methods and of a method proposed in a previous research. The calibrated values of the standards are utilized for validation. The characterization results may differ notably or slightly, depending on the properties of the data and the algorithm.

Thermalized collisional pre-sheath detected in dense plasma with coherent and incoherent Thomson scattering

In the direct vicinity of plasma-facing surfaces, the incident plasma particles interact with surface-recombined neutrals. Remarkably high near-surface plasma pressure losses were observed in the high-flux linear plasma generator Magnum-PSI. Combining the incoherent and coherent Thomson scattering diagnostics, we directly measured particle, momentum and energy fluxes down to 3 mm from the plasma target surface. At the surface, the particle and total heat flux were also measured, using respectively an in-target Langmuir probe and thermographic methods. The near-surface momentum and energy losses scale with density, and amount to at least 50% and 20%, respectively, at n e = 8 × 1020 m−3. These losses are attributed to the efficient exchange of charge, momentum and energy between incident plasma and surface-recombined neutrals. In low-temperature plasmas with sufficient density, incident particles go through several cycles of interaction and surface deposition before leaving the plasma, thereby providing an effective alternative dissipation channel to the incident plasma. Parallel plasma parameter profiles exhibit a transition with increasing plasma density. In low-density conditions, the plasma temperature is constant and near-surface ion acceleration is observed, attributed to the ambipolar electric field. Conversely, deceleration and plasma cooling are observed in dense conditions. These results are explained by the combined effect of ion–neutral friction and electron–ion thermal equilibration in the so-called thermalized collisional pre-sheath. The energy available for ambipolar acceleration is thus reduced, as well as the upstream flow velocity. In the ITER divertor, enhanced near-surface p–n interaction is expected as well, given the overlap in plasma conditions. Including these effects in finite-element scrape-off layer models requires a near-surface resolution smaller than the neutral mean free path. This amounts to 1 mm in Magnum-PSI, and possibly an order of magnitude smaller in ITER.

Nr5a homologues in the ricefield eel Monopterus albus: Alternative splicing, tissue-specific expression, and differential roles on the activation of cyp19a1a promoter in vitro

Nr5a (Fushi tarazu factor 1, Ftz-F1) homologues belong to the nuclear receptor superfamily, and are involved in the regulation of reproduction in vertebrates. Four genes encoding Nr5a homologues were present in the genome of ricefield eel, which are designated as nr5a1a, nr5a1b, nr5a2, and nr5a5 in the present study. Alternatively spliced transcripts were identified for nr5a1a and nr5a1b genes. Sequence analysis indicated that nr5a5 is possibly a paralog of nr5a2, and nr5a1b is lost during evolution in some teleosts including tilapia and medaka. Ricefield eel nr5a genes exhibit tissue-specific expression patterns, with nr5a1a and nr5a1b resembling that of the SF-1/Ad4BP (NR5A1) subfamily, and nr5a2 and nr5a5 resembling that of the NR5A2/LRH/FTF subfamily. Transcriptomic analysis revealed parallel expression profiles of nr5a1a, foxl2, and cyp19a1a in ovarian follicles during vitellogenesis, with peak values at the late vitellogenic stage. Real-time PCR indicated that the expression levels of nr5a1a and foxl2 in gonads were decreased significantly during the sexual transition from female to the late intersexual stage. In vitro transient transfection assay showed that Nr5a1a up-regulated ricefield eel cyp19a1a promoter activities synergistically with Foxl2. However, Nr5a1b, Nr5a2, and Nr5a5 could neither activate ricefield eel cyp19a1a promoter alone nor enhance the stimulatory effects of Foxl2 on cyp19a1a promoter activities. Collectively, the above data suggest that Nr5a homologues may have diverse and differential roles in the tissues of ricefield eels. The up-regulation of gonadal nr5a1a and foxl2 during vitellogenesis may be important for the ovarian development whereas their down-regulation during the sexual transition period may be important for the sex change process of ricefield eels, possibly through the regulation of cyp19a1a gene expression.

Hydrophobically modified melamine‐formaldehyde sponge used for conformance control and water shutoff during oil production

AbstractPolymer or polymer gels have been widely used to control excessive water during oil production by homogenizing injection profile and reducing water cut in the produced fluids. However, the gels used are generally unable to selectively minimize water production, and face the challenge of syneresis of gels under high temperature and high salinity environment. In this work, melamine‐formaldehyde sponge was modified with AlCl3 solution, rendering a transition from hydrophilic to hydrophobic state with a water contact angle of 130° on the surface of the modified product. Filtration results show that mineral oil and water can be selectively separated with the hydrophobically modified sponge powders. Simulated water shutoff experiments demonstrated the blockage efficiency against water was 30% higher than that against oil, and the oil production was increased 7.4% after blocking. The parallel profile control tests confirmed that the fraction flow of high permeable channel decreased about 75%, accompanied with 60% rise of oil recovery factor. These results indicated that such hydrophobic materials can significantly reduce excessive water production, and this work provided a new idea to offer a low‐cost hydrophobic material for conformance control and water shutoff during oil production.

Multiple Origins of Neurons From Secretory Cells.

The elusive diversity of neurons puzzled neuroscientists since discovering the first nerve cells in the 1830s. Quantitative information about neuronal diversity began to flow from the middle of the twentieth century. At that time, microelectrode and histochemical tools were applied to vertebrate and invertebrate preparations. Simpler nervous systems of some gastropod mollusks, annelids, and nematodes revealed identified neurons with defined transmitter specificity and functions. Early systematic studies pointed out that most of the neurons composing their nervous systems might be unique (Bullock and Horridge, 1965). That revelation provided tractable experimental preparations to decipher cellular bases of behaviors (Kandel, 1976, 2001; Kuffler and Nicholls, 1976). Today, with advances in single-cell (epi)genomics and transcriptomics, the astonishing diversity of neuronal cell types exceeds any imagination (Moroz, 2018). The most straightforward question is, how different are the neurons? But more fundamental questions are: Why are neurons different? Why are there so many neurotransmitters? Why are neurotransmitters different? These questions have been addressed by many (Kandel, 1979; Van Vallen, 1982; Bloom, 1984), aiming for functional aspects. In 1968–1974 these questions were asked from an evolutionary standpoint, and Dmitry Sakharov had proposed the hypothesis of neuronal polygeny (=multiple origins of neurons) (Sakharov, 1970a,b, 1972, 1974a,b). Using minimal comparative data available 50 years ago, Sakharov suggested that neurons evolved from genetically different secretory cells. The evolutionary view of neuronal evolution can be summarized as follows. Each of these populations of secretory cells could use chemically distinct transmitter(s) and different (distant) receptors for communications in early neural systems, where synapses are not required. Ancestral diversity of secretory cell types (=secretory phenotypes) has been preserved over 500+ million years of biological evolution, forming lineages of homologous neurons across phyla. Thus, neurons are different because they have different genealogies. Subsequent functional “demands” and specifications could further tune these different ancestral neurosecretory phenotypes. In other words, the traditional one-root genealogy of neurons was transformed into multiple genealogies or a net of phyletic cell/neuronal lineages, as schematically presented in Figure 1. Open in a separate window Figure 1 Multiple origins of neurons and secretory cells. Schematic illustration of the ancestral cell lineages (different color trajectories) that led to the exant neural systems in four basal metazoan clades with Placozoa as nerveless animals. Neural systems might consist of genetically diverged cell types with different ancestries, gene regulatory networks, and signal molecules. This diagram integrates both the hypothesis of independent origins of neurons (as in ctenophores, Moroz et al., 2014) and the sister-cell model (Arendt et al., 2016), which suggests that novel neuronal types arise in pairs, through sub-specialization of ancestral cell types. Thus, sister neuronal subtypes can share gene-regulatory networks, perhaps, evolutionary conserved developmental pathways, and are expected to have more similar expression profiles than each of them compared to other neuronal types. The key prediction of this model is that gene expression profiles from sister-cell types will form a hierarchical tree structure in phylogenetic reconstructions. A complementary model predicts that neurons and novel neuronal subtypes arise through “co-options” or “fusions” of regulatory modules and pathways “recruited” from genetically unrelated cell types. As a result, their expression profiles would be substantially different, leading to net-type rather than tree-type cellular genealogies in phylogenetic reconstructions. We expect that both scenarios can coexist in any given nervous system. But the tremendous diversity of neural systems across phyla suggests variable contributions of each historical scenario. Combining tools of (i) statistical geometry, artificial intelligence and (ii) modern phylogenomics with (iii) massive parallel single-neuron transcriptome profiling would allow us to unbiasedly reconstruct the genealogy of neurons by testing the treeness statistics as it was recently used for cancer and placental cells. The top illustrations are photos of Mnemiopsis, Trichoplax, Podocoryne, Priapulus, and Aplysia. Some cell lineages (different colors) might become eliminated in the course of evolution (loss) or be expanded or evolved in parallel from different secretory cell types.

Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast.

Ageing-related processes are largely conserved, with simple organisms remaining the main platform to discover and dissect new ageing-associated genes. Yeasts provide potent model systems to study cellular ageing owing their amenability to systematic functional assays under controlled conditions. Even with yeast cells, however, ageing assays can be laborious and resource-intensive. Here we present improved experimental and computational methods to study chronological lifespan in Schizosaccharomyces pombe. We decoded the barcodes for 3206 mutants of the latest gene-deletion library, enabling the parallel profiling of ~700 additional mutants compared to previous screens. We then applied a refined method of barcode sequencing (Bar-seq), addressing technical and statistical issues raised by persisting DNA in dead cells and sampling bottlenecks in aged cultures, to screen for mutants showing altered lifespan during stationary phase. This screen identified 341 long-lived mutants and 1246 short-lived mutants which point to many previously unknown ageing-associated genes, including 46 conserved but entirely uncharacterized genes. The ageing-associated genes showed coherent enrichments in processes also associated with human ageing, particularly with respect to ageing in non-proliferative brain cells. We also developed an automated colony-forming unit assay to facilitate medium- to high-throughput chronological-lifespan studies by saving time and resources compared to the traditional assay. Results from the Bar-seq screen showed good agreement with this new assay. This study provides an effective methodological platform and identifies many new ageing-associated genes as a framework for analysing cellular ageing in yeast and beyond.

Lithospheric structures of the northern Hegenshan-Heihe suture: Implications for the Paleozoic metallogenic setting at the eastern segment of the central Asian orogenic belt

The Hegenshan-Heihe Suture (HHS) is regarded as the collision boundary between the Erguna-Xing’an and Songnen Blocks at the eastern segment of the Central Asian Orogenic Belt (CAOB). However, the convergent processes associated with these two blocks are still controversial due to the lack of definitive geological evidence (i.e., ophiolites, accretionary prisms), which leads to a poor understanding of the relevant metallogenic setting. This paper provides new geophysical constraints on the lithospheric structures of the northern HHS from Dashizhai to Heihe. By the comprehensive interpretation of two parallel deep seismic profiles, the Qiqihaer-Chaihe profile and the newly acquired Duobaoshan profile, the configuration of the subduction-trench-arc-back-arc systems are studied. The subducted continental margin of the Songnen Block is recognized by a set of westward dipping reflections with an apparent dip angle of 20 to 25°, while the accretion complex with a lateral extension of more than 70 km is inferred as an area of short reflections with a westward tendency. The magmatic arc belts and the back-arc area have a quite different seismic reflection patterns. The former are recognized by inverted triangular-shaped transparent reflections, while the latter is featured by arched reflections as clusters. They are bounded by a set of remarkable inclined reflections from the topmost crust to the bottom of the middle crust. It is inferred that the final subduction relict of the northern HHS went through Qiqihaer to the west of Sunwu. Magmatic arc belts forming over two stages are recognized to be located to the west of the subduction relict, and they have a consistent distribution with the magnetic anomaly. A detailed model of the formation of the northern HHS is proposed, which includes two stages of westward oceanic subduction and the final collision.

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.

Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA for clonal tracking, capturing three distinct modalities in single cells. ASAP-seq uses a bridging approach that repurposes antibody:oligonucleotide conjugates designed for existing technologies that pair protein measurements with single-cell RNA sequencing. Together with DOGMA-seq, an adaptation of CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) for measuring gene activity across the central dogma of gene regulation, we demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA and surface proteins during native hematopoietic differentiation and peripheral blood mononuclear cell stimulation and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.

Redox Metabolism Measurement in Mammalian Cells and Tissues by LC-MS.

Cellular redox state is highly dynamic and delicately balanced between constant production of reactive oxygen species (ROS), and neutralization by endogenous antioxidants, such as glutathione. Physiologic ROS levels can function as signal transduction messengers, while high levels of ROS can react with and damage various molecules eliciting cellular toxicity. The redox state is reflective of the cell’s metabolic status and can inform on regulated cell-state transitions or various pathologies including aging and cancer. Therefore, methods that enable reliable, quantitative readout of the cellular redox state are imperative for scientists from multiple fields. Liquid-chromatography mass-spectrometry (LC-MS) based methods to detect small molecules that reflect the redox balance in the cell such as glutathione, NADH, and NADPH, have been developed and applied successfully, but because redox metabolites are very labile, these methods are not easily standardized or consolidated. Here, we report a robust LC-MS method for the simultaneous detection of several redox-reactive metabolites that is compatible with parallel global metabolic profiling in mammalian cells. We performed a comprehensive comparison between three commercial hydrophilic interaction chromatography (HILIC) columns, and we describe the application of our method in mammalian cells and tissues. The presented method is easily applicable and will enable the study of ROS function and oxidative stress in mammalian cells by researchers from various fields.

191 Dream features of the Italian population across the first and second wave of the COVID-19 pandemic

IntroductionThe Italian government has responded to the second wave of the COVID-19 pandemic (autumn 2020) with a partial lockdown (PL). Here we aim to investigate the effects of the PL on dream features in the Italian population and to follow up on previous data collected during the total lockdown (TL) effected during the first wave of the pandemic (spring 2020).MethodsUsing a longitudinal approach, 214 participants (Mage=36.78±14.2y; 159F) who had participated in a previous survey (April 2020 – TL) completed the same online survey from November 10th to December 1st (PL). The questionnaires administered included the Pittsburgh Sleep Quality Index (PSQI) and a set of specific ad hoc questions on dream features (frequency, length, vividness, emotional tone, relation of content to the current health emergency) and their possible changes relative to the month preceding the lockdown, resulting in four time points (pre-TL, TL, pre-PL, PL).ResultsFrequency and length of dreams significantly increased from pre-PL to PL (both p’s<.01), while no difference emerged for vividness. As in TL, almost 30% of the subjects reported having COVID-19-related dreams during PL and, among these, 51% reported to face, in these dreams, problematic situations similar to those of their daily life. Both PSQI and dream negative emotionality scores significantly increased from pre-TL to TL, decreased in pre-PL and increased again in PL, indicating a parallel worsening of sleep quality and dream emotionality with both lockdowns. Dream negative emotionality in PL also showed positive correlations with PSQI scores and with negative mood, stress levels, general fear and fear about the COVID-19.ConclusionIn line with the continuity hypothesis on the relationships between dreaming and the wake state, our data confirm that dream features are significantly and immediately affected by major life changes such as those brought about by the COVID-19 pandemic and related restrictions. Interestingly, dream emotionality and subjective sleep quality show a parallel profile across the different time points, suggesting the possible role of sleep quality as a modulating factor on dream affect.Support (if any)N/A

Formation of edge pressure pedestal and reversed magnetic shear due to toroidal rotation in a tokamak equilibrium

Toroidal rotation is well known to play significant roles in the edge transport and L–H transition dynamics of tokamaks. Our recent calculation finds that a sufficiently strong localized toroidal rotation can directly bring out the formation of edge pressure pedestal with reversed magnetic shear that is reminiscent of an H-mode plasma, purely through the effects of toroidal rotation on the tokamak MHD equilibrium itself. In particular, the enhanced edge toroidal rotation enables a substantial peaking of the parallel current profile near edge in higher β regimes, which leads to the flattening or reversal of the local q (safety factor) profile. Here the formation of pressure pedestal along with the reversed magnetic shear region is shown to be the natural outcome of the MHD tokamak equilibrium in a self-consistent response to the presence of a localized toroidal rotation typically observed in high confinement-mode (H-mode) or quiescent H-mode.

Joint Interpretation of Geophysical Results and Geological Observations for Detecting Buried Active Faults: The Case of the “Il Lago” Plain (Pettoranello del Molise, Italy)

We report a geophysical study across an active normal fault in the Southern Apennines. The surveyed area is the “Il Lago” Plain (Pettoranello del Molise), at the foot of Mt. Patalecchia (Molise Apennines, Southern Italy), a small tectonic basin filled by Holocene deposits located at the NW termination of the major Quaternary Bojano basin structure. This basin, on the NE flank of the Matese Massif, was the epicentral area of the very strong 26 July, 1805, Sant’Anna earthquake (I0 = X MCS, Mw = 6.7). The “Il Lago” Plain is bordered by a portion of the right-stepping normal fault system bounding the whole Bojano Quaternary basin (28 km long). The seismic source responsible for the 1805 earthquake is regarded as one of the most hazardous structures of the Apennines; however, the position of its NW boundary of this seismic source is debated. Geological, geomorphological and macroseismic data show that some coseismic surface faulting also occurred in correspondence with the border fault of the “Il Lago” Plain. The study of the “Il Lago” Plain subsurface might help to constrain the NW segment boundary of the 1805 seismogenic source, suggesting that it is possibly a capable fault, source for moderate (Mw &lt; 5.5) to strong earthquakes (Mw ≥ 5.5). Therefore, we constrained the geometry of the fault beneath the plain using low-frequency Ground Penetrating Radar (GPR) data supported by seismic tomography. Seismic tomography yielded preliminary information on the subsurface structures and the dielectric permittivity of the subsoil. A set of GPR parallel profiles allowed a quick and high-resolution characterization of the lateral extension of the fault, and of its geometry at depth. The result of our study demonstrates the optimal potential of combined seismic and deep GPR surveys for investigating the geometry of buried active normal faults. Moreover, our study could be used for identifying suitable sites for paleoseismic analyses, where record of earthquake surface faulting might be preserved in Holocene lacustrine sedimentary deposits. The present case demonstrates the possibility to detect with high accuracy the complexity of a fault-zone within a basin, inferred by GPR data, not only in its shallower part, but also down to about 100 m depth.

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling.

Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.

Paleowind directions from the magnetic fabric of loess deposits in the western Chinese Loess Plateau and implications for dust provenance

AbstractThe aeolian loess-paleosol sequences in the Chinese Loess Plateau (CLP) are an excellent archive of variations in atmospheric circulation in the geological past. However, there is no consensus regarding the roles of the East Asian winter monsoon and westerly winds in transporting the dust responsible for loess deposition during glacial and interstadial periods. We conducted detailed measurements of the anisotropy of magnetic susceptibility (AMS) on two parallel loess profiles covering the most recent 130 ka in the western CLP to determine paleowind directions. Results show that the magnetic lineations of the loess and paleosol units in both sections are significantly clustered along the northwest to southeast direction. These observations demonstrate that the prevailing wind system responsible for dust transport in the western CLP was the northwesterly winter monsoon, rather than the westerly winds. The AMS-derived dust-bearing wind direction was relatively stable during the last glacial and interglacial cycle in the western CLP, consistent with sedimentary and AMS evidence from the eastern CLP. Accordingly, it is reasonable to conclude that large areas of deserts and Gobi deserts areas located in the upwind direction were the dominant sources for the aeolian deposits of the Loess Plateau.

Ground Penetrating Radar as a Functional Tool to Outline the Presence of Buried Waste: A Case Study in South Italy

The ability of the ground penetrating radar (GPR) method as a rapid preliminary survey to detect the presence of illegally buried waste is presented in this paper. The test site is located in the countryside of “Sannicandro di Bari” (Southern Italy) and has a surface area of 1500 m2. A total of five parallel profiles were acquired in 2014 using a geophysical survey system instrument (GSSI) equipped with 400 and 200 MHz antennae in the monostatic configuration. Two of the five profiles were registered in a control area to compare a natural condition to a suspected waste buried zone. As a result of a processing and elaboration workflow, GPR investigations allowed us to interpret the signal qualitatively within a maximum depth of about 3 m, identifying many signal anomalies, whose characteristics can be considered typical of buried waste. The GPR response of the three profiles acquired in the suspected area showed substantial differences not found in the control’s profiles. Anomalies related to the presence of intense scattering, of dome structures not attributable to cavities, but rather to a flattening and compacting of different layers, therefore, less electrically conductive, were identified in the suspected area. The interpretation of the results obtained by the GPR profiles was confirmed by excavations carried out with bulldozers. Large quantities of solid waste illegally buried (e.g., waste deriving from construction and demolition activities, bituminous mixtures, discarded tires, glass, plastic, municipal waste) were revealed in all the sites where anomalies and non-conformities appeared compared to the control natural soil.

Massively Parallel Kinetic Profiling of Natural and Engineered CRISPR Nucleases

Engineered SpCas9s and AsCas12a cleave fewer off-target genomic sites than natural SpCas9. However, understanding their fidelity, mechanisms and cleavage outcomes requires systematic profiling across mispaired target DNAs. Here we describe NucleaSeq—nuclease digestion and deep sequencing—a massively parallel platform that measures the cleavage kinetics and time-resolved cleavage products for over 10,000 targets containing mismatches, insertions and deletions relative to the guide RNA. Combining cleavage rates and binding specificities on the same target libraries, we benchmarked five SpCas9 variants and AsCas12a. A biophysical model built from these data sets revealed mechanistic insights into off-target cleavage. Engineered SpCas9s, especially Cas9-HF1, dramatically increased cleavage specificity but not binding specificity compared to natural SpCas9. Surprisingly, AsCas12a cleavage specificity differed little from that of SpCas9. Initial DNA cleavage sites and end trimming varied by nuclease, guide RNA and the positions of mispaired nucleotides. More broadly, NucleaSeq enables rapid, quantitative and systematic comparisons of specificity and cleavage outcomes across engineered and natural nucleases.

Recombinant cellulase of Caulobacter crescentus: potential applications for biofuels and textile industries

Caulobacter crescentus (C. crescentus) has a single celA gene encoding the bacterial cellulase (EC 3.2.1.4) of the GH9 family that is induced at transcriptional levels (q-PCR) by agroindustrial residues. Corn straw (1%, w/v) was more efficient in inducing bacterial mRNA-celA expression than corn cob (1%, w/v) and a parallel protein expression profile was observed, since enzyme activity was also higher in presence of corn straw in the bacterium. In order to evaluate the biotechnological role of cellulase from C. crescentus (NA1000), the celA gene of 1,878 bp (CCNA_02310) was cloned in the pTrCHisA vector and successfully expressed in Escherichia coli. The recombinant cellulase CelA purified showed 73 kDa, specificity to CMC, optimal pH of 5.5 and pH stability of 6, optimal temperature at 40 °C and thermostability at 35 °C, KM = 0.66 mg/mL and VMax = 2.41 U/mg/min. CelA was strongly activated by ions Mn2+ (70%), Sn2+ (49%) and Co2+ (46%) and was efficient in the hydrolysis of corn straw and corn cob (1%; w/v) releasing 2.62 µmol/mL and 1.02 µmol/mL of reducing sugar, respectively, being an alternative for the production of chemicals and biofuels. CelA was applied directly to the jeans fiber and scanning electron micrographs (SEM) generated showed a clean and smooth surface of the fibers compared to the control, indicating the application of enzyme for the biopolishing of denim jeans. This work supports a set of biotechnological capabilities of cellulase from C. crescentus suggested by the bacterial genomic sequence that has not been described yet.